[med-svn] [cnvkit] 01/03: New upstream version 0.9.0
Andreas Tille
tille at debian.org
Fri Sep 29 08:22:57 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository cnvkit.
commit 42bc6195b6aa5834a9d60dd597926e38eb22c367
Author: Andreas Tille <tille at debian.org>
Date: Fri Sep 29 09:13:59 2017 +0200
New upstream version 0.9.0
---
.codecov.yml | 2 +
.gitignore | 1 +
.travis.yml | 63 +-
CITATION | 17 +-
README.rst | 46 +-
cnvkit.py | 2 +
cnvlib/__init__.py | 9 +-
cnvlib/_cnarray.py | 600 -
cnvlib/_version.py | 2 +-
cnvlib/access.py | 102 +-
cnvlib/antitarget.py | 156 +-
cnvlib/autobin.py | 185 +
cnvlib/batch.py | 205 +
cnvlib/call.py | 110 +-
cnvlib/cmdutil.py | 90 +
cnvlib/cnary.py | 398 +-
cnvlib/commands.py | 1759 ++-
cnvlib/core.py | 155 +-
cnvlib/coverage.py | 247 +-
cnvlib/descriptives.py | 274 +
cnvlib/diagram.py | 35 +-
cnvlib/export.py | 229 +-
cnvlib/fix.py | 147 +-
cnvlib/gary.py | 490 -
cnvlib/heatmap.py | 119 +
cnvlib/importers.py | 145 +-
cnvlib/jenks.py | 9 +-
cnvlib/metrics.py | 283 +-
cnvlib/ngfrills/__init__.py | 113 -
cnvlib/ngfrills/faidx.py | 34 -
cnvlib/ngfrills/regions.py | 248 -
cnvlib/ngfrills/shared.py | 10 -
cnvlib/parallel.py | 81 +-
cnvlib/params.py | 7 +-
cnvlib/plots.py | 425 +-
cnvlib/rary.py | 176 -
cnvlib/reference.py | 246 +-
cnvlib/reports.py | 60 +-
cnvlib/{ngfrills => }/samutil.py | 62 +-
cnvlib/scatter.py | 533 +
cnvlib/segfilters.py | 153 +
cnvlib/segmentation/__init__.py | 208 +-
cnvlib/segmentation/cbs.py | 4 +-
cnvlib/segmentation/flasso.py | 10 +-
cnvlib/segmentation/haar.py | 134 +-
cnvlib/smoothing.py | 79 +-
cnvlib/target.py | 313 +-
cnvlib/vary.py | 409 +-
devtools/conda-recipe/build.sh | 2 +
devtools/conda-recipe/meta.yaml | 43 +
devtools/travis-ci/install_miniconda.sh | 19 +
doc/baf.rst | 45 +
doc/calling.rst | 36 +-
doc/cnvlib.rst | 141 +-
doc/conf.py | 19 +-
doc/fileformats.rst | 75 +-
doc/germline.rst | 33 +
doc/heterogeneity.rst | 44 +-
doc/importexport.rst | 47 +-
doc/index.rst | 82 +-
doc/nonhybrid.rst | 115 +-
doc/pipeline.rst | 170 +-
doc/plots.rst | 96 +-
doc/quickstart.rst | 50 +-
doc/reports.rst | 70 +-
doc/scripts.rst | 56 +-
doc/sex.rst | 73 +
doc/skgenome.rst | 112 +
doc/tumor.rst | 42 +
doc/workflow.svg | 17 +-
docker/Dockerfile | 24 +-
scripts/cnn_annotate.py | 35 +
scripts/cnn_updater.py | 51 +
scripts/genome2access.py | 46 -
scripts/guess_baits.py | 238 +
scripts/refFlat2bed.py | 168 +-
scripts/reference2targets.py | 43 +-
scripts/skg_convert.py | 35 +
setup.cfg | 2 +
setup.py | 22 +-
skgenome/__init__.py | 2 +
skgenome/chromsort.py | 61 +
skgenome/combiners.py | 67 +
skgenome/gary.py | 615 +
skgenome/intersect.py | 181 +
skgenome/merge.py | 178 +
skgenome/rangelabel.py | 69 +
skgenome/subdivide.py | 62 +
skgenome/subtract.py | 72 +
skgenome/tabio/__init__.py | 267 +
skgenome/tabio/bedio.py | 125 +
skgenome/tabio/genepred.py | 163 +
skgenome/tabio/gff.py | 55 +
skgenome/tabio/picard.py | 90 +
skgenome/tabio/seg.py | 228 +
skgenome/tabio/simplevcf.py | 41 +
skgenome/tabio/tab.py | 33 +
skgenome/tabio/textcoord.py | 30 +
skgenome/tabio/util.py | 14 +
skgenome/tabio/vcfio.py | 305 +
test/.coveragerc | 4 +-
test/Makefile | 33 +-
test/formats/amplicon.cnr | 2868 ++---
test/formats/blank.vcf | 140 +
test/formats/chrM-Y-trunc.hg19.fa | 821 ++
test/formats/dac-my.bed | 3 +
test/formats/example.gff | 8 +
test/formats/my-refflat.bed | 276 +
test/formats/my-targets.bed | 4 +
test/formats/na12878-chrM-Y-trunc.bam | Bin 0 -> 4397336 bytes
test/formats/na12878_na12882_mix.vcf | 4703 ++++++++
test/formats/nosample.vcf | 140 +
test/formats/p2-20_1.cnr | 19090 ++++++++++++++++++++++++++++++
test/formats/p2-20_2.cnr | 19090 ++++++++++++++++++++++++++++++
test/formats/refflat-mini.txt | 100 +
test/formats/tr95t.cns | 251 +-
test/formats/tr95t.segmetrics.cns | 125 +
test/formats/warning.seg | 13 +
test/test_cnvlib.py | 493 +-
test/test_genome.py | 543 +
test/test_io.py | 130 +
test/test_r.py | 39 +-
122 files changed, 55500 insertions(+), 7268 deletions(-)
diff --git a/.codecov.yml b/.codecov.yml
new file mode 100644
index 0000000..66b868e
--- /dev/null
+++ b/.codecov.yml
@@ -0,0 +1,2 @@
+ignore:
+ - "cnvlib/commands.py"
diff --git a/.gitignore b/.gitignore
index d7aaeb7..e676194 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,6 +8,7 @@
# Testing & coverage shrapnel
.coverage
coverage.xml
+*.bai
# Backup files from some Unix editors
*~
diff --git a/.travis.yml b/.travis.yml
index 1d26503..bcbed1a 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,49 +1,38 @@
-# Configuration file to run tests on Travis-CI via GitHub notifications
-language: python
-python:
- - "2.7"
+language: c
+sudo: false
-notifications:
- email: false
-
-sudo: required
-dist: trusty
-
-# Install these Debian packages without sudo
-# https://docs.travis-ci.com/user/migrating-from-legacy/#Adding-APT-Packages
-addons:
- apt:
- packages:
- - gfortran
- - libblas-dev
- - libfreetype6-dev
- - liblapack-dev
- - python-dev
- - python-biopython
- - python-dateutil
- - python-matplotlib
- - python-numpy
- - python-reportlab
- - python-scipy
- - python-tk
- - python-tz
-
-# Cache the compiled pip package dependencies
-# https://docs.travis-ci.com/user/caching/#pip-cache
-cache: pip
-
-# Use the default install step for Python (which installs deps & CNVkit itself):
-# pip install -r requirements.txt
-# https://docs.travis-ci.com/user/languages/python/#Dependency-Management
+install:
+ - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install md5sha1sum; fi
+ - source devtools/travis-ci/install_miniconda.sh
before_script:
+ - conda create -q -y --name testenv python=$CONDA_PY
+ - source activate testenv
+ - conda build -c bioconda -c R --python $CONDA_PY ./devtools/conda-recipe/ # Build the conda recipe for the latest dev
+ - conda install -c bioconda -c R --use-local -yq cnvkit # Install the locally built package and its requirements
+ - conda install -c bioconda -c R -yq pandas==$PANDAS pysam==$PYSAM # Install the versions desired for testing
+ - conda remove cnvkit -y -q # Remove the conda cnvkit package but keep the dependencies installed
+ - python setup.py install # Install directly from source
- cd test/
# For codecov.io
- pip install codecov
script:
- - coverage run test_cnvlib.py
+ - coverage run test_io.py
+ - coverage run -a test_genome.py
+ - coverage run -a test_cnvlib.py
+ - coverage run -a test_r.py
after_success:
- coverage report
- codecov
+
+os:
+ # - osx
+ - linux
+
+env:
+ - CONDA_PY=2.7 PANDAS=0.18.1 PYSAM=0.10.0
+ - CONDA_PY=2.7 PANDAS=0.20.2 PYSAM=0.11.2.2
+ - CONDA_PY=3.5 PANDAS=0.18.1 PYSAM=0.10.0
+ - CONDA_PY=3.5 PANDAS=0.20.2 PYSAM=0.11.2.2
diff --git a/CITATION b/CITATION
index b45ee5e..9ed154f 100644
--- a/CITATION
+++ b/CITATION
@@ -1,18 +1,19 @@
To cite CNVkit in publications, please use:
Talevich, E., Shain, A. H., Botton, T., & Bastian, B. C. (2014).
- CNVkit: Copy number detection and visualization for targeted sequencing using
- off-target reads. bioRxiv doi: http://dx.doi.org/10.1101/010876
+ CNVkit: Genome-wide copy number detection and visualization from
+ targeted sequencing. PLOS Computational Biology 12(4): e1004873.
+ doi: 10.1371/journal.pcbi.1004873
A BibTeX entry for LaTeX users is:
@article{,
- title = {{CNVkit: Copy number detection and visualization for targeted sequencing using off-target reads}},
+ title = {{CNVkit: Genome-wide copy number detection and visualization from targeted sequencing}},
author = {Talevich, Eric and Shain, A. Hunter and Botton, Thomas and Bastian, Boris C.},
- journal = {bioRxiv},
- month = oct,
- year = {2014}
- doi = {10.1101/010876},
- url = {http://dx.doi.org/10.1101/010876},
+ journal = {PLOS Computational Biology},
+ month = apr,
+ year = {2016}
+ doi = {10.1371/journal.pcbi.1004873},
+ url = {http://dx.doi.org/10.1371/journal.pcbi.1004873},
}
diff --git a/README.rst b/README.rst
index 31aceda..7cf6358 100644
--- a/README.rst
+++ b/README.rst
@@ -5,14 +5,19 @@ CNVkit
A command-line toolkit and Python library for detecting copy number variants
and alterations genome-wide from targeted DNA sequencing.
-Read the full documentation at: http://cnvkit.readthedocs.org
+Read the full documentation at: http://cnvkit.readthedocs.io
.. image:: https://travis-ci.org/etal/cnvkit.svg?branch=master
:target: https://travis-ci.org/etal/cnvkit
+ :alt: Build status
.. image:: https://landscape.io/github/etal/cnvkit/master/landscape.svg
- :target: https://landscape.io/github/etal/cnvkit/master
- :alt: Code Health
+ :target: https://landscape.io/github/etal/cnvkit/master
+ :alt: Code health
+
+.. image:: https://codecov.io/github/etal/cnvkit/coverage.svg?branch=master
+ :target: https://codecov.io/github/etal/cnvkit?branch=master
+ :alt: Test coverage
Support
@@ -36,7 +41,8 @@ A `Galaxy tool <https://testtoolshed.g2.bx.psu.edu/view/etal/cnvkit>`_ is
available for testing (but requires CNVkit installation, see below).
A `Docker container <https://registry.hub.docker.com/u/etal/cnvkit/>`_ is also
-available on Docker Hub.
+available on Docker Hub, and the BioContainers community provides another on
+`Quay <https://quay.io/repository/biocontainers/cnvkit>`_.
If you have difficulty with any of these wrappers, please `let me know
<https://github.com/etal/cnvkit/issues/>`_!
@@ -72,7 +78,7 @@ This approach is preferred on Mac OS X, and is a solid choice on Linux, too.
To download and install CNVkit and its Python dependencies::
- conda install -c bioconda -c r cnvkit
+ conda install cnvkit -c bioconda -c r -c conda-forge
From a Python package repository
@@ -81,7 +87,7 @@ From a Python package repository
Reasonably up-to-date CNVkit packages are available on `PyPI
<https://pypi.python.org/pypi/CNVkit>`_ and can be installed using `pip
<https://pip.pypa.io/en/latest/installing.html>`_ (usually works on Linux if the
-dependencies listed below are installed)::
+system dependencies listed below are installed)::
pip install cnvkit
@@ -111,28 +117,26 @@ these Python packages via ``pip`` or ``conda``:
- `NumPy <http://www.numpy.org/>`_
- `SciPy <http://www.scipy.org/>`_
- `Pandas <http://pandas.pydata.org/>`_
+- `pyfaidx <https://github.com/mdshw5/pyfaidx>`_
- `pysam <https://github.com/pysam-developers/pysam>`_
-- `PyVCF <https://github.com/jamescasbon/PyVCF>`_
On Ubuntu or Debian Linux::
- sudo apt-get install python-numpy python-scipy python-matplotlib python-reportlab python-pip
- sudo pip install pandas biopython pysam pyvcf --upgrade
-
+ sudo apt-get install python-numpy python-scipy python-matplotlib python-reportlab python-pandas
+ sudo pip install biopython pyfaidx pysam pyvcf --upgrade
-On Mac OS X you may instead find it much easier to first install the Python
-package manager `Miniconda`_, or the full `Anaconda`_ distribution, which
-includes most of the dependencies. Then install the rest of CNVkit's
-dependencies::
+On Mac OS X you may find it much easier to first install the Python package
+manager `Miniconda`_, or the full `Anaconda`_ distribution (see above).
+Then install the rest of CNVkit's dependencies::
- conda install numpy scipy pandas matplotlib reportlab biopython pysam pyvcf
+ conda install numpy scipy pandas matplotlib reportlab biopython pyfaidx pysam pyvcf
-Otherwise, we recommend using `Homebrew <http://brew.sh/>`_ to install an
+Alternatively, you can use `Homebrew <http://brew.sh/>`_ to install an
up-to-date Python (e.g. ``brew install python``) and as many of the Python
-packages as possible (primarily NumPy, SciPy and matplotlib). Then, proceed with
-pip::
+packages as possible (primarily NumPy, SciPy, matplotlib and pandas).
+Then, proceed with pip::
- sudo pip install numpy scipy pandas matplotlib reportlab biopython pysam pyvcf
+ pip install numpy scipy pandas matplotlib reportlab biopython pyfaidx pysam pyvcf
R dependencies
@@ -169,9 +173,7 @@ installed CNVkit correctly. On a multi-core machine you can parallelize this
with ``make -j``.
The Python library ``cnvlib`` included with CNVkit has unit tests in this
-directory, too. To run the test suite::
-
- python test_cnvlib.py
+directory, too. Run the test suite with ``make test``.
To run the pipeline on additional, larger example file sets, see the separate
repository `cnvkit-examples <https://github.com/etal/cnvkit-examples>`_.
diff --git a/cnvkit.py b/cnvkit.py
index b666720..e7dedce 100755
--- a/cnvkit.py
+++ b/cnvkit.py
@@ -1,6 +1,8 @@
#!/usr/bin/env python
"""Command-line interface for CNVkit, the Copy Number Variation toolkit."""
+from future import standard_library
+standard_library.install_aliases()
import logging
from cnvlib import commands
diff --git a/cnvlib/__init__.py b/cnvlib/__init__.py
index 980802c..8501a47 100644
--- a/cnvlib/__init__.py
+++ b/cnvlib/__init__.py
@@ -1,6 +1,5 @@
-from .cnary import CopyNumArray as _CNA
from ._version import __version__
-
-def read(fname):
- """Parse a file as a copy number or copy ratio table (.cnn, .cnr)."""
- return _CNA.read(fname)
+from .cmdutil import read_cna as read
+from .commands import *
+from .diagram import create_diagram as do_diagram
+from skgenome import tabio
diff --git a/cnvlib/_cnarray.py b/cnvlib/_cnarray.py
deleted file mode 100644
index c12b0fc..0000000
--- a/cnvlib/_cnarray.py
+++ /dev/null
@@ -1,600 +0,0 @@
-"""Definitions for the core data structure, a copy number array."""
-from __future__ import print_function
-
-import sys
-
-import numpy
-from numpy.lib import recfunctions as rfn
-from Bio.File import as_handle
-from Bio._py3k import basestring, map, zip
-
-from . import core, metrics, ngfrills, smoothing
-
-
-class CopyNumArray(object):
- """An array of genomic intervals, treated like aCGH probes."""
- # http://docs.scipy.org/doc/numpy/user/basics.rec.html
-
- _dtype = (('chromosome', 'O'),
- ('start', 'i4'),
- ('end', 'i4'),
- ('gene', 'O'),
- ('coverage', 'f4'))
- _dtype_gc = ('gc', 'f4')
- _dtype_rmask = ('rmask', 'f4')
- _dtype_spread = ('spread', 'f4')
- _dtype_weight = ('weight', 'f4')
- _dtype_probes = ('probes', 'i4')
-
- def __init__(self, sample_id, extra_column_names=()):
- """Initialize an empty CopyNumArray with the requested columns."""
- xtra = []
- dtype = list(self._dtype)
- for col_name, col_dtype in (
- ('gc', self._dtype_gc),
- ('rmask', self._dtype_rmask),
- ('spread', self._dtype_spread),
- ('weight', self._dtype_weight),
- ('probes', self._dtype_probes)):
- if col_name in extra_column_names:
- xtra.append(col_name)
- dtype.append(col_dtype)
- self._xtra = tuple(xtra)
- self.data = numpy.empty(0, dtype=dtype)
- self.sample_id = sample_id
-
- @classmethod
- def from_array(cls, sample_id, array):
- cnarr = cls(sample_id, array.dtype.names[5:])
- cnarr.data = numpy.asarray(array, dtype=cnarr.data.dtype)
- return cnarr
-
- @classmethod
- def from_columns(cls, sample_id, **columns):
- these_cols = set(columns)
- required_cols = {'chromosome', 'start', 'end', 'gene', 'coverage'}
- optional_cols = {'gc', 'rmask', 'spread', 'weight', 'probes'}
- missing_cols = required_cols - these_cols
- if missing_cols:
- raise ValueError("Missing required column(s): " +
- " ".join(sorted(missing_cols)))
- extra_cols = these_cols - required_cols
- bogus_cols = extra_cols - optional_cols
- if bogus_cols:
- raise ValueError("Unrecognized column name(s): " +
- " ".join(sorted(bogus_cols)))
- cnarr = cls(sample_id, list(extra_cols))
- # XXX better way?
- table = list(zip(*[columns[key] for key in cnarr.data.dtype.names]))
- cnarr.data = numpy.asarray(table, dtype=cnarr.data.dtype)
- return cnarr
-
- @classmethod
- def from_rows(cls, sample_id, row_data, extra_keys=()):
- new_cna = cls(sample_id, extra_keys)
- if len(row_data) == 1:
- row_data = [tuple(row_data[0])]
- try:
- # Rows might be plain tuples
- new_array = numpy.asarray(row_data, dtype=new_cna.data.dtype)
- except ValueError:
- # "Setting void-array with object members using buffer"
- # All rows are numpy.ndarray
- new_array = rfn.stack_arrays(row_data, usemask=False,
- asrecarray=True, autoconvert=False)
- # print(new_array.dtype)
-
- new_cna.data = new_array
- return new_cna
-
- # Container-like behavior
-
- def __eq__(self, other):
- return (isinstance(other, self.__class__) and
- (self.data == other.data).all())
-
- def __len__(self):
- return len(self.data)
-
- def __contains__(self, key):
- return (key in self.data.dtype.fields)
-
- def __getitem__(self, index):
- return self.data[index]
-
- def __setitem__(self, index, value):
- if isinstance(value, numpy.void) and isinstance(index, int):
- # Avoid "Setting void-array with object members using buffer"
- value = tuple(value)
- self.data[index] = value
-
- def __delitem__(self, index):
- return NotImplemented
-
- def __iter__(self):
- return iter(self.data)
-
- def __next__(self):
- return next(self.data)
-
- @property
- def coverage(self):
- return self.data['coverage']
-
- @property
- def chromosome(self):
- return self.data['chromosome']
-
- @property
- def start(self):
- return self.data['start']
-
- @property
- def end(self):
- return self.data['end']
-
- @property
- def gene(self):
- return self.data['gene']
-
- def labels(self):
- return (row2label(row) for row in self.data)
-
- def by_bin(self, bins):
- """Group rows by another CopyNumArray; trim row start/end to bin edges.
-
- Returns an iterable of (bin, CopyNumArray of overlapping cnarray rows))
-
- If a probe overlaps with a bin boundary, the probe start or end position
- is replaced with the bin boundary position. Probes outside any segments
- are skipped. This is appropriate for most other comparisons between
- CopyNumArray objects.
- """
- cn_by_chrom = dict(self.by_chromosome())
- for chrom, bin_rows in bins.by_chromosome():
- cn_rows = cn_by_chrom.get(chrom)
- if not cn_rows:
- continue
-
- # Traverse rows and bins together, matching up start/end points
- # cn_rows = iter(cn_rows)
- # curr_row = next(cn_rows)
- # row_start, row_end = curr_row['start'], curr_row['end']
- for bin_row in bin_rows:
- # Iterate over rows until we're clear of the bin
- # while True:
- # if row_start < bin_row['start']:
- # # Skip a gap in bin1
- # row_start = bin_row['start']
- # elif row_start > bin_row['start']:
- # # Skip a gap in bin2
- # bin_row['start'] = row_start
- # # Row start points match now: emit up to the next endpoint
- # bin_row['end'] = min(bin_row['end'], row_end)
- # selected_rows.append(bin_row)
- # if row_end > bin_row['end']:
- # # Trim & hold bin2; take next bin1
- # row_start = bin_row['end']
- # break
- # elif row_end < bin_row['end']:
- # try:
- # # Trim & hold bin1; take next bin2
- # bin_row['start'] = row_end
- # curr_row = next(bin_rows)
- # row_start, row_end = curr_row['start'], curr_row['end']
- # continue
- # except StopIteration:
- # # At the 3' telomere
- # break
- # elif row_end == bin_row['end']:
- # try:
- # # Take next of each of bin1 and bin2
- # curr_row = next(bin_rows)
- # row_start, row_end = curr_row['start'], curr_row['end']
- # except StopIteration:
- # # At the 3' telomere
- # pass
- # break
-
- # ENH - use a faster 1-pass implementation
- binned_rows = cn_rows.in_range(chrom, bin_row['start'],
- bin_row['end'], trim=True)
-
- yield bin_row, self.to_rows(binned_rows)
-
- def by_chromosome(self):
- """Iterate over probes grouped by chromosome name."""
- uniq_chrom, idx = numpy.unique(self.chromosome, True)
- sort_idx = idx.argsort()
- idx = idx.take(sort_idx)
- uniq_chrom = uniq_chrom.take(sort_idx)
- idx2 = numpy.concatenate((idx[1:], [len(self.data)]))
- for chrom, start, end in zip(uniq_chrom, idx, idx2):
- subarr = self.to_array(self.data[start:end])
- yield chrom, subarr
-
- def by_gene(self, ignore=('-', 'CGH', '.')):
- """Iterate over probes grouped by gene name.
-
- Emits pairs of (gene name, CNA of rows with same name)
-
- Groups each series of intergenic bins as a 'Background' gene; any
- 'Background' bins within a gene are grouped with that gene.
- Bins with names in `ignore` are treated as 'Background' bins, but retain
- their name.
- """
- curr_chrom = None
- curr_bg_rows_idx = []
- curr_gene_name = None
- curr_gene_rows_idx = []
-
- for i, row in enumerate(self.data):
- gene = str(row['gene'])
- if gene == 'Background' or gene in ignore:
- # This background *may* be in an intergenic region
- if curr_chrom != row['chromosome']:
- # New chromosome (not intergenic): emit the BG & reset
- if curr_bg_rows_idx:
- yield ('Background',
- self.to_array(self.data.take(curr_bg_rows_idx)))
- curr_bg_rows_idx = []
- # Include this row in the current background
- curr_chrom = row['chromosome']
- curr_bg_rows_idx.append(i)
- elif gene == curr_gene_name:
- # Continue the current gene
- # Any "background" was intronic; include in the current gene
- if curr_bg_rows_idx:
- curr_gene_rows_idx.extend(curr_bg_rows_idx)
- curr_bg_rows_idx = []
- # Add this row to the current gene
- curr_gene_rows_idx.append(i)
- else:
- # New gene
- # Emit the last gene, if any
- if curr_gene_rows_idx:
- yield (curr_gene_name,
- self.to_array(self.data.take(curr_gene_rows_idx)))
- # Emit the subsequent background, if any
- if curr_bg_rows_idx:
- yield ('Background',
- self.to_array(self.data.take(curr_bg_rows_idx)))
- # Reset BG trackers
- curr_bg_rows_idx = []
- # Start tracking the new gene
- curr_gene_rows_idx = [i]
- curr_chrom = row['chromosome']
- curr_gene_name = gene
-
- # Remainder
- if curr_gene_rows_idx:
- yield (curr_gene_name,
- self.to_array(self.data.take(curr_gene_rows_idx)))
- if curr_bg_rows_idx:
- yield 'Background', self.to_array(self.data.take(curr_bg_rows_idx))
-
- def by_segment(self, segments):
- """Group cnarray rows by the segments that row midpoints land in.
-
- Returns an iterable of segments and rows grouped by overlap with each
- segment.
-
- Note that segments don't necessarily cover all probes (some near
- telo/centromeres may have been dropped as outliers during segmentation).
- These probes are grouped with the nearest segment, so the endpoint of
- the first/last probe may not match the corresponding segment endpoint.
- This is appropriate if the segments were obtained from this probe array.
- """
- curr_probes_idx = []
- segments = iter(segments)
- curr_segment = next(segments)
- next_segment = None
- for i, row in enumerate(self.data):
- probe_midpoint = 0.5 * (row['start'] + row['end'])
- if (row['chromosome'] == curr_segment['chromosome'] and
- curr_segment['start'] <= probe_midpoint <= curr_segment['end']):
- # Probe is within the current segment
- curr_probes_idx.append(i)
-
- elif row['chromosome'] != curr_segment['chromosome']:
- # Probe should be at the start of the next chromosome.
- # Find the matching segment.
- if next_segment is None:
- next_segment = next(segments)
-
- # Skip any extra segments on the chromosome after the current
- # probes (e.g. probes are targets, trailing segments are based
- # on antitargets alone)
- while row['chromosome'] != next_segment['chromosome']:
- try:
- next_segment = next(segments)
- except StopIteration:
- raise ValueError("Segments are missing chromosome %r"
- % row['chromosome'])
-
- # Emit the current (completed) group
- yield (curr_segment,
- self.to_array(self.data.take(curr_probes_idx)))
- # Begin a new group of probes
- curr_segment, next_segment = next_segment, None
- curr_probes_idx = [i]
-
- elif row['start'] < curr_segment['start']:
- # Probe is near the start of the current chromosome, but we've
- # already seen another outlier here (rare/nonexistent case).
- # Group with the current (upcoming) segment.
- curr_probes_idx.append(i)
-
- elif row['end'] > curr_segment['end']:
- # Probe is at the end of an accessible region (e.g. p or q arm)
- # on the current chromosome.
- # Group this probe with whichever of the current or next
- # segments is closer.
- if next_segment is None:
- next_segment = next(segments)
- if (next_segment['chromosome'] != row['chromosome']
- or (next_segment['start'] - probe_midpoint) >
- (probe_midpoint - curr_segment['end'])):
- # The current segment is closer than the next. Group here.
- curr_probes_idx.append(i)
- else:
- # The next segment is closer. Emit the current group
- # Begin a new group of probes
- yield (curr_segment,
- self.to_array(self.data.take(curr_probes_idx)))
- # Reset/update trackers for the next group of probes
- curr_segment, next_segment = next_segment, None
- curr_probes_idx = [i]
- else:
- raise ValueError("Mismatch between probes and segments\n" +
- "Probe: %s\nSegment: %s"
- % (row2label(row), row2label(curr_segment)))
- # Emit the remaining probes
- yield curr_segment, self.to_array(self.data.take(curr_probes_idx))
-
- def center_all(self, peak=False):
- """Recenter coverage values to the autosomes' average (in-place)."""
- chr_x = core.guess_chr_x(self)
- chr_y = ('chrY' if chr_x.startswith('chr') else 'Y')
- mask_autosome = ((self.chromosome != chr_x) &
- (self.chromosome != chr_y))
- mid = numpy.median(self.coverage[mask_autosome])
- mask_cvg = (mask_autosome &
- (self.coverage >= mid - 1.1) &
- (self.coverage <= mid + 1.1))
- if peak and sum(mask_cvg) > 210:
- # Estimate the location of peak density
- # hack: from a smoothed histogram -- enh: kernel density estimate
- x = self.coverage[mask_cvg]
- w = self['weight'][mask_cvg] if 'weight' in self else None
- resn = int(round(numpy.sqrt(len(x))))
- x_vals, x_edges = numpy.histogram(x, bins=8*resn, weights=w)
- xs = smoothing.smoothed(x_vals, resn)
- # DBG: Check the fit
- # ngfrills.echo("Centering: median", mid,
- # ", mode", x_edges[numpy.argmax(xs)],
- # ", resolution", x_edges[2] - x_edges[1])
- # from matplotlib import pyplot
- # _fig, ax = pyplot.subplots()
- # ax.plot(x_vals, c='k', alpha=.5)
- # ax.plot(xs, c='r', lw=2)
- # median_idx = x_edges.searchsorted(mid)
- # ax.axvspan(median_idx - 1, median_idx, color='teal', alpha=.3)
- # ax.vlines(numpy.argmax(xs), *ax.get_ylim(), colors='salmon')
- # pyplot.show()
- # --
- mid = x_edges[numpy.argmax(xs)]
- self.data['coverage'] -= mid
-
- def copy(self):
- """Create an independent copy of this object."""
- return self.to_rows(numpy.copy(self.data))
-
- def add_columns(self, **columns):
- """Create a new CNA, adding the specified extra columns to this CNA."""
- cols = {key: self.data[key]
- for key in self.data.dtype.names}
- cols.update(columns)
- return self.__class__.from_columns(self.sample_id, **cols)
-
- def drop_extra_columns(self):
- """Remove any optional columns from this CopyNumArray.
-
- Returns a new copy with only the core columns retained:
- log2 value, chromosome, start, end, bin name.
- """
- result = self.__class__(self.sample_id)
- result.data = rfn.drop_fields(self.data, self._xtra)
- return result
-
- def merge(self, other):
- """Combine this array's data with another CopyNumArray (in-place).
-
- Any optional columns must match between both arrays.
- """
- assert isinstance(other, CopyNumArray), (
- "Argument (type %s) is not a CopyNumArray instance" % type(other))
- self.data = numpy.concatenate((self.data, other.data))
- self.sort()
-
- def in_range(self, chrom, start=0, end=None, trim=False):
- """Get the CopyNumArray portion within the given genomic range.
-
- If trim=True, include bins straddling the range boundaries, and trim
- the bins endpoints to the boundaries.
- """
- rows = self.data[self.chromosome == chrom]
- if not len(rows):
- raise ValueError("Chromosome %s is not in this probe set" % chrom)
- if start:
- if trim:
- # Include all rows overlapping the start point
- rows = rows[rows['end'].searchsorted(start, 'right'):]
- # Update 5' endpoints to the boundary
- rows['start'][rows['start'] < start] = start
- else:
- # Only rows entirely after the start point
- rows = rows[rows['start'].searchsorted(start):]
- if end:
- if trim:
- rows = rows[:rows['start'].searchsorted(end)]
- # Update 3' endpoints to the boundary
- rows['end'][rows['end'] > end] = end
- else:
- rows = rows[:rows['end'].searchsorted(end, 'right')]
- return self.to_rows(rows)
-
- def select(self, selector=None, **kwargs):
- """Take a subset of rows where the given condition is true.
-
- Arguments can be a function (lambda expression) returning a bool, which
- will be used to select True rows, and/or keyword arguments like
- gene="Background" or chromosome="chr7", which will select rows where the
- keyed field equals the specified value.
- """
- outrows = self.data
- if selector is not None:
- assert callable(selector)
- condition = numpy.apply_along_axis(selector, 0, outrows)
- outrows = numpy.extract(condition, outrows)
- for key, val in kwargs.items():
- assert key in self
- outrows = outrows[outrows[key] == val]
- return self.to_rows(outrows)
-
- def shuffle(self):
- """Randomize the order of bins in this array (in-place)."""
- numpy.random.seed(0xA5EED) # For reproducible results
- order = numpy.arange(len(self.data))
- numpy.random.shuffle(order)
- self.data = self.data[order]
- return order
-
- def sort(self, key=None):
- """Sort the bins in this array (in-place).
-
- Optional argument 'key' is one of:
-
- - a function that computes a sorting key from a CopyNumArray row
- - a string identifier for an existing data column
- - a list/array/iterable of precomputed keys equal in length to the
- number of rows in this CopyNumArray.
-
- By default, bins are sorted by chromosomal coordinates.
- """
- if key is None:
- # Sort by chrom, then by start position
- chrom_keys = list(map(core.sorter_chrom, self.data['chromosome']))
- order = numpy.lexsort((self.data['start'], chrom_keys))
- else:
- # Sort by the given key, using a stable sort algorithm
- if isinstance(key, basestring):
- keys = self.data[key]
- elif callable(key):
- keys = list(map(key, self.data))
- else:
- if not len(key) == len(self):
- raise ValueError("Sort key, as an array, must have the "
- "same length as the CopyNumArray to sort "
- "(%d vs. %d)." % (len(key), len(self)))
- keys = key
- order = numpy.argsort(keys, kind='mergesort')
- self.data = self.data.take(order)
-
- def squash_genes(self, ignore=('-', 'CGH', '.'), squash_background=False,
- summary_stat=metrics.biweight_location):
- """Combine consecutive bins with the same targeted gene name.
-
- The `ignore` parameter lists bin names that not be counted as genes to
- be output.
-
- Parameter `summary_stat` is a function that summarizes an array of
- coverage values to produce the "squashed" gene's coverage value. By
- default this is the biweight location, but you might want median, mean,
- max, min or something else in some cases.
-
- Optional columns, if present, are dropped.
- """
- def squash_rows(name, rows):
- """Combine multiple rows (for the same gene) into one row."""
- chrom = core.check_unique(rows['chromosome'], 'chromosome')
- start = rows[0]['start']
- end = rows[-1]['end']
- cvg = summary_stat(rows['coverage'])
- outrow = [chrom, start, end, name, cvg]
- # Handle extra fields
- # ENH - no coverage stat; do weighted average as appropriate
- for xfield in ('gc', 'rmask', 'spread', 'weight'):
- if xfield in self:
- outrow.append(summary_stat(rows[xfield]))
- if 'probes' in self:
- outrow.append(sum(rows['probes']))
- return tuple(outrow)
-
- outrows = []
- for name, subarr in self.by_gene(ignore):
- if name == 'Background' and not squash_background:
- outrows.extend(map(tuple, subarr))
- else:
- outrows.append(squash_rows(name, subarr))
- return self.to_rows(outrows)
-
- def to_array(self, array):
- return self.__class__.from_array(self.sample_id, array)
-
- def to_rows(self, rows):
- """Like from_rows, reusing this instance's metadata."""
- return self.__class__.from_rows(self.sample_id, rows, self._xtra)
-
- # I/O
-
- @classmethod
- def read(cls, infile, sample_id=None):
- """Parse a tabular table of coverage data from a handle or filename."""
- if sample_id is None:
- if isinstance(infile, basestring):
- sample_id = core.fbase(infile)
- else:
- sample_id = '<unknown>'
- with as_handle(infile) as handle:
- try:
- header = next(handle)
- except StopIteration:
- # Don't crash on empty files
- return cls(sample_id)
- # Build CNA...
- xtra = _sniff_xtra(header)
- cnarr = cls(sample_id, xtra)
- arr = numpy.loadtxt(handle, delimiter="\t", dtype=cnarr.data.dtype, ndmin=1)
- cnarr.data = arr
- return cnarr
-
- def write(self, outfile=sys.stdout):
- """Write coverage data to a file or handle in tabular format.
-
- This is similar to BED or BedGraph format, but with extra columns.
-
- To combine multiple samples in one file and/or convert to another
- format, see the 'export' subcommand.
- """
- colnames = ['chromosome', 'start', 'end', 'gene', 'log2']
- colnames.extend(self._xtra)
- rows = (list(map(str, row)) for row in self.data)
- with ngfrills.safe_write(outfile) as handle:
- header = '\t'.join(colnames) + '\n'
- handle.write(header)
- handle.writelines('\t'.join(row) + '\n' for row in rows)
-
-
-def _sniff_xtra(header_line):
- colnames = tuple(map(str.strip, header_line.split('\t')))
- assert colnames[:5] == ('chromosome', 'start', 'end', 'gene', 'log2'), \
- colnames[:5]
- xtra = colnames[5:]
- assert all(x in ('gc', 'rmask', 'spread', 'weight', 'probes')
- for x in xtra)
- return xtra
-
-
-def row2label(row):
- return "{}:{}-{}".format(row['chromosome'], row['start'], row['end'])
diff --git a/cnvlib/_version.py b/cnvlib/_version.py
index 9ff9982..3e2f46a 100644
--- a/cnvlib/_version.py
+++ b/cnvlib/_version.py
@@ -1 +1 @@
-__version__ = "0.7.11"
+__version__ = "0.9.0"
diff --git a/cnvlib/access.py b/cnvlib/access.py
old mode 100755
new mode 100644
index db075b5..b50d49b
--- a/cnvlib/access.py
+++ b/cnvlib/access.py
@@ -6,20 +6,22 @@ Inaccessible regions, e.g. telomeres and centromeres, are masked out with N in
the reference genome sequence; this script scans those to identify the
coordinates of the accessible regions (those between the long spans of N's).
"""
+from __future__ import absolute_import, division, print_function
+from builtins import next, zip
-import itertools
import logging
import numpy as np
+from skgenome import tabio, GenomicArray as GA
-from cnvlib.ngfrills import parse_regions
-
-def log_this(chrom, run_start, run_end):
- """Log a coordinate range, then return it as a tuple."""
- logging.info("\tAccessible region %s:%d-%d (size %d)",
- chrom, run_start, run_end, run_end - run_start)
- return (chrom, run_start, run_end)
+def do_access(fa_fname, exclude_fnames=(), min_gap_size=5000):
+ """List the locations of accessible sequence regions in a FASTA file."""
+ access_regions = GA.from_rows(get_regions(fa_fname))
+ for ex_fname in exclude_fnames:
+ excluded = tabio.read(ex_fname, 'bed3')
+ access_regions = access_regions.subtract(excluded)
+ return GA.from_rows(join_regions(access_regions, min_gap_size))
def get_regions(fasta_fname):
@@ -47,7 +49,7 @@ def get_regions(fasta_fname):
else:
# Slow route: line is a mix of N and non-N chars
line_chars = np.array(line, dtype='c')
- n_indices = np.where(line_chars == 'N')[0]
+ n_indices = np.where(line_chars == b'N')[0]
# Emit the first block of non-N chars, if any
if run_start is not None:
yield log_this(chrom, run_start, cursor + n_indices[0])
@@ -56,7 +58,7 @@ def get_regions(fasta_fname):
# Emit any short intermediate blocks
gap_mask = np.diff(n_indices) > 1
if gap_mask.any():
- ok_starts = n_indices[gap_mask] + 1 + cursor
+ ok_starts = n_indices[:-1][gap_mask] + 1 + cursor
ok_ends = n_indices[1:][gap_mask] + cursor
for start, end in zip(ok_starts, ok_ends):
yield log_this(chrom, start, end)
@@ -75,17 +77,19 @@ def get_regions(fasta_fname):
yield log_this(chrom, run_start, cursor)
-def group_regions_by_chromosome(rows):
- """Iterate through BED3 rows: (chrom, BED3-rows-in-this-chrom)"""
- for chrom, rows in itertools.groupby(rows, lambda bed3: bed3[0]):
- yield chrom, [(start, end) for _chrom, start, end in rows]
+def log_this(chrom, run_start, run_end):
+ """Log a coordinate range, then return it as a tuple."""
+ logging.info("\tAccessible region %s:%d-%d (size %d)",
+ chrom, run_start, run_end, run_end - run_start)
+ return (chrom, run_start, run_end)
def join_regions(regions, min_gap_size):
"""Filter regions, joining those separated by small gaps."""
- for chrom, coords in group_regions_by_chromosome(regions):
+ min_gap_size = min_gap_size or 0
+ for chrom, rows in regions.by_chromosome():
logging.info("%s: Joining over small gaps", chrom)
- coords = iter(coords)
+ coords = iter(zip(rows['start'], rows['end']))
prev_start, prev_end = next(coords)
for start, end in coords:
gap = start - prev_end
@@ -103,69 +107,3 @@ def join_regions(regions, min_gap_size):
yield (chrom, prev_start, prev_end)
prev_start, prev_end = start, end
yield (chrom, prev_start, prev_end)
-
-
-def exclude_regions(bed_fname, access_rows):
- ex_by_chrom = dict(group_regions_by_chromosome(
- parse_regions(bed_fname, coord_only=True)))
- if len(ex_by_chrom) == 0:
- # Nothing to exclude -> emit the input regions unmodified
- for row in access_rows:
- yield row
- else:
- # Check if each input region overlaps an excluded region
- for chrom, a_rows in group_regions_by_chromosome(access_rows):
- if chrom in ex_by_chrom:
- logging.info("%s: Subtracting excluded regions", chrom)
- exclude_rows = iter(ex_by_chrom[chrom])
- ex_start, ex_end = next_or_inf(exclude_rows)
- for a_start, a_end in a_rows:
- for row in exclude_in_region(exclude_rows, chrom, a_start,
- a_end, ex_start, ex_end):
- yield row
- else:
- logging.info("%s: No excluded regions", chrom)
- for a_start, a_end in a_rows:
- yield (chrom, a_start, a_end)
-
-
-def exclude_in_region(exclude_rows, chrom, a_start, a_end, ex_start, ex_end):
- """Take region exclusions from an iterable and apply, perhaps recursively.
-
- Returns an iterable (usually length 1) of two tuples:
- (accessible chromosome, start, end)
- (current exclusion start, end)
- """
- # If we've leapfrogged the excluded area, catch up
- while ex_end <= a_start:
- ex_start, ex_end = next_or_inf(exclude_rows)
- if a_end <= ex_start:
- # Excluded area does not overlap this one
- yield (chrom, a_start, a_end)
- else:
- # Excluded area overlaps this one -> trim this region
- logging.info("\tExclusion %s:%d-%d overlaps accessible region %d-%d",
- chrom, ex_start, ex_end, a_start, a_end)
- if ex_start <= a_start:
- if ex_end < a_end:
- # Exclusion covers this region's left (start) edge only
- for row in exclude_in_region(exclude_rows, chrom, ex_end, a_end,
- ex_start, ex_end):
- yield row
- # Otherwise: Exclusion covers the whole region
- else:
- yield (chrom, a_start, ex_start)
- if ex_end < a_end:
- # Exclusion is in the middle of this region
- for row in exclude_in_region(exclude_rows, chrom, ex_end,
- a_end, ex_start, ex_end):
- yield row
- # Otherwise: Exclusion covers this region's right (end) edge only
-
-
-def next_or_inf(iterable):
- try:
- return next(iterable)
- except StopIteration:
- return float("Inf"), float("Inf")
-
diff --git a/cnvlib/antitarget.py b/cnvlib/antitarget.py
index 1dc70b4..01f6e31 100644
--- a/cnvlib/antitarget.py
+++ b/cnvlib/antitarget.py
@@ -1,18 +1,25 @@
"""Supporting functions for the 'antitarget' command."""
from __future__ import absolute_import, division, print_function
-import re
-import sys
+from builtins import map
+
import logging
+import re
+
+from skgenome import GenomicArray as GA
+
+from .params import INSERT_SIZE, MIN_REF_COVERAGE, ANTITARGET_NAME
-from Bio._py3k import range
-iteritems = (dict.iteritems if sys.version_info[0] < 3 else dict.items)
-from .params import INSERT_SIZE
-from .rary import RegionArray as RA
+def do_antitarget(targets, access=None, avg_bin_size=150000,
+ min_bin_size=None):
+ """Derive off-targt ("antitarget") bins from target regions."""
+ if not min_bin_size:
+ min_bin_size = 2 * int(avg_bin_size * (2 ** MIN_REF_COVERAGE))
+ return get_antitargets(targets, access, avg_bin_size, min_bin_size)
-def get_background(target_bed, access_bed, avg_bin_size, min_bin_size):
- """Generate background intervals from target intervals.
+def get_antitargets(targets, accessible, avg_bin_size, min_bin_size):
+ """Generate antitarget intervals between/around target intervals.
Procedure:
@@ -25,112 +32,61 @@ def get_background(target_bed, access_bed, avg_bin_size, min_bin_size):
- Divide into equal-size (region_size/avg_bin_size) portions
- Emit the (chrom, start, end) coords of each portion
"""
- target_chroms = dict(RA.read(target_bed).by_chromosome())
- if access_bed:
+ if accessible:
# Chromosomes' accessible sequence regions are given -- use them
- access_chroms = dict(RA.read(access_bed).by_chromosome())
- if access_chroms and set(access_chroms).isdisjoint(target_chroms):
- raise ValueError("Chromosome names in the accessible regions file "
- "%s %r do not match those in targets %s %r"
- % (access_bed,
- tuple(sorted(access_chroms.keys())[:3]),
- target_bed,
- tuple(sorted(target_chroms.keys())[:3])))
+ access_chroms, target_chroms = compare_chrom_names(accessible, targets)
# But filter out untargeted alternative contigs and mitochondria
- untgt_chroms = set(access_chroms) - set(target_chroms)
+ untgt_chroms = access_chroms - target_chroms
# Autosomes typically have numeric names, allosomes are X and Y
is_canonical = re.compile(r"(chr)?(\d+|[XYxy])$")
if any(is_canonical.match(c) for c in target_chroms):
chroms_to_skip = [c for c in untgt_chroms
if not is_canonical.match(c)]
else:
- # Alternative contigs have long names -- skip them
+ # Alternative contigs have longer names -- skip them
max_tgt_chr_name_len = max(map(len, target_chroms))
chroms_to_skip = [c for c in untgt_chroms
if len(c) > max_tgt_chr_name_len]
- for untgt_chr in chroms_to_skip:
- logging.info("Skipping untargeted chromosome %s", untgt_chr)
- del access_chroms[untgt_chr]
+ if chroms_to_skip:
+ logging.info("Skipping untargeted chromosomes %s",
+ ' '.join(sorted(chroms_to_skip)))
+ skip_idx = accessible.chromosome.isin(chroms_to_skip)
+ accessible = accessible[~skip_idx]
else:
# Chromosome accessible sequence regions not known -- use heuristics
# (chromosome length is endpoint of last probe; skip initial
# <magic number> of bases that are probably telomeric)
TELOMERE_SIZE = 150000
- access_chroms = guess_chromosome_regions(target_chroms, TELOMERE_SIZE)
-
- backgrounds = find_background_regions(access_chroms, target_chroms,
- 2 * INSERT_SIZE)
- bg_arr = RA.from_rows(backgrounds)
- bg_arr.sort()
-
- # Emit regions as antitarget bins according to avg_bin_size and min_bin_size
- out_rows = []
- for chrom, start, end in bg_arr.coords():
- span = end - start
- if span >= min_bin_size:
- nbins = int(round(span / avg_bin_size)) or 1
- if nbins == 1:
- out_rows.append((chrom, start, end))
- else:
- # Divide the background region into equal-sized bins
- bin_size = span / nbins
- bin_start = start
- bin_end = None
- for i in range(1, nbins):
- bin_end = start + int(i * bin_size)
- out_rows.append((chrom, bin_start, bin_end))
- bin_start = bin_end
- out_rows.append((chrom, bin_start, end))
- out_arr = RA.from_rows(out_rows)
- out_arr["name"] = "Background"
- return out_arr
-
-
-def guess_chromosome_regions(target_chroms, telomere_size):
+ accessible = guess_chromosome_regions(targets, TELOMERE_SIZE)
+
+ pad_size = 2 * INSERT_SIZE
+ bg_arr = (accessible.resize_ranges(-pad_size)
+ .subtract(targets.resize_ranges(pad_size))
+ .subdivide(avg_bin_size, min_bin_size))
+ bg_arr['gene'] = ANTITARGET_NAME
+ return bg_arr
+
+
+def compare_chrom_names(a_regions, b_regions):
+ a_chroms = set(a_regions.chromosome.unique())
+ b_chroms = set(b_regions.chromosome.unique())
+ if a_chroms and a_chroms.isdisjoint(b_chroms):
+ msg = "Chromosome names do not match between files"
+ a_fname = a_regions.meta.get('filename')
+ b_fname = b_regions.meta.get('filename')
+ if a_fname and b_fname:
+ msg += " {} and {}".format(a_fname, b_fname)
+ msg += ": {} vs. {}".format(', '.join(map(repr, sorted(a_chroms)[:3])),
+ ', '.join(map(repr, sorted(b_chroms)[:3])))
+ raise ValueError(msg)
+ return a_chroms, b_chroms
+
+
+def guess_chromosome_regions(targets, telomere_size):
"""Determine (minimum) chromosome lengths from target coordinates."""
- endpoints = [target_region[len(target_region) - 1, 'end']
- for _chrom, target_region in target_chroms.iteritems()]
- whole_chroms = RA.from_columns({"chromosome": target_chroms.keys(),
- "start": telomere_size,
- "end": endpoints})
- return dict(whole_chroms.by_chromosome())
-
-
-def find_background_regions(access_chroms, target_chroms, pad_size):
- """Take coordinates of accessible regions and targets; emit antitargets."""
- for chrom, access_arr in access_chroms.iteritems():
- if chrom in target_chroms:
- target_regions = target_chroms[chrom].coords()
-
- # Split each access_region at the targets it contains
- _, tgt_start, tgt_end = next(target_regions)
- assert tgt_start < tgt_end
- for _, acc_start, acc_end in access_arr.coords():
- if acc_end - acc_start <= 2 * pad_size:
- # Accessible region is way too small
- continue
-
- bg_start = acc_start + pad_size
- while tgt_start < acc_end:
- # There may be at least one more target in this region
- if tgt_end + pad_size > bg_start:
- # Yes, there is a target in this region
- if tgt_start - pad_size > bg_start:
- # Split the background region at this target
- yield (chrom, bg_start, tgt_start - pad_size)
- bg_start = tgt_end + pad_size
-
- # Done splitting that target; is there another?
- try:
- _, tgt_start, tgt_end = next(target_regions)
- except StopIteration:
- # Ensure all the remaining access_regions are unbroken
- tgt_start = tgt_end = float('Inf')
-
- # No remaining targets in this region - emit the rest of it
- if acc_end - pad_size - bg_start > 0:
- yield (chrom, bg_start, acc_end - pad_size)
- else:
- for _, acc_start, acc_end in access_arr.coords():
- yield (chrom, acc_start + pad_size, acc_end - pad_size)
-
+ endpoints = [subarr.end.iat[-1] for _c, subarr in targets.by_chromosome()]
+ whole_chroms = GA.from_columns({
+ 'chromosome': targets.chromosome.drop_duplicates(),
+ 'start': telomere_size,
+ 'end': endpoints})
+ return whole_chroms
diff --git a/cnvlib/autobin.py b/cnvlib/autobin.py
new file mode 100644
index 0000000..ba88133
--- /dev/null
+++ b/cnvlib/autobin.py
@@ -0,0 +1,185 @@
+"""Estimate reasonable bin sizes from BAM read counts or depths."""
+from __future__ import absolute_import, division, print_function
+import logging
+import os
+import tempfile
+
+import numpy as np
+import pandas as pd
+from skgenome import tabio, GenomicArray as GA
+
+from . import coverage, samutil
+from .descriptives import weighted_median
+
+
+def midsize_file(fnames):
+ """Select the median-size file from several given filenames.
+
+ If an even number of files is given, selects the file just below the median.
+ """
+ return sorted(fnames, key=lambda f: os.stat(f).st_size
+ )[len(fnames) // 2 - 1]
+
+
+def do_autobin(bam_fname, method, targets=None, access=None,
+ bp_per_bin=100000., target_min_size=20, target_max_size=20000,
+ antitarget_min_size=500, antitarget_max_size=500000):
+ """Quickly calculate reasonable bin sizes from BAM read counts.
+
+ Parameters
+ ----------
+ bam_fname : string
+ BAM filename.
+ method : string
+ One of: 'wgs' (whole-genome sequencing), 'amplicon' (targeted amplicon
+ capture), 'hybrid' (hybridization capture).
+ targets : GenomicArray
+ Targeted genomic regions (for 'hybrid' and 'amplicon').
+ access : GenomicArray
+ Sequencing-accessible regions of the reference genome (for 'hybrid' and
+ 'wgs').
+ bp_per_bin : int
+ Desired number of sequencing read nucleotide bases mapped to each bin.
+
+ Returns
+ -------
+ 2-tuple of 2-tuples:
+ ((target depth, target avg. bin size),
+ (antitarget depth, antitarget avg. bin size))
+ """
+ # Closes over bp_per_bin
+ def depth2binsize(depth, min_size, max_size):
+ if depth:
+ bin_size = int(round(bp_per_bin / depth))
+ if bin_size < min_size:
+ logging.info("Limiting est. bin size %d to given min. %d",
+ bin_size, min_size)
+ bin_size = min_size
+ elif bin_size > max_size:
+ logging.info("Limiting est. bin size %d to given max. %d",
+ bin_size, max_size)
+ bin_size = max_size
+ return bin_size
+
+ samutil.ensure_bam_index(bam_fname)
+ rc_table = samutil.idxstats(bam_fname, drop_unmapped=True)
+ read_len = samutil.get_read_length(bam_fname)
+ logging.info("Estimated read length %s", read_len)
+
+ # Dispatch
+ if method == 'amplicon':
+ # From BAM index
+ # rc_table = update_chrom_length(rc_table, targets)
+ # tgt_depth = average_depth(rc_table, read_len)
+ # By sampling
+ tgt_depth = sample_region_cov(bam_fname, targets)
+ anti_depth = None
+ elif method == 'hybrid':
+ tgt_depth, anti_depth = hybrid(rc_table, read_len, bam_fname, targets,
+ access)
+ elif method == 'wgs':
+ if access is not None and len(access):
+ rc_table = update_chrom_length(rc_table, access)
+ tgt_depth = average_depth(rc_table, read_len)
+ anti_depth = None
+
+ # Clip bin sizes to specified ranges
+ tgt_bin_size = depth2binsize(tgt_depth, target_min_size, target_max_size)
+ anti_bin_size = depth2binsize(anti_depth, antitarget_min_size,
+ antitarget_max_size)
+ return ((tgt_depth, tgt_bin_size),
+ (anti_depth, anti_bin_size))
+
+
+def hybrid(rc_table, read_len, bam_fname, targets, access=None):
+ """Hybrid capture sequencing."""
+ # Identify off-target regions
+ if access is None:
+ access = idxstats2ga(rc_table)
+ antitargets = access.subtract(targets)
+ # Only examine chromosomes present in all 2-3 input datasets
+ rc_table, targets, antitargets = shared_chroms(rc_table, targets,
+ antitargets)
+ # Deal with targets
+ target_depth = sample_region_cov(bam_fname, targets)
+ # Antitargets: subtract captured reads from total
+ target_length = region_size_by_chrom(targets)['length']
+ target_reads = (target_length * target_depth / read_len).values
+ anti_table = update_chrom_length(rc_table, antitargets)
+ anti_table = anti_table.assign(mapped=anti_table.mapped - target_reads)
+ anti_depth = average_depth(anti_table, read_len)
+ return target_depth, anti_depth
+
+
+# ---
+
+def average_depth(rc_table, read_length):
+ """Estimate the average read depth across the genome.
+
+ Returns
+ -------
+ float
+ Median of the per-chromosome mean read depths, weighted by chromosome
+ size.
+ """
+ mean_depths = read_length * rc_table.mapped / rc_table.length
+ return weighted_median(mean_depths, rc_table.length)
+
+
+def idxstats2ga(table):
+ return GA(table.assign(start=0, end=table.length)
+ .loc[:, ('chromosome', 'start', 'end')])
+
+
+def sample_region_cov(bam_fname, regions, max_num=100):
+ """Calculate read depth in a randomly sampled subset of regions."""
+ midsize_regions = sample_midsize_regions(regions, max_num)
+ with tempfile.NamedTemporaryFile(suffix='.bed', mode='w+t') as f:
+ tabio.write(regions.as_dataframe(midsize_regions), f, 'bed4')
+ f.flush()
+ table = coverage.bedcov(f.name, bam_fname, 0)
+ # Mean read depth across all sampled regions
+ return table.basecount.sum() / (table.end - table.start).sum()
+
+
+def sample_midsize_regions(regions, max_num):
+ """Randomly select a subset of up to `max_num` regions."""
+ sizes = regions.end - regions.start
+ lo_size, hi_size = np.percentile(sizes[sizes > 0], [25, 75])
+ midsize_regions = regions.data[(sizes >= lo_size) & (sizes <= hi_size)]
+ if len(midsize_regions) > max_num:
+ midsize_regions = midsize_regions.sample(max_num, random_state=0xA5EED)
+ return midsize_regions
+
+
+def shared_chroms(*tables):
+ """Intersection of DataFrame .chromosome values."""
+ chroms = tables[0].chromosome.drop_duplicates()
+ for tab in tables[1:]:
+ if tab is not None:
+ new_chroms = tab.chromosome.drop_duplicates()
+ chroms = chroms[chroms.isin(new_chroms)]
+ return [None if tab is None else tab[tab.chromosome.isin(chroms)]
+ for tab in tables]
+
+
+def update_chrom_length(rc_table, regions):
+ if regions is not None and len(regions):
+ chrom_sizes = region_size_by_chrom(regions)
+ rc_table = rc_table.merge(chrom_sizes, on='chromosome', how='inner')
+ rc_table['length'] = rc_table['length_y'] # ?
+ rc_table = rc_table.drop(['length_x', 'length_y'], axis=1)
+ return rc_table
+
+
+def region_size_by_chrom(regions):
+ chromgroups = regions.data.groupby('chromosome', sort=False)
+ # sizes = chromgroups.apply(total_region_size) # XXX
+ sizes = [total_region_size(g) for _key, g in chromgroups]
+ return pd.DataFrame({'chromosome': regions.chromosome.drop_duplicates(),
+ 'length': sizes})
+
+
+def total_region_size(regions):
+ """Aggregate area of all genomic ranges in `regions`."""
+ return (regions.end - regions.start).sum()
diff --git a/cnvlib/batch.py b/cnvlib/batch.py
new file mode 100644
index 0000000..93206ce
--- /dev/null
+++ b/cnvlib/batch.py
@@ -0,0 +1,205 @@
+"""The 'batch' command."""
+from __future__ import absolute_import, division, print_function
+
+import logging
+import os
+
+from matplotlib import pyplot
+from skgenome import tabio, GenomicArray as GA
+
+from . import (access, antitarget, autobin, core, coverage, diagram, fix,
+ parallel, reference, scatter, segmentation, target)
+from .cmdutil import read_cna
+
+
+def batch_make_reference(normal_bams, target_bed, antitarget_bed,
+ male_reference, fasta, annotate, short_names,
+ target_avg_size, access_bed, antitarget_avg_size,
+ antitarget_min_size, output_reference, output_dir,
+ processes, by_count, method):
+ """Build the CN reference from normal samples, targets and antitargets."""
+ if method in ("wgs", "amplicon"):
+ if antitarget_bed:
+ raise ValueError("%r protocol: antitargets should not be "
+ "given/specified." % method)
+ if access_bed and target_bed and access_bed != target_bed:
+ raise ValueError("%r protocol: targets and access should not be "
+ "different." % method)
+
+ bait_arr = None
+ if method == "wgs":
+ if not annotate:
+ # TODO check if target_bed has gene names
+ raise ValueError("WGS protocol: need '--annotate' option "
+ "(e.g. refFlat.txt) to avoid later problems "
+ "locating genes in data.")
+ access_arr = None
+ if not target_bed:
+ # TODO - drop weird contigs before writing, see antitargets.py
+ if access_bed:
+ target_bed = access_bed
+ elif fasta:
+ # Run 'access' on the fly
+ access_arr = access.do_access(fasta)
+ # Take filename base from FASTA, lacking any other clue
+ target_bed = os.path.splitext(os.path.basename(fasta)
+ )[0] + ".bed"
+ tabio.write(access_arr, target_bed, "bed3")
+ else:
+ raise ValueError("WGS protocol: need to provide --targets, "
+ "--access, or --fasta options.")
+
+ # Tweak default parameters
+ if not target_avg_size:
+ if normal_bams:
+ # Calculate bin size from .bai & access
+ if fasta and not access_arr:
+ # Calculate wgs depth from all
+ # sequencing-accessible area (it doesn't take that long
+ # compared to WGS coverage); user-provided access might be
+ # something else that excludes a significant number of
+ # mapped reads.
+ access_arr = access.do_access(fasta)
+ if access_arr:
+ autobin_args = ['wgs', access_arr]
+ else:
+ # Don't assume the given targets/access covers the whole
+ # genome; use autobin sampling to estimate bin size, as we
+ # do for amplicon
+ bait_arr = tabio.read_auto(target_bed)
+ autobin_args = ['amplicon', bait_arr]
+ # Choose median-size normal bam or tumor bam
+ bam_fname = autobin.midsize_file(normal_bams)
+ (wgs_depth, target_avg_size), _ = autobin.do_autobin(
+ bam_fname, *autobin_args, bp_per_bin=50000.)
+ logging.info("WGS average depth %.2f --> using bin size %d",
+ wgs_depth, target_avg_size)
+ else:
+ # This bin size is OK down to 10x
+ target_avg_size = 5000
+
+ # To make temporary filenames for processed targets or antitargets
+ tgt_name_base, _tgt_ext = os.path.splitext(os.path.basename(target_bed))
+ if output_dir:
+ tgt_name_base = os.path.join(output_dir, tgt_name_base)
+
+ # Pre-process baits/targets
+ new_target_fname = tgt_name_base + '.target.bed'
+ if bait_arr is None:
+ bait_arr = tabio.read_auto(target_bed)
+ target_arr = target.do_target(bait_arr, annotate, short_names, True,
+ **({'avg_size': target_avg_size}
+ if target_avg_size
+ else {}))
+ tabio.write(target_arr, new_target_fname, 'bed4')
+ target_bed = new_target_fname
+
+ if not antitarget_bed:
+ # Devise a temporary antitarget filename
+ antitarget_bed = tgt_name_base + '.antitarget.bed'
+ if method == "hybrid":
+ # Build antitarget BED from the given targets
+ anti_kwargs = {}
+ if access_bed:
+ anti_kwargs['access'] = tabio.read_auto(access_bed)
+ if antitarget_avg_size:
+ anti_kwargs['avg_bin_size'] = antitarget_avg_size
+ if antitarget_min_size:
+ anti_kwargs['min_bin_size'] = antitarget_min_size
+ anti_arr = antitarget.do_antitarget(target_arr, **anti_kwargs)
+ else:
+ # No antitargets for wgs, amplicon
+ anti_arr = GA([])
+ tabio.write(anti_arr, antitarget_bed, "bed4")
+
+ if len(normal_bams) == 0:
+ logging.info("Building a flat reference...")
+ ref_arr = reference.do_reference_flat(target_bed, antitarget_bed, fasta,
+ male_reference)
+ else:
+ logging.info("Building a copy number reference from normal samples...")
+ # Run coverage on all normals
+ with parallel.pick_pool(processes) as pool:
+ tgt_futures = []
+ anti_futures = []
+ procs_per_cnn = max(1, processes // (2 * len(normal_bams)))
+ for nbam in normal_bams:
+ sample_id = core.fbase(nbam)
+ sample_pfx = os.path.join(output_dir, sample_id)
+ tgt_futures.append(
+ pool.submit(batch_write_coverage,
+ target_bed, nbam,
+ sample_pfx + '.targetcoverage.cnn',
+ by_count, procs_per_cnn))
+ anti_futures.append(
+ pool.submit(batch_write_coverage,
+ antitarget_bed, nbam,
+ sample_pfx + '.antitargetcoverage.cnn',
+ by_count, procs_per_cnn))
+
+ target_fnames = [tf.result() for tf in tgt_futures]
+ antitarget_fnames = [af.result() for af in anti_futures]
+ # Build reference from *.cnn
+ ref_arr = reference.do_reference(target_fnames, antitarget_fnames,
+ fasta, male_reference, None,
+ do_gc=True,
+ do_edge=(method == "hybrid"),
+ do_rmask=True)
+ if not output_reference:
+ output_reference = os.path.join(output_dir, "reference.cnn")
+ core.ensure_path(output_reference)
+ tabio.write(ref_arr, output_reference)
+ return output_reference, target_bed, antitarget_bed
+
+
+def batch_write_coverage(bed_fname, bam_fname, out_fname, by_count, processes):
+ """Run coverage on one sample, write to file."""
+ cnarr = coverage.do_coverage(bed_fname, bam_fname, by_count, 0, processes)
+ tabio.write(cnarr, out_fname)
+ return out_fname
+
+
+def batch_run_sample(bam_fname, target_bed, antitarget_bed, ref_fname,
+ output_dir, male_reference, plot_scatter, plot_diagram,
+ rlibpath, by_count, skip_low, method, processes):
+ """Run the pipeline on one BAM file."""
+ # ENH - return probes, segments (cnarr, segarr)
+ logging.info("Running the CNVkit pipeline on %s ...", bam_fname)
+ sample_id = core.fbase(bam_fname)
+ sample_pfx = os.path.join(output_dir, sample_id)
+
+ raw_tgt = coverage.do_coverage(target_bed, bam_fname, by_count, 0,
+ processes)
+ tabio.write(raw_tgt, sample_pfx + '.targetcoverage.cnn')
+
+ raw_anti = coverage.do_coverage(antitarget_bed, bam_fname, by_count, 0,
+ processes)
+ tabio.write(raw_anti, sample_pfx + '.antitargetcoverage.cnn')
+
+ cnarr = fix.do_fix(raw_tgt, raw_anti, read_cna(ref_fname),
+ do_gc=True, do_edge=(method == "hybrid"), do_rmask=True)
+ tabio.write(cnarr, sample_pfx + '.cnr')
+
+ logging.info("Segmenting %s.cnr ...", sample_pfx)
+ segments = segmentation.do_segmentation(cnarr, 'cbs',
+ rlibpath=rlibpath,
+ skip_low=skip_low,
+ processes=processes,
+ **({'threshold': 1e-6}
+ if method == 'wgs'
+ else {}))
+ tabio.write(segments, sample_pfx + '.cns')
+
+ if plot_scatter:
+ scatter.do_scatter(cnarr, segments)
+ pyplot.savefig(sample_pfx + '-scatter.pdf', format='pdf',
+ bbox_inches="tight")
+ logging.info("Wrote %s-scatter.pdf", sample_pfx)
+
+ if plot_diagram:
+ is_xx = cnarr.guess_xx(male_reference)
+ outfname = sample_pfx + '-diagram.pdf'
+ diagram.create_diagram(cnarr.shift_xx(male_reference, is_xx),
+ segments.shift_xx(male_reference, is_xx),
+ 0.5, 3, outfname)
+ logging.info("Wrote %s", outfname)
diff --git a/cnvlib/call.py b/cnvlib/call.py
index 4a0b3c1..0e179fa 100644
--- a/cnvlib/call.py
+++ b/cnvlib/call.py
@@ -1,9 +1,78 @@
"""Call copy number variants from segmented log2 ratios."""
from __future__ import absolute_import, division, print_function
+import logging
+
import numpy as np
import pandas as pd
+from . import segfilters
+
+
+def do_call(cnarr, variants=None, method="threshold", ploidy=2, purity=None,
+ is_reference_male=False, is_sample_female=False, filters=None,
+ thresholds=(-1.1, -0.25, 0.2, 0.7)):
+ if method not in ("threshold", "clonal", "none"):
+ raise ValueError("Argument `method` must be one of: clonal, threshold")
+
+ outarr = cnarr.copy()
+ if filters:
+ # Apply any filters that use segmetrics but not cn fields
+ for filt in ('ci', 'sem'):
+ if filt in filters:
+ logging.info("Applying filter '%s'", filt)
+ outarr = getattr(segfilters, filt)(outarr)
+ filters.remove(filt)
+
+ if variants:
+ outarr["baf"] = variants.baf_by_ranges(outarr)
+
+ if purity and purity < 1.0:
+ logging.info("Rescaling sample with purity %g, ploidy %d",
+ purity, ploidy)
+ absolutes = absolute_clonal(outarr, ploidy, purity,
+ is_reference_male, is_sample_female)
+ # Recalculate sample log2 ratios after rescaling for purity
+ outarr["log2"] = log2_ratios(outarr, absolutes, ploidy,
+ is_reference_male)
+ if variants:
+ # Rescale b-allele frequencies for purity
+ outarr["baf"] = rescale_baf(purity, outarr["baf"])
+ elif method == "clonal":
+ # Estimate absolute copy numbers from the original log2 values
+ logging.info("Calling copy number with clonal ploidy %d", ploidy)
+ absolutes = absolute_pure(outarr, ploidy, is_reference_male)
+
+ if method == "threshold":
+ # Apply cutoffs to either original or rescaled log2 values
+ tokens = ["%g => %d" % (thr, i) for i, thr in enumerate(thresholds)]
+ logging.info("Calling copy number with thresholds: %s",
+ ", ".join(tokens))
+ absolutes = absolute_threshold(outarr, ploidy, thresholds,
+ is_reference_male)
+
+ if method != 'none':
+ outarr['cn'] = absolutes.round().astype('int')
+ if 'baf' in outarr:
+ # Calculate major and minor allelic copy numbers (s.t. cn1 >= cn2)
+ upper_baf = ((outarr['baf'] - .5).abs() + .5).fillna(1.0).values
+ outarr['cn1'] = ((absolutes * upper_baf).round()
+ .clip(0, outarr['cn'])
+ .astype('int'))
+ outarr['cn2'] = outarr['cn'] - outarr['cn1']
+ is_null = (outarr['baf'].isnull() & (outarr['cn'] > 0))
+ outarr[is_null, 'cn1'] = np.nan
+ outarr[is_null, 'cn2'] = np.nan
+
+ if filters:
+ # Apply the remaining cn-based filters
+ for filt in filters:
+ logging.info("Applying filter '%s'", filt)
+ outarr = getattr(segfilters, filt)(outarr)
+
+ outarr.sort_columns()
+ return outarr
+
def log2_ratios(cnarr, absolutes, ploidy, is_reference_male,
min_abs_val=1e-3, round_to_int=False):
@@ -11,11 +80,11 @@ def log2_ratios(cnarr, absolutes, ploidy, is_reference_male,
Optionally round copy numbers to integers.
- Account for reference gender & ploidy of sex chromosomes.
+ Account for reference sex & ploidy of sex chromosomes.
"""
# Round absolute copy numbers to integer values
if round_to_int:
- absolutes = np.rint(absolutes)
+ absolutes = absolutes.round()
# Avoid a logarithm domain error
ratios = np.log2(np.maximum(absolutes / ploidy, min_abs_val))
# Adjust sex chromosomes to be relative to the reference
@@ -111,7 +180,7 @@ def absolute_expect(cnarr, ploidy, is_sample_female):
"""Absolute integer number of expected copies in each bin.
I.e. the given ploidy for autosomes, and XY or XX sex chromosome counts
- according to the sample's specified gender.
+ according to the sample's specified chromosomal sex.
"""
exp_copies = np.repeat(ploidy, len(cnarr))
is_y = np.asarray(cnarr.chromosome == cnarr._chr_y_label)
@@ -127,7 +196,7 @@ def absolute_reference(cnarr, ploidy, is_reference_male):
"""Absolute integer number of reference copies in each bin.
I.e. the given ploidy for autosomes, 1 or 2 X according to the reference
- gender, and always 1 copy of Y.
+ sex, and always 1 copy of Y.
"""
ref_copies = np.repeat(ploidy, len(cnarr))
is_x = np.asarray(cnarr.chromosome == cnarr._chr_x_label)
@@ -144,12 +213,15 @@ def _reference_expect_copies(chrom, ploidy, is_sample_female, is_reference_male)
For sex chromosomes, these values may not be the same ploidy as the
autosomes. The "reference" number is the chromosome's ploidy in the
CNVkit reference, while "expect" is the chromosome's neutral ploidy in the
- given sample, based on the specified gender of each. E.g., given a female
+ given sample, based on the specified sex of each. E.g., given a female
sample and a male reference, on chromosome X the "reference" value is 1 but
"expect" is 2.
- Return a pair of integers: number of copies in the reference, and expected in
- the sample.
+ Returns
+ -------
+ tuple
+ A pair of integers: number of copies in the reference, and expected in
+ the sample.
"""
chrom = chrom.lower()
if chrom in ["chrx", "x"]:
@@ -166,7 +238,10 @@ def _reference_expect_copies(chrom, ploidy, is_sample_female, is_reference_male)
def _reference_copies_pure(chrom, ploidy, is_reference_male):
"""Determine the reference number of chromosome copies (pure sample).
- Return the integer number of copies in the reference.
+ Returns
+ -------
+ int
+ Number of copies in the reference.
"""
chrom = chrom.lower()
if chrom in ["chry", "y"] or (is_reference_male and chrom in ["chrx", "x"]):
@@ -215,9 +290,22 @@ def _log2_ratio_to_absolute_pure(log2_ratio, ref_copies):
Purity adjustment is skipped. This is appropriate if the sample is germline
or if scaling for tumor heterogeneity was done beforehand.
- Math::
-
- n = r*2^v
+ .. math :: n = r*2^v
"""
ncopies = ref_copies * 2 ** log2_ratio
return ncopies
+
+
+def rescale_baf(purity, observed_baf, normal_baf=0.5):
+ """Adjust B-allele frequencies for sample purity.
+
+ Math::
+
+ t_baf*purity + n_baf*(1-purity) = obs_baf
+ obs_baf - n_baf * (1-purity) = t_baf * purity
+ t_baf = (obs_baf - n_baf * (1-purity))/purity
+ """
+ # ENH: use normal_baf array if available
+ tumor_baf = (observed_baf - normal_baf * (1-purity)) / purity
+ # ENH: warn if tumor_baf < 0 -- purity estimate may be too low
+ return tumor_baf
diff --git a/cnvlib/cmdutil.py b/cnvlib/cmdutil.py
new file mode 100644
index 0000000..baf3bfc
--- /dev/null
+++ b/cnvlib/cmdutil.py
@@ -0,0 +1,90 @@
+"""Functions reused within command-line implementations."""
+from __future__ import absolute_import, division, print_function
+
+import logging
+import sys
+
+from skgenome import tabio
+
+from .cnary import CopyNumArray as CNA
+
+
+def read_cna(infile, sample_id=None, meta=None):
+ """Read a CNVkit file (.cnn, .cnr, .cns) to create a CopyNumArray object."""
+ return tabio.read(infile, into=CNA, sample_id=sample_id, meta=meta)
+
+
+def load_het_snps(vcf_fname, sample_id=None, normal_id=None,
+ min_variant_depth=20, zygosity_freq=None, tumor_boost=False):
+ if vcf_fname is None:
+ return None
+ varr = tabio.read(vcf_fname, 'vcf',
+ sample_id=sample_id,
+ normal_id=normal_id,
+ min_depth=min_variant_depth,
+ skip_somatic=True)
+ if (zygosity_freq is None and 'n_zygosity' in varr and
+ not varr['n_zygosity'].any()):
+ # Mutect2 sets all normal genotypes to 0/0 -- work around it
+ logging.warn("VCF normal sample's genotypes are all 0/0 or missing; "
+ "inferring genotypes from allele frequency instead")
+ zygosity_freq = 0.25
+ if zygosity_freq is not None:
+ varr = varr.zygosity_from_freq(zygosity_freq, 1 - zygosity_freq)
+ if 'n_zygosity' in varr:
+ # Infer & drop (more) somatic loci based on genotype
+ somatic_idx = (varr['zygosity'] != 0.0) & (varr['n_zygosity'] == 0.0)
+ if somatic_idx.any() and not somatic_idx.all():
+ logging.info("Skipping %d additional somatic record based on "
+ "T/N genotypes", somatic_idx.sum())
+ varr = varr[~somatic_idx]
+ orig_len = len(varr)
+ varr = varr.heterozygous()
+ logging.info("Kept %d heterozygous of %d VCF records",
+ len(varr), orig_len)
+ # TODO use/explore tumor_boost option
+ if tumor_boost:
+ varr['alt_freq'] = varr.tumor_boost()
+ return varr
+
+
+def verify_sample_sex(cnarr, sex_arg, is_male_reference):
+ is_sample_female = cnarr.guess_xx(is_male_reference, verbose=False)
+ if sex_arg:
+ is_sample_female_given = (sex_arg.lower() not in ['y', 'm', 'male'])
+ if is_sample_female != is_sample_female_given:
+ logging.warn("Sample sex specified as %s "
+ "but chromosomal X/Y ploidy looks like %s",
+ "female" if is_sample_female_given else "male",
+ "female" if is_sample_female else "male")
+ is_sample_female = is_sample_female_given
+ logging.info("Treating sample %s as %s",
+ cnarr.sample_id or '',
+ "female" if is_sample_female else "male")
+ return is_sample_female
+
+
+def write_tsv(outfname, rows, colnames=None):
+ """Write rows, with optional column header, to tabular file."""
+ with tabio.safe_write(outfname or sys.stdout) as handle:
+ if colnames:
+ header = '\t'.join(colnames) + '\n'
+ handle.write(header)
+ handle.writelines('\t'.join(map(str, row)) + '\n'
+ for row in rows)
+
+
+def write_text(outfname, text, *more_texts):
+ """Write one or more strings (blocks of text) to a file."""
+ with tabio.safe_write(outfname or sys.stdout) as handle:
+ handle.write(text)
+ if more_texts:
+ for mtext in more_texts:
+ handle.write(mtext)
+
+
+def write_dataframe(outfname, dframe, header=True):
+ """Write a pandas.DataFrame to a tabular file."""
+ with tabio.safe_write(outfname or sys.stdout) as handle:
+ dframe.to_csv(handle, header=header,
+ index=False, sep='\t', float_format='%.6g')
diff --git a/cnvlib/cnary.py b/cnvlib/cnary.py
index 6924756..14cb740 100644
--- a/cnvlib/cnary.py
+++ b/cnvlib/cnary.py
@@ -1,15 +1,20 @@
"""CNVkit's core data structure, a copy number array."""
from __future__ import print_function, absolute_import, division
+from builtins import map
+from past.builtins import basestring
import logging
import numpy as np
import pandas as pd
+from scipy.stats import median_test
+from skgenome import GenomicArray
-from . import core, gary, metrics, params, smoothing
+from . import core, descriptives, params, smoothing
+from .metrics import segment_mean
-class CopyNumArray(gary.GenomicArray):
+class CopyNumArray(GenomicArray):
"""An array of genomic intervals, treated like aCGH probes.
Required columns: chromosome, start, end, gene, log2
@@ -17,13 +22,13 @@ class CopyNumArray(gary.GenomicArray):
Optional columns: gc, rmask, spread, weight, probes
"""
_required_columns = ("chromosome", "start", "end", "gene", "log2")
- _required_dtypes = ("string", "int", "int", "string", "float")
+ _required_dtypes = (str, int, int, str, float)
# ENH: make gene optional
# Extra columns, in order:
- # "gc", "rmask", "spread", "weight", "probes"
+ # "depth", "gc", "rmask", "spread", "weight", "probes"
def __init__(self, data_table, meta_dict=None):
- gary.GenomicArray.__init__(self, data_table, meta_dict)
+ GenomicArray.__init__(self, data_table, meta_dict)
@property
def log2(self):
@@ -37,8 +42,7 @@ class CopyNumArray(gary.GenomicArray):
def _chr_x_label(self):
if 'chr_x' in self.meta:
return self.meta['chr_x']
- chr_x = ('chrX' if self[0, 'chromosome'].startswith('chr')
- else 'X')
+ chr_x = ('chrX' if self.chromosome.iat[0].startswith('chr') else 'X')
self.meta['chr_x'] = chr_x
return chr_x
@@ -53,29 +57,37 @@ class CopyNumArray(gary.GenomicArray):
# More meta to store:
# is_sample_male = bool
# is_reference_male = bool
- # file_path
# * invalidate 'chr_x' if .chromosome/['chromosome'] is set
# Traversal
- # XXX hair: some genes overlap; some bins cover multiple genes
- # -> option: whether to split gene names on commas
def by_gene(self, ignore=params.IGNORE_GENE_NAMES):
"""Iterate over probes grouped by gene name.
- Emits pairs of (gene name, CNA of rows with same name)
+ Group each series of intergenic bins as an "Antitarget" gene; any
+ "Antitarget" bins within a gene are grouped with that gene.
- Groups each series of intergenic bins as a 'Background' gene; any
- 'Background' bins within a gene are grouped with that gene.
- Bins with names in `ignore` are treated as 'Background' bins, but retain
- their name.
+ Bins' gene names are split on commas to accommodate overlapping genes
+ and bins that cover multiple genes.
+
+ Parameters
+ ----------
+ ignore : list or tuple of str
+ Gene names to treat as "Antitarget" bins instead of real genes,
+ grouping these bins with the surrounding gene or intergenic region.
+ These bins will still retain their name in the output.
+
+ Yields
+ ------
+ tuple
+ Pairs of: (gene name, CNA of rows with same name)
"""
+ ignore += params.ANTITARGET_ALIASES
start_idx = end_idx = None
for _chrom, subgary in self.by_chromosome():
prev_idx = 0
- for gene in pd.unique(subgary.data['gene']):
- if not (gene == 'Background' or gene in ignore):
- gene_idx = (subgary.data['gene'] == gene).nonzero()[0]
+ for gene, gene_idx in subgary._get_gene_map().items():
+ if gene not in ignore:
if not len(gene_idx):
logging.warn("Specified gene name somehow missing: %s",
gene)
@@ -84,25 +96,42 @@ class CopyNumArray(gary.GenomicArray):
end_idx = gene_idx[-1] + 1
if prev_idx < start_idx:
# Include intergenic regions
- yield "Background", subgary.as_dataframe(
+ yield params.ANTITARGET_NAME, subgary.as_dataframe(
subgary.data.iloc[prev_idx:start_idx])
yield gene, subgary.as_dataframe(
subgary.data.iloc[start_idx:end_idx])
prev_idx = end_idx
if prev_idx < len(subgary) - 1:
# Include the telomere
- yield "Background", subgary.as_dataframe(
+ yield params.ANTITARGET_NAME, subgary.as_dataframe(
subgary.data.iloc[prev_idx:])
# Manipulation
- def center_all(self, estimator=np.median, skip_low=False):
- """Recenter coverage values to the autosomes' average (in-place)."""
+ def center_all(self, estimator=pd.Series.median, by_chrom=True,
+ skip_low=False, verbose=False):
+ """Re-center log2 values to the autosomes' average (in-place).
+
+ Parameters
+ ----------
+ estimator : str or callable
+ Function to estimate central tendency. If a string, must be one of
+ 'mean', 'median', 'mode', 'biweight' (for biweight location). Median
+ by default.
+ skip_low : bool
+ Whether to drop very-low-coverage bins (via `drop_low_coverage`)
+ before estimating the center value.
+ by_chrom : bool
+ If True, first apply `estimator` to each chromosome separately, then
+ apply `estimator` to the per-chromosome values, to reduce the impact
+ of uneven targeting or extreme aneuploidy. Otherwise, apply
+ `estimator` to all log2 values directly.
+ """
est_funcs = {
- "mean": np.mean,
- "median": np.median,
- "mode": metrics.modal_location,
- "biweight": metrics.biweight_location,
+ "mean": pd.Series.mean,
+ "median": pd.Series.median,
+ "mode": descriptives.modal_location,
+ "biweight": descriptives.biweight_location,
}
if isinstance(estimator, basestring):
if estimator in est_funcs:
@@ -110,45 +139,86 @@ class CopyNumArray(gary.GenomicArray):
else:
raise ValueError("Estimator must be a function or one of: %s"
% ", ".join(map(repr, est_funcs)))
- table = (self.drop_low_coverage() if skip_low else self).autosomes()
- if table:
- self.data['log2'] -= estimator(table['log2'])
-
- def drop_low_coverage(self):
- """Drop bins with extremely low log2 coverage values.
-
- These are generally bins that had no reads mapped, and so were
- substituted with a small dummy log2 value to avoid divide-by-zero
- errors.
+ cnarr = (self.drop_low_coverage(verbose=verbose) if skip_low else self
+ ).autosomes()
+ if cnarr:
+ if by_chrom:
+ values = pd.Series([estimator(subarr['log2'])
+ for _c, subarr in cnarr.by_chromosome()
+ if len(subarr)])
+ else:
+ values = cnarr['log2']
+ shift = -estimator(values)
+ if verbose:
+ logging.info("Shifting log2 values by %f", shift)
+ self.data['log2'] += shift
+
+ def drop_low_coverage(self, verbose=False):
+ """Drop bins with extremely low log2 coverage or copy ratio values.
+
+ These are generally bins that had no reads mapped due to sample-specific
+ issues. A very small log2 ratio or coverage value may have been
+ substituted to avoid domain or divide-by-zero errors.
"""
- return self.as_dataframe(self.data[self.data['log2'] >
- params.NULL_LOG2_COVERAGE -
- params.MIN_REF_COVERAGE])
-
- def squash_genes(self, summary_func=metrics.biweight_location,
- squash_background=False, ignore=params.IGNORE_GENE_NAMES):
+ min_cvg = params.NULL_LOG2_COVERAGE - params.MIN_REF_COVERAGE
+ drop_idx = self.data['log2'] < min_cvg
+ if 'depth' in self:
+ drop_idx |= self.data['depth'] == 0
+ if verbose and drop_idx.any():
+ logging.info("Dropped %d low-coverage bins",
+ drop_idx.sum())
+ return self[~drop_idx]
+
+ def squash_genes(self, summary_func=descriptives.biweight_location,
+ squash_antitarget=False, ignore=params.IGNORE_GENE_NAMES,
+ squash_background=None, # DEPRECATED in 0.9.0
+ ):
"""Combine consecutive bins with the same targeted gene name.
- The `ignore` parameter lists bin names that not be counted as genes to
- be output.
-
- Parameter `summary_func` is a function that summarizes an array of
- coverage values to produce the "squashed" gene's coverage value. By
- default this is the biweight location, but you might want median, mean,
- max, min or something else in some cases.
+ Parameters
+ ----------
+ summary_func : callable
+ Function to summarize an array of log2 values to produce a
+ new log2 value for a "squashed" (i.e. reduced) region. By default
+ this is the biweight location, but you might want median, mean, max,
+ min or something else in some cases.
+ squash_antitarget : bool
+ If True, also reduce consecutive "Antitarget" bins into a single
+ bin. Otherwise, keep "Antitarget" and ignored bins as they are in
+ the output.
+ ignore : list or tuple of str
+ Bin names to be treated as "Antitarget" instead of as unique genes.
+
+ Return
+ ------
+ CopyNumArray
+ Another, usually smaller, copy of `self` with each gene's bins
+ reduced to a single bin with appropriate values.
"""
+ # Handle the deprecated argument
+ if squash_background is not None:
+ if squash_antitarget == squash_background:
+ logging.warn("Keyword argument squash_background=%r was given; "
+ "use squash_antitarget instead.", squash_background)
+ squash_antitarget = squash_background
+ else:
+ raise ValueError(
+ "Deprecated keyword argument squash_background=%r was given, "
+ "but conflicts with its successor squash_antitarget=%r"
+ % (squash_background, squash_antitarget))
+
def squash_rows(name, rows):
"""Combine multiple rows (for the same gene) into one row."""
if len(rows) == 1:
return tuple(rows.iloc[0])
chrom = core.check_unique(rows.chromosome, 'chromosome')
- start = rows.iloc[0]['start']
- end = rows.iloc[-1]['end']
+ start = rows.start.iat[0]
+ end = rows.end.iat[-1]
cvg = summary_func(rows.log2)
outrow = [chrom, start, end, name, cvg]
# Handle extra fields
# ENH - no coverage stat; do weighted average as appropriate
- for xfield in ('gc', 'rmask', 'spread', 'weight'):
+ for xfield in ('depth', 'gc', 'rmask', 'spread', 'weight'):
if xfield in self:
outrow.append(summary_func(rows[xfield]))
if 'probes' in self:
@@ -157,18 +227,19 @@ class CopyNumArray(gary.GenomicArray):
outrows = []
for name, subarr in self.by_gene(ignore):
- if name == 'Background' and not squash_background:
+ if name in params.ANTITARGET_ALIASES and not squash_antitarget:
outrows.extend(subarr.data.itertuples(index=False))
else:
outrows.append(squash_rows(name, subarr.data))
return self.as_rows(outrows)
- # Chromosomal gender
+ # Chromosomal sex
- def shift_xx(self, male_reference=False):
- """Adjust chrX coverages (divide in half) for apparent female samples."""
+ def shift_xx(self, male_reference=False, is_xx=None):
+ """Adjust chrX log2 ratios (subtract 1) for apparent female samples."""
outprobes = self.copy()
- is_xx = self.guess_xx(male_reference=male_reference)
+ if is_xx is None:
+ is_xx = self.guess_xx(male_reference=male_reference)
if is_xx and male_reference:
# Female: divide X coverages by 2 (in log2: subtract 1)
outprobes[outprobes.chromosome == self._chr_x_label, 'log2'] -= 1.0
@@ -180,47 +251,152 @@ class CopyNumArray(gary.GenomicArray):
return outprobes
def guess_xx(self, male_reference=False, verbose=True):
- """Guess whether a sample is female from chrX relative coverages.
-
- Recommended cutoff values:
- -0.5 -- raw target data, not yet corrected
- +0.5 -- probe data already corrected on a male profile
+ """Detect chromosomal sex; return True if a sample is probably female.
+
+ Uses `compare_sex_chromosomes` to calculate coverage ratios of the X and
+ Y chromosomes versus autosomes.
+
+ Parameters
+ ----------
+ male_reference : bool
+ Was this sample normalized to a male reference copy number profile?
+ verbose : bool
+ If True, print (i.e. log to console) the ratios of the log2
+ coverages of the X and Y chromosomes versus autosomes, the
+ "maleness" ratio of male vs. female expectations for each sex
+ chromosome, and the inferred chromosomal sex.
+
+ Returns
+ -------
+ bool
+ True if the coverage ratios indicate the sample is female.
+ """
+ is_xy, stats = self.compare_sex_chromosomes(male_reference)
+ if is_xy is None:
+ return None
+ elif verbose:
+ logging.info("Relative log2 coverage of %s=%.3g, %s=%.3g "
+ "(maleness=%.3g x %.3g = %.3g) --> assuming %s",
+ self._chr_x_label, stats['chrx_ratio'],
+ self._chr_y_label, stats['chry_ratio'],
+ stats['chrx_male_lr'], stats['chry_male_lr'],
+ stats['chrx_male_lr'] * stats['chry_male_lr'],
+ ('female', 'male')[is_xy])
+ return ~is_xy
+
+ def compare_sex_chromosomes(self, male_reference=False, skip_low=False):
+ """Compare coverage ratios of sex chromosomes versus autosomes.
+
+ Perform 4 Mood's median tests of the log2 coverages on chromosomes X and
+ Y, separately shifting for assumed male and female chromosomal sex.
+ Compare the chi-squared values obtained to infer whether the male or
+ female assumption fits the data better.
+
+ Parameters
+ ----------
+ male_reference : bool
+ Whether a male reference copy number profile was used to normalize
+ the data. If so, a male sample should have log2 values of 0 on X and
+ Y, and female +1 on X, deep negative (below -3) on Y. Otherwise, a
+ male sample should have log2 values of -1 on X and 0 on
+ Y, and female 0 on X, deep negative (below -3) on Y.
+ skip_low : bool
+ If True, drop very-low-coverage bins (via `drop_low_coverage`)
+ before comparing log2 coverage ratios. Included for completeness,
+ but shouldn't affect the result much since the M-W test is
+ nonparametric and p-values are not used here.
+
+ Returns
+ -------
+ bool
+ True if the sample appears male.
+ dict
+ Calculated values used for the inference: relative log2 ratios of
+ chromosomes X and Y versus the autosomes; the Mann-Whitney U values
+ from each test; and ratios of U values for male vs. female
+ assumption on chromosomes X and Y.
"""
- cutoff = 0.5 if male_reference else -0.5
- # ENH - better coverage approach: take Z-scores or rank of +1,0 or 0,-1
- # based on the available probes, then choose which is more probable
- rel_chrx_cvg = self.get_relative_chrx_cvg()
- if rel_chrx_cvg is None:
- return
- is_xx = (rel_chrx_cvg >= cutoff)
- if verbose:
- logging.info("Relative log2 coverage of X chromosome: %g "
- "(assuming %s)",
- rel_chrx_cvg, ('male', 'female')[is_xx])
- return is_xx
-
- def get_relative_chrx_cvg(self):
- """Get the relative log-coverage of chrX in a sample."""
- chromosome_x = self[self.chromosome == self._chr_x_label]
- if not len(chromosome_x):
+ chrx = self[self.chromosome == self._chr_x_label]
+ if not len(chrx):
logging.warn("*WARNING* No %s found in probes; check the input",
self._chr_x_label)
- return
- autosomes = self.autosomes()
- auto_cvgs = autosomes['log2']
- x_cvgs = chromosome_x['log2']
- if 'probes' in self:
- # Weight segments by number of probes to ensure good behavior
- auto_sizes = autosomes['probes']
- x_sizes = chromosome_x['probes']
- # ENH: weighted median
- rel_chrx_cvg = (np.average(x_cvgs, weights=x_sizes) -
- np.average(auto_cvgs, weights=auto_sizes))
+ return None, {}
+
+ auto = self.autosomes()
+ if skip_low:
+ chrx = chrx.drop_low_coverage()
+ auto = auto.drop_low_coverage()
+ auto_l = auto['log2'].values
+ use_weight = ('weight' in self)
+ auto_w = auto['weight'].values if use_weight else None
+
+ def compare_to_auto(vals, weights):
+ # Mood's median test stat is chisq -- near 0 for similar median
+ try:
+ stat, _p, _med, cont = median_test(auto_l, vals, ties='ignore',
+ lambda_='log-likelihood')
+ except ValueError:
+ # "All values are below the grand median (0.0)"
+ stat = None
+ else:
+ if stat == 0 and 0 in cont:
+ stat = None
+ # In case Mood's test failed for either sex
+ if use_weight:
+ med_diff = abs(descriptives.weighted_median(auto_l, auto_w) -
+ descriptives.weighted_median(vals, weights))
+ else:
+ med_diff = abs(np.median(auto_l) - np.median(vals))
+ return (stat, med_diff)
+
+ def compare_chrom(vals, weights, female_shift, male_shift):
+ """Calculate "maleness" ratio of test statistics.
+
+ The ratio is of the female vs. male chi-square test statistics from
+ the median test. If the median test fails for either sex, (due to
+ flat/trivial input), use the ratio of the absolute difference in
+ medians.
+ """
+ female_stat, f_diff = compare_to_auto(vals + female_shift, weights)
+ male_stat, m_diff = compare_to_auto(vals + male_shift, weights)
+ # Statistic is smaller for similar-median sets
+ if female_stat is not None and male_stat is not None:
+ return female_stat / max(male_stat, 0.01)
+ # Difference in medians is also smaller for similar-median sets
+ return f_diff / max(m_diff, 0.01)
+
+ female_x_shift, male_x_shift = (-1, 0) if male_reference else (0, +1)
+ chrx_male_lr = compare_chrom(chrx['log2'].values,
+ (chrx['weight'].values if use_weight
+ else None),
+ female_x_shift, male_x_shift)
+ combined_score = chrx_male_lr
+ # Similar for chrY if it's present
+ chry = self[self.chromosome == self._chr_y_label]
+ if len(chry):
+ chry_male_lr = compare_chrom(chry['log2'].values,
+ (chry['weight'].values if use_weight
+ else None),
+ +3, 0)
+ if np.isfinite(chry_male_lr):
+ combined_score *= chry_male_lr
else:
- rel_chrx_cvg = np.median(x_cvgs) - np.median(auto_cvgs)
- return rel_chrx_cvg
-
- def expect_flat_cvg(self, is_male_reference=None):
+ # If chrY is missing, don't sabotage the inference
+ chry_male_lr = np.nan
+ # Relative log2 values, for convenient reporting
+ auto_mean = segment_mean(auto, skip_low=skip_low)
+ chrx_mean = segment_mean(chrx, skip_low=skip_low)
+ chry_mean = segment_mean(chry, skip_low=skip_low)
+ return (combined_score > 1.0,
+ dict(chrx_ratio=chrx_mean - auto_mean,
+ chry_ratio=chry_mean - auto_mean,
+ combined_score=combined_score,
+ # For debugging, mainly
+ chrx_male_lr=chrx_male_lr,
+ chry_male_lr=chry_male_lr,
+ ))
+
+ def expect_flat_log2(self, is_male_reference=None):
"""Get the uninformed expected copy ratios of each bin.
Create an array of log2 coverages like a "flat" reference.
@@ -246,11 +422,22 @@ class CopyNumArray(gary.GenomicArray):
def residuals(self, segments=None):
"""Difference in log2 value of each bin from its segment mean.
- If segments are just regions (e.g. RegionArray) with no log2 values
- precalculated, subtract the median of this array's log2 values within
- each region. If no segments are given, subtract each chromosome's
- median.
-
+ Parameters
+ ----------
+ segments : GenomicArray, CopyNumArray, or None
+ Determines the "mean" value to which `self` log2 values are relative:
+
+ - If CopyNumArray, use the log2 values as the segment means to
+ subtract.
+ - If GenomicArray with no log2 values, group `self` by these ranges
+ and subtract each group's median log2 value.
+ - If None, subtract each chromosome's median.
+
+ Returns
+ -------
+ array
+ Residual log2 values from `self` relative to `segments`; same length
+ as `self`.
"""
if not segments:
resids = [subcna.log2 - subcna.log2.median()
@@ -263,7 +450,7 @@ class CopyNumArray(gary.GenomicArray):
for _seg, subcna in self.by_ranges(segments)]
return np.concatenate(resids) if resids else np.array([])
- def guess_average_depth(self, segments=None, window=100):
+ def _guess_average_depth(self, segments=None, window=100):
"""Estimate the effective average read depth from variance.
Assume read depths are Poisson distributed, converting log2 values to
@@ -287,12 +474,13 @@ class CopyNumArray(gary.GenomicArray):
cnarr = self
# Remove variations due to real/likely CNVs
y_log2 = cnarr.residuals(segments)
- if window:
+ if segments is None and window:
y_log2 -= smoothing.smoothed(y_log2, window)
# Guess Poisson parameter from absolute-scale values
y = np.exp2(y_log2)
# ENH: use weight argument to these stats
- loc = metrics.biweight_location(y)
- spread = metrics.biweight_midvariance(y, loc)
- scale = loc / spread**2
- return scale
+ loc = descriptives.biweight_location(y)
+ spread = descriptives.biweight_midvariance(y, loc)
+ if spread > 0:
+ return loc / spread**2
+ return loc
diff --git a/cnvlib/commands.py b/cnvlib/commands.py
index 8571cdd..586f2c1 100644
--- a/cnvlib/commands.py
+++ b/cnvlib/commands.py
@@ -3,40 +3,42 @@
# "_cmd_*" handles I/O and arguments processing for the command
# "do_*" runs the command's functionality as an API
from __future__ import absolute_import, division, print_function
+from builtins import map, zip
+
import argparse
-import collections
import logging
import os
import sys
-import numpy as np
-import pandas as pd
-
-from Bio._py3k import map, range, zip
-iteritems = (dict.iteritems if sys.version_info[0] < 3 else dict.items)
-
# If running headless, use a suitable GUI-less plotting backend
if not os.environ.get('DISPLAY'):
import matplotlib
- try:
- matplotlib.use("Agg", force=True)
- except TypeError:
- # Older matplotlib doesn't have 'force' argument
- matplotlib.use("Agg")
+ matplotlib.use("Agg", force=True)
from matplotlib import pyplot
from matplotlib.backends.backend_pdf import PdfPages
pyplot.ioff()
-from . import (core, ngfrills, parallel, params,
- access, antitarget, call, coverage, export, fix, importers,
- metrics, plots, reference, reports, segmentation, target)
-from .cnary import CopyNumArray as _CNA
-from .vary import VariantArray as _VA
-from .rary import RegionArray as _RA
+import numpy as np
+import pandas as pd
+from skgenome import tabio, GenomicArray as _GA
+from skgenome.rangelabel import to_label
+
+from . import (access, antitarget, autobin, batch, call, core, coverage,
+ descriptives, diagram, export, fix, heatmap, importers, metrics,
+ parallel, reference, reports, scatter, segmentation, target)
+from .cmdutil import (load_het_snps, read_cna, verify_sample_sex,
+ write_tsv, write_text, write_dataframe)
+
from ._version import __version__
+__all__ = []
+def public(fn):
+ __all__.append(fn.__name__)
+ return fn
+
+
AP = argparse.ArgumentParser(
description="CNVkit, a command-line toolkit for copy number analysis.",
epilog="Contact Eric Talevich <eric.talevich at ucsf.edu> for help.")
@@ -51,7 +53,9 @@ AP_subparsers = AP.add_subparsers(
def _cmd_batch(args):
"""Run the complete CNVkit pipeline on one or more BAM files."""
+ logging.info("CNVkit %s", __version__)
# Validate/restrict options, beyond what argparse mutual exclusion can do
+ bad_args_msg = ""
if args.reference:
bad_flags = [flag
for is_used, flag in (
@@ -62,20 +66,23 @@ def _cmd_batch(args):
(args.access, '-g/--access'),
(args.annotate, '--annotate'),
(args.short_names, '--short-names'),
- (args.split, '--split'),
(args.target_avg_size, '--target-avg-size'),
(args.antitarget_avg_size, '--antitarget-avg-size'),
(args.antitarget_min_size, '--antitarget-min-size'),
) if is_used]
if bad_flags:
- sys.exit("If -r/--reference is given, options to construct a new " +
- "reference (" + ", ".join(bad_flags) +
- ") should not be used." +
- "\n(See: cnvkit.py batch -h)")
- elif not args.targets or args.normal is None:
- sys.exit("Options -n/--normal and -t/--targets (at least) must be "
- "given to build a new reference if -r/--reference is not used."
- "\n(See: cnvkit.py batch -h)")
+ bad_args_msg = ("If -r/--reference is given, options to construct "
+ "a new reference (%s) should not be used."
+ % ", ".join(bad_flags))
+ elif args.normal is None:
+ bad_args_msg = ("Option -n/--normal must be given to build a new "
+ "reference if -r/--reference is not used.")
+ elif args.method in ('hybrid', 'amplicon') and not args.targets:
+ bad_args_msg = ("For the '%r' sequencing method, option -t/--targets "
+ "(at least) must be given to build a new reference if "
+ "-r/--reference is not used." % args.method)
+ if bad_args_msg:
+ sys.exit(bad_args_msg + "\n(See: cnvkit.py batch -h)")
# Ensure sample IDs are unique to avoid overwriting outputs
seen_sids = {}
@@ -86,162 +93,74 @@ def _cmd_batch(args):
% (sid, fname, seen_sids[sid]))
seen_sids[sid] = fname
+ if args.processes < 1:
+ import multiprocessing
+ args.processes = multiprocessing.cpu_count()
+
if not args.reference:
# Build a copy number reference; update (anti)targets upon request
- args.reference, args.targets, args.antitargets = batch_make_reference(
+ args.reference, args.targets, args.antitargets = batch.batch_make_reference(
args.normal, args.targets, args.antitargets, args.male_reference,
- args.fasta, args.annotate, args.short_names, args.split,
- args.target_avg_size, args.access, args.antitarget_avg_size,
- args.antitarget_min_size, args.output_reference, args.output_dir,
- args.processes, args.count_reads)
+ args.fasta, args.annotate, args.short_names, args.target_avg_size,
+ args.access, args.antitarget_avg_size, args.antitarget_min_size,
+ args.output_reference, args.output_dir, args.processes,
+ args.count_reads, args.method)
elif args.targets is None and args.antitargets is None:
# Extract (anti)target BEDs from the given, existing CN reference
- ref_arr = _CNA.read(args.reference)
- target_coords, antitarget_coords = reference.reference2regions(ref_arr)
+ ref_arr = read_cna(args.reference)
+ targets, antitargets = reference.reference2regions(ref_arr)
ref_pfx = os.path.join(args.output_dir, core.fbase(args.reference))
args.targets = ref_pfx + '.target-tmp.bed'
args.antitargets = ref_pfx + '.antitarget-tmp.bed'
- core.write_tsv(args.targets, target_coords)
- core.write_tsv(args.antitargets, antitarget_coords)
+ tabio.write(targets, args.targets, 'bed4')
+ tabio.write(antitargets, args.antitargets, 'bed4')
if args.bam_files:
- logging.info("Running %d samples in %s",
- len(args.bam_files),
- ("serial" if args.processes == 1
- else ("%d processes" % args.processes)))
- pool = parallel.pick_pool(args.processes)
- for bam in args.bam_files:
- pool.apply_async(batch_run_sample,
- (bam, args.targets, args.antitargets, args.reference,
- args.output_dir, args.male_reference, args.scatter,
- args.diagram, args.rlibpath, args.count_reads))
- pool.close()
- pool.join()
-
-
-def batch_make_reference(normal_bams, target_bed, antitarget_bed, male_reference,
- fasta, annotate, short_names, split, target_avg_size,
- access, antitarget_avg_size, antitarget_min_size,
- output_reference, output_dir, processes, by_count):
- """Build the CN reference from normal samples, targets and antitargets."""
- # To make temporary filenames for processed targets or antitargets
- tgt_name_base, tgt_name_ext = os.path.splitext(os.path.basename(target_bed))
- if output_dir:
- tgt_name_base = os.path.join(output_dir, tgt_name_base)
-
- if annotate or short_names or split:
- # Pre-process baits/targets
- new_target_fname = tgt_name_base + '.target.bed'
- tgt_rarr = do_targets(target_bed, annotate, short_names, split,
- **({'avg_size': target_avg_size}
- if split and target_avg_size
- else {}))
- tgt_rarr.write(new_target_fname, "bed4")
- target_bed = new_target_fname
-
- if not antitarget_bed:
- # Build antitarget BED from the given targets
- anti_kwargs = {}
- if access:
- anti_kwargs['access_bed'] = access
- if antitarget_avg_size:
- anti_kwargs['avg_bin_size'] = antitarget_avg_size
- if antitarget_min_size:
- anti_kwargs['min_bin_size'] = antitarget_min_size
- anti_rarr = do_antitarget(target_bed, **anti_kwargs)
- # Devise a temporary antitarget filename
- antitarget_bed = tgt_name_base + '.antitarget.bed'
- anti_rarr.write(antitarget_bed, "bed4")
-
- if len(normal_bams) == 0:
- logging.info("Building a flat reference...")
- ref_arr = do_reference_flat(target_bed, antitarget_bed, fasta,
- male_reference)
+ if args.processes == 1:
+ procs_per_bam = 1
+ logging.info("Running %d samples in serial", len(args.bam_files))
+ else:
+ procs_per_bam = max(1, args.processes // len(args.bam_files))
+ logging.info("Running %d samples in %d processes "
+ "(that's %d processes per bam)",
+ len(args.bam_files), args.processes, procs_per_bam)
+
+ with parallel.pick_pool(args.processes) as pool:
+ for bam in args.bam_files:
+ pool.submit(batch.batch_run_sample,
+ bam, args.targets, args.antitargets, args.reference,
+ args.output_dir, args.male_reference, args.scatter,
+ args.diagram, args.rlibpath, args.count_reads,
+ args.drop_low_coverage, args.method, procs_per_bam)
else:
- logging.info("Building a copy number reference from normal samples...")
- target_fnames = []
- antitarget_fnames = []
- # Run coverage on all normals
- pool = parallel.pick_pool(processes)
- for nbam in normal_bams:
- sample_id = core.fbase(nbam)
- sample_pfx = os.path.join(output_dir, sample_id)
- tgt_fname = sample_pfx + '.targetcoverage.cnn'
- pool.apply_async(batch_write_coverage,
- (target_bed, nbam, tgt_fname, by_count))
- target_fnames.append(tgt_fname)
- anti_fname = sample_pfx + '.antitargetcoverage.cnn'
- pool.apply_async(batch_write_coverage,
- (antitarget_bed, nbam, anti_fname, by_count))
- antitarget_fnames.append(anti_fname)
- pool.close()
- pool.join()
- # Build reference from *.cnn
- ref_arr = do_reference(target_fnames, antitarget_fnames, fasta,
- male_reference)
- if not output_reference:
- output_reference = os.path.join(output_dir, "reference.cnn")
- ngfrills.ensure_path(output_reference)
- ref_arr.write(output_reference)
-
- return output_reference, target_bed, antitarget_bed
-
-
-def batch_write_coverage(bed_fname, bam_fname, out_fname, by_count):
- """Run coverage on one sample, write to file."""
- cnarr = do_coverage(bed_fname, bam_fname, by_count)
- cnarr.write(out_fname)
-
-
-def batch_run_sample(bam_fname, target_bed, antitarget_bed, ref_fname,
- output_dir, male_reference=False, scatter=False,
- diagram=False, rlibpath=None, by_count=False):
- """Run the pipeline on one BAM file."""
- # ENH - return probes, segments (cnarr, segarr)
- logging.info("Running the CNVkit pipeline on %s ...", bam_fname)
- sample_id = core.fbase(bam_fname)
- sample_pfx = os.path.join(output_dir, sample_id)
-
- raw_tgt = do_coverage(target_bed, bam_fname, by_count)
- raw_tgt.write(sample_pfx + '.targetcoverage.cnn')
-
- raw_anti = do_coverage(antitarget_bed, bam_fname, by_count)
- raw_anti.write(sample_pfx + '.antitargetcoverage.cnn')
-
- cnarr = do_fix(raw_tgt, raw_anti, _CNA.read(ref_fname))
- cnarr.write(sample_pfx + '.cnr')
-
- logging.info("Segmenting %s.cnr ...", sample_pfx)
- segments = segmentation.do_segmentation(cnarr, 'cbs', rlibpath=rlibpath)
- segments.write(sample_pfx + '.cns')
-
- if scatter:
- do_scatter(cnarr, segments)
- pyplot.savefig(sample_pfx + '-scatter.pdf', format='pdf',
- bbox_inches="tight")
- logging.info("Wrote %s-scatter.pdf", sample_pfx)
-
- if diagram:
- from cnvlib import diagram
- outfname = sample_pfx + '-diagram.pdf'
- diagram.create_diagram(cnarr, segments, 0.5, 3, outfname,
- male_reference)
- logging.info("Wrote %s", outfname)
+ logging.info("No tumor/test samples (but %d normal/control samples) "
+ "specified on the command line.",
+ len(args.normal))
P_batch = AP_subparsers.add_parser('batch', help=_cmd_batch.__doc__)
P_batch.add_argument('bam_files', nargs='*',
help="Mapped sequence reads (.bam)")
+P_batch.add_argument('-m', '--method',
+ choices=('hybrid', 'amplicon', 'wgs'), default='hybrid',
+ help="""Sequencing protocol: hybridization capture ('hybrid'), targeted
+ amplicon sequencing ('amplicon'), or whole genome sequencing
+ ('wgs'). Determines whether and how to use antitarget bins.
+ [Default: %(default)s]""")
P_batch.add_argument('-y', '--male-reference', action='store_true',
help="""Use or assume a male reference (i.e. female samples will have +1
log-CNR of chrX; otherwise male samples would have -1 chrX).""")
P_batch.add_argument('-c', '--count-reads', action='store_true',
help="""Get read depths by counting read midpoints within each bin.
(An alternative algorithm).""")
-P_batch.add_argument('-p', '--processes', type=int, default=1,
+P_batch.add_argument("--drop-low-coverage", action='store_true',
+ help="""Drop very-low-coverage bins before segmentation to avoid
+ false-positive deletions in poor-quality tumor samples.""")
+P_batch.add_argument('-p', '--processes',
+ nargs='?', type=int, const=0, default=1,
help="""Number of subprocesses used to running each of the BAM files in
- parallel. Give 0 or a negative value to use the maximum number
- of available CPUs. [Default: process each BAM in serial]""")
+ parallel. Without an argument, use the maximum number of
+ available CPUs. [Default: process each BAM in serial]""")
P_batch.add_argument("--rlibpath",
help="Path to an alternative site-library to use for R packages.")
@@ -249,24 +168,23 @@ P_batch.add_argument("--rlibpath",
P_batch_newref = P_batch.add_argument_group(
"To construct a new copy number reference")
P_batch_newref.add_argument('-n', '--normal', nargs='*',
- help="""Normal samples (.bam) to construct the pooled reference.
- If this option is used but no files are given, a "flat"
- reference will be built.""")
+ help="""Normal samples (.bam) used to construct the pooled, paired, or
+ flat reference. If this option is used but no filenames are
+ given, a "flat" reference will be built. Otherwise, all
+ filenames following this option will be used.""")
P_batch_newref.add_argument('-f', '--fasta',
help="Reference genome, FASTA format (e.g. UCSC hg19.fa)")
-P_batch_newref.add_argument('-t', '--targets', #required=True,
+P_batch_newref.add_argument('-t', '--targets',
help="Target intervals (.bed or .list)")
-P_batch_newref.add_argument('-a', '--antitargets', #required=True,
+P_batch_newref.add_argument('-a', '--antitargets',
help="Antitarget intervals (.bed or .list)")
# For pre-processing targets
P_batch_newref.add_argument('--annotate',
- help="""UCSC refFlat.txt or ensFlat.txt file for the reference genome.
- Pull gene names from this file and assign them to the target
- regions.""")
+ help="""Use gene models from this file to assign names to the target
+ regions. Format: UCSC refFlat.txt or ensFlat.txt file
+ (preferred), or BED, interval list, GFF, or similar.""")
P_batch_newref.add_argument('--short-names', action='store_true',
help="Reduce multi-accession bait labels to be short and consistent.")
-P_batch_newref.add_argument('--split', action='store_true',
- help="Split large tiled intervals into smaller, consecutive targets.")
P_batch_newref.add_argument('--target-avg-size', type=int,
help="Average size of split target bins (results are approximate).")
# For antitargets:
@@ -295,47 +213,31 @@ P_batch_report.add_argument('-d', '--output-dir', default='.',
P_batch_report.add_argument('--scatter', action='store_true',
help="Create a whole-genome copy ratio profile as a PDF scatter plot.")
P_batch_report.add_argument('--diagram', action='store_true',
- help="Create a diagram of copy ratios on chromosomes as a PDF.")
+ help="Create an ideogram of copy ratios on chromosomes as a PDF.")
P_batch.set_defaults(func=_cmd_batch)
# target ----------------------------------------------------------------------
-def _cmd_target(args):
- """Transform bait intervals into targets more suitable for CNVkit."""
- rarr = do_targets(args.interval, args.annotate, args.short_names,
- args.split, args.avg_size)
- rarr.write(args.output, "bed4")
+do_target = public(target.do_target)
-def do_targets(bed_fname, annotate=None, do_short_names=False, do_split=False,
- avg_size=200/.75):
+def _cmd_target(args):
"""Transform bait intervals into targets more suitable for CNVkit."""
- bed_rows = ngfrills.parse_regions(bed_fname, False,
- keep_strand=bool(annotate))
- if annotate:
- logging.info("Applying annotations as target names")
- bed_rows = target.add_refflat_names(bed_rows, annotate)
- if do_short_names:
- logging.info("Shortening interval labels")
- bed_rows = target.shorten_labels(bed_rows)
- if do_split:
- logging.info("Splitting large targets")
- bed_rows = target.split_targets(bed_rows, avg_size)
- bed_rarr = _RA.from_rows(bed_rows,
- ['chromosome', 'start', 'end', 'name'])
- bed_rarr.sort()
- return bed_rarr
+ regions = tabio.read_auto(args.interval)
+ regions = target.do_target(regions, args.annotate, args.short_names,
+ args.split, args.avg_size)
+ tabio.write(regions, args.output, "bed4")
P_target = AP_subparsers.add_parser('target', help=_cmd_target.__doc__)
P_target.add_argument('interval',
help="""BED or interval file listing the targeted regions.""")
P_target.add_argument('--annotate',
- help="""UCSC refFlat.txt or ensFlat.txt file for the reference genome.
- Pull gene names from this file and assign them to the target
- regions.""")
+ help="""Use gene models from this file to assign names to the target
+ regions. Format: UCSC refFlat.txt or ensFlat.txt file
+ (preferred), or BED, interval list, GFF, or similar.""")
P_target.add_argument('--short-names', action='store_true',
help="Reduce multi-accession bait labels to be short and consistent.")
P_target.add_argument('--split', action='store_true',
@@ -352,24 +254,14 @@ P_target.set_defaults(func=_cmd_target)
# access ----------------------------------------------------------------------
-def _cmd_access(args):
- """List the locations of accessible sequence regions in a FASTA file."""
- # Closes over args.output
- def write_row(chrom, run_start, run_end):
- args.output.write("%s\t%s\t%s\n" % (chrom, run_start, run_end))
- args.output.flush()
-
- for row in do_access(args.fa_fname, args.exclude, args.min_gap_size):
- write_row(*row)
+do_access = public(access.do_access)
-def do_access(fa_fname, exclude_fnames=(), min_gap_size=5000):
+def _cmd_access(args):
"""List the locations of accessible sequence regions in a FASTA file."""
- access_regions = access.get_regions(fa_fname)
- for ex_fname in exclude_fnames:
- access_regions = access.exclude_regions(ex_fname, access_regions)
- for row in access.join_regions(access_regions, min_gap_size):
- yield row
+ access_arr = access.do_access(args.fa_fname, args.exclude,
+ args.min_gap_size)
+ tabio.write(access_arr, args.output, "bed3")
P_access = AP_subparsers.add_parser('access', help=_cmd_access.__doc__)
@@ -390,33 +282,27 @@ P_access.set_defaults(func=_cmd_access)
# antitarget ------------------------------------------------------------------
-def _cmd_antitarget(args):
- """Derive a background/antitarget BED file from a target BED file."""
- out_rarr = do_antitarget(args.interval, args.access,
- args.avg_size, args.min_size)
+do_antitarget = public(antitarget.do_antitarget)
+def _cmd_antitarget(args):
+ """Derive off-target ("antitarget") bins from target regions."""
+ targets = tabio.read_auto(args.targets)
+ access = tabio.read_auto(args.access) if args.access else None
+ out_arr = antitarget.do_antitarget(targets, access, args.avg_size,
+ args.min_size)
if not args.output:
base, ext = args.interval.rsplit('.', 1)
args.output = base + '.antitarget.' + ext
- out_rarr.write(args.output, "bed4")
-
-
-def do_antitarget(target_bed, access_bed=None, avg_bin_size=100000,
- min_bin_size=None):
- """Derive a background/antitarget BED file from a target BED file."""
- if not min_bin_size:
- min_bin_size = 2 * int(avg_bin_size * (2 ** params.MIN_REF_COVERAGE))
- return antitarget.get_background(target_bed, access_bed, avg_bin_size,
- min_bin_size)
+ tabio.write(out_arr, args.output, "bed4")
P_anti = AP_subparsers.add_parser('antitarget', help=_cmd_antitarget.__doc__)
-P_anti.add_argument('interval',
+P_anti.add_argument('targets',
help="""BED or interval file listing the targeted regions.""")
P_anti.add_argument('-g', '--access',
help="""Regions of accessible sequence on chromosomes (.bed), as
output by genome2access.py.""")
-P_anti.add_argument('-a', '--avg-size', type=int, default=100000,
+P_anti.add_argument('-a', '--avg-size', type=int, default=150000,
help="""Average size of antitarget bins (results are approximate).
[Default: %(default)s]""")
P_anti.add_argument('-m', '--min-size', type=int,
@@ -426,35 +312,132 @@ P_anti.add_argument('-o', '--output', help="""Output file name.""")
P_anti.set_defaults(func=_cmd_antitarget)
+# autobin ---------------------------------------------------------------------
+
+do_autobin = public(autobin.do_autobin)
+
+
+def _cmd_autobin(args):
+ """Quickly calculate reasonable bin sizes from BAM read counts."""
+ if args.method in ('hybrid', 'amplicon') and not args.targets:
+ raise RuntimeError("Sequencing method %r requires targets", args.method)
+ elif args.method == 'wgs' and args.targets:
+ logging.warn("Targets will be ignored: %s", args.targets)
+ if args.method == 'amplicon' and args.access:
+ logging.warn("Sequencing-accessible regions will be ignored: %s",
+ args.access)
+
+ def read_regions(bed_fname):
+ if bed_fname:
+ regions = tabio.read_auto(bed_fname)
+ if len(regions):
+ return regions
+ else:
+ logging.warn("No regions to estimate depth from %s",
+ regions.meta.get('filename', ''))
+
+ tgt_arr = read_regions(args.targets)
+ access_arr = read_regions(args.access)
+ bam_fname = autobin.midsize_file(args.bams)
+ fields = autobin.do_autobin(bam_fname, args.method, tgt_arr, access_arr,
+ args.bp_per_bin, args.target_min_size,
+ args.target_max_size, args.antitarget_min_size,
+ args.antitarget_max_size)
+ (_tgt_depth, tgt_bin_size), (_anti_depth, anti_bin_size) = fields
+
+ # Create & write BED files
+ target_out_arr = target.do_target(access_arr if args.method == 'wgs'
+ else tgt_arr,
+ args.annotate, args.short_names,
+ do_split=True, avg_size=tgt_bin_size)
+ tgt_name_base = tgt_arr.sample_id if tgt_arr else core.fbase(bam_fname)
+ target_bed = tgt_name_base + '.target.bed'
+ tabio.write(target_out_arr, target_bed, "bed4")
+ if args.method == "hybrid" and anti_bin_size:
+ # Build antitarget BED from the given targets
+ anti_arr = antitarget.do_antitarget(target_out_arr,
+ access=access_arr,
+ avg_bin_size=anti_bin_size,
+ min_bin_size=args.antitarget_min_size)
+ else:
+ # No antitargets for wgs, amplicon
+ anti_arr = _GA([])
+ antitarget_bed = tgt_name_base + '.antitarget.bed'
+ tabio.write(anti_arr, antitarget_bed, "bed4")
+
+ # Print depths & bin sizes as a table on stdout
+ labels = ("Target", "Antitarget")
+ width = max(map(len, labels)) + 1
+ print(" " * width, "Depth", "Bin size", sep='\t')
+ for label, (depth, binsize) in zip(labels, fields):
+ if depth is not None:
+ print((label + ":").ljust(width),
+ format(depth, ".3f"),
+ binsize,
+ sep='\t')
+
+
+P_autobin = AP_subparsers.add_parser('autobin', help=_cmd_autobin.__doc__)
+P_autobin.add_argument('bams', nargs='+',
+ help="""Sample BAM file(s) to test for target coverage""")
+P_autobin.add_argument('-m', '--method',
+ choices=('hybrid', 'amplicon', 'wgs'), default='hybrid',
+ help="""Sequencing protocol: hybridization capture ('hybrid'), targeted
+ amplicon sequencing ('amplicon'), or whole genome sequencing
+ ('wgs'). Determines whether and how to use antitarget bins.
+ [Default: %(default)s]""")
+P_autobin.add_argument('-g', '--access',
+ help="""Sequencing-accessible genomic regions, or exons to use as
+ possible targets (e.g. output of refFlat2bed.py)""")
+P_autobin.add_argument('-t', '--targets',
+ help="""Potentially targeted genomic regions, e.g. all possible exons
+ for the reference genome. Format: BED, interval list, etc.""")
+P_autobin.add_argument('-b', '--bp-per-bin', type=float, default=100000.,
+ help="""Desired average number of sequencing read bases mapped to each
+ bin. [Default: %(default)s]""")
+
+P_autobin.add_argument('--target-max-size', type=int, default=20000,
+ help="Maximum size of target bins.")
+P_autobin.add_argument('--target-min-size', type=int, default=20,
+ help="Minimum size of target bins.")
+P_autobin.add_argument('--antitarget-max-size', type=int, default=500000,
+ help="Maximum size of antitarget bins.")
+P_autobin.add_argument('--antitarget-min-size', type=int, default=500,
+ help="Minimum size of antitarget bins.")
+
+P_autobin.add_argument('--annotate',
+ help="""Use gene models from this file to assign names to the target
+ regions. Format: UCSC refFlat.txt or ensFlat.txt file
+ (preferred), or BED, interval list, GFF, or similar.""")
+P_autobin.add_argument('--short-names', action='store_true',
+ help="Reduce multi-accession bait labels to be short and consistent.")
+ # Option: --dry-run to not write BED files?
+
+# P_autobin.add_argument('-o', '--output', help="Output filename.")
+P_autobin.set_defaults(func=_cmd_autobin)
+
+
# coverage --------------------------------------------------------------------
+do_coverage = public(coverage.do_coverage)
+
+
def _cmd_coverage(args):
"""Calculate coverage in the given regions from BAM read depths."""
- pset = do_coverage(args.interval, args.bam_file, args.count, args.min_mapq)
+ pset = coverage.do_coverage(args.interval, args.bam_file, args.count,
+ args.min_mapq, args.processes)
if not args.output:
# Create an informative but unique name for the coverage output file
bambase = core.fbase(args.bam_file)
- bedbase = core.rbase(args.interval)
+ bedbase = core.fbase(args.interval)
tgtbase = ('antitargetcoverage'
if 'anti' in bedbase.lower()
else 'targetcoverage')
args.output = '%s.%s.cnn' % (bambase, tgtbase)
if os.path.exists(args.output):
args.output = '%s.%s.cnn' % (bambase, bedbase)
- ngfrills.ensure_path(args.output)
- pset.write(args.output)
-
-
-def do_coverage(bed_fname, bam_fname, by_count=False, min_mapq=0):
- """Calculate coverage in the given regions from BAM read depths."""
- if not ngfrills.ensure_bam_sorted(bam_fname):
- raise RuntimeError("BAM file %s must be sorted by coordinates"
- % bam_fname)
- ngfrills.ensure_bam_index(bam_fname)
- # ENH: count importers.TOO_MANY_NO_COVERAGE & warn
- cnarr = coverage.interval_coverages(bed_fname, bam_fname, by_count,
- min_mapq)
- return cnarr
+ core.ensure_path(args.output)
+ tabio.write(pset, args.output)
P_coverage = AP_subparsers.add_parser('coverage', help=_cmd_coverage.__doc__)
@@ -467,19 +450,29 @@ P_coverage.add_argument('-q', '--min-mapq', type=int, default=0,
help="""Minimum mapping quality score (phred scale 0-60) to count a read
for coverage depth. [Default: %(default)s]""")
P_coverage.add_argument('-o', '--output', help="""Output file name.""")
+P_coverage.add_argument('-p', '--processes',
+ nargs='?', type=int, const=0, default=1,
+ help="""Number of subprocesses to calculate coverage in parallel.
+ Without an argument, use the maximum number of available CPUs.
+ [Default: use 1 process]""")
P_coverage.set_defaults(func=_cmd_coverage)
# reference -------------------------------------------------------------------
+do_reference = public(reference.do_reference)
+do_reference_flat = public(reference.do_reference_flat)
+
+
def _cmd_reference(args):
"""Compile a coverage reference from the given files (normal samples)."""
usage_err_msg = ("Give .cnn samples OR targets and antitargets.")
if args.targets and args.antitargets:
# Flat refence
assert not args.references, usage_err_msg
- ref_probes = do_reference_flat(args.targets, args.antitargets,
- args.fasta, args.male_reference)
+ ref_probes = reference.do_reference_flat(args.targets, args.antitargets,
+ args.fasta,
+ args.male_reference)
elif args.references:
# Pooled reference
assert not args.targets and not args.antitargets, usage_err_msg
@@ -494,62 +487,18 @@ def _cmd_reference(args):
antitargets = [f for f in filenames if 'antitarget' in f]
logging.info("Number of target and antitarget files: %d, %d",
len(targets), len(antitargets))
- ref_probes = do_reference(targets, antitargets, args.fasta,
- args.male_reference,
- args.do_gc, args.do_edge, args.do_rmask)
+ female_samples = ((args.sample_sex.lower() not in ['y', 'm', 'male'])
+ if args.sample_sex else None)
+ ref_probes = reference.do_reference(targets, antitargets, args.fasta,
+ args.male_reference, female_samples,
+ args.do_gc, args.do_edge,
+ args.do_rmask)
else:
raise ValueError(usage_err_msg)
ref_fname = args.output or "cnv_reference.cnn"
- ngfrills.ensure_path(ref_fname)
- ref_probes.write(ref_fname)
-
-
-def do_reference(target_fnames, antitarget_fnames, fa_fname=None,
- male_reference=False, do_gc=True, do_edge=True, do_rmask=True):
- """Compile a coverage reference from the given files (normal samples)."""
- core.assert_equal("Unequal number of target and antitarget files given",
- targets=len(target_fnames),
- antitargets=len(antitarget_fnames))
- if not fa_fname:
- logging.info("No FASTA reference genome provided; "
- "skipping GC, RM calculations")
-
- # Calculate & save probe centers
- ref_probes = reference.combine_probes(target_fnames, fa_fname,
- male_reference, True,
- do_gc, do_edge, False)
- ref_probes.add(reference.combine_probes(antitarget_fnames, fa_fname,
- male_reference, False,
- do_gc, False, do_rmask))
- ref_probes.center_all(skip_low=True)
- ref_probes.sort_columns()
- reference.warn_bad_probes(ref_probes)
- return ref_probes
-
-
-def do_reference_flat(targets, antitargets, fa_fname=None,
- male_reference=False):
- """Compile a neutral-coverage reference from the given intervals.
-
- Combines the intervals, shifts chrX values if requested, and calculates GC
- and RepeatMasker content from the genome FASTA sequence.
- """
- ref_probes = reference.bed2probes(targets)
- ref_probes.add(reference.bed2probes(antitargets))
- # Set sex chromosomes by "reference" gender
- ref_probes['log2'] = ref_probes.expect_flat_cvg(male_reference)
- # Calculate GC and RepeatMasker content for each probe's genomic region
- if fa_fname:
- gc, rmask = reference.get_fasta_stats(ref_probes, fa_fname)
- ref_probes['gc'] = gc
- ref_probes['rmask'] = rmask
- reference.warn_bad_probes(ref_probes)
- else:
- logging.info("No FASTA reference genome provided; "
- "skipping GC, RM calculations")
- ref_probes.sort_columns()
- return ref_probes
+ core.ensure_path(ref_fname)
+ tabio.write(ref_probes, ref_fname)
P_reference = AP_subparsers.add_parser('reference', help=_cmd_reference.__doc__)
@@ -558,27 +507,43 @@ P_reference.add_argument('references', nargs='*',
directory that contains them.""")
P_reference.add_argument('-f', '--fasta',
help="Reference genome, FASTA format (e.g. UCSC hg19.fa)")
-P_reference.add_argument('-t', '--targets',
- help="Target intervals (.bed or .list)")
-P_reference.add_argument('-a', '--antitargets',
- help="Antitarget intervals (.bed or .list)")
+P_reference.add_argument('-o', '--output', help="Output file name.")
P_reference.add_argument('-y', '--male-reference', action='store_true',
help="""Create a male reference: shift female samples' chrX
log-coverage by -1, so the reference chrX average is -1.
Otherwise, shift male samples' chrX by +1, so the reference chrX
average is 0.""")
-P_reference.add_argument('--no-gc', dest='do_gc', action='store_false',
+P_reference.add_argument('-x', '--sample-sex', '-g', '--gender',
+ dest='sample_sex',
+ choices=('m', 'y', 'male', 'Male', 'f', 'x', 'female', 'Female'),
+ help="""Specify the chromosomal sex of all given samples as male or
+ female. (Default: guess each sample from coverage of X and Y
+ chromosomes).""")
+
+P_reference_flat = P_reference.add_argument_group(
+ "To construct a generic, \"flat\" copy number reference with neutral "
+ "expected coverage")
+P_reference_flat.add_argument('-t', '--targets',
+ help="Target intervals (.bed or .list)")
+P_reference_flat.add_argument('-a', '--antitargets',
+ help="Antitarget intervals (.bed or .list)")
+
+P_reference_bias = P_reference.add_argument_group(
+ "To disable specific automatic bias corrections")
+P_reference_bias.add_argument('--no-gc', dest='do_gc', action='store_false',
help="Skip GC correction.")
-P_reference.add_argument('--no-edge', dest='do_edge', action='store_false',
+P_reference_bias.add_argument('--no-edge', dest='do_edge', action='store_false',
help="Skip edge-effect correction.")
-P_reference.add_argument('--no-rmask', dest='do_rmask', action='store_false',
+P_reference_bias.add_argument('--no-rmask', dest='do_rmask', action='store_false',
help="Skip RepeatMasker correction.")
-P_reference.add_argument('-o', '--output', help="Output file name.")
P_reference.set_defaults(func=_cmd_reference)
# fix -------------------------------------------------------------------------
+do_fix = public(fix.do_fix)
+
+
def _cmd_fix(args):
"""Combine target and antitarget coverages and correct for biases.
@@ -586,44 +551,15 @@ def _cmd_fix(args):
biases and re-center.
"""
# Verify that target and antitarget are from the same sample
- tgt_raw = _CNA.read(args.target)
- anti_raw = _CNA.read(args.antitarget)
- if tgt_raw.sample_id != anti_raw.sample_id:
+ tgt_raw = read_cna(args.target)
+ anti_raw = read_cna(args.antitarget)
+ if len(anti_raw) and tgt_raw.sample_id != anti_raw.sample_id:
raise ValueError("Sample IDs do not match:"
"'%s' (target) vs. '%s' (antitarget)"
% (tgt_raw.sample_id, anti_raw.sample_id))
- target_table = do_fix(tgt_raw, anti_raw, _CNA.read(args.reference),
- args.do_gc, args.do_edge, args.do_rmask)
- target_table.write(args.output or tgt_raw.sample_id + '.cnr')
-
-
-def do_fix(target_raw, antitarget_raw, reference,
- do_gc=True, do_edge=True, do_rmask=True):
- """Combine target and antitarget coverages and correct for biases."""
- # Load, recenter and GC-correct target & antitarget probes separately
- logging.info("Processing target: %s", target_raw.sample_id)
- cnarr = fix.load_adjust_coverages(target_raw, reference, True,
- do_gc, do_edge, False)
- logging.info("Processing antitarget: %s", antitarget_raw.sample_id)
- anti_cnarr = fix.load_adjust_coverages(antitarget_raw, reference, False,
- do_gc, False, do_rmask)
- if len(anti_cnarr):
- # Down-weight the more variable probe set (targets or antitargets)
- tgt_iqr = metrics.interquartile_range(cnarr.drop_low_coverage().residuals())
- anti_iqr = metrics.interquartile_range(anti_cnarr.drop_low_coverage().residuals())
- iqr_ratio = max(tgt_iqr, .01) / max(anti_iqr, .01)
- if iqr_ratio > 1:
- logging.info("Targets are %.2f x more variable than antitargets",
- iqr_ratio)
- cnarr["weight"] /= iqr_ratio
- else:
- logging.info("Antitargets are %.2f x more variable than targets",
- 1. / iqr_ratio)
- anti_cnarr["weight"] *= iqr_ratio
- # Combine target and antitarget bins
- cnarr.add(anti_cnarr)
- cnarr.center_all(skip_low=True)
- return cnarr
+ target_table = fix.do_fix(tgt_raw, anti_raw, read_cna(args.reference),
+ args.do_gc, args.do_edge, args.do_rmask)
+ tabio.write(target_table, args.output or tgt_raw.sample_id + '.cnr')
P_fix = AP_subparsers.add_parser('fix', help=_cmd_fix.__doc__)
@@ -652,17 +588,21 @@ P_fix.set_defaults(func=_cmd_fix)
# segment ---------------------------------------------------------------------
+do_segmentation = public(segmentation.do_segmentation)
+
+
def _cmd_segment(args):
"""Infer copy number segments from the given coverage table."""
- cnarr = _CNA.read(args.filename)
- variants = (_VA.read_vcf(args.vcf, skip_hom=True, skip_somatic=True)
- if args.vcf else None)
+ cnarr = read_cna(args.filename)
+ variants = load_het_snps(args.vcf, args.sample_id, args.normal_id,
+ args.min_variant_depth, args.zygosity_freq)
results = segmentation.do_segmentation(cnarr, args.method, args.threshold,
variants=variants,
skip_low=args.drop_low_coverage,
skip_outliers=args.drop_outliers,
save_dataframe=bool(args.dataframe),
- rlibpath=args.rlibpath)
+ rlibpath=args.rlibpath,
+ processes=args.processes)
if args.dataframe:
segments, dframe = results
with open(args.dataframe, 'w') as handle:
@@ -670,7 +610,7 @@ def _cmd_segment(args):
logging.info("Wrote %s", args.dataframe)
else:
segments = results
- segments.write(args.output or segments.sample_id + '.cns')
+ tabio.write(segments, args.output or segments.sample_id + '.cns')
P_segment = AP_subparsers.add_parser('segment', help=_cmd_segment.__doc__)
@@ -688,9 +628,6 @@ P_segment.add_argument('-m', '--method',
P_segment.add_argument('-t', '--threshold', type=float,
help="""Significance threshold (p-value or FDR, depending on method) to
accept breakpoints during segmentation.""")
-P_segment.add_argument('-v', '--vcf',
- help="""VCF file name containing variants for segmentation by allele
- frequencies.""")
P_segment.add_argument("--drop-low-coverage", action='store_true',
help="""Drop very-low-coverage bins before segmentation to avoid
false-positive deletions in poor-quality tumor samples.""")
@@ -702,178 +639,85 @@ P_segment.add_argument("--drop-outliers",
[Default: %(default)g]""")
P_segment.add_argument("--rlibpath",
help="Path to an alternative site-library to use for R packages.")
-P_segment.set_defaults(func=_cmd_segment)
-
-
-# rescale ---------------------------------------------------------------------
-
-def _cmd_rescale(args):
- """[DEPRECATED] Rescale segment copy ratios given known purity and ploidy.
-
- Instead, use the command "call -m none".
- """
- if args.purity and not 0.0 < args.purity <= 1.0:
- raise RuntimeError("Purity must be between 0 and 1.")
-
- cnarr = _CNA.read(args.filename)
- if args.center:
- cnarr.center_all(args.center)
- if args.purity and args.purity < 1.0:
- is_sample_female = verify_gender_arg(cnarr, args.gender,
- args.male_reference)
- cnarr = do_rescale(cnarr, args.ploidy, args.purity,
- args.male_reference, is_sample_female)
- cnarr.write(args.output)
-
+P_segment.add_argument('-p', '--processes',
+ nargs='?', type=int, const=0, default=1,
+ help="""Number of subprocesses to segment in parallel.
+ Give 0 or a negative value to use the maximum number
+ of available CPUs. [Default: use 1 process]""")
+
+P_segment_vcf = P_segment.add_argument_group(
+ "To additionally segment SNP b-allele frequencies")
+P_segment_vcf.add_argument('-v', '--vcf', metavar="FILENAME",
+ help="""VCF file name containing variants for segmentation by allele
+ frequencies.""")
+P_segment_vcf.add_argument('-i', '--sample-id',
+ help="""Specify the name of the sample in the VCF (-v/--vcf) to use for
+ b-allele frequency extraction and as the default plot title.""")
+P_segment_vcf.add_argument('-n', '--normal-id',
+ help="""Corresponding normal sample ID in the input VCF (-v/--vcf).
+ This sample is used to select only germline SNVs to plot
+ b-allele frequencies.""")
+P_segment_vcf.add_argument('--min-variant-depth', type=int, default=20,
+ help="""Minimum read depth for a SNV to be displayed in the b-allele
+ frequency plot. [Default: %(default)s]""")
+P_segment_vcf.add_argument('-z', '--zygosity-freq',
+ metavar='ALT_FREQ', nargs='?', type=float, const=0.25,
+ help="""Ignore VCF's genotypes (GT field) and instead infer zygosity
+ from allele frequencies. [Default if used without a number:
+ %(const)s]""")
-def do_rescale(cnarr, ploidy=2, purity=None, is_reference_male=False,
- is_sample_female=False):
- absolutes = call.absolute_clonal(cnarr, ploidy, purity,
- is_reference_male, is_sample_female)
- # Convert back to log2 ratios; avoid a logarithm domain error
- outarr = cnarr.copy()
- outarr['log2'] = call.log2_ratios(cnarr, absolutes, ploidy,
- is_reference_male)
- return outarr
+P_segment.set_defaults(func=_cmd_segment)
-P_rescale = AP_subparsers.add_parser('rescale', help=_cmd_rescale.__doc__)
-P_rescale.add_argument('filename',
- help="Copy ratios (.cnr or .cns).")
-P_rescale.add_argument("--center",
- choices=('mean', 'median', 'mode', 'biweight'),
- help="""Re-center the log2 ratio values using this estimate of the
- center or average value.""")
-P_rescale.add_argument("--ploidy", type=int, default=2,
- help="Ploidy of the sample cells. [Default: %(default)d]")
-P_rescale.add_argument("--purity", type=float,
- help="Estimated tumor cell fraction, a.k.a. purity or cellularity.")
-P_rescale.add_argument("-g", "--gender",
- choices=('m', 'male', 'Male', 'f', 'female', 'Female'),
- help="""Specify the sample's gender as male or female. (Otherwise
- guessed from chrX copy number).""")
-P_rescale.add_argument('-y', '--male-reference', action='store_true',
- help="""Was a male reference used? If so, expect half ploidy on
- chrX and chrY; otherwise, only chrY has half ploidy. In CNVkit,
- if a male reference was used, the "neutral" copy number (ploidy)
- of chrX is 1; chrY is haploid for either gender reference.""")
-P_rescale.add_argument('-o', '--output',
- help="Output table file name (CNR-like table of segments, .cns).")
-P_rescale.set_defaults(func=_cmd_rescale)
+# call ------------------------------------------------------------------------
+do_call = public(call.do_call)
-# call ------------------------------------------------------------------------
def _cmd_call(args):
"""Call copy number variants from segmented log2 ratios."""
if args.purity and not 0.0 < args.purity <= 1.0:
raise RuntimeError("Purity must be between 0 and 1.")
- cnarr = _CNA.read(args.filename)
- if args.center:
- cnarr.center_all(args.center)
- is_sample_female = (verify_gender_arg(cnarr, args.gender,
+ cnarr = read_cna(args.filename)
+ if args.center_at:
+ logging.info("Shifting log2 values by %f", -args.center_at)
+ cnarr['log2'] -= args.center_at
+ elif args.center:
+ cnarr.center_all(args.center, verbose=True)
+
+ varr = load_het_snps(args.vcf, args.sample_id, args.normal_id,
+ args.min_variant_depth, args.zygosity_freq)
+ is_sample_female = (verify_sample_sex(cnarr, args.sample_sex,
args.male_reference)
if args.purity and args.purity < 1.0
else None)
- vcf = (_VA.read_vcf(args.vcf, skip_hom=True, skip_somatic=True)
- if args.vcf
- else None)
- cnarr = do_call(cnarr, vcf, args.method, args.ploidy, args.purity,
- args.male_reference, is_sample_female, args.thresholds)
- cnarr.write(args.output or cnarr.sample_id + '.call.cns')
-
-
-def do_call(cnarr, variants=None, method="threshold", ploidy=2, purity=None,
- is_reference_male=False, is_sample_female=False,
- thresholds=(-1.1, -0.25, 0.2, 0.7)):
- if method not in ("threshold", "clonal", "none"):
- raise ValueError("Argument `method` must be one of: clonal, threshold")
-
- outarr = cnarr.copy()
- if variants:
- # baf_median = lambda x: np.median(np.abs(x - .5)) + .5
- baf_median = export.mirrored_baf_median
- outarr["baf"] = outarr.match_to_bins(variants, 'alt_freq', np.nan,
- summary_func=baf_median)
-
- if purity and purity < 1.0:
- logging.info("Rescaling sample with purity %g, ploidy %d",
- purity, ploidy)
- absolutes = call.absolute_clonal(outarr, ploidy, purity,
- is_reference_male, is_sample_female)
- # Recalculate sample log2 ratios after rescaling for purity
- outarr["log2"] = call.log2_ratios(outarr, absolutes, ploidy,
- is_reference_male)
- if variants:
- # Rescale b-allele frequencies for purity
- outarr["baf"] = rescale_baf(purity, outarr["baf"])
- elif method == "clonal":
- # Estimate absolute copy numbers from the original log2 values
- logging.info("Calling copy number with clonal ploidy %d", ploidy)
- absolutes = call.absolute_pure(outarr, ploidy, is_reference_male)
-
- if method == "threshold":
- # Apply cutoffs to either original or rescaled log2 values
- tokens = ["%g => %d" % (thr, i) for i, thr in enumerate(thresholds)]
- logging.info("Calling copy number with thresholds: %s",
- ", ".join(tokens))
- absolutes = call.absolute_threshold(outarr, ploidy, thresholds,
- is_reference_male)
-
- if method != "none":
- outarr["cn"] = np.asarray(np.rint(absolutes), dtype=np.int_)
- if "baf" in outarr:
- # Major and minor allelic copy numbers
- outarr["cn1"] = np.asarray(np.rint(absolutes * outarr["baf"]),
- dtype=np.int_).clip(0, outarr["cn"])
- outarr["cn2"] = outarr["cn"] - outarr["cn1"]
- is_null = outarr["baf"].isnull()
- outarr[is_null, "cn1"] = np.nan
- outarr[is_null, "cn2"] = np.nan
- return outarr
-
-
-def rescale_baf(purity, observed_baf, normal_baf=0.5):
- """Adjust B-allele frequencies for sample purity.
-
- Math:
- t_baf*purity + n_baf*(1-purity) = obs_baf
- obs_baf - n_baf * (1-purity) = t_baf * purity
- t_baf = (obs_baf - n_baf * (1-purity))/purity
- """
- # ENH: use normal_baf array if available
- tumor_baf = (observed_baf - normal_baf * (1-purity)) / purity
- # ENH: warn if tumor_baf < 0 -- purity estimate may be too low
- return tumor_baf
+ cnarr = call.do_call(cnarr, varr, args.method, args.ploidy, args.purity,
+ args.male_reference, is_sample_female, args.filters,
+ args.thresholds)
+ tabio.write(cnarr, args.output or cnarr.sample_id + '.call.cns')
def csvstring(text):
return tuple(map(float, text.split(",")))
-def verify_gender_arg(cnarr, gender_arg, is_male_reference):
- is_sample_female = cnarr.guess_xx(is_male_reference, verbose=False)
- if gender_arg:
- is_sample_female_given = (gender_arg.lower() not in ["m", "male"])
- if is_sample_female != is_sample_female_given:
- logging.info("Sample gender specified as %s "
- "but chrX copy number looks like %s",
- gender_arg,
- "female" if is_sample_female else "male")
- is_sample_female = is_sample_female_given
- logging.info("Treating sample gender as %s",
- "female" if is_sample_female else "male")
- return is_sample_female
-
-
P_call = AP_subparsers.add_parser('call', help=_cmd_call.__doc__)
P_call.add_argument('filename',
help="Copy ratios (.cnr or .cns).")
-P_call.add_argument("--center",
+P_call.add_argument("--center", nargs='?', const='median',
choices=('mean', 'median', 'mode', 'biweight'),
- help="""Re-center the log2 ratio values using this estimate of the
- center or average value.""")
+ help="""Re-center the log2 ratio values using this estimator of the
+ center or average value. ('median' if no argument given.)""")
+P_call.add_argument("--center-at", type=float,
+ help="""Subtract a constant number from all log2 values. For "manual"
+ re-centering, in case the --center option gives unsatisfactory
+ results.)""")
+P_call.add_argument('--filter', action='append', default=[], dest='filters',
+ choices=('ampdel', 'cn', 'ci', 'sem', # 'bic'
+ ),
+ help="""Merge segments flagged by the specified filter(s) with the
+ adjacent segment(s).""")
P_call.add_argument('-m', '--method',
choices=('threshold', 'clonal', 'none'), default='threshold',
help="""Calling method. [Default: %(default)s]""")
@@ -886,20 +730,39 @@ P_call.add_argument("--ploidy", type=int, default=2,
help="Ploidy of the sample cells. [Default: %(default)d]")
P_call.add_argument("--purity", type=float,
help="Estimated tumor cell fraction, a.k.a. purity or cellularity.")
-P_call.add_argument('-v', '--vcf',
- help="""VCF file name containing variants for assigning allele
- frequencies and copy number.""")
-P_call.add_argument("-g", "--gender",
- choices=('m', 'male', 'Male', 'f', 'female', 'Female'),
- help="""Specify the sample's gender as male or female. (Otherwise
- guessed from chrX copy number).""")
+P_call.add_argument('-x', '--sample-sex', '-g', '--gender', dest='sample_sex',
+ choices=('m', 'y', 'male', 'Male', 'f', 'x', 'female', 'Female'),
+ help="""Specify the sample's chromosomal sex as male or female.
+ (Otherwise guessed from X and Y coverage).""")
P_call.add_argument('-y', '--male-reference', action='store_true',
help="""Was a male reference used? If so, expect half ploidy on
chrX and chrY; otherwise, only chrY has half ploidy. In CNVkit,
if a male reference was used, the "neutral" copy number (ploidy)
- of chrX is 1; chrY is haploid for either gender reference.""")
+ of chrX is 1; chrY is haploid for either reference sex.""")
P_call.add_argument('-o', '--output',
help="Output table file name (CNR-like table of segments, .cns).")
+
+P_call_vcf = P_call.add_argument_group(
+ "To additionally process SNP b-allele frequencies for allelic copy number")
+P_call_vcf.add_argument('-v', '--vcf', metavar="FILENAME",
+ help="""VCF file name containing variants for calculation of b-allele
+ frequencies.""")
+P_call_vcf.add_argument('-i', '--sample-id',
+ help="""Name of the sample in the VCF (-v/--vcf) to use for b-allele
+ frequency extraction.""")
+P_call_vcf.add_argument('-n', '--normal-id',
+ help="""Corresponding normal sample ID in the input VCF (-v/--vcf).
+ This sample is used to select only germline SNVs to calculate
+ b-allele frequencies.""")
+P_call_vcf.add_argument('--min-variant-depth', type=int, default=20,
+ help="""Minimum read depth for a SNV to be used in the b-allele
+ frequency calculation. [Default: %(default)s]""")
+P_call_vcf.add_argument('-z', '--zygosity-freq',
+ metavar='ALT_FREQ', nargs='?', type=float, const=0.25,
+ help="""Ignore VCF's genotypes (GT field) and instead infer zygosity
+ from allele frequencies. [Default if used without a number:
+ %(const)s]""")
+
P_call.set_defaults(func=_cmd_call)
@@ -914,12 +777,21 @@ def _cmd_diagram(args):
If both the raw probes and segments are given, show them side-by-side on
each chromosome (segments on the left side, probes on the right side).
"""
- from cnvlib import diagram
- cnarr = _CNA.read(args.filename) if args.filename else None
- segarr = _CNA.read(args.segment) if args.segment else None
+ if not args.filename and not args.segment:
+ raise ValueError("Must specify a filename as an argument or with "
+ "the '-s' option, or both. You did neither.")
+
+ cnarr = read_cna(args.filename) if args.filename else None
+ segarr = read_cna(args.segment) if args.segment else None
+ if args.adjust_xy:
+ is_sample_female = verify_sample_sex(cnarr or segarr, args.sample_sex,
+ args.male_reference)
+ if cnarr:
+ cnarr = cnarr.shift_xx(args.male_reference, is_sample_female)
+ if segarr:
+ segarr = segarr.shift_xx(args.male_reference, is_sample_female)
outfname = diagram.create_diagram(cnarr, segarr, args.threshold,
- args.min_probes, args.output,
- args.male_reference)
+ args.min_probes, args.output, args.title)
logging.info("Wrote %s", outfname)
@@ -939,373 +811,157 @@ P_diagram.add_argument('-y', '--male-reference', action='store_true',
help="""Assume inputs are already corrected against a male
reference (i.e. female samples will have +1 log-CNR of
chrX; otherwise male samples would have -1 chrX).""")
+P_diagram.add_argument('-x', '--sample-sex', '-g', '--gender',
+ dest='sample_sex',
+ choices=('m', 'y', 'male', 'Male', 'f', 'x', 'female', 'Female'),
+ help="""Specify the sample's chromosomal sex as male or female.
+ (Otherwise guessed from X and Y coverage).""")
+P_diagram.add_argument('--no-shift-xy', dest='adjust_xy', action='store_false',
+ help="Don't adjust the X and Y chromosomes according to sample sex.")
P_diagram.add_argument('-o', '--output',
help="Output PDF file name.")
+P_diagram_aes = P_diagram.add_argument_group("Plot aesthetics")
+P_diagram_aes.add_argument('--title',
+ help="Plot title. [Default: sample ID, from filename or -i]")
P_diagram.set_defaults(func=_cmd_diagram)
# scatter ---------------------------------------------------------------------
+do_scatter = public(scatter.do_scatter)
+
+
def _cmd_scatter(args):
"""Plot probe log2 coverages and segmentation calls together."""
- cnarr = _CNA.read(args.filename, args.sample_id
- ) if args.filename else None
- segarr = _CNA.read(args.segment
- ) if args.segment else None
- if not args.sample_id and (cnarr or segarr):
- args.sample_id = (cnarr or segarr).sample_id
- varr = _VA.read_vcf(args.vcf, args.sample_id, args.normal_id,
- args.min_variant_depth, skip_hom=True, skip_somatic=True
- ) if args.vcf else None
-
+ cnarr = read_cna(args.filename, sample_id=args.sample_id
+ ) if args.filename else None
+ segarr = read_cna(args.segment, sample_id=args.sample_id
+ ) if args.segment else None
+ varr = load_het_snps(args.vcf, args.sample_id, args.normal_id,
+ args.min_variant_depth, args.zygosity_freq)
if args.range_list:
with PdfPages(args.output) as pdf_out:
- for chrom, start, end in _RA.read(args.range_list).coords():
- region = "{}:{}-{}".format(chrom, start, end)
- do_scatter(cnarr, segarr, varr, region, False,
- args.background_marker, args.trend,
- args.width, args.y_min, args.y_max)
- pyplot.title(region)
+ for region in tabio.read_auto(args.range_list).coords():
+ try:
+ scatter.do_scatter(cnarr, segarr, varr, region, None,
+ args.antitarget_marker, args.trend,
+ args.width, args.y_min, args.y_max,
+ ("%s %s" % (args.title,
+ region.chromosome)
+ if args.title else None),
+ args.segment_color)
+ except ValueError as exc:
+ # Probably no bins in the selected region
+ logging.warn("Not plotting region %r: %s",
+ to_label(region), exc)
pdf_out.savefig()
pyplot.close()
else:
- do_scatter(cnarr, segarr, varr, args.chromosome, args.gene,
- args.background_marker, args.trend, args.width,
- args.y_min, args.y_max)
+ scatter.do_scatter(cnarr, segarr, varr, args.chromosome, args.gene,
+ args.antitarget_marker, args.trend, args.width,
+ args.y_min, args.y_max, args.title,
+ args.segment_color)
if args.output:
- pyplot.savefig(args.output, format='pdf', bbox_inches="tight")
+ oformat = os.path.splitext(args.output)[-1].replace(".", "")
+ pyplot.savefig(args.output, format=oformat, bbox_inches="tight")
logging.info("Wrote %s", args.output)
else:
pyplot.show()
-def do_scatter(cnarr, segments=None, variants=None,
- show_range=None, show_gene=None,
- background_marker=None, do_trend=False, window_width=1e6,
- y_min=None, y_max=None, title=None):
- """Plot probe log2 coverages and CBS calls together.
-
- show_gene: name of gene to highligh
- show_range: chromosome name or coordinate string like "chr1:20-30"
- """
- if title is None:
- title = (cnarr or segments or variants).sample_id
-
- if not show_gene and not show_range:
- # Plot all chromosomes, concatenated on one plot
- PAD = 1e7
- if (cnarr or segments) and variants:
- # Lay out top 3/5 for the CN scatter, bottom 2/5 for SNP plot
- axgrid = pyplot.GridSpec(5, 1, hspace=.85)
- axis = pyplot.subplot(axgrid[:3])
- axis2 = pyplot.subplot(axgrid[3:], sharex=axis)
- # Place chromosome labels between the CNR and SNP plots
- axis2.tick_params(labelbottom=False)
- chrom_sizes = plots.chromosome_sizes(cnarr or segments)
- plots.snv_on_genome(axis2, variants, chrom_sizes, segments,
- do_trend, PAD)
- else:
- _fig, axis = pyplot.subplots()
- if cnarr or segments:
- axis.set_title(title)
- plots.cnv_on_genome(axis, cnarr, segments, PAD, do_trend, y_min, y_max)
- else:
- axis.set_title("Variant allele frequencies: %s" % title)
- chrom_sizes = collections.OrderedDict(
- (chrom, subarr["end"].max())
- for chrom, subarr in variants.by_chromosome())
- plots.snv_on_genome(axis, variants, chrom_sizes, segments, do_trend,
- PAD)
-
- else:
- # Plot a specified region on one chromosome
- # -r \ -g | None | Some
- # None | genome| genes w/ auto window
- # chr | chr | genes w/ no window *
- # chr:s-e | window| genes w/ given window
- chrom, start, end = plots.unpack_range(show_range)
- window_coords = ()
- genes = []
- if show_gene:
- gene_names = show_gene.split(',')
- # Scan for probes matching the specified gene
- gene_coords = plots.gene_coords_by_name(cnarr, gene_names)
- if not len(gene_coords) == 1:
- raise ValueError("Genes %s are split across chromosomes %s"
- % (show_gene, gene_coords.keys()))
- g_chrom, genes = gene_coords.popitem()
- if chrom:
- # Confirm that the selected chromosomes match
- core.assert_equal("Chromosome also selected by region (-r)"
- "does not match",
- **{"chromosome": chrom,
- "gene(s)": g_chrom})
- else:
- chrom = g_chrom
- # Set the display window to the selected genes +/- a margin
- genes.sort()
- window_coords = (max(0, genes[0][0] - window_width),
- genes[-1][1] + window_width)
-
- if start is not None or end is not None:
- # Default selection endpoint to the maximum chromosome position
- if not end:
- end = (cnarr or segments or variants
- ).select(chromosome=chrom).end.iat[-1]
- if window_coords:
- # Genes were specified, & window was set around them
- if start > window_coords[0] or end < window_coords[1]:
- raise ValueError("Selected gene range " + chrom +
- (":%d-%d" % window_coords) +
- " is outside specified range " +
- show_range)
- window_coords = (max(0, start - window_width), end + window_width)
- if cnarr and not genes:
- genes = plots.gene_coords_by_range(cnarr, chrom,
- start, end)[chrom]
- if not genes and window_width > (end - start) / 10.0:
- # No genes in the selected region, so highlight the region
- # itself (unless the selection is ~entire displayed window)
- logging.info("No genes found in selection; will show the "
- "selected range itself instead")
- genes = [(start, end, "Selection")]
- elif show_range and window_coords:
- # Specified range is only chrom, no start-end
- # Reset window around selected genes to show the whole chromosome
- window_coords = ()
-
- # Prune plotted elements to the selected region
- sel_probes = (cnarr.in_range(chrom, *window_coords)
- if cnarr else _CNA([]))
- sel_seg = (segments.in_range(chrom, *window_coords, mode='trim')
- if segments else _CNA([]))
-
- logging.info("Showing %d probes and %d selected genes in range %s",
- len(sel_probes), len(genes),
- (chrom + ":%d-%d" % window_coords if window_coords
- else chrom))
-
- # Similarly for SNV allele freqs, if given
- if (cnarr or segments) and variants:
- # Lay out top 3/5 for the CN scatter, bottom 2/5 for SNP plot
- axgrid = pyplot.GridSpec(5, 1, hspace=.5)
- axis = pyplot.subplot(axgrid[:3])
- axis2 = pyplot.subplot(axgrid[3:], sharex=axis)
- # Plot allele freqs for only the selected region
- sel_snvs = variants.in_range(chrom, *window_coords)
- plots.snv_on_chromosome(axis2, sel_snvs, sel_seg, genes,
- do_trend, # do_boost,
- )
- elif variants:
- # XXX tangle
- # nb: don't do the last call to cnv_on_chromosome
- _fig, axis = pyplot.subplots()
- sel_snvs = variants.in_range(chrom, *window_coords)
- plots.snv_on_chromosome(axis, sel_snvs, sel_seg, genes,
- do_trend, # do_boost,
- )
- return
-
- else:
- _fig, axis = pyplot.subplots()
- axis.set_xlabel("Position (Mb)")
-
- # Plot CNVs
- axis.set_title("%s %s" % (title, chrom))
- plots.cnv_on_chromosome(axis, sel_probes, sel_seg, genes,
- background_marker=background_marker,
- do_trend=do_trend, y_min=y_min, y_max=y_max)
-
-
P_scatter = AP_subparsers.add_parser('scatter', help=_cmd_scatter.__doc__)
P_scatter.add_argument('filename', nargs="?",
help="""Processed bin-level copy ratios (*.cnr), the output
of the 'fix' sub-command.""")
-P_scatter.add_argument('-s', '--segment',
+P_scatter.add_argument('-s', '--segment', metavar="FILENAME",
help="Segmentation calls (.cns), the output of the 'segment' command.")
-P_scatter.add_argument('-c', '--chromosome',
- help="""Chromosome (e.g. 'chr1') or chromosomal range (e.g.
- 'chr1:2333000-2444000') to display. If a range is given,
+P_scatter.add_argument('-c', '--chromosome', metavar="RANGE",
+ help="""Chromosome or chromosomal range, e.g. 'chr1' or
+ 'chr1:2333000-2444000', to display. If a range is given,
all targeted genes in this range will be shown, unless
- '--gene'/'-g' is already given.""")
+ -g/--gene is also given.""")
P_scatter.add_argument('-g', '--gene',
help="Name of gene or genes (comma-separated) to display.")
P_scatter.add_argument('-l', '--range-list',
help="""File listing the chromosomal ranges to display, as BED, interval
- list or "chr:start-end" text. Creates focal plots similar to
+ list or 'chr:start-end' text. Creates focal plots similar to
-c/--chromosome for each listed region, combined into a
multi-page PDF. The output filename must also be
specified (-o/--output).""")
-P_scatter.add_argument("-i", "--sample-id",
- help="""Specify the name of the sample in the VCF to use for b-allele
- frequency extraction and to show in plot title.""")
-P_scatter.add_argument("-n", "--normal-id",
- help="Corresponding normal sample ID in the input VCF.")
-P_scatter.add_argument('-b', '--background-marker', default=None,
- help="""Plot antitargets with this symbol, in zoomed/selected regions.
- [Default: same as targets]""")
-P_scatter.add_argument('-t', '--trend', action='store_true',
- help="Draw a smoothed local trendline on the scatter plot.")
-P_scatter.add_argument('-v', '--vcf',
- help="""VCF file name containing variants to plot for SNV allele
- frequencies.""")
-P_scatter.add_argument('-m', '--min-variant-depth', type=int, default=20,
- help="""Minimum read depth for a SNV to be displayed in the b-allele
- frequency plot. [Default: %(default)s]""")
P_scatter.add_argument('-w', '--width', type=float, default=1e6,
- help="""Width of margin to show around the selected gene or region
- on the chromosome (use with --gene or --region).
- [Default: %(default)d]""")
-P_scatter.add_argument('--y-min', type=float, help="""y-axis lower limit.""")
-P_scatter.add_argument('--y-max', type=float, help="""y-axis upper limit.""")
-P_scatter.add_argument('-o', '--output',
- help="Output table file name.")
-P_scatter.set_defaults(func=_cmd_scatter)
-
-
-# loh -------------------------------------------------------------------------
+ help="""Width of margin to show around the selected gene or chromosomal
+ region (-g/--gene or -c/--chromosome). [Default: %(default)d]
+ """)
+P_scatter.add_argument('-o', '--output', metavar="FILENAME",
+ help="Output PDF file name.")
-def _cmd_loh(args):
- """[DEPRECATED] Plot allelic frequencies at each variant position in a VCF file.
+P_scatter_aes = P_scatter.add_argument_group("Plot aesthetics")
+P_scatter_aes.add_argument('-a', '--antitarget-marker',
+ '-b', '--background-marker', # DEPRECATED in 0.9.0
+ metavar='CHARACTER', dest='antitarget_marker', default=None,
+ help="""Plot antitargets using this symbol when plotting in a selected
+ chromosomal region (-g/--gene or -c/--chromosome).
+ [Default: same as targets]""")
+# Alternative shim (enable in 0.9.1)
+# P_scatter_aes.add_argument('-b', '--background-marker',
+# dest='antitarget_marker', help=argparse.SUPPRESS)
+P_scatter_aes.add_argument('--segment-color', default=scatter.SEG_COLOR,
+ help="""Plot segment lines in this color. Value can be any string
+ accepted by matplotlib, e.g. 'red' or '#CC0000'.""")
+P_scatter_aes.add_argument('--title',
+ help="Plot title. [Default: sample ID, from filename or -i]")
+P_scatter_aes.add_argument('-t', '--trend', action='store_true',
+ help="Draw a smoothed local trendline on the scatter plot.")
+P_scatter_aes.add_argument('--y-max', type=float, help="y-axis upper limit.")
+P_scatter_aes.add_argument('--y-min', type=float, help="y-axis lower limit.")
- Divergence from 0.5 indicates loss of heterozygosity in a tumor sample.
+P_scatter_vcf = P_scatter.add_argument_group(
+ "To plot SNP b-allele frequencies")
+P_scatter_vcf.add_argument('-v', '--vcf', metavar="FILENAME",
+ help="""VCF file name containing variants to plot for SNV b-allele
+ frequencies.""")
+P_scatter_vcf.add_argument('-i', '--sample-id',
+ help="""Name of the sample in the VCF to use for b-allele frequency
+ extraction and as the default plot title.""")
+P_scatter_vcf.add_argument('-n', '--normal-id',
+ help="""Corresponding normal sample ID in the input VCF. This sample is
+ used to select only germline SNVs to plot.""")
+P_scatter_vcf.add_argument('-m', '--min-variant-depth', type=int, default=20,
+ help="""Minimum read depth for a SNV to be used in the b-allele
+ frequency calculation. [Default: %(default)s]""")
+P_scatter_vcf.add_argument('-z', '--zygosity-freq',
+ metavar='ALT_FREQ', nargs='?', type=float, const=0.25,
+ help="""Ignore VCF's genotypes (GT field) and instead infer zygosity
+ from allele frequencies. [Default if used without a number:
+ %(const)s]""")
- Instead, use the command "scatter -v".
- """
- variants = _VA.read_vcf(args.variants, args.sample_id, args.normal_id,
- args.min_depth, skip_hom=True, skip_somatic=True)
- segments = _CNA.read(args.segment) if args.segment else None
- _fig, axis = pyplot.subplots()
- axis.set_title("Variant allele frequencies: %s" % variants.sample_id)
- chrom_sizes = collections.OrderedDict(
- (chrom, subarr["end"].max())
- for chrom, subarr in variants.by_chromosome())
- PAD = 2e7
- plots.snv_on_genome(axis, variants, chrom_sizes, segments, args.trend, PAD)
- if args.output:
- pyplot.savefig(args.output, format='pdf', bbox_inches="tight")
- else:
- pyplot.show()
+P_scatter.set_defaults(func=_cmd_scatter)
-P_loh = AP_subparsers.add_parser('loh', help=_cmd_loh.__doc__)
-P_loh.add_argument('variants',
- help="Sample variants in VCF format.")
-P_loh.add_argument('-s', '--segment',
- help="Segmentation calls (.cns), the output of the 'segment' command.")
-P_loh.add_argument('-m', '--min-depth', type=int, default=20,
- help="""Minimum read depth for a variant to be displayed.
- [Default: %(default)s]""")
-P_loh.add_argument("-i", "--sample-id",
- help="Sample name to use for LOH calculations from the input VCF.")
-P_loh.add_argument("-n", "--normal-id",
- help="Corresponding normal sample ID in the input VCF.")
-P_loh.add_argument('-t', '--trend', action='store_true',
- help="Draw a smoothed local trendline on the scatter plot.")
-P_loh.add_argument('-o', '--output',
- help="Output PDF file name.")
-P_loh.set_defaults(func=_cmd_loh)
+# heatmap ---------------------------------------------------------------------
+do_heatmap = public(heatmap.do_heatmap)
-# heatmap ---------------------------------------------------------------------
def _cmd_heatmap(args):
"""Plot copy number for multiple samples as a heatmap."""
- cnarrs = list(map(_CNA.read, args.filenames))
- do_heatmap(cnarrs, args.chromosome, args.desaturate)
+ cnarrs = []
+ for fname in args.filenames:
+ cnarr = read_cna(fname)
+ if args.adjust_xy:
+ is_sample_female = verify_sample_sex(cnarr, args.sample_sex,
+ args.male_reference)
+ cnarr = cnarr.shift_xx(args.male_reference, is_sample_female)
+ cnarrs.append(cnarr)
+ heatmap.do_heatmap(cnarrs, args.chromosome, args.desaturate)
if args.output:
- pyplot.savefig(args.output, format='pdf', bbox_inches="tight")
+ oformat = os.path.splitext(args.output)[-1].replace(".", "")
+ pyplot.savefig(args.output, format=oformat, bbox_inches="tight")
logging.info("Wrote %s", args.output)
else:
pyplot.show()
-def do_heatmap(cnarrs, show_range=None, do_desaturate=False):
- """Plot copy number for multiple samples as a heatmap."""
- from matplotlib.collections import BrokenBarHCollection
-
- _fig, axis = pyplot.subplots()
-
- # List sample names on the y-axis
- axis.set_yticks([i + 0.5 for i in range(len(cnarrs))])
- axis.set_yticklabels([c.sample_id for c in cnarrs])
- axis.set_ylim(0, len(cnarrs))
- axis.invert_yaxis()
- axis.set_ylabel("Samples")
- axis.set_axis_bgcolor('#DDDDDD')
-
- r_chrom, r_start, r_end = plots.unpack_range(show_range)
- if r_start is not None or r_end is not None:
- logging.info("Showing log2 ratios in range %s:%d-%s",
- r_chrom, r_start, r_end or '*')
- elif r_chrom:
- logging.info("Showing log2 ratios on chromosome %s", r_chrom)
-
- # Closes over do_desaturate
- def cna2df(cna):
- """Extract a dataframe of plotting points from a CopyNumArray."""
- points = cna.data.loc[:, ["start", "end"]]
- points["color"] = cna.log2.apply(plots.cvg2rgb, args=(do_desaturate,))
- return points
-
- # Group each file's probes/segments by chromosome
- sample_data = [collections.defaultdict(list) for _c in cnarrs]
- # Calculate the size (max endpoint value) of each chromosome
- chrom_sizes = collections.OrderedDict()
- for i, cnarr in enumerate(cnarrs):
- if r_chrom:
- subcna = cnarr.in_range(r_chrom, r_start, r_end, mode="trim")
- sample_data[i][r_chrom] = cna2df(subcna)
- chrom_sizes[r_chrom] = max(subcna.end.iat[-1] if subcna else 0,
- chrom_sizes.get(r_chrom, 0))
- else:
- for chrom, subcna in cnarr.by_chromosome():
- sample_data[i][chrom] = cna2df(subcna)
- chrom_sizes[chrom] = max(subcna.end.iat[-1] if subcna else 0,
- chrom_sizes.get(r_chrom, 0))
-
- # Closes over axis
- def plot_sample_chrom(i, sample):
- """Draw the given coordinates and colors as a horizontal series."""
- xranges = [(start, end - start)
- for start, end in zip(sample.start, sample.end)]
- bars = BrokenBarHCollection(xranges, (i, i+1),
- edgecolors="none",
- facecolors=sample["color"])
- axis.add_collection(bars)
-
- if show_range:
- # Lay out only the selected chromosome
- # Set x-axis the chromosomal positions (in Mb), title as the selection
- axis.set_xlim((r_start or 0) * plots.MB,
- (r_end or chrom_sizes[r_chrom]) * plots.MB)
- axis.set_title(show_range)
- axis.set_xlabel("Position (Mb)")
- axis.tick_params(which='both', direction='out')
- axis.get_xaxis().tick_bottom()
- axis.get_yaxis().tick_left()
- # Plot the individual probe/segment coverages
- for i, sample in enumerate(sample_data):
- crow = sample[r_chrom]
- crow["start"] *= plots.MB
- crow["end"] *= plots.MB
- plot_sample_chrom(i, crow)
-
- else:
- # Lay out chromosome dividers and x-axis labels
- # (Just enough padding to avoid overlap with the divider line)
- chrom_offsets = plots.plot_x_dividers(axis, chrom_sizes, 1)
- # Plot the individual probe/segment coverages
- for i, sample in enumerate(sample_data):
- for chrom, curr_offset in iteritems(chrom_offsets):
- crow = sample[chrom]
- crow["start"] += curr_offset
- crow["end"] += curr_offset
- plot_sample_chrom(i, crow)
-
- return axis
-
-
P_heatmap = AP_subparsers.add_parser('heatmap', help=_cmd_heatmap.__doc__)
P_heatmap.add_argument('filenames', nargs='+',
help="Sample coverages as raw probes (.cnr) or segments (.cns).")
@@ -1318,6 +974,18 @@ P_heatmap.add_argument('-c', '--chromosome',
# help="Name of gene to display.")
P_heatmap.add_argument('-d', '--desaturate', action='store_true',
help="Tweak color saturation to focus on significant changes.")
+P_heatmap.add_argument('-y', '--male-reference', action='store_true',
+ help="""Assume inputs are already corrected against a male
+ reference (i.e. female samples will have +1 log-CNR of
+ chrX; otherwise male samples would have -1 chrX).""")
+P_heatmap.add_argument('-x', '--sample-sex', '-g', '--gender',
+ dest='sample_sex',
+ choices=('m', 'y', 'male', 'Male', 'f', 'x', 'female', 'Female'),
+ help="""Specify the chromosomal sex of all given samples as male or
+ female. (Default: guess each sample from coverage of X and Y
+ chromosomes).""")
+P_heatmap.add_argument('--no-shift-xy', dest='adjust_xy', action='store_false',
+ help="Don't adjust the X and Y chromosomes according to sample sex.")
P_heatmap.add_argument('-o', '--output',
help="Output PDF file name.")
P_heatmap.set_defaults(func=_cmd_heatmap)
@@ -1330,20 +998,22 @@ P_heatmap.set_defaults(func=_cmd_heatmap)
def _cmd_breaks(args):
"""List the targeted genes in which a copy number breakpoint occurs."""
- cnarr = _CNA.read(args.filename)
- segarr = _CNA.read(args.segment)
+ cnarr = read_cna(args.filename)
+ segarr = read_cna(args.segment)
bpoints = do_breaks(cnarr, segarr, args.min_probes)
logging.info("Found %d gene breakpoints", len(bpoints))
- core.write_tsv(args.output, bpoints,
- colnames=['Gene', 'Chrom.', 'Location', 'Change',
- 'ProbesLeft', 'ProbesRight'])
+ write_dataframe(args.output, bpoints)
+ at public
def do_breaks(probes, segments, min_probes=1):
"""List the targeted genes in which a copy number breakpoint occurs."""
intervals = reports.get_gene_intervals(probes)
bpoints = reports.get_breakpoints(intervals, segments, min_probes)
- return bpoints
+ return pd.DataFrame.from_records(bpoints,
+ columns=['gene', 'chromosome',
+ 'location', 'change',
+ 'probes_left', 'probes_right'])
P_breaks = AP_subparsers.add_parser('breaks', help=_cmd_breaks.__doc__)
@@ -1364,27 +1034,37 @@ P_breaks.set_defaults(func=_cmd_breaks)
def _cmd_gainloss(args):
"""Identify targeted genes with copy number gain or loss."""
- pset = _CNA.read(args.filename)
- segs = _CNA.read(args.segment) if args.segment else None
- gainloss = do_gainloss(pset, segs, args.male_reference, args.threshold,
- args.min_probes, args.drop_low_coverage)
+ cnarr = read_cna(args.filename)
+ segarr = read_cna(args.segment) if args.segment else None
+ is_sample_female = verify_sample_sex(cnarr, args.sample_sex,
+ args.male_reference)
+ gainloss = do_gainloss(cnarr, segarr, args.threshold,
+ args.min_probes, args.drop_low_coverage,
+ args.male_reference, is_sample_female)
logging.info("Found %d gene-level gains and losses", len(gainloss))
- core.write_tsv(args.output, gainloss,
- colnames=['Gene', 'Chrom.', 'Start', 'End', 'Log2Ratio',
- 'Probes'])
+ write_dataframe(args.output, gainloss)
-def do_gainloss(probes, segments=None, male_reference=False, threshold=0.2,
- min_probes=3, skip_low=False):
+ at public
+def do_gainloss(cnarr, segments=None, threshold=0.2, min_probes=3,
+ skip_low=False, male_reference=False, is_sample_female=None):
"""Identify targeted genes with copy number gain or loss."""
- probes = probes.shift_xx(male_reference)
+ if is_sample_female is None:
+ is_sample_female = cnarr.guess_xx(male_reference=male_reference)
+ cnarr = cnarr.shift_xx(male_reference, is_sample_female)
if segments:
- segments = segments.shift_xx(male_reference)
- gainloss = reports.gainloss_by_segment(probes, segments, threshold,
+ segments = segments.shift_xx(male_reference, is_sample_female)
+ gainloss = reports.gainloss_by_segment(cnarr, segments, threshold,
skip_low)
else:
- gainloss = reports.gainloss_by_gene(probes, threshold, skip_low)
- return [row for row in gainloss if row[5] >= min_probes]
+ gainloss = reports.gainloss_by_gene(cnarr, threshold, skip_low)
+ gainloss = list(gainloss)
+ columns = (gainloss[0].index if len(gainloss) else cnarr._required_columns)
+ columns = ["gene"] + [col for col in columns if col != "gene"]
+ gainloss = pd.DataFrame.from_records(gainloss).reindex(columns=columns)
+ if min_probes and len(gainloss):
+ gainloss = gainloss[gainloss.probes >= min_probes]
+ return gainloss
P_gainloss = AP_subparsers.add_parser('gainloss', help=_cmd_gainloss.__doc__)
@@ -1406,79 +1086,94 @@ P_gainloss.add_argument('-y', '--male-reference', action='store_true',
help="""Assume inputs are already corrected against a male
reference (i.e. female samples will have +1 log-coverage of
chrX; otherwise male samples would have -1 chrX).""")
+P_gainloss.add_argument('-x', '--sample-sex', '-g', '--gender',
+ dest='sample_sex',
+ choices=('m', 'y', 'male', 'Male', 'f', 'x', 'female', 'Female'),
+ help="""Specify the sample's chromosomal sex as male or female.
+ (Otherwise guessed from X and Y coverage).""")
P_gainloss.add_argument('-o', '--output',
help="Output table file name.")
P_gainloss.set_defaults(func=_cmd_gainloss)
-# gender ----------------------------------------------------------------------
+# sex/gender ------------------------------------------------------------------
-def _cmd_gender(args):
- """Guess samples' gender from the relative coverage of chromosome X."""
- outrows = []
- for fname in args.targets:
- rel_chrx_cvg = _CNA.read(fname).get_relative_chrx_cvg()
- if args.male_reference:
- is_xx = (rel_chrx_cvg >= 0.5)
- else:
- is_xx = (rel_chrx_cvg >= -0.5)
- outrows.append((fname,
- ("Female" if is_xx else "Male"),
- "%s%.3g" % ('+' if rel_chrx_cvg > 0 else '',
- rel_chrx_cvg)))
- core.write_tsv(args.output, outrows)
+def _cmd_sex(args):
+ """Guess samples' sex from the relative coverage of chromosomes X and Y."""
+ cnarrs = map(read_cna, args.filenames)
+ table = do_sex(cnarrs, args.male_reference)
+ write_dataframe(args.output, table, header=True)
-P_gender = AP_subparsers.add_parser('gender', help=_cmd_gender.__doc__)
-P_gender.add_argument('targets', nargs='+',
+ at public
+def do_sex(cnarrs, is_male_reference):
+ """Guess samples' sex from the relative coverage of chromosomes X and Y."""
+ def strsign(num):
+ if num > 0:
+ return "+%.3g" % num
+ return "%.3g" % num
+
+ def guess_and_format(cna):
+ is_xy, stats = cna.compare_sex_chromosomes(is_male_reference)
+ return (cna.meta["filename"] or cna.sample_id,
+ "Male" if is_xy else "Female",
+ strsign(stats['chrx_ratio']),
+ strsign(stats['chry_ratio']))
+
+ rows = (guess_and_format(cna) for cna in cnarrs)
+ columns = ["sample", "sex", "X_logratio", "Y_logratio"]
+ return pd.DataFrame.from_records(rows, columns=columns)
+
+
+P_sex = AP_subparsers.add_parser('sex', help=_cmd_sex.__doc__)
+P_sex.add_argument('filenames', nargs='+',
help="Copy number or copy ratio files (*.cnn, *.cnr).")
-P_gender.add_argument('-y', '--male-reference', action='store_true',
+P_sex.add_argument('-y', '--male-reference', action='store_true',
help="""Assume inputs are already normalized to a male reference
(i.e. female samples will have +1 log-coverage of chrX;
otherwise male samples would have -1 chrX).""")
-P_gender.add_argument('-o', '--output',
+P_sex.add_argument('-o', '--output',
help="Output table file name.")
-P_gender.set_defaults(func=_cmd_gender)
+P_sex.set_defaults(func=_cmd_sex)
+
+# Shims
+AP_subparsers._name_parser_map['gender'] = P_sex
+do_gender = public(do_sex)
# metrics ---------------------------------------------------------------------
+do_metrics = public(metrics.do_metrics)
+
+
def _cmd_metrics(args):
- """Compute coverage deviations and other metrics for self-evaluation.
- """
- if (len(args.cnarrays) > 1 and len(args.segments) > 1 and
+ """Compute coverage deviations and other metrics for self-evaluation."""
+ if (len(args.cnarrays) > 1 and
+ args.segments and len(args.segments) > 1 and
len(args.cnarrays) != len(args.segments)):
raise ValueError("Number of coverage/segment filenames given must be "
"equal, if more than 1 segment file is given.")
- # Repeat a single segment file to match the number of coverage files
- if len(args.cnarrays) > 1 and len(args.segments) == 1:
- args.segments = [args.segments[0] for _i in range(len(args.cnarrays))]
-
- # Calculate all metrics
- outrows = []
- for probes_fname, segs_fname in zip(args.cnarrays, args.segments):
- cnarr = _CNA.read(probes_fname)
- segments = _CNA.read(segs_fname)
- values = metrics.ests_of_scale(cnarr.drop_low_coverage()
- .residuals(segments))
- outrows.append([core.rbase(probes_fname), len(segments)] +
- ["%.7f" % val for val in values])
-
- core.write_tsv(args.output, outrows,
- colnames=("sample", "segments", "stdev", "mad", "iqr",
- "bivar"))
+ cnarrs = map(read_cna, args.cnarrays)
+ if args.segments:
+ args.segments = map(read_cna, args.segments)
+ table = metrics.do_metrics(cnarrs, args.segments, args.drop_low_coverage)
+ write_dataframe(args.output, table)
P_metrics = AP_subparsers.add_parser('metrics', help=_cmd_metrics.__doc__)
P_metrics.add_argument('cnarrays', nargs='+',
help="""One or more bin-level coverage data files (*.cnn, *.cnr).""")
-P_metrics.add_argument('-s', '--segments', nargs='+', required=True,
+P_metrics.add_argument('-s', '--segments', nargs='+',
help="""One or more segmentation data files (*.cns, output of the
'segment' command). If more than one file is given, the number
must match the coverage data files, in which case the input
files will be paired together in the given order. Otherwise, the
same segments will be used for all coverage files.""")
+P_metrics.add_argument("--drop-low-coverage", action='store_true',
+ help="""Drop very-low-coverage bins before calculations to reduce
+ negative "fat tail" of bin log2 values in poor-quality
+ tumor samples.""")
P_metrics.add_argument('-o', '--output',
help="Output table file name.")
P_metrics.set_defaults(func=_cmd_metrics)
@@ -1491,11 +1186,21 @@ def _cmd_segmetrics(args):
if not 0.0 < args.alpha <= 1.0:
raise RuntimeError("alpha must be between 0 and 1.")
+ from scipy.stats import sem
+ # silence sem's "Degrees of freedom <= 0 for slice"; NaN is OK
+ import warnings
+ warnings.simplefilter("ignore", RuntimeWarning)
+
stats = {
+ 'mean': np.mean,
+ 'median': np.median,
+ 'mode': descriptives.modal_location,
'stdev': np.std,
- 'mad': metrics.median_absolute_deviation,
- 'iqr': metrics.interquartile_range,
- 'bivar': metrics.biweight_midvariance,
+ 'mad': descriptives.median_absolute_deviation,
+ 'mse': descriptives.mean_squared_error,
+ 'iqr': descriptives.interquartile_range,
+ 'bivar': descriptives.biweight_midvariance,
+ 'sem': sem,
'ci': lambda x: metrics.confidence_interval_bootstrap(x, args.alpha,
args.bootstrap),
'pi': lambda x: metrics.prediction_interval(x, args.alpha),
@@ -1505,28 +1210,32 @@ def _cmd_segmetrics(args):
return
# Calculate all metrics
- cnarr = _CNA.read(args.cnarray)
+ cnarr = read_cna(args.cnarray)
if args.drop_low_coverage:
cnarr = cnarr.drop_low_coverage()
- segarr = _CNA.read(args.segments)
- deviations = [segbins.log2 - segment.log2
- for segment, segbins in cnarr.by_ranges(segarr)]
+ segarr = read_cna(args.segments)
+ segments, segbins = zip(*cnarr.by_ranges(segarr))
+ # Measures of location
+ for statname in ("mean", "median", "mode"):
+ if getattr(args, statname):
+ func = stats[statname]
+ segarr[statname] = np.asfarray([func(sb.log2) for sb in segbins])
# Measures of spread
- for statname in ("StDev", "MAD", "IQR", "BiVar"):
- option = statname.lower()
- if getattr(args, option):
- func = stats[option]
+ deviations = [sb.log2 - seg.log2 for seg, sb in zip(segments, segbins)]
+ for statname in ("stdev", "sem", "mad", "mse", "iqr", "bivar"):
+ if getattr(args, statname):
+ func = stats[statname]
segarr[statname] = np.asfarray([func(d) for d in deviations])
# Interval calculations
if args.ci:
- segarr["CI_lo"], segarr["CI_hi"] = _segmetric_interval(segarr, cnarr,
+ segarr["ci_lo"], segarr["ci_hi"] = _segmetric_interval(segarr, cnarr,
stats['ci'])
if args.pi:
- segarr["PI_lo"], segarr["PI_hi"] = _segmetric_interval(segarr, cnarr,
+ segarr["pi_lo"], segarr["pi_hi"] = _segmetric_interval(segarr, cnarr,
stats['pi'])
- segarr.write(args.output or segarr.sample_id + ".segmetrics.cns")
+ tabio.write(segarr, args.output or segarr.sample_id + ".segmetrics.cns")
def _segmetric_interval(segarr, cnarr, func):
@@ -1545,17 +1254,27 @@ P_segmetrics.add_argument('cnarray',
P_segmetrics.add_argument('-s', '--segments', required=True,
help="Segmentation data file (*.cns, output of the 'segment' command).")
P_segmetrics.add_argument("--drop-low-coverage", action='store_true',
- help="""Drop very-low-coverage bins before segmentation to avoid
- false-positive deletions in poor-quality tumor samples.""")
+ help="""Drop very-low-coverage bins before calculations to avoid
+ negative bias in poor-quality tumor samples.""")
P_segmetrics.add_argument('-o', '--output',
help="Output table file name.")
P_segmetrics_stats = P_segmetrics.add_argument_group(
"Statistics available")
+P_segmetrics_stats.add_argument('--mean', action='store_true',
+ help="Mean log2 value (unweighted).")
+P_segmetrics_stats.add_argument('--median', action='store_true',
+ help="Median.")
+P_segmetrics_stats.add_argument('--mode', action='store_true',
+ help="Mode (i.e. peak density of log2 values).")
P_segmetrics_stats.add_argument('--stdev', action='store_true',
help="Standard deviation.")
+P_segmetrics_stats.add_argument('--sem', action='store_true',
+ help="Standard error of the mean.")
P_segmetrics_stats.add_argument('--mad', action='store_true',
help="Median absolute deviation (standardized).")
+P_segmetrics_stats.add_argument('--mse', action='store_true',
+ help="Mean squared error.")
P_segmetrics_stats.add_argument('--iqr', action='store_true',
help="Inter-quartile range.")
P_segmetrics_stats.add_argument('--bivar', action='store_true',
@@ -1583,23 +1302,30 @@ def _cmd_import_picard(args):
The input file is generated by the PER_TARGET_COVERAGE option in the
CalculateHsMetrics script in Picard tools.
+
+ If 'antitarget' is in the input filename, the generated output filename will
+ have the suffix '.antitargetcoverage.cnn', otherwise '.targetcoverage.cnn'.
"""
- for fname in importers.find_picard_files(args.targets):
- cnarr = importers.import_picard_pertargetcoverage(fname)
- outfname = os.path.basename(fname)[:-4] + '.cnn'
+ for fname in args.targets:
+ if not os.path.isfile(fname):
+ # Legacy usage: previously accepted directory as an argument
+ raise ValueError("Not a file: %s" % fname)
+ garr = importers.do_import_picard(fname)
+ outfname = ("{}.{}targetcoverage.cnn"
+ .format(garr.sample_id,
+ 'anti' if 'antitarget' in fname else ''))
if args.output_dir:
if not os.path.isdir(args.output_dir):
os.mkdir(args.output_dir)
logging.info("Created directory %s", args.output_dir)
outfname = os.path.join(args.output_dir, outfname)
- cnarr.write(outfname)
+ tabio.write(garr, outfname)
P_import_picard = AP_subparsers.add_parser('import-picard',
help=_cmd_import_picard.__doc__)
-P_import_picard.add_argument('targets', nargs='*', default=['.'],
- help="""Sample coverage .csv files (target and antitarget), or the
- directory that contains them.""")
+P_import_picard.add_argument('targets', nargs='+',
+ help="""Sample coverage .csv files (target and antitarget).""")
P_import_picard.add_argument('-d', '--output-dir', default='.',
help="Output directory name.")
P_import_picard.set_defaults(func=_cmd_import_picard)
@@ -1609,6 +1335,7 @@ P_import_picard.set_defaults(func=_cmd_import_picard)
def _cmd_import_seg(args):
"""Convert a SEG file to CNVkit .cns files."""
+ from .cnary import CopyNumArray as _CNA
if args.chromosomes:
if args.chromosomes == 'human':
chrom_names = {'23': 'X', '24': 'Y', '25': 'M'}
@@ -1617,10 +1344,10 @@ def _cmd_import_seg(args):
for kv in args.chromosomes.split(','))
else:
chrom_names = args.chromosomes
-
- for segset in importers.import_seg(args.segfile, chrom_names, args.prefix,
- args.from_log10):
- segset.write(os.path.join(args.output_dir, segset.sample_id + '.cns'))
+ for sid, segtable in tabio.seg.parse_seg(args.segfile, chrom_names,
+ args.prefix, args.from_log10):
+ segarr = _CNA(segtable, {"sample_id": sid})
+ tabio.write(segarr, os.path.join(args.output_dir, sid + '.cns'))
P_import_seg = AP_subparsers.add_parser('import-seg',
@@ -1643,32 +1370,21 @@ P_import_seg.set_defaults(func=_cmd_import_seg)
# import-theta ---------------------------------------------------------------
+do_import_theta = public(importers.do_import_theta)
+
+
def _cmd_import_theta(args):
"""Convert THetA output to a BED-like, CNVkit-like tabular format.
Equivalently, use the THetA results file to convert CNVkit .cns segments to
integer copy number calls.
"""
- tumor_segs = _CNA.read(args.tumor_cns)
+ tumor_segs = read_cna(args.tumor_cns)
for i, new_cns in enumerate(do_import_theta(tumor_segs, args.theta_results,
args.ploidy)):
- new_cns.write(os.path.join(args.output_dir,
- "%s-%d.cns" % (tumor_segs.sample_id, i + 1)))
-
-
-def do_import_theta(segarr, theta_results_fname, ploidy=2):
- theta = importers.parse_theta_results(theta_results_fname)
- for copies in theta['C']:
- # Drop any segments where the C value is None
- mask_drop = np.array([c is None for c in copies], dtype='bool')
- segarr = segarr[~mask_drop].copy()
- ok_copies = np.array([c for c in copies if c is not None], dtype='int')
- # Replace remaining segment values with these integers
- segarr["cn"] = ok_copies.copy()
- ok_copies[ok_copies == 0] = 0.5
- segarr["log2"] = np.log2(ok_copies / ploidy)
- segarr.sort_columns()
- yield segarr
+ tabio.write(new_cns,
+ os.path.join(args.output_dir,
+ "%s-%d.cns" % (tumor_segs.sample_id, i + 1)))
P_import_theta = AP_subparsers.add_parser('import-theta',
@@ -1697,16 +1413,11 @@ def _cmd_export_bed(args):
Input is a segmentation file (.cns) where, preferably, log2 ratios have
already been adjusted to integer absolute values using the 'call' command.
"""
- if args.show_all and args.show == "ploidy":
- # Until this option is removed, let it override the default
- logging.warn("Option '--show-all' is deprecated; "
- "use '--show all' instead.")
- args.show = "all"
bed_tables = []
for segfname in args.segments:
- segments = _CNA.read(segfname)
- # ENH: args.gender as a comma-separated list of genders
- is_sample_female = verify_gender_arg(segments, args.gender,
+ segments = read_cna(segfname)
+ # ENH: args.sample_sex as a comma-separated list
+ is_sample_female = verify_sample_sex(segments, args.sample_sex,
args.male_reference)
tbl = export.export_bed(segments, args.ploidy,
args.male_reference, is_sample_female,
@@ -1714,7 +1425,7 @@ def _cmd_export_bed(args):
args.show)
bed_tables.append(tbl)
table = pd.concat(bed_tables)
- core.write_dataframe(args.output, table, header=False)
+ write_dataframe(args.output, table, header=False)
P_export_bed = P_export_subparsers.add_parser('bed',
help=_cmd_export_bed.__doc__)
@@ -1726,10 +1437,11 @@ P_export_bed.add_argument("-i", "--sample-id", metavar="LABEL",
[Default: use the sample ID, taken from the file name]""")
P_export_bed.add_argument("--ploidy", type=int, default=2,
help="Ploidy of the sample cells. [Default: %(default)d]")
-P_export_bed.add_argument("-g", "--gender",
- choices=('m', 'male', 'Male', 'f', 'female', 'Female'),
- help="""Specify the sample's gender as male or female. (Otherwise
- guessed from chrX copy number).""")
+P_export_bed.add_argument('-x', '--sample-sex', '-g', '--gender',
+ dest='sample_sex',
+ choices=('m', 'y', 'male', 'Male', 'f', 'x', 'female', 'Female'),
+ help="""Specify the sample's chromosomal sex as male or female.
+ (Otherwise guessed from X and Y coverage).""")
P_export_bed.add_argument("--show",
choices=('ploidy', 'variant', 'all'), default="ploidy",
help="""Which segmented regions to show:
@@ -1737,14 +1449,11 @@ P_export_bed.add_argument("--show",
'variant' = CNA regions with non-neutral copy number;
'ploidy' = CNA regions with non-default ploidy.
[Default: %(default)s]""")
-P_export_bed.add_argument("--show-all", action="store_true",
- help="""Write all segmented regions.
- [DEPRECATED; use "--show all" instead]""")
P_export_bed.add_argument("-y", "--male-reference", action="store_true",
help="""Was a male reference used? If so, expect half ploidy on
chrX and chrY; otherwise, only chrY has half ploidy. In CNVkit,
if a male reference was used, the "neutral" copy number (ploidy)
- of chrX is 1; chrY is haploid for either gender reference.""")
+ of chrX is 1; chrY is haploid for either reference sex.""")
P_export_bed.add_argument('-o', '--output', help="Output file name.")
P_export_bed.set_defaults(func=_cmd_export_bed)
@@ -1756,7 +1465,7 @@ def _cmd_export_seg(args):
Compatible with IGV and GenePattern.
"""
table = export.export_seg(args.filenames)
- core.write_dataframe(args.output, table)
+ write_dataframe(args.output, table)
P_export_seg = P_export_subparsers.add_parser('seg',
help=_cmd_export_seg.__doc__)
@@ -1774,33 +1483,39 @@ def _cmd_export_vcf(args):
Input is a segmentation file (.cns) where, preferably, log2 ratios have
already been adjusted to integer absolute values using the 'call' command.
"""
- segments = _CNA.read(args.segments)
- is_sample_female = verify_gender_arg(segments,
- args.gender,
+ segarr = read_cna(args.segments)
+ cnarr = read_cna(args.cnr) if args.cnr else None
+ is_sample_female = verify_sample_sex(segarr, args.sample_sex,
args.male_reference)
- header, body = export.export_vcf(segments, args.ploidy, args.male_reference,
- is_sample_female, args.sample_id)
- core.write_text(args.output, header, body)
+ header, body = export.export_vcf(segarr, args.ploidy, args.male_reference,
+ is_sample_female, args.sample_id, cnarr)
+ write_text(args.output, header, body)
P_export_vcf = P_export_subparsers.add_parser('vcf',
help=_cmd_export_vcf.__doc__)
P_export_vcf.add_argument('segments', #nargs='1',
help="""Segmented copy ratio data file (*.cns), the output of the
'segment' or 'call' sub-commands.""")
+# ENH?: Incorporate left/right CI into .cns via 'segment' or 'segmetrics',
+# potentially calculated another way besides adjacent bin boundaries
+P_export_vcf.add_argument("--cnr",
+ help="""Bin-level copy ratios (*.cnr). Used to indicate fuzzy boundaries
+ for segments in the output VCF via the CIPOS and CIEND tags.""")
P_export_vcf.add_argument("-i", "--sample-id", metavar="LABEL",
help="""Sample name to write in the genotype field of the output VCF file.
[Default: use the sample ID, taken from the file name]""")
P_export_vcf.add_argument("--ploidy", type=int, default=2,
help="Ploidy of the sample cells. [Default: %(default)d]")
-P_export_vcf.add_argument("-g", "--gender",
- choices=('m', 'male', 'Male', 'f', 'female', 'Female'),
- help="""Specify the sample's gender as male or female. (Otherwise
- guessed from chrX copy number).""")
+P_export_vcf.add_argument('-x', '--sample-sex', '-g', '--gender',
+ dest='sample_sex',
+ choices=('m', 'y', 'male', 'Male', 'f', 'x', 'female', 'Female'),
+ help="""Specify the sample's chromosomal sex as male or female.
+ (Otherwise guessed from X and Y coverage).""")
P_export_vcf.add_argument("-y", "--male-reference", action="store_true",
help="""Was a male reference used? If so, expect half ploidy on
chrX and chrY; otherwise, only chrY has half ploidy. In CNVkit,
if a male reference was used, the "neutral" copy number (ploidy)
- of chrX is 1; chrY is haploid for either gender reference.""")
+ of chrX is 1; chrY is haploid for either reference sex.""")
P_export_vcf.add_argument('-o', '--output', help="Output file name.")
P_export_vcf.set_defaults(func=_cmd_export_vcf)
@@ -1808,25 +1523,25 @@ P_export_vcf.set_defaults(func=_cmd_export_vcf)
# THetA special case: takes tumor .cns and normal .cnr or reference.cnn
def _cmd_export_theta(args):
"""Convert segments to THetA2 input file format (*.input)."""
- tumor_cn = _CNA.read(args.tumor_segment)
- # Handle deprecated positional reference
- if args.normal_reference:
- logging.warn("Second positional argument normal_reference is "
- "deprecated; use --reference instead.")
- if not args.reference:
- args.reference = args.normal_reference
- normal_cn = (_CNA.read(args.reference) if args.reference else None)
+ tumor_cn = read_cna(args.tumor_segment)
+ normal_cn = read_cna(args.reference) if args.reference else None
table = export.export_theta(tumor_cn, normal_cn)
if not args.output:
args.output = tumor_cn.sample_id + ".interval_count"
table.to_csv(args.output, sep='\t', index=False)
logging.info("Wrote %s", args.output)
if args.vcf:
- variants = _VA.read_vcf(args.vcf,
- sample_id=args.sample_id or tumor_cn.sample_id,
- normal_id=args.normal_id, min_depth=args.min_depth,
- skip_somatic=True, skip_hom=False)
- tumor_snps, normal_snps = export.export_theta_snps(variants)
+ variants = load_het_snps(args.vcf,
+ args.sample_id, # or tumor_cn.sample_id,
+ args.normal_id, args.min_variant_depth,
+ args.zygosity_freq)
+ if not len(variants):
+ raise ValueError("VCF contains no usable SNV records")
+ try:
+ tumor_snps, normal_snps = export.export_theta_snps(variants)
+ except ValueError:
+ raise ValueError("VCF does not contain any tumor/normal paired "
+ "samples")
for title, table in [("tumor", tumor_snps), ("normal", normal_snps)]:
out_fname = "{}.{}.snp_formatted.txt".format(tumor_cn.sample_id, title)
table.to_csv(out_fname, sep='\t', index=False)
@@ -1836,34 +1551,41 @@ P_export_theta = P_export_subparsers.add_parser('theta',
help=_cmd_export_theta.__doc__)
P_export_theta.add_argument('tumor_segment',
help="""Tumor-sample segmentation file from CNVkit (.cns).""")
-P_export_theta.add_argument("normal_reference", nargs='?',
- help="""Reference copy number profile (.cnn), or normal-sample bin-level
- log2 copy ratios (.cnr). [DEPRECATED]""")
-P_export_theta.add_argument("-r", "--reference",
+P_export_theta.add_argument('-r', '--reference',
help="""Reference copy number profile (.cnn), or normal-sample bin-level
log2 copy ratios (.cnr). Use if the tumor_segment input file
does not contain a "weight" column.""")
-P_export_theta.add_argument("-v", "--vcf",
+P_export_theta.add_argument('-o', '--output', help="Output file name.")
+
+P_extheta_vcf = P_export_theta.add_argument_group(
+ "To also output tables of SNP b-allele frequencies for THetA2")
+P_extheta_vcf.add_argument('-v', '--vcf',
help="""VCF file containing SNVs observed in both the tumor and normal
samples. Tumor sample ID should match the `tumor_segment`
filename or be specified with -i/--sample-id.""")
-P_export_theta.add_argument("-i", "--sample-id",
+P_extheta_vcf.add_argument('-i', '--sample-id',
help="""Specify the name of the tumor sample in the VCF (given with
-v/--vcf). [Default: taken the tumor_segment file name]""")
-P_export_theta.add_argument("-n", "--normal-id",
+P_extheta_vcf.add_argument('-n', '--normal-id',
help="Corresponding normal sample ID in the input VCF.")
-P_export_theta.add_argument('-m', '--min-depth', type=int, default=20,
+P_extheta_vcf.add_argument('-m', '--min-variant-depth', type=int, default=20,
help="""Minimum read depth for a SNP in the VCF to be counted.
[Default: %(default)s]""")
-P_export_theta.add_argument('-o', '--output', help="Output file name.")
+P_extheta_vcf.add_argument('-z', '--zygosity-freq',
+ metavar='ALT_FREQ', nargs='?', type=float, const=0.25,
+ help="""Ignore VCF's genotypes (GT field) and instead infer zygosity
+ from allele frequencies. [Default if used without a number:
+ %(const)s]""")
+
P_export_theta.set_defaults(func=_cmd_export_theta)
# Nexus "basic" special case: can only represent 1 sample
def _cmd_export_nb(args):
"""Convert bin-level log2 ratios to Nexus Copy Number "basic" format."""
- table = export.export_nexus_basic(args.filename)
- core.write_dataframe(args.output, table)
+ cnarr = read_cna(args.filename)
+ table = export.export_nexus_basic(cnarr)
+ write_dataframe(args.output, table)
P_export_nb = P_export_subparsers.add_parser('nexus-basic',
help=_cmd_export_nb.__doc__)
@@ -1877,9 +1599,11 @@ P_export_nb.set_defaults(func=_cmd_export_nb)
# Nexus "Custom-OGT" special case: can only represent 1 sample
def _cmd_export_nbo(args):
"""Convert log2 ratios and b-allele freqs to Nexus "Custom-OGT" format."""
- table = export.export_nexus_ogt(args.filename, args.vcf, args.sample_id,
- args.min_variant_depth, args.min_weight)
- core.write_dataframe(args.output, table)
+ cnarr = read_cna(args.filename)
+ varr = load_het_snps(args.vcf, args.sample_id, args.normal_id,
+ args.min_variant_depth, args.zygosity_freq)
+ table = export.export_nexus_ogt(cnarr, varr, args.min_weight)
+ write_dataframe(args.output, table)
P_export_nbo = P_export_subparsers.add_parser('nexus-ogt',
help=_cmd_export_nbo.__doc__)
@@ -1889,12 +1613,19 @@ P_export_nbo.add_argument('filename',
P_export_nbo.add_argument('vcf',
help="""VCF of SNVs for the same sample, to calculate b-allele
frequencies.""")
-P_export_nbo.add_argument("-i", "--sample-id",
+P_export_nbo.add_argument('-i', '--sample-id',
help="""Specify the name of the sample in the VCF to use to extract
b-allele frequencies.""")
+P_export_nbo.add_argument('-n', '--normal-id',
+ help="Corresponding normal sample ID in the input VCF.")
P_export_nbo.add_argument('-m', '--min-variant-depth', type=int, default=20,
help="""Minimum read depth for a SNV to be included in the b-allele
frequency calculation. [Default: %(default)s]""")
+P_export_nbo.add_argument('-z', '--zygosity-freq',
+ metavar='ALT_FREQ', nargs='?', type=float, const=0.25,
+ help="""Ignore VCF's genotypes (GT field) and instead infer zygosity
+ from allele frequencies. [Default if used without a number:
+ %(const)s]""")
P_export_nbo.add_argument('-w', '--min-weight', type=float, default=0.0,
help="""Minimum weight (between 0 and 1) for a bin to be included in
the output. [Default: %(default)s]""")
@@ -1904,25 +1635,37 @@ P_export_nbo.set_defaults(func=_cmd_export_nbo)
# All else: export any number of .cnr or .cns files
-for fmt_key, fmt_descr in (
- ('cdt', "Convert log2 ratios to CDT format. Compatible with Java TreeView."),
- ('jtv', "Convert log2 ratios to Java TreeView's native format."),
- # Not implemented yet:
- # 'gct' (GenePattern).
-):
- def _cmd_export_simple(args):
- sample_ids = list(map(core.fbase, args.filenames))
- table = export.merge_samples(args.filenames)
- formatter = export.EXPORT_FORMATS[fmt_key]
- outheader, outrows = formatter(sample_ids, table)
- core.write_tsv(args.output, outrows, colnames=outheader)
-
- P_export_simple = P_export_subparsers.add_parser(fmt_key, help=fmt_descr)
- P_export_simple.add_argument('filenames', nargs='+',
- help="""Log2 copy ratio data file(s) (*.cnr), the output of the
- 'fix' sub-command.""")
- P_export_simple.add_argument('-o', '--output', help="Output file name.")
- P_export_simple.set_defaults(func=_cmd_export_simple)
+def _cmd_export_cdt(args):
+ """Convert log2 ratios to CDT format. Compatible with Java TreeView."""
+ sample_ids = list(map(core.fbase, args.filenames))
+ table = export.merge_samples(args.filenames)
+ formatter = export.EXPORT_FORMATS['cdt']
+ outheader, outrows = formatter(sample_ids, table)
+ write_tsv(args.output, outrows, colnames=outheader)
+
+P_export_cdt = P_export_subparsers.add_parser('cdt',
+ help=_cmd_export_cdt.__doc__)
+P_export_cdt.add_argument('filenames', nargs='+',
+ help="""Log2 copy ratio data file(s) (*.cnr), the output of the
+ 'fix' sub-command.""")
+P_export_cdt.add_argument('-o', '--output', help="Output file name.")
+P_export_cdt.set_defaults(func=_cmd_export_cdt)
+
+def _cmd_export_jtv(args):
+ """Convert log2 ratios to Java TreeView's native format."""
+ sample_ids = list(map(core.fbase, args.filenames))
+ table = export.merge_samples(args.filenames)
+ formatter = export.EXPORT_FORMATS['jtv']
+ outheader, outrows = formatter(sample_ids, table)
+ write_tsv(args.output, outrows, colnames=outheader)
+
+P_export_jtv = P_export_subparsers.add_parser('jtv',
+ help=_cmd_export_jtv.__doc__)
+P_export_jtv.add_argument('filenames', nargs='+',
+ help="""Log2 copy ratio data file(s) (*.cnr), the output of the
+ 'fix' sub-command.""")
+P_export_jtv.add_argument('-o', '--output', help="Output file name.")
+P_export_jtv.set_defaults(func=_cmd_export_jtv)
# version ---------------------------------------------------------------------
diff --git a/cnvlib/core.py b/cnvlib/core.py
index 69a51a1..d151f03 100644
--- a/cnvlib/core.py
+++ b/cnvlib/core.py
@@ -1,73 +1,80 @@
"""CNV utilities."""
from __future__ import absolute_import, division, print_function
-import sys
-import os.path
-from itertools import takewhile
+from builtins import map
+from past.builtins import basestring
-from .ngfrills import safe_write
-
-# __________________________________________________________________________
-# I/O helpers
-
-def write_tsv(outfname, rows, colnames=None):
- """Write rows, with optional column header, to tabular file."""
- with safe_write(outfname or sys.stdout) as handle:
- if colnames:
- header = '\t'.join(colnames) + '\n'
- handle.write(header)
- handle.writelines('\t'.join(map(str, row)) + '\n'
- for row in rows)
-
-
-def write_text(outfname, text, *more_texts):
- """Write one or more strings (blocks of text) to a file."""
- with safe_write(outfname or sys.stdout) as handle:
- handle.write(text)
- if more_texts:
- for mtext in more_texts:
- handle.write(mtext)
-
-
-def write_dataframe(outfname, dframe, header=True):
- """Write a pandas.DataFrame to a tabular file."""
- with safe_write(outfname or sys.stdout) as handle:
- dframe.to_csv(handle, header=header,
- index=False, sep='\t', float_format='%.6g')
+import contextlib
+import logging
+import os
+import subprocess
+import tempfile
# __________________________________________________________________________
-# Sorting key functions
-
-def sorter_chrom(label):
- """Create a sorting key from chromosome label.
+# I/O helpers
- Sort by integers first, then letters or strings. The prefix "chr"
- (case-insensitive), if present, is stripped automatically for sorting.
+def call_quiet(*args):
+ """Safely run a command and get stdout; print stderr if there's an error.
- E.g. chr1 < chr2 < chr10 < chrX < chrY < chrM
+ Like subprocess.check_output, but silent in the normal case where the
+ command logs unimportant stuff to stderr. If there is an error, then the
+ full error message(s) is shown in the exception message.
"""
- # Strip "chr" prefix
- chrom = (label[3:] if label.lower().startswith('chr')
- else label)
- if chrom in ('X', 'Y'):
- key = (1000, chrom)
- else:
- # Separate numeric and special chromosomes
- nums = ''.join(takewhile(str.isdigit, chrom))
- chars = chrom[len(nums):]
- nums = int(nums) if nums else 0
- if not chars:
- key = (nums, '')
- elif len(chars) == 1:
- key = (2000 + nums, chars)
- else:
- key = (3000 + nums, chars)
- return key
-
-
-def sorter_chrom_at(index):
- """Create a sort key function that gets chromosome label at a list index."""
- return lambda row: sorter_chrom(row[index])
+ # args = map(str, args)
+ if not len(args):
+ raise ValueError("Must supply at least one argument (the command name)")
+ try:
+ proc = subprocess.Popen(args, stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE)
+ except OSError as exc:
+ raise RuntimeError("Could not find the executable %r" % args[0]
+ + " -- is it installed correctly?"
+ + "\n(Original error: %s)" % exc)
+ out, err = proc.communicate()
+ if proc.returncode != 0:
+ raise RuntimeError("Subprocess command failed:\n$ %s\n\n%s"
+ % (' '.join(args), err))
+ return out
+
+
+def ensure_path(fname):
+ """Create dirs and move an existing file to avoid overwriting, if necessary.
+
+ If a file already exists at the given path, it is renamed with an integer
+ suffix to clear the way.
+ """
+ if '/' in os.path.normpath(fname):
+ # Ensure the output directory exists
+ dname = os.path.dirname(os.path.abspath(fname))
+ if dname and not os.path.isdir(dname):
+ try:
+ os.makedirs(dname)
+ except OSError as exc:
+ raise OSError("Output path " + fname +
+ " contains a directory " + dname +
+ " that cannot be created: %s" % exc)
+ if os.path.isfile(fname):
+ # Add an integer suffix to the existing file name
+ cnt = 1
+ bak_fname = "%s.%d" % (fname, cnt)
+ while os.path.isfile(bak_fname):
+ cnt += 1
+ bak_fname = "%s.%d" % (fname, cnt)
+ os.rename(fname, bak_fname)
+ logging.info("Moved existing file %s -> %s", fname, bak_fname)
+ return True
+
+
+ at contextlib.contextmanager
+def temp_write_text(text, mode="w+b"):
+ """Save text to a temporary file.
+
+ NB: This won't work on Windows b/c the file stays open.
+ """
+ with tempfile.NamedTemporaryFile(mode=mode) as tmp:
+ tmp.write(text)
+ tmp.flush()
+ yield tmp.name
# __________________________________________________________________________
@@ -89,7 +96,7 @@ def assert_equal(msg, **values):
ok = True
key1, val1 = values.popitem()
msg += ": %s = %r" % (key1, val1)
- for okey, oval in values.iteritems():
+ for okey, oval in values.items():
msg += ", %s = %r" % (okey, oval)
if oval != val1:
ok = False
@@ -107,9 +114,21 @@ def check_unique(items, title):
def fbase(fname):
"""Strip directory and all extensions from a filename."""
- return os.path.basename(fname).split('.', 1)[0]
-
-
-def rbase(fname):
- """Strip directory and final extension from a filename."""
- return os.path.basename(fname).rsplit('.', 1)[0]
+ base = os.path.basename(fname)
+ # Gzip extension usually follows another extension
+ if base.endswith('.gz'):
+ base = base[:-3]
+ # Cases to drop more than just the last dot
+ known_multipart_exts = (
+ '.antitargetcoverage.cnn', '.targetcoverage.cnn',
+ '.antitargetcoverage.csv', '.targetcoverage.csv',
+ # Pipeline suffixes
+ '.recal.bam', '.deduplicated.realign.bam',
+ )
+ for ext in known_multipart_exts:
+ if base.endswith(ext):
+ base = base[:-len(ext)]
+ break
+ else:
+ base = base.rsplit('.', 1)[0]
+ return base
diff --git a/cnvlib/coverage.py b/cnvlib/coverage.py
index 2257dca..6dcf741 100644
--- a/cnvlib/coverage.py
+++ b/cnvlib/coverage.py
@@ -1,23 +1,41 @@
"""Supporting functions for the 'antitarget' command."""
-from __future__ import absolute_import, division
+from __future__ import absolute_import, division, print_function
+from builtins import zip
+from past.builtins import basestring
import logging
import math
import os.path
import time
+from concurrent import futures
-from Bio._py3k import map, zip
+import numpy as np
+import pandas as pd
import pysam
+from Bio._py3k import StringIO
+from skgenome import tabio
+from . import core, samutil
from .cnary import CopyNumArray as CNA
-from .rary import RegionArray as RA
-from .core import fbase
+from .parallel import rm, to_chunks
+from .params import NULL_LOG2_COVERAGE
-from .params import NULL_LOG2_COVERAGE, READ_LEN
+def do_coverage(bed_fname, bam_fname, by_count=False, min_mapq=0, processes=1):
+ """Calculate coverage in the given regions from BAM read depths."""
+ if not samutil.ensure_bam_sorted(bam_fname):
+ raise RuntimeError("BAM file %s must be sorted by coordinates"
+ % bam_fname)
+ samutil.ensure_bam_index(bam_fname)
+ # ENH: count importers.TOO_MANY_NO_COVERAGE & warn
+ cnarr = interval_coverages(bed_fname, bam_fname, by_count, min_mapq,
+ processes)
+ return cnarr
-def interval_coverages(bed_fname, bam_fname, by_count, min_mapq):
+
+def interval_coverages(bed_fname, bam_fname, by_count, min_mapq, processes):
"""Calculate log2 coverages in the BAM file at each interval."""
+ meta = {'sample_id': core.fbase(bam_fname)}
start_time = time.time()
# Skip processing if the BED file is empty
@@ -28,17 +46,28 @@ def interval_coverages(bed_fname, bam_fname, by_count, min_mapq):
else:
logging.info("Skip processing %s with empty regions file %s",
os.path.basename(bam_fname), bed_fname)
- return CNA.from_rows([], meta_dict={'sample_id': fbase(bam_fname)})
+ return CNA.from_rows([], meta_dict=meta)
# Calculate average read depth in each bin
- ic_func = (interval_coverages_count if by_count
- else interval_coverages_pileup)
- results = ic_func(bed_fname, bam_fname, min_mapq)
- read_counts, cna_rows = zip(*list(results))
+ if by_count:
+ results = interval_coverages_count(bed_fname, bam_fname, min_mapq,
+ processes)
+ read_counts, cna_rows = zip(*results)
+ read_counts = pd.Series(read_counts)
+ cnarr = CNA.from_rows(list(cna_rows),
+ columns=CNA._required_columns + ('depth',),
+ meta_dict=meta)
+ else:
+ table = interval_coverages_pileup(bed_fname, bam_fname, min_mapq,
+ processes)
+ read_len = samutil.get_read_length(bam_fname)
+ read_counts = table['basecount'] / read_len
+ table = table.drop('basecount', axis=1)
+ cnarr = CNA(table, meta)
# Log some stats
tot_time = time.time() - start_time
- tot_reads = sum(read_counts)
+ tot_reads = read_counts.sum()
logging.info("Time: %.3f seconds (%d reads/sec, %s bins/sec)",
tot_time,
int(round(tot_reads / tot_time, 0)),
@@ -48,9 +77,9 @@ def interval_coverages(bed_fname, bam_fname, by_count, min_mapq):
len(read_counts),
tot_reads,
(tot_reads / len(read_counts)),
- min(read_counts),
- max(read_counts))
- tot_mapped_reads = bam_total_reads(bam_fname)
+ read_counts.min(),
+ read_counts.max())
+ tot_mapped_reads = samutil.bam_total_reads(bam_fname)
if tot_mapped_reads:
logging.info("Percent reads in regions: %.3f (of %d mapped)",
100. * tot_reads / tot_mapped_reads,
@@ -58,25 +87,41 @@ def interval_coverages(bed_fname, bam_fname, by_count, min_mapq):
else:
logging.info("(Couldn't calculate total number of mapped reads)")
- return CNA.from_rows(list(cna_rows),
- meta_dict={'sample_id': fbase(bam_fname)})
+ return cnarr
-def interval_coverages_count(bed_fname, bam_fname, min_mapq):
+def interval_coverages_count(bed_fname, bam_fname, min_mapq, procs=1):
"""Calculate log2 coverages in the BAM file at each interval."""
- bamfile = pysam.Samfile(bam_fname, 'rb')
- for chrom, subregions in RA.read(bed_fname).by_chromosome():
- logging.info("Processing chromosome %s of %s",
- chrom, os.path.basename(bam_fname))
- for _chrom, start, end, name, in subregions.coords(["name"]):
- count, depth = region_depth_count(bamfile, chrom, start, end,
- min_mapq)
- yield [count,
- (chrom, start, end, name,
- math.log(depth, 2) if depth else NULL_LOG2_COVERAGE)]
-
-
-def region_depth_count(bamfile, chrom, start, end, min_mapq):
+ regions = tabio.read_auto(bed_fname)
+ if procs == 1:
+ bamfile = pysam.Samfile(bam_fname, 'rb')
+ for chrom, subregions in regions.by_chromosome():
+ logging.info("Processing chromosome %s of %s",
+ chrom, os.path.basename(bam_fname))
+ for count, row in _rdc_chunk(bamfile, subregions, min_mapq):
+ yield [count, row]
+ else:
+ with futures.ProcessPoolExecutor(procs) as pool:
+ args_iter = ((bam_fname, subr, min_mapq)
+ for _c, subr in regions.by_chromosome())
+ for chunk in pool.map(_rdc, args_iter):
+ for count, row in chunk:
+ yield [count, row]
+
+
+def _rdc(args):
+ """Wrapper for parallel."""
+ return list(_rdc_chunk(*args))
+
+
+def _rdc_chunk(bamfile, regions, min_mapq):
+ if isinstance(bamfile, basestring):
+ bamfile = pysam.Samfile(bamfile, 'rb')
+ for chrom, start, end, gene in regions.coords(["gene"]):
+ yield region_depth_count(bamfile, chrom, start, end, gene, min_mapq)
+
+
+def region_depth_count(bamfile, chrom, start, end, gene, min_mapq):
"""Calculate depth of a region via pysam count.
i.e. counting the number of read starts in a region, then scaling for read
@@ -92,25 +137,60 @@ def region_depth_count(bamfile, chrom, start, end, min_mapq):
or read.is_qcfail
or read.mapq < min_mapq)
- # Count the number of read midpoints in the interval
- count = sum((start <= (read.pos + .5*read.rlen) <= end and filter_read(read))
- for read in bamfile.fetch(reference=chrom,
- start=start, end=end))
- # Scale read counts to region length
- # Depth := #Bases / Span
- depth = (READ_LEN * count / (end - start)
- if end > start else 0)
- return count, depth
-
-
-def interval_coverages_pileup(bed_fname, bam_fname, min_mapq):
+ count = 0
+ bases = 0
+ for read in bamfile.fetch(reference=chrom, start=start, end=end):
+ if filter_read(read):
+ count += 1
+ # Only count the bases aligned to the region
+ rlen = read.query_length
+ if read.pos < start:
+ rlen -= start - read.pos
+ if read.pos + read.query_length > end:
+ rlen -= read.pos + read.query_length - end
+ bases += rlen
+ depth = bases / (end - start) if end > start else 0
+ row = (chrom, start, end, gene,
+ math.log(depth, 2) if depth else NULL_LOG2_COVERAGE,
+ depth)
+ return count, row
+
+
+def interval_coverages_pileup(bed_fname, bam_fname, min_mapq, procs=1):
"""Calculate log2 coverages in the BAM file at each interval."""
logging.info("Processing reads in %s", os.path.basename(bam_fname))
- for chrom, start, end, name, count, depth in bedcov(bed_fname, bam_fname,
- min_mapq):
- yield [count,
- (chrom, start, end, name,
- math.log(depth, 2) if depth else NULL_LOG2_COVERAGE)]
+ if procs == 1:
+ table = bedcov(bed_fname, bam_fname, min_mapq)
+ else:
+ chunks = []
+ with futures.ProcessPoolExecutor(procs) as pool:
+ args_iter = ((bed_chunk, bam_fname, min_mapq)
+ for bed_chunk in to_chunks(bed_fname))
+ for bed_chunk_fname, table in pool.map(_bedcov, args_iter):
+ chunks.append(table)
+ rm(bed_chunk_fname)
+ table = pd.concat(chunks, ignore_index=True)
+ # Fill in CNA required columns
+ if 'gene' in table:
+ table['gene'] = table['gene'].fillna('-')
+ else:
+ table['gene'] = '-'
+ # NB: User-supplied bins might be zero-width or reversed -- skip those
+ spans = table.end - table.start
+ ok_idx = (spans > 0)
+ table = table.assign(depth=0, log2=NULL_LOG2_COVERAGE)
+ table.loc[ok_idx, 'depth'] = (table.loc[ok_idx, 'basecount']
+ / spans[ok_idx])
+ ok_idx = (table['depth'] > 0)
+ table.loc[ok_idx, 'log2'] = np.log2(table.loc[ok_idx, 'depth'])
+ return table
+
+
+def _bedcov(args):
+ """Wrapper for parallel."""
+ bed_fname = args[0]
+ table = bedcov(*args)
+ return bed_fname, table
def bedcov(bed_fname, bam_fname, min_mapq):
@@ -119,53 +199,28 @@ def bedcov(bed_fname, bam_fname, min_mapq):
i.e. mean pileup depth across each region.
"""
# Count bases in each region; exclude low-MAPQ reads
- if min_mapq > 0:
- bedcov_args = ['-Q', str(min_mapq)]
- else:
- bedcov_args = []
+ cmd = [bed_fname, bam_fname]
+ if min_mapq and min_mapq > 0:
+ cmd.extend(['-Q', bytes(min_mapq)])
try:
- lines = pysam.bedcov(bed_fname, bam_fname, *bedcov_args)
+ raw = pysam.bedcov(*cmd, split_lines=False)
except pysam.SamtoolsError as exc:
- raise ValueError("Failed processing %r coverages in %r regions. PySAM error: %s"
- % (bam_fname, bed_fname, exc))
- if not lines:
- raise ValueError("BED file %r sequence IDs don't match any in BAM file %r"
- % (bed_fname, bam_fname))
- # Return an iterable...
- if isinstance(lines, basestring):
- lines = lines.splitlines()
- for line in lines:
- fields = line.split('\t')
- if len(fields) == 5:
- chrom, start_s, end_s, name, basecount_s = fields
- elif len(fields) == 4:
- chrom, start_s, end_s, basecount_s = fields
- name = "-"
- else:
- raise RuntimeError("Bad line from bedcov:\n" + line)
- start, end, basecount = map(int, (start_s, end_s, basecount_s.strip()))
- span = end - start
- if span > 0:
- # Algebra from above
- count = basecount / READ_LEN
- mean_depth = basecount / span
- else:
- # User-supplied bins might be oddly constructed
- count = mean_depth = 0
- yield chrom, start, end, name, count, mean_depth
-
-
-def bam_total_reads(bam_fname):
- """Count the total number of mapped reads in a BAM file.
-
- Uses the BAM index to do this quickly.
- """
- lines = pysam.idxstats(bam_fname)
- if isinstance(lines, basestring):
- lines = lines.splitlines()
- tot_mapped_reads = 0
- for line in lines:
- _seqname, _seqlen, nmapped, _nunmapped = line.split()
- tot_mapped_reads += int(nmapped)
- return tot_mapped_reads
-
+ raise ValueError("Failed processing %r coverages in %r regions. "
+ "PySAM error: %s" % (bam_fname, bed_fname, exc))
+ if not raw:
+ raise ValueError("BED file %r chromosome names don't match any in "
+ "BAM file %r" % (bed_fname, bam_fname))
+ columns = detect_bedcov_columns(raw)
+ table = pd.read_table(StringIO(raw), names=columns, usecols=columns)
+ return table
+
+
+def detect_bedcov_columns(text):
+ # NB: gene is optional; may be trailing cols
+ firstline = text[:text.index('\n')]
+ tabcount = firstline.count('\t')
+ if tabcount >= 4:
+ return ['chromosome', 'start', 'end', 'gene', 'basecount']
+ elif tabcount == 3:
+ return ['chromosome', 'start', 'end', 'basecount']
+ raise RuntimeError("Bad line from bedcov:\n%r" % firstline)
diff --git a/cnvlib/descriptives.py b/cnvlib/descriptives.py
new file mode 100644
index 0000000..036651d
--- /dev/null
+++ b/cnvlib/descriptives.py
@@ -0,0 +1,274 @@
+"""Robust estimators of central tendency and scale.
+
+See:
+ https://en.wikipedia.org/wiki/Robust_measures_of_scale
+ https://astropy.readthedocs.io/en/latest/_modules/astropy/stats/funcs.html
+
+"""
+from __future__ import division
+import sys
+from functools import wraps
+
+import numpy as np
+from scipy import stats
+
+
+# Decorators to coerce input and short-circuit trivial cases
+
+def on_array(default=None):
+ """Ensure `a` is a numpy array with no missing/NaN values."""
+ def outer(f):
+ @wraps(f)
+ def wrapper(a, **kwargs):
+ a = np.asfarray(a)
+ a = a[~np.isnan(a)]
+ if not len(a):
+ return np.nan
+ if len(a) == 1:
+ if default is None:
+ return a[0]
+ return default
+ return f(a, **kwargs)
+ return wrapper
+ return outer
+
+
+def on_weighted_array(default=None):
+ """Ensure `a` and `w` are equal-length numpy arrays with no NaN values.
+
+ For weighted descriptives -- `a` is the array of values, `w` is weights.
+
+ 1. Drop any cells in `a` that are NaN from both `a` and `w`
+ 2. Replace any remaining NaN cells in `w` with 0.
+ """
+ def outer(f):
+ @wraps(f)
+ def wrapper(a, w, **kwargs):
+ if len(a) != len(w):
+ raise ValueError("Unequal array lengths: a=%d, w=%d"
+ % (len(a), len(w)))
+ if not len(a):
+ return np.nan
+ a = np.asfarray(a)
+ w = np.asfarray(w)
+ # Drop a's NaN indices from both arrays
+ a_nan = np.isnan(a)
+ if a_nan.any():
+ a = a[~a_nan]
+ if not len(a):
+ return np.nan
+ w = w[~a_nan]
+ if len(a) == 1:
+ if default is None:
+ return a[0]
+ return default
+ # Fill w's NaN indices
+ w_nan = np.isnan(w)
+ if w_nan.any():
+ w[w_nan] = 0.0
+ return f(a, w, **kwargs)
+ return wrapper
+ return outer
+
+
+# M-estimators of central location
+
+ at on_array()
+def biweight_location(a, initial=None, c=6.0, epsilon=1e-3, max_iter=5):
+ """Compute the biweight location for an array.
+
+ The biweight is a robust statistic for estimating the central location of a
+ distribution.
+ """
+ def biloc_iter(a, initial):
+ # Weight the observations by distance from initial estimate
+ d = a - initial
+ mad = np.median(np.abs(d))
+ w = d / max(c * mad, epsilon)
+ w = (1 - w**2)**2
+ # Omit the outlier points
+ mask = (w < 1)
+ weightsum = w[mask].sum()
+ if weightsum == 0:
+ # Insufficient variation to improve the initial estimate
+ return initial
+ return initial + (d[mask] * w[mask]).sum() / weightsum
+
+ if initial is None:
+ initial = np.median(a)
+ for _i in range(max_iter):
+ result = biloc_iter(a, initial)
+ if abs(result - initial) <= epsilon:
+ break
+ initial = result
+ return result
+
+
+ at on_array()
+def modal_location(a):
+ """Return the modal value of an array's values.
+
+ The "mode" is the location of peak density among the values, estimated using
+ a Gaussian kernel density estimator.
+
+ Parameters
+ ----------
+ a : np.array
+ A 1-D array of floating-point values, e.g. bin log2 ratio values.
+ """
+ sarr = np.sort(a)
+ kde = stats.gaussian_kde(sarr)
+ y = kde.evaluate(sarr)
+ peak = sarr[y.argmax()]
+ return peak
+
+
+ at on_weighted_array()
+def weighted_median(a, weights):
+ """Weighted median of a 1-D numeric array."""
+ order = a.argsort()
+ a = a[order]
+ weights = weights[order]
+ midpoint = 0.5 * weights.sum()
+ if (weights > midpoint).any():
+ # Any point with the majority of total weight must be the median
+ return a[weights.argmax()]
+ cumulative_weight = weights.cumsum()
+ midpoint_idx = cumulative_weight.searchsorted(midpoint)
+ if (midpoint_idx > 0 and
+ cumulative_weight[midpoint_idx-1] - midpoint < sys.float_info.epsilon):
+ # Midpoint of 2 array values
+ return a[midpoint_idx-1 : midpoint_idx+1].mean()
+ return a[midpoint_idx]
+
+
+# Estimators of scale
+
+ at on_array(0)
+def biweight_midvariance(a, initial=None, c=9.0, epsilon=1e-3):
+ """Compute the biweight midvariance for an array.
+
+ The biweight midvariance is a robust statistic for determining the
+ midvariance (i.e. the standard deviation) of a distribution.
+
+ See:
+
+ - https://en.wikipedia.org/wiki/Robust_measures_of_scale#The_biweight_midvariance
+ - https://astropy.readthedocs.io/en/latest/_modules/astropy/stats/funcs.html
+ """
+ if initial is None:
+ initial = biweight_location(a)
+ # Difference of observations from initial location estimate
+ d = a - initial
+ # Weighting (avoid dividing by zero)
+ mad = np.median(np.abs(d))
+ w = d / max(c * mad, epsilon)
+ # Omit the outlier points
+ mask = np.abs(w) < 1
+ if w[mask].sum() == 0:
+ # Insufficient variation to improve on MAD
+ return mad * 1.4826
+ n = mask.sum()
+ d_ = d[mask]
+ w_ = (w**2)[mask]
+ return np.sqrt((n * (d_**2 * (1 - w_)**4).sum())
+ / (((1 - w_) * (1 - 5 * w_)).sum()**2))
+
+
+ at on_array(0)
+def gapper_scale(a):
+ """Scale estimator based on gaps between order statistics.
+
+ See:
+
+ - Wainer & Thissen (1976)
+ - Beers, Flynn, and Gebhardt (1990)
+ """
+ gaps = np.diff(np.sort(a))
+ n = len(a)
+ idx = np.arange(1, n)
+ weights = idx * (n - idx)
+ return (gaps * weights).sum() * np.sqrt(np.pi) / (n * (n - 1))
+
+
+ at on_array(0)
+def interquartile_range(a):
+ """Compute the difference between the array's first and third quartiles."""
+ return np.percentile(a, 75) - np.percentile(a, 25)
+
+
+ at on_array(0)
+def median_absolute_deviation(a, scale_to_sd=True):
+ """Compute the median absolute deviation (MAD) of array elements.
+
+ The MAD is defined as: ``median(abs(a - median(a)))``.
+
+ See: https://en.wikipedia.org/wiki/Median_absolute_deviation
+ """
+ a_median = np.median(a)
+ mad = np.median(np.abs(a - a_median))
+ if scale_to_sd:
+ mad *= 1.4826
+ return mad
+
+
+ at on_array(0)
+def mean_squared_error(a, initial=None):
+ """Mean squared error (MSE).
+
+ By default, assume the input array `a` is the residuals/deviations/error,
+ so MSE is calculated from zero. Another reference point for calculating the
+ error can be specified with `initial`.
+ """
+ if initial is None:
+ initial = a.mean()
+ if initial:
+ a = a - initial
+ return (a ** 2).mean()
+
+
+ at on_array(0)
+def q_n(a):
+ """Rousseeuw & Croux's (1993) Q_n, an alternative to MAD.
+
+ ``Qn := Cn first quartile of (|x_i - x_j|: i < j)``
+
+ where Cn is a constant depending on n.
+
+ Finite-sample correction factors must be used to calibrate the
+ scale of Qn for small-to-medium-sized samples.
+
+ n E[Qn]
+ -- -----
+ 10 1.392
+ 20 1.193
+ 40 1.093
+ 60 1.064
+ 80 1.048
+ 100 1.038
+ 200 1.019
+
+ """
+ # First quartile of: (|x_i - x_j|: i < j)
+ vals = []
+ for i, x_i in enumerate(a):
+ for x_j in a[i+1:]:
+ vals.append(abs(x_i - x_j))
+ quartile = np.percentile(vals, 25)
+
+ # Cn: a scaling factor determined by sample size
+ n = len(a)
+ if n <= 10:
+ # ENH: warn when extrapolating beyond the data
+ # ENH: simulate for values up to 10
+ # (unless the equation below is reliable)
+ scale = 1.392
+ elif 10 < n < 400:
+ # I fitted the simulated values (above) to a power function in Excel:
+ # f(x) = 1.0 + 3.9559 * x ^ -1.0086
+ # This should be OK for interpolation. (Does it apply generally?)
+ scale = 1.0 + (4 / n)
+ else:
+ scale = 1.0
+
+ return quartile / scale
diff --git a/cnvlib/diagram.py b/cnvlib/diagram.py
index c19172f..28f3041 100644
--- a/cnvlib/diagram.py
+++ b/cnvlib/diagram.py
@@ -4,7 +4,7 @@ This uses and abuses Biopython's BasicChromosome module. It depends on
ReportLab, too, so we isolate this functionality here so that the rest of CNVkit
will run without it. (And also to keep the codebase tidy.)
"""
-from __future__ import division
+from __future__ import absolute_import, division
import collections
import math
import warnings
@@ -26,7 +26,7 @@ CHROM_FATNESS = 0.3
PAGE_SIZE = (11.0*inch, 8.5*inch)
-def create_diagram(cnarr, segarr, threshold, min_probes, outfname, male_reference):
+def create_diagram(cnarr, segarr, threshold, min_probes, outfname, title=None):
"""Create the diagram."""
if cnarr and segarr:
do_both = True # Draw segments on left, probes on right.
@@ -38,23 +38,19 @@ def create_diagram(cnarr, segarr, threshold, min_probes, outfname, male_referenc
cnarr = segarr
cnarr_is_seg = True
else:
- raise ValueError("Must specify a filename as an argument or with "
- "the '-s' option, or both. You did neither.")
+ raise ValueError("Must provide argument cnarr or segarr, or both. ")
do_both = False
# Label genes where copy ratio value exceeds threshold
- cnarr = cnarr.shift_xx(male_reference)
if cnarr_is_seg:
sel = cnarr.data[(cnarr.data.log2.abs() >= threshold) &
~cnarr.data.gene.isin(params.IGNORE_GENE_NAMES)]
- gainloss = [(s.gene, s.chromosome, s.start, s.end, s.log2, s.probes)
- for s in sel.itertuples(index=False)]
+ gainloss = sel.itertuples(index=False)
elif segarr:
- segarr = segarr.shift_xx(male_reference)
gainloss = reports.gainloss_by_segment(cnarr, segarr, threshold)
else:
gainloss = reports.gainloss_by_gene(cnarr, threshold)
- gene_labels = [gl_row[0] for gl_row in gainloss if gl_row[5] >= min_probes]
+ gene_labels = [gl_row.gene for gl_row in gainloss if gl_row.probes >= min_probes]
# NB: If multiple segments cover the same gene (gene contains breakpoints),
# all those segments are marked as "hits". We'll uniquify them.
# TODO - use different logic to only label the gene's signficant segment(s)
@@ -91,7 +87,7 @@ def create_diagram(cnarr, segarr, threshold, min_probes, outfname, male_referenc
# Generate the diagram PDF
if not outfname:
outfname = cnarr.sample_id + '-diagram.pdf'
- drawing = build_chrom_diagram(features, chrom_sizes, cnarr.sample_id)
+ drawing = build_chrom_diagram(features, chrom_sizes, cnarr.sample_id, title)
cvs = canvas.Canvas(outfname, pagesize=PAGE_SIZE)
renderPDF.draw(drawing, cvs, 0, 0)
cvs.showPage()
@@ -99,7 +95,7 @@ def create_diagram(cnarr, segarr, threshold, min_probes, outfname, male_referenc
return outfname
-def build_chrom_diagram(features, chr_sizes, sample_id):
+def build_chrom_diagram(features, chr_sizes, sample_id, title=None):
"""Create a PDF of color-coded features on chromosomes."""
max_chr_len = max(chr_sizes.values())
@@ -107,7 +103,7 @@ def build_chrom_diagram(features, chr_sizes, sample_id):
chr_diagram.page_size = PAGE_SIZE
chr_diagram.title_size = 18
- for chrom, length in chr_sizes.items():
+ for chrom, length in list(chr_sizes.items()):
chrom_features = features.get(chrom)
if not chrom_features:
continue
@@ -136,7 +132,8 @@ def build_chrom_diagram(features, chr_sizes, sample_id):
cur_chromosome.add(tel_end)
chr_diagram.add(cur_chromosome)
- title = "Sample " + sample_id
+ if not title:
+ title = "Sample " + sample_id
return bc_organism_draw(chr_diagram, title)
@@ -146,9 +143,15 @@ def bc_organism_draw(org, title, wrap=12):
Instead of stacking chromosomes horizontally (along the x-axis), stack rows
vertically, then proceed with the chromosomes within each row.
- Arguments:
-
- - title: The output title of the produced document.
+ Parameters
+ ----------
+ org :
+ The chromosome diagram object being modified.
+ title : str
+ The output title of the produced document.
+ wrap : int
+ Maximum number of chromosomes per row; the remainder will be wrapped to
+ the next row(s).
"""
margin_top = 1.25*inch
margin_bottom = 0.1*inch
diff --git a/cnvlib/export.py b/cnvlib/export.py
index e96218a..b2094a0 100644
--- a/cnvlib/export.py
+++ b/cnvlib/export.py
@@ -1,17 +1,16 @@
"""Export CNVkit objects and files to other formats."""
from __future__ import absolute_import, division, print_function
+from builtins import range, str, zip
-import collections
import logging
import time
import numpy as np
import pandas as pd
-from Bio._py3k import map, range, zip
+from skgenome import tabio
-from . import call, core, params
-from .cnary import CopyNumArray as CNA
-from .vary import VariantArray as VA
+from . import call
+from .cmdutil import read_cna
from ._version import __version__
@@ -30,15 +29,14 @@ def merge_samples(filenames):
if not filenames:
return []
- first_cnarr = CNA.read(filenames[0])
+ first_cnarr = read_cna(filenames[0])
out_table = first_cnarr.data.loc[:, ["chromosome", "start", "end", "gene"]]
out_table["label"] = label_with_gene(first_cnarr)
out_table[first_cnarr.sample_id] = first_cnarr["log2"]
for fname in filenames[1:]:
- cnarr = CNA.read(fname)
- # Verify labels match
- labels = label_with_gene(cnarr)
- if not (labels == out_table["label"]).all():
+ cnarr = read_cna(fname)
+ if not (len(cnarr) == len(out_table)
+ and (label_with_gene(cnarr) == out_table["label"]).all()):
raise ValueError("Mismatched row coordinates in %s" % fname)
# Copy the next column by sample ID
if cnarr.sample_id in out_table.columns:
@@ -51,19 +49,26 @@ def merge_samples(filenames):
# Supported formats:
def fmt_cdt(sample_ids, table):
- """Format as CDT."""
+ """Format as CDT.
+
+ See:
+
+ - http://jtreeview.sourceforge.net/docs/JTVUserManual/ch02s11.html
+ - http://www.eisenlab.org/FuzzyK/cdt.html
+ """
outheader = ['GID', 'CLID', 'NAME', 'GWEIGHT'] + sample_ids
header2 = ['AID', '', '', '']
header2.extend(['ARRY' + str(i).zfill(3) + 'X'
for i in range(len(sample_ids))])
- outrows = [header2]
+ header3 = ['EWEIGHT', '', '', ''] + ['1'] * len(sample_ids)
+ outrows = [header2, header3]
outtable = pd.concat([
- pd.DataFrame({
- "GID": table.index.apply(lambda x: "GENE%dX" % x),
- "CLID": table.index.apply(lambda x: "IMAGE:%d" % x),
- "NAME": table["label"],
- "GWEIGHT": 1,
- }),
+ pd.DataFrame.from_items([
+ ("GID", pd.Series(table.index).apply(lambda x: "GENE%dX" % x)),
+ ("CLID", pd.Series(table.index).apply(lambda x: "IMAGE:%d" % x)),
+ ("NAME", table["label"]),
+ ("GWEIGHT", 1),
+ ]),
table.drop(["chromosome", "start", "end", "gene", "label"],
axis=1)],
axis=1)
@@ -93,36 +98,31 @@ def fmt_jtv(sample_ids, table):
# Special cases
-def export_nexus_basic(sample_fname):
+def export_nexus_basic(cnarr):
"""Biodiscovery Nexus Copy Number "basic" format.
Only represents one sample per file.
"""
- cnarr = CNA.read(sample_fname)
out_table = cnarr.data.loc[:, ['chromosome', 'start', 'end', 'gene', 'log2']]
out_table['probe'] = cnarr.labels()
return out_table
-def export_nexus_ogt(sample_fname, vcf_fname, sample_id,
- min_depth=20, min_weight=0.0):
+def export_nexus_ogt(cnarr, varr, min_weight=0.0):
"""Biodiscovery Nexus Copy Number "Custom-OGT" format.
To create the b-allele frequencies column, alterate allele frequencies from
the VCF are aligned to the .cnr file bins. Bins that contain no variants
are left blank; if a bin contains multiple variants, then the frequencies
- are all "mirrored" to be above .5, then the median of those values is taken.
+ are all "mirrored" to be above or below .5 (majority rules), then the median
+ of those values is taken.
"""
- cnarr = CNA.read(sample_fname)
if min_weight and "weight" in cnarr:
mask_low_weight = (cnarr["weight"] < min_weight)
logging.info("Dropping %d bins with weight below %f",
mask_low_weight.sum(), min_weight)
cnarr.data = cnarr.data[~mask_low_weight]
- varr = VA.read_vcf(vcf_fname, sample_id=sample_id or cnarr.sample_id,
- min_depth=min_depth, skip_hom=True, skip_somatic=True)
- bafs = cnarr.match_to_bins(varr, 'alt_freq', np.nan,
- summary_func=mirrored_baf_median)
+ bafs = varr.baf_by_ranges(cnarr)
logging.info("Placed %d variants into %d bins",
sum(~np.isnan(bafs)), len(cnarr))
out_table = cnarr.data.loc[:, ['chromosome', 'start', 'end', 'log2']]
@@ -136,56 +136,24 @@ def export_nexus_ogt(sample_fname, vcf_fname, sample_id,
return out_table
-def mirrored_baf_median(vals):
- shift = np.median(np.abs(vals - .5))
- if np.median(vals) > .5:
- return .5 + shift
- else:
- return .5 - shift
-
-
-def export_seg(sample_fnames):
+def export_seg(sample_fnames, chrom_ids=None):
"""SEG format for copy number segments.
Segment breakpoints are not the same across samples, so samples are listed
in serial with the sample ID as the left column.
"""
- out_tables = []
- chrom_ids = None
- for fname in sample_fnames:
- segments = CNA.read(fname)
- if chrom_ids is None:
- # Create & store
- chrom_ids = create_chrom_ids(segments)
- else:
- # Verify
- core.assert_equal("Segment chromosome names differ",
- previous=chrom_ids.keys(),
- current=create_chrom_ids(segments).keys())
- table = segments.data.loc[:, ["start", "end"]]
- table["ID"] = segments.sample_id
- table["mean"] = segments.data["log2"]
- table["chromosome"] = [chrom_ids[chrom]
- for chrom in segments["chromosome"]]
- if "probes" in segments:
- table["num_probes"] = segments["probes"]
- sorted_cols = ["ID", "chromosome", "start", "end", "num_probes",
- "mean"]
- else:
- sorted_cols = ["ID", "chromosome", "start", "end", "mean"]
- out_tables.append(table.reindex(columns=sorted_cols))
- return pd.concat(out_tables)
+ dframes, sample_ids = zip(*(_load_seg_dframe_id(fname)
+ for fname in sample_fnames))
+ out_table = tabio.seg.write_seg(dframes, sample_ids, chrom_ids)
+ return out_table
-def create_chrom_ids(segments):
- """Map chromosome names to integers in the order encountered."""
- mapping = collections.OrderedDict()
- curr_idx = 1
- for chrom in segments.chromosome:
- if chrom not in mapping:
- mapping[chrom] = curr_idx
- curr_idx += 1
- return mapping
+def _load_seg_dframe_id(fname):
+ segarr = read_cna(fname)
+ assert segarr is not None
+ assert segarr.data is not None
+ assert segarr.sample_id is not None
+ return segarr.data, segarr.sample_id
# _____________________________________________________________________________
@@ -212,8 +180,8 @@ def export_bed(segments, ploidy, is_reference_male, is_sample_female,
out = segments.data.loc[:, ["chromosome", "start", "end"]]
out["label"] = label
out["ncopies"] = (segments["cn"] if "cn" in segments
- else np.rint(call.absolute_pure(segments, ploidy,
- is_reference_male)))
+ else call.absolute_pure(segments, ploidy, is_reference_male)
+ .round().astype('int'))
if show == "ploidy":
# Skip regions of default ploidy
out = out[out["ncopies"] != ploidy]
@@ -228,7 +196,7 @@ def export_bed(segments, ploidy, is_reference_male, is_sample_female,
# VCF
VCF_HEADER = """\
-##fileformat=VCFv4.0
+##fileformat=VCFv4.2
##fileDate={date}
##source=CNVkit v{version}
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
@@ -256,7 +224,7 @@ VCF_HEADER = """\
def export_vcf(segments, ploidy, is_reference_male, is_sample_female,
- sample_id=None):
+ sample_id=None, cnarr=None):
"""Convert segments to Variant Call Format.
For now, only 1 sample per VCF. (Overlapping CNVs seem tricky.)
@@ -265,6 +233,8 @@ def export_vcf(segments, ploidy, is_reference_male, is_sample_female,
"""
vcf_columns = ["#CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER",
"INFO", "FORMAT", sample_id or segments.sample_id]
+ if cnarr:
+ segments = assign_ci_start_end(segments, cnarr)
vcf_rows = segments2vcf(segments, ploidy, is_reference_male,
is_sample_female)
table = pd.DataFrame.from_records(vcf_rows, columns=vcf_columns)
@@ -273,25 +243,42 @@ def export_vcf(segments, ploidy, is_reference_male, is_sample_female,
return VCF_HEADER, vcf_body
+def assign_ci_start_end(segarr, cnarr):
+ """Assign ci_start and ci_end fields to segments.
+
+ Values for each segment indicate the CI boundary points within that segment,
+ i.e. the right CI boundary for the left-side breakpoint (segment start), and
+ left CI boundary for the right-side breakpoint (segment end).
+
+ This is a little unintuitive because the CI refers to the breakpoint, not
+ the segment, but we're storing the info in an array of segments.
+
+ Calculation: Just use the boundaries of the bins left- and right-adjacent to
+ each segment breakpoint.
+ """
+ lefts_rights = ((bins.end.iat[0], bins.start.iat[-1])
+ for _seg, bins in cnarr.by_ranges(segarr, mode="outer"))
+ ci_lefts, ci_rights = zip(*lefts_rights)
+ return segarr.as_dataframe(
+ segarr.data.assign(ci_left=ci_lefts, ci_right=ci_rights))
+
+
def segments2vcf(segments, ploidy, is_reference_male, is_sample_female):
"""Convert copy number segments to VCF records."""
out_dframe = segments.data.loc[:, ["chromosome", "end", "log2", "probes"]]
+ out_dframe["start"] = segments.start.replace(0, 1)
+
if "cn" in segments:
out_dframe["ncopies"] = segments["cn"]
abs_expect = call.absolute_expect(segments, ploidy, is_sample_female)
-
else:
abs_dframe = call.absolute_dataframe(segments, ploidy, 1.0,
is_reference_male,
is_sample_female)
- out_dframe["ncopies"] = np.rint(abs_dframe["absolute"])
+ out_dframe["ncopies"] = abs_dframe["absolute"].round().astype('int')
abs_expect = abs_dframe["expect"]
idx_losses = (out_dframe["ncopies"] < abs_expect)
- starts = segments.start.copy()
- starts[starts == 0] = 1
- out_dframe["start"] = starts
-
svlen = segments.end - segments.start
svlen[idx_losses] *= -1
out_dframe["svlen"] = svlen
@@ -302,6 +289,18 @@ def segments2vcf(segments, ploidy, is_reference_male, is_sample_female):
out_dframe["format"] = "GT:GQ:CN:CNQ"
out_dframe.loc[idx_losses, "format"] = "GT:GQ" # :CN:CNQ ?
+ if "ci_left" in segments and "ci_right" in segments:
+ has_ci = True
+ # Calculate fuzzy left&right coords for CIPOS and CIEND
+ left_margin = segments["ci_left"].values - segments.start.values
+ right_margin = segments.end.values - segments["ci_right"].values
+ out_dframe["ci_pos_left"] = np.r_[0, -right_margin[:-1]]
+ out_dframe["ci_pos_right"] = left_margin
+ out_dframe["ci_end_left"] = right_margin
+ out_dframe["ci_end_right"] = np.r_[left_margin[1:], 0]
+ else:
+ has_ci = False
+
# Reformat this data to create INFO and genotype
# TODO be more clever about this
for out_row, abs_exp in zip(out_dframe.itertuples(index=False), abs_expect):
@@ -323,15 +322,20 @@ def segments2vcf(segments, ploidy, is_reference_male, is_sample_female):
gt = "0/1"
genotype = "%s:%d" % (gt, out_row.probes)
- info = ";".join(["IMPRECISE",
- "SVTYPE=%s" % out_row.svtype,
- "END=%d" % out_row.end,
- "SVLEN=%d" % out_row.svlen,
- "FOLD_CHANGE=%f" % 2.0 ** out_row.log2,
- "FOLD_CHANGE_LOG=%f" % out_row.log2,
- "PROBES=%d" % out_row.probes
- # CIPOS=-56,20;CIEND=-10,62
- ])
+ fields = ["IMPRECISE",
+ "SVTYPE=%s" % out_row.svtype,
+ "END=%d" % out_row.end,
+ "SVLEN=%d" % out_row.svlen,
+ "FOLD_CHANGE=%f" % 2.0 ** out_row.log2,
+ "FOLD_CHANGE_LOG=%f" % out_row.log2,
+ "PROBES=%d" % out_row.probes
+ ]
+ if has_ci:
+ fields.extend([
+ "CIPOS=(%d,%d)" % (out_row.ci_pos_left, out_row.ci_pos_right),
+ "CIEND=(%d,%d)" % (out_row.ci_end_left, out_row.ci_end_right),
+ ])
+ info = ";".join(fields)
yield (out_row.chromosome, out_row.start, '.', 'N',
"<%s>" % out_row.svtype, '.', '.',
@@ -357,11 +361,17 @@ def export_theta(tumor_segs, normal_cn):
where chromosome IDs ("chrm") are integers 1 through 24.
"""
+ out_columns = ["#ID", "chrm", "start", "end", "tumorCount", "normalCount"]
+ if not tumor_segs:
+ return pd.DataFrame(columns=out_columns)
+
# Drop any chromosomes that are not integer or XY
# THetA hard-codes X & Y, so we can, too
- xy_names = (["chrX", "chrY"]
- if tumor_segs.chromosome.iat[0].startswith('chr')
- else ["X", "Y"])
+ # xy_names = (["chrX", "chrY"]
+ # if tumor_segs.chromosome.iat[0].startswith('chr')
+ # else ["X", "Y"])
+ # NB: THetA2 now apparently just drops X and Y (#153)
+ xy_names = []
tumor_segs = tumor_segs.autosomes(also=xy_names)
if normal_cn:
normal_cn = normal_cn.autosomes(also=xy_names)
@@ -370,7 +380,7 @@ def export_theta(tumor_segs, normal_cn):
# Convert chromosome names to 1-based integer indices
chr2idx = {c: i+1
- for i, c in enumerate(tumor_segs.chromosome.drop_duplicates())}
+ for i, c in enumerate(tumor_segs.chromosome.drop_duplicates())}
table["chrm"] = tumor_segs.chromosome.replace(chr2idx)
# Unique string identifier for each row, e.g. "start_1_93709:end_1_19208166"
table["#ID"] = ["start_%d_%d:end_%d_%d"
@@ -381,7 +391,7 @@ def export_theta(tumor_segs, normal_cn):
ref_means, nbins = ref_means_nbins(tumor_segs, normal_cn)
table["tumorCount"] = theta_read_counts(tumor_segs.log2, nbins)
table["normalCount"] = theta_read_counts(ref_means, nbins)
- return table[["#ID", "chrm", "start", "end", "tumorCount", "normalCount"]]
+ return table[out_columns]
def ref_means_nbins(tumor_segs, normal_cn):
@@ -439,9 +449,9 @@ def ref_means_nbins(tumor_segs, normal_cn):
def theta_read_counts(log2_ratio, nbins,
- # These two scaling factors don't meaningfully affect
+ # These scaling factors don't meaningfully affect
# THetA's calculation unless they're too small
- avg_depth=500, avg_bin_width=200):
+ avg_depth=500, avg_bin_width=200, read_len=100):
"""Calculate segments' read counts from log2-ratios.
Math:
@@ -456,31 +466,34 @@ def theta_read_counts(log2_ratio, nbins,
read_count = bin_width * read_depth / read_length
"""
read_depth = (2 ** log2_ratio) * avg_depth
- read_count = nbins * avg_bin_width * read_depth / params.READ_LEN
- return read_count.round().astype('int')
+ read_count = nbins * avg_bin_width * read_depth / read_len
+ return read_count.round().fillna(0).astype('int')
def export_theta_snps(varr):
"""Generate THetA's SNP per-allele read count "formatted.txt" files."""
# Drop any chromosomes that are not integer or XY
- varr = varr.autosomes(also=(["chrX", "chrY"]
- if varr.chromosome.iat[0].startswith("chr")
- else ["X", "Y"]))
+ varr = varr.autosomes(also=(['chrX', 'chrY']
+ if varr.chromosome.iat[0].startswith('chr')
+ else ['X', 'Y']))
# Skip indels
varr = varr[(varr["ref"].str.len() == 1) & (varr["alt"].str.len() == 1)]
# Drop rows with any NaN
- varr.data.dropna(subset=["depth", "n_depth", "alt_count", "n_alt_count"],
- inplace=True)
+ varr.data.dropna(subset=["depth", "alt_count"], inplace=True)
+ if "n_depth" in varr and "n_alt_count" in varr:
+ varr.data.dropna(subset=["n_depth", "alt_count"], inplace=True)
# Avoid weird situation I've seen on alt contigs
varr = varr[varr["depth"] >= varr["alt_count"]]
# Reformat for THetA2
for depth_key, alt_key in (("depth", "alt_count"),
("n_depth", "n_alt_count")):
# Extract the SNP allele counts that THetA2 uses
- table = varr.data.loc[:, ("chromosome", "start", depth_key, alt_key)]
- table["ref_depth"] = (table[depth_key] - table[alt_key]).astype("int")
- table[alt_key] = table[alt_key].astype("int")
- table = table.loc[:, ("chromosome", "start", "ref_depth", alt_key)]
+ table = varr.data.loc[:, ('chromosome', 'start', depth_key, alt_key)]
+ table = (table.assign(ref_depth=table[depth_key] - table[alt_key])
+ .loc[:, ('chromosome', 'start', 'ref_depth', alt_key)]
+ .dropna())
+ table['ref_depth'] = table['ref_depth'].astype('int')
+ table[alt_key] = table[alt_key].astype('int')
table.columns = ["#Chrm", "Pos", "Ref_Allele", "Mut_Allele"]
yield table
diff --git a/cnvlib/fix.py b/cnvlib/fix.py
index 1139022..5b7d1ed 100644
--- a/cnvlib/fix.py
+++ b/cnvlib/fix.py
@@ -1,107 +1,153 @@
"""Supporting functions for the 'fix' command."""
from __future__ import absolute_import, division, print_function
+from builtins import map
import logging
import numpy as np
import pandas as pd
-from . import params, smoothing
+from . import descriptives, params, smoothing
+
+
+def do_fix(target_raw, antitarget_raw, reference,
+ do_gc=True, do_edge=True, do_rmask=True):
+ """Combine target and antitarget coverages and correct for biases."""
+ # Load, recenter and GC-correct target & antitarget probes separately
+ logging.info("Processing target: %s", target_raw.sample_id)
+ cnarr = load_adjust_coverages(target_raw, reference, True,
+ do_gc, do_edge, False)
+ logging.info("Processing antitarget: %s", antitarget_raw.sample_id)
+ anti_cnarr = load_adjust_coverages(antitarget_raw, reference, False,
+ do_gc, False, do_rmask)
+ if len(anti_cnarr):
+ anti_resid = anti_cnarr.drop_low_coverage().residuals()
+ frac_anti_low = 1 - (len(anti_resid) / len(anti_cnarr))
+ if frac_anti_low > .5:
+ # Off-target bins are mostly garbage -- skip reweighting
+ logging.warn("WARNING: Most antitarget bins ({:.2f}%, {:d}/{:d}) "
+ "have low or no coverage; is this amplicon/WGS?"
+ .format(100 * frac_anti_low,
+ len(anti_cnarr) - len(anti_resid),
+ len(anti_cnarr)))
+ else:
+ # Down-weight the more variable probe set (targets or antitargets)
+ tgt_iqr = descriptives.interquartile_range(cnarr.drop_low_coverage()
+ .residuals())
+ anti_iqr = descriptives.interquartile_range(anti_resid)
+ iqr_ratio = max(tgt_iqr, .01) / max(anti_iqr, .01)
+ if iqr_ratio > 1:
+ logging.info("Targets are %.2f x more variable than antitargets",
+ iqr_ratio)
+ cnarr["weight"] /= iqr_ratio
+ else:
+ logging.info("Antitargets are %.2f x more variable than targets",
+ 1. / iqr_ratio)
+ anti_cnarr["weight"] *= iqr_ratio
+ # Combine target and antitarget bins
+ cnarr.add(anti_cnarr)
+ cnarr.center_all(skip_low=True)
+ return cnarr
-def load_adjust_coverages(pset, ref_pset, skip_low,
+def load_adjust_coverages(cnarr, ref_cnarr, skip_low,
fix_gc, fix_edge, fix_rmask):
"""Load and filter probe coverages; correct using reference and GC."""
- if 'gc' in pset:
+ if 'gc' in cnarr:
# Don't choke on Picard-derived files that have the GC column
- pset = pset.drop_extra_columns()
+ cnarr = cnarr.keep_columns(cnarr._required_columns + ('depth',))
# No corrections needed if there are no data rows (e.g. no antitargets)
- if not len(pset):
- return pset
+ if not len(cnarr):
+ return cnarr
- ref_matched = match_ref_to_probes(ref_pset, pset)
+ ref_matched = match_ref_to_sample(ref_cnarr, cnarr)
- # Drop probes that had poor coverage in the pooled reference
- ok_cvg_indices = ~mask_bad_probes(ref_matched)
+ # Drop bins that had poor coverage in the pooled reference
+ ok_cvg_indices = ~mask_bad_bins(ref_matched)
logging.info("Keeping %d of %d bins", sum(ok_cvg_indices), len(ref_matched))
- pset = pset[ok_cvg_indices]
+ cnarr = cnarr[ok_cvg_indices]
ref_matched = ref_matched[ok_cvg_indices]
# Apply corrections for known systematic biases in coverage
- pset.center_all(skip_low=skip_low)
+ cnarr.center_all(skip_low=skip_low)
# Skip bias corrections if most bins have no coverage (e.g. user error)
- if (pset['log2'] > params.NULL_LOG2_COVERAGE - params.MIN_REF_COVERAGE
- ).sum() <= len(pset) // 2:
- logging.warn("WARNING: most bins have no or very low coverage; "
- "check that the right BED file was used")
+ if (cnarr['log2'] > params.NULL_LOG2_COVERAGE - params.MIN_REF_COVERAGE
+ ).sum() <= len(cnarr) // 2:
+ logging.warn("WARNING: most bins have no or very low coverage; "
+ "check that the right BED file was used")
else:
if fix_gc:
if 'gc' in ref_matched:
logging.info("Correcting for GC bias...")
- pset = center_by_window(pset, .1, ref_matched['gc'])
+ cnarr = center_by_window(cnarr, .1, ref_matched['gc'])
else:
logging.warn("WARNING: Skipping correction for GC bias")
if fix_edge:
logging.info("Correcting for density bias...")
- edge_bias = get_edge_bias(pset, params.INSERT_SIZE)
- pset = center_by_window(pset, .1, edge_bias)
+ edge_bias = get_edge_bias(cnarr, params.INSERT_SIZE)
+ cnarr = center_by_window(cnarr, .1, edge_bias)
if fix_rmask:
if 'rmask' in ref_matched:
logging.info("Correcting for RepeatMasker bias...")
- pset = center_by_window(pset, .1, ref_matched['rmask'])
+ cnarr = center_by_window(cnarr, .1, ref_matched['rmask'])
else:
logging.warn("WARNING: Skipping correction for RepeatMasker bias")
# Normalize coverages according to the reference
# (Subtract the reference log2 copy number to get the log2 ratio)
- pset.data['log2'] -= ref_matched['log2']
- pset.center_all(skip_low=skip_low)
- return apply_weights(pset, ref_matched)
+ cnarr.data['log2'] -= ref_matched['log2']
+ cnarr.center_all(skip_low=skip_low)
+ return apply_weights(cnarr, ref_matched)
-def mask_bad_probes(probes):
- """Flag the probes with excessively low or inconsistent coverage.
+def mask_bad_bins(cnarr):
+ """Flag the bins with excessively low or inconsistent coverage.
- Returns a bool array where True indicates probes that failed the checks.
+ Returns
+ -------
+ np.array
+ A boolean array where True indicates bins that failed the checks.
"""
- mask = ((probes['log2'] < params.MIN_REF_COVERAGE) |
- (probes['log2'] > -params.MIN_REF_COVERAGE) |
- (probes['spread'] > params.MAX_REF_SPREAD))
+ mask = ((cnarr['log2'] < params.MIN_REF_COVERAGE) |
+ (cnarr['log2'] > -params.MIN_REF_COVERAGE) |
+ (cnarr['spread'] > params.MAX_REF_SPREAD))
+ if 'depth' in cnarr:
+ mask |= cnarr['depth'] == 0
return mask
-def match_ref_to_probes(ref_pset, probes):
- """Filter the reference probes to match the target or antitarget probe set.
- """
- probes_labeled = probes.data.set_index(pd.Index(probes.coords()))
- ref_labeled = ref_pset.data.set_index(pd.Index(ref_pset.coords()))
+def match_ref_to_sample(ref_cnarr, samp_cnarr):
+ """Filter the reference bins to match the sample (target or antitarget)."""
+ samp_labeled = samp_cnarr.data.set_index(pd.Index(samp_cnarr.coords()))
+ ref_labeled = ref_cnarr.data.set_index(pd.Index(ref_cnarr.coords()))
# Safety
- for dset, name in ((probes_labeled, "probe"),
+ for dset, name in ((samp_labeled, "sample"),
(ref_labeled, "reference")):
dupes = dset.index.duplicated()
if dupes.any():
raise ValueError("Duplicated genomic coordinates in " + name +
" set:\n" + "\n".join(map(str, dset.index[dupes])))
- ref_matched = ref_labeled.reindex(index=probes_labeled.index)
+ ref_matched = ref_labeled.reindex(index=samp_labeled.index)
# Check for signs that the wrong reference was used
num_missing = pd.isnull(ref_matched.start).sum()
if num_missing > 0:
raise ValueError("Reference is missing %d bins found in %s"
- % (num_missing, probes.sample_id))
- return ref_pset.as_dataframe(ref_matched.reset_index(drop=True))
+ % (num_missing, samp_cnarr.sample_id))
+ return ref_cnarr.as_dataframe(ref_matched.reset_index(drop=True))
def center_by_window(cnarr, fraction, sort_key):
"""Smooth out biases according to the trait specified by sort_key.
- E.g. correct GC-biased probes by windowed averaging across similar-GC
- probes; or for similar interval sizes.
+ E.g. correct GC-biased bins by windowed averaging across similar-GC
+ bins; or for similar interval sizes.
"""
- # Separate neighboring probes that could have the same key
+ # Separate neighboring bins that could have the same key
# (to avoid re-centering actual CNV regions -- only want an independently
- # sampled subset of presumably overall-CN-neutral probes)
+ # sampled subset of presumably overall-CN-neutral bins)
df = cnarr.data.reset_index(drop=True)
+ np.random.seed(0xA5EED)
shuffle_order = np.random.permutation(df.index)
df = df.reindex(shuffle_order)
# Apply the same shuffling to the key array as to the target probe set
@@ -154,13 +200,13 @@ def edge_losses(target_sizes, insert_size):
"""Calculate coverage losses at the edges of baited regions.
Letting i = insert size and t = target size, the proportional loss of
- coverage near the two edges of the baited region (combined) is::
+ coverage near the two edges of the baited region (combined) is:
- i/2t
+ .. math :: i/2t
- If the "shoulders" extend outside the bait $(t < i), reduce by::
+ If the "shoulders" extend outside the bait $(t < i), reduce by:
- (i-t)^2 / 4it
+ .. math :: (i-t)^2 / 4it
on each side, or (i-t)^2 / 2it total.
"""
@@ -179,11 +225,11 @@ def edge_gains(target_sizes, gap_sizes, insert_size):
Letting i = insert size, t = target size, g = gap to neighboring bait,
the gain of coverage due to a nearby bait, if g < i, is::
- (i-g)^2 / 4it
+ .. math :: (i-g)^2 / 4it
If the neighbor flank extends beyond the target (t+g < i), reduce by::
- (i-t-g)^2 / 4it
+ .. math :: (i-t-g)^2 / 4it
If a neighbor overlaps the target, treat it as adjacent (gap size 0).
"""
@@ -216,13 +262,13 @@ def apply_weights(cnarr, ref_matched, epsilon=1e-4):
weights = sizes / sizes.max()
if (np.abs(np.mod(ref_matched['log2'], 1)) > epsilon).any():
# NB: Not used with a flat reference
- logging.info("Weighting bins by relative coverage depths in reference")
+ logging.debug("Weighting bins by relative coverage depths in reference")
# Penalize bins that deviate from neutral coverage
- flat_cvgs = ref_matched.expect_flat_cvg()
+ flat_cvgs = ref_matched.expect_flat_log2()
weights *= np.exp2(-np.abs(ref_matched['log2'] - flat_cvgs))
if (ref_matched['spread'] > epsilon).any():
# NB: Not used with a flat or paired reference
- logging.info("Weighting bins by coverage spread in reference")
+ logging.debug("Weighting bins by coverage spread in reference")
# Inverse of variance, 0--1
variances = ref_matched['spread'] ** 2
invvars = 1.0 - (variances / variances.max())
@@ -230,4 +276,3 @@ def apply_weights(cnarr, ref_matched, epsilon=1e-4):
# Avoid 0-value bins -- CBS doesn't like these
weights = np.maximum(weights, epsilon)
return cnarr.add_columns(weight=weights)
-
diff --git a/cnvlib/gary.py b/cnvlib/gary.py
deleted file mode 100644
index bd6cf4c..0000000
--- a/cnvlib/gary.py
+++ /dev/null
@@ -1,490 +0,0 @@
-"""A generic array of genomic positions."""
-from __future__ import print_function, absolute_import, division
-
-import logging
-import sys
-import warnings
-
-import numpy as np
-import pandas as pd
-
-from . import core, ngfrills
-
-
-class GenomicArray(object):
- """An array of genomic intervals. Base class for genomic data structures.
-
- Can represent most BED-like tabular formats with arbitrary additional
- columns.
- """
- _required_columns = ("chromosome", "start", "end")
- _required_dtypes = ("string", "int", "int")
-
- def __init__(self, data_table, meta_dict=None):
- # Validation
- if len(data_table):
- if not all(c in data_table.columns for c in self._required_columns):
- raise ValueError("data table must have at least columns "
- + repr(self._required_columns))
- # Ensure chromosomes are strings to avoid integer conversion of 1, 2...
- if not isinstance(data_table.chromosome.iat[0], basestring):
- data_table["chromosome"] = (data_table["chromosome"]
- .astype("string"))
- elif not isinstance(data_table, pd.DataFrame):
- # Empty but conformant table
- data_table = self._make_blank()
- self.data = data_table
- self.meta = (dict(meta_dict)
- if meta_dict is not None and len(meta_dict)
- else {})
-
- @staticmethod
- def row2label(row):
- return "{}:{}-{}".format(row.chromosome, row.start, row.end)
-
- @classmethod
- def _make_blank(cls):
- """Create an empty dataframe with the columns required by this class."""
- table = pd.DataFrame({key: [] for key in cls._required_columns})
- for col, dtype in zip(cls._required_columns, cls._required_dtypes):
- table[col] = table[col].astype(dtype)
- return table
-
- @classmethod
- def from_columns(cls, columns, meta_dict=None):
- """Create a new instance from column arrays, given as a dict."""
- table = pd.DataFrame.from_dict(columns)
- ary = cls(table, meta_dict)
- ary.sort_columns()
- return ary
-
- @classmethod
- def from_rows(cls, rows, columns=None, meta_dict=None):
- """Create a new instance from a list of rows, as tuples or arrays."""
- if columns is None:
- columns = cls._required_columns
- table = pd.DataFrame.from_records(rows, columns=columns)
- return cls(table, meta_dict)
-
- def as_columns(self, **columns):
- """Wrap the named columns in this instance's metadata."""
- return self.__class__.from_columns(columns, self.meta)
- # return self.__class__(self.data.loc[:, columns], self.meta.copy())
-
- def as_dataframe(self, dframe):
- """Wrap the given pandas dataframe in this instance's metadata."""
- return self.__class__(dframe.reset_index(drop=True), self.meta.copy())
-
- # def as_index(self, index):
- # """Subset with fancy/boolean indexing; reuse this instance's metadata."""
- # """Extract rows by indices, reusing this instance's metadata."""
- # if isinstance(index, (int, slice)):
- # return self.__class__(self.data.iloc[index], self.meta.copy())
- # else:
- # return self.__class__(self.data[index], self.meta.copy())
-
- def as_rows(self, rows):
- """Wrap the given rows in this instance's metadata."""
- return self.from_rows(rows,
- columns=self.data.columns,
- meta_dict=self.meta)
-
- # Container behaviour
-
- def __eq__(self, other):
- return (isinstance(other, self.__class__) and
- self.data.equals(other.data))
-
- def __len__(self):
- return len(self.data)
-
- def __contains__(self, key):
- return key in self.data.columns
-
- def __getitem__(self, index):
- """Access a portion of the data.
-
- Cases:
-
- - single integer: a row, as pd.Series
- - string row name: a column, as pd.Series
- - a boolean array: masked rows, as_dataframe
- - tuple of integers: selected rows, as_dataframe
- """
- if isinstance(index, int):
- # A single row
- return self.data.iloc[index]
- # return self.as_dataframe(self.data.iloc[index:index+1])
- elif isinstance(index, basestring):
- # A column, by name
- return self.data[index]
- elif (isinstance(index, tuple) and
- len(index) == 2 and
- index[1] in self.data.columns):
- # Row index, column index -> cell value
- return self.data.loc[index]
- elif isinstance(index, slice):
- # return self.as_dataframe(self.data.take(index))
- return self.as_dataframe(self.data[index])
- else:
- # Iterable -- selected row indices or boolean array, probably
- try:
- if isinstance(index, type(None)) or len(index) == 0:
- empty = pd.DataFrame(columns=self.data.columns)
- return self.as_dataframe(empty)
- except TypeError:
- raise TypeError("object of type %r " % type(index) +
- "cannot be used as an index into a " +
- self.__class__.__name__)
- return self.as_dataframe(self.data[index])
- # return self.as_dataframe(self.data.take(index))
-
- def __setitem__(self, index, value):
- """Assign to a portion of the data.
- """
- # self.data[index] = value
- if isinstance(index, int):
- self.data.iloc[index] = value
- elif isinstance(index, basestring):
- self.data[index] = value
- elif (isinstance(index, tuple) and
- len(index) == 2 and
- index[1] in self.data.columns):
- self.data.loc[index] = value
- else:
- assert isinstance(index, slice) or len(index) > 0
- self.data[index] = value
-
- def __delitem__(self, index):
- return NotImplemented
-
- def __iter__(self):
- return self.data.itertuples(index=False)
-
- __next__ = next
-
- @property
- def chromosome(self):
- return self.data['chromosome']
-
- @property
- def start(self):
- return self.data['start']
-
- @property
- def end(self):
- return self.data['end']
-
- @property
- def sample_id(self):
- return self.meta.get('sample_id')
-
- # Traversal
-
- def autosomes(self, also=()):
- """Select chromosomes w/ integer names, ignoring any 'chr' prefixes."""
- with warnings.catch_warnings():
- # NB: We're not using the deprecated part of this pandas method
- warnings.simplefilter("ignore", UserWarning)
- is_auto = self.chromosome.str.match(r"(chr)?\d+$",
- as_indexer=True, na=False)
- if not is_auto.any():
- # The autosomes, if any, are not named with plain integers
- return self
- if also:
- if isinstance(also, basestring):
- also = [also]
- for a_chrom in also:
- is_auto |= (self.chromosome == a_chrom)
- return self[is_auto]
-
- def by_chromosome(self):
- """Iterate over bins grouped by chromosome name."""
- for chrom, subtable in self.data.groupby("chromosome", sort=False):
- yield chrom, self.as_dataframe(subtable)
-
- def by_ranges(self, other, mode='inner', keep_empty=True):
- """Group rows by another GenomicArray's bin coordinate ranges.
-
- Returns an iterable of (bin, GenomicArray of overlapping rows)). Usually
- used for grouping probes or SNVs by CNV segments.
-
- `mode` determines what to do with bins that overlap a boundary of the
- selection. Values are:
-
- - ``inner``: Drop the bins on the selection boundary, don't emit them.
- - ``outer``: Keep/emit those bins as they are.
- - ``trim``: Emit those bins but alter their boundaries to match the
- selection; the bin start or end position is replaced with the
- selection boundary position.
-
- Bins in this array that fall outside the other array's bins are skipped.
- """
- chrom_lookup = dict(self.by_chromosome())
- for chrom, bin_rows in other.by_chromosome():
- if chrom in chrom_lookup:
- subranges = chrom_lookup[chrom]._iter_ranges(
- None, bin_rows['start'], bin_rows['end'], mode)
- for bin_row, subrange in zip(bin_rows, subranges):
- yield bin_row, subrange
- else:
- if keep_empty:
- for bin_row in bin_rows:
- yield bin_row, self.as_rows([])
-
- def coords(self, also=()):
- """Iterate over plain coordinates of each bin: chromosome, start, end.
-
- With `also`, also include those columns.
-
- Example, yielding rows in BED format:
-
- >>> probes.coords(also=["name", "strand"])
- """
- cols = list(GenomicArray._required_columns)
- if also:
- if isinstance(also, basestring):
- cols.append(also)
- else:
- cols.extend(also)
- coordframe = self.data.loc[:, cols]
- return coordframe.itertuples(index=False)
-
- def labels(self):
- return self.data.apply(self.row2label, axis=1)
-
- def in_range(self, chrom=None, start=None, end=None, mode='inner'):
- """Get the GenomicArray portion within the given genomic range.
-
- `mode` works as in `by_ranges`: ``outer`` includes bins straddling the
- range boundaries, ``trim`` additionally alters the straddling bins'
- endpoints to match the range boundaries, and ``inner`` excludes those
- bins.
- """
- if isinstance(start, (int, float, np.float64)):
- start = [int(start)]
- if isinstance(end, (int, float, np.float64)):
- end = [int(end)]
- results = self._iter_ranges(chrom, start, end, mode)
- return next(results)
-
- def in_ranges(self, chrom=None, starts=None, ends=None, mode='inner'):
- """Get the GenomicArray portion within the specified ranges.
-
- Same as `in_ranges` but the `starts` and `ends` are arrays of equal
- length, and the output concatenates all the selected bins.
- """
- return self.concat(self._iter_ranges(chrom, starts, ends, mode))
-
- def _iter_ranges(self, chrom, starts, ends, mode):
- """Iterate through sub-ranges."""
- assert mode in ('inner', 'outer', 'trim')
- if chrom:
- assert isinstance(chrom, basestring) # ENH: accept array?
- try:
- table = self.data[self.data['chromosome'] == chrom]
- except KeyError:
- raise KeyError("Chromosome %s is not in this probe set" % chrom)
- else:
- # Unsafe, but faster if we've already subsetted by chromosome
- table = self.data
-
- # Edge cases
- if not len(table):
- yield self.as_rows([])
- raise StopIteration
-
- if starts is None and ends is None:
- yield self.as_dataframe(table)
- raise StopIteration
-
- if starts is not None and len(starts):
- if mode == 'inner':
- # Only rows entirely after the start point
- start_idxs = table.start.searchsorted(starts)
- else:
- # Include all rows overlapping the start point
- start_idxs = table.end.searchsorted(starts, 'right')
- else:
- starts = np.zeros(len(ends) if ends is not None else 1,
- dtype=np.int_)
- start_idxs = starts.copy()
-
- if ends is not None and len(ends):
- if mode == 'inner':
- end_idxs = table.end.searchsorted(ends, 'right')
- else:
- end_idxs = table.start.searchsorted(ends)
- else:
- end_idxs = np.repeat(len(table), len(starts))
- ends = [None] * len(starts)
-
- for start_idx, start_val, end_idx, end_val in zip(start_idxs, starts,
- end_idxs, ends):
- subtable = table[start_idx:end_idx]
- if mode == 'trim':
- subtable = subtable.copy()
- # Update 5' endpoints to the boundary
- if start_val:
- subtable.start = subtable.start.clip_lower(start_val)
- # Update 3' endpoints to the boundary
- if end_val:
- subtable.end = subtable.end.clip_upper(end_val)
- yield self.as_dataframe(subtable)
-
- def match_to_bins(self, other, key, default=0.0, fill=False,
- summary_func=np.median):
- """Take values of the other array at each of this array's bins.
-
- Assign `default` to indices that fall outside the other array's bins, or
- chromosomes that appear in `self` but not `other`.
-
- Return an array of the `key` column values in `other` corresponding to this
- array's bin locations, the same length as this array.
- """
- def rows2value(rows):
- if len(rows) == 0:
- return default
- elif len(rows) == 1:
- return rows[0, key]
- else:
- return summary_func(rows[key])
-
- all_out_vals = [rows2value(other_rows) for _bin, other_rows in
- other.by_ranges(self, mode='outer', keep_empty=True)]
- return np.asarray(all_out_vals)
-
- # Modification
-
- def add(self, other):
- """Combine this array's data with another GenomicArray (in-place).
-
- Any optional columns must match between both arrays.
- """
- if not isinstance(other, self.__class__):
- raise ValueError("Argument (type %s) is not a %s instance"
- % (type(other), self.__class__))
- if not len(other.data):
- return self.copy()
- self.data = pd.concat([self.data, other.data])
- self.sort()
-
- def concat(self, others):
- """Concatenate several GenomicArrays, keeping this array's metadata.
-
- This array's data table is not implicitly included in the result.
- """
- result = self.as_dataframe(pd.concat([otr.data for otr in others]))
- result.sort()
- return result
-
- def copy(self):
- """Create an independent copy of this object."""
- return self.as_dataframe(self.data.copy())
-
- def add_columns(self, **columns):
- """Create a new CNA, adding the specified extra columns to this CNA."""
- # return self.as_dataframe(self.data.assign(**columns))
- result = self.copy()
- for key, values in columns.iteritems():
- result[key] = values
- return result
-
- def keep_columns(self, columns):
- """Extract a subset of columns, reusing this instance's metadata."""
- return self.__class__(self.data.loc[:, columns], self.meta.copy())
-
- def drop_extra_columns(self):
- """Remove any optional columns from this GenomicArray.
-
- Returns a new copy with only the core columns retained:
- log2 value, chromosome, start, end, bin name.
- """
- table = self.data.loc[:, self._required_columns]
- return self.as_dataframe(table)
-
- def select(self, selector=None, **kwargs):
- """Take a subset of rows where the given condition is true.
-
- Arguments can be a function (lambda expression) returning a bool, which
- will be used to select True rows, and/or keyword arguments like
- gene="Background" or chromosome="chr7", which will select rows where the
- keyed field equals the specified value.
- """
- table = self.data
- if selector is not None:
- table = table[table.apply(selector, axis=1)]
- for key, val in kwargs.items():
- assert key in self
- table = table[table[key] == val]
- return self.as_dataframe(table)
-
- def shuffle(self):
- """Randomize the order of bins in this array (in-place)."""
- np.random.seed(0xA5EED) # For reproducible results
- order = np.arange(len(self.data))
- np.random.shuffle(order)
- self.data = self.data.iloc[order]
- return order
-
- def sort(self):
- """Sort this array's bins in-place, with smart chromosome ordering."""
- table = self.data.copy()
- table['SORT_KEY'] = self.chromosome.apply(core.sorter_chrom)
- table.sort_values(by=['SORT_KEY', 'start'], inplace=True)
- del table['SORT_KEY']
- self.data = table.reset_index(drop=True)
-
- def sort_columns(self):
- """Sort this array's columns in-place, per class definition."""
- extra_cols = []
- for col in self.data.columns:
- if col not in self._required_columns:
- extra_cols.append(col)
- sorted_colnames = list(self._required_columns) + sorted(extra_cols)
- assert len(sorted_colnames) == len(self.data.columns)
- self.data = self.data.reindex(columns=sorted_colnames)
-
- # I/O
-
- @classmethod
- def read(cls, infile, sample_id=None):
- if sample_id is None:
- if isinstance(infile, basestring):
- sample_id = core.fbase(infile)
- else:
- sample_id = '<unknown>'
- try:
- table = pd.read_table(infile,
- dtype={'chromosome': 'string'})
- if "log2" in table.columns:
- # Every bin needs a log2 value; the others can be NaN
- t2 = table.dropna(subset=["log2"])
- if len(t2) < len(table):
- logging.warn("Dropped %d rows with missing log2 values",
- len(table) - len(t2))
- table = t2
- except ValueError:
- # File is blank/empty, most likely
- logging.warn("Blank file?: %s", infile)
- table = cls._make_blank()
- # ENH
- # table['chromosome'] = pd.Categorical(table['chromosome'],
- # table.chromosome.drop_duplicates(),
- # ordered=True)
- # Create a multi-index of genomic coordinates (like GRanges)
- # table.set_index(['chromosome', 'start'], inplace=True)
- return cls(table, {"sample_id": sample_id})
-
- def write(self, outfile=None):
- """Write the wrapped data table to a file or handle in tabular format.
-
- The format is BED-like, but with a header row included and with
- arbitrary extra columns.
-
- To combine multiple samples in one file and/or convert to another
- format, see the 'export' subcommand.
- """
- with ngfrills.safe_write(outfile or sys.stdout) as handle:
- self.data.to_csv(handle, index=False, sep='\t', float_format='%.6g')
-
diff --git a/cnvlib/heatmap.py b/cnvlib/heatmap.py
new file mode 100644
index 0000000..3d63360
--- /dev/null
+++ b/cnvlib/heatmap.py
@@ -0,0 +1,119 @@
+"""The 'heatmap' command."""
+from __future__ import absolute_import, division, print_function
+from builtins import zip
+
+import collections
+import logging
+
+import numpy as np
+import matplotlib as mpl
+from matplotlib import pyplot as plt
+from matplotlib.collections import BrokenBarHCollection
+from skgenome.rangelabel import unpack_range
+
+from . import plots
+
+
+def do_heatmap(cnarrs, show_range=None, do_desaturate=False):
+ """Plot copy number for multiple samples as a heatmap."""
+ _fig, axis = plt.subplots()
+ set_colorbar(axis)
+
+ # List sample names on the y-axis
+ axis.set_yticks([i + 0.5 for i in range(len(cnarrs))])
+ axis.set_yticklabels([c.sample_id for c in cnarrs])
+ axis.set_ylim(0, len(cnarrs))
+ axis.invert_yaxis()
+ axis.set_ylabel("Samples")
+ axis.set_axis_bgcolor('#DDDDDD')
+
+ r_chrom, r_start, r_end = unpack_range(show_range)
+ if r_start is not None or r_end is not None:
+ logging.info("Showing log2 ratios in range %s:%d-%s",
+ r_chrom, r_start, r_end or '*')
+ elif r_chrom:
+ logging.info("Showing log2 ratios on chromosome %s", r_chrom)
+
+ # Closes over do_desaturate
+ def cna2df(cna):
+ """Extract a dataframe of plotting points from a CopyNumArray."""
+ points = cna.data.loc[:, ["start", "end"]]
+ points["color"] = cna.log2.apply(plots.cvg2rgb, args=(do_desaturate,))
+ return points
+
+ # Group each file's probes/segments by chromosome
+ sample_data = [collections.defaultdict(list) for _c in cnarrs]
+ # Calculate the size (max endpoint value) of each chromosome
+ chrom_sizes = collections.OrderedDict()
+ for i, cnarr in enumerate(cnarrs):
+ if r_chrom:
+ subcna = cnarr.in_range(r_chrom, r_start, r_end, mode="trim")
+ sample_data[i][r_chrom] = cna2df(subcna)
+ chrom_sizes[r_chrom] = max(subcna.end.iat[-1] if subcna else 0,
+ chrom_sizes.get(r_chrom, 0))
+ else:
+ for chrom, subcna in cnarr.by_chromosome():
+ sample_data[i][chrom] = cna2df(subcna)
+ chrom_sizes[chrom] = max(subcna.end.iat[-1] if subcna else 0,
+ chrom_sizes.get(r_chrom, 0))
+
+ # Closes over axis
+ def plot_sample_chrom(i, sample):
+ """Draw the given coordinates and colors as a horizontal series."""
+ xranges = [(start, end - start)
+ for start, end in zip(sample.start, sample.end)]
+ bars = BrokenBarHCollection(xranges, (i, i+1),
+ edgecolors="none",
+ facecolors=sample["color"])
+ axis.add_collection(bars)
+
+ if show_range:
+ # Lay out only the selected chromosome
+ # Set x-axis the chromosomal positions (in Mb), title as the selection
+ axis.set_xlim((r_start or 0) * plots.MB,
+ (r_end or chrom_sizes[r_chrom]) * plots.MB)
+ axis.set_title(show_range)
+ axis.set_xlabel("Position (Mb)")
+ axis.tick_params(which='both', direction='out')
+ axis.get_xaxis().tick_bottom()
+ axis.get_yaxis().tick_left()
+ # Plot the individual probe/segment coverages
+ for i, sample in enumerate(sample_data):
+ crow = sample[r_chrom]
+ crow["start"] *= plots.MB
+ crow["end"] *= plots.MB
+ plot_sample_chrom(i, crow)
+
+ else:
+ # Lay out chromosome dividers and x-axis labels
+ # (Just enough padding to avoid overlap with the divider line)
+ chrom_offsets = plots.plot_x_dividers(axis, chrom_sizes, 1)
+ # Plot the individual probe/segment coverages
+ for i, sample in enumerate(sample_data):
+ for chrom, curr_offset in chrom_offsets.items():
+ crow = sample[chrom]
+ if len(crow):
+ crow["start"] += curr_offset
+ crow["end"] += curr_offset
+ plot_sample_chrom(i, crow)
+
+ return axis
+
+
+def set_colorbar(axis):
+ # Create our colormap
+ # ENH: refactor to use colormap to colorize the BrokenBarHCollection
+ # - maybe also refactor plots.cvg2rgb
+ cmap = mpl.colors.LinearSegmentedColormap.from_list('cnvheat',
+ [(0, 0, .75),
+ (1, 1, 1),
+ (.75, 0, 0)])
+ # Add a colorbar
+ norm = mpl.colors.Normalize(-1.33, 1.33)
+ mappable = mpl.cm.ScalarMappable(norm=norm, cmap=cmap)
+ mappable.set_array(np.linspace(-1.33, 1.33, 30))
+ cbar = plt.colorbar(mappable, ax=axis, orientation='vertical',
+ fraction=0.04, pad=0.03, shrink=0.6,
+ # label="log2",
+ ticks=(-1, 0, 1))
+ cbar.set_label("log2", labelpad=0)
diff --git a/cnvlib/importers.py b/cnvlib/importers.py
index 5b46ffc..8fa2732 100644
--- a/cnvlib/importers.py
+++ b/cnvlib/importers.py
@@ -1,79 +1,30 @@
"""Import from other formats to the CNVkit format."""
from __future__ import absolute_import, division, print_function
+from builtins import map, next, zip
import logging
-import math
-import os.path
-import subprocess
import numpy as np
-import pandas as pd
+from skgenome import tabio
-from . import core, params
-from .cnary import CopyNumArray as CNA
+from . import params
# __________________________________________________________________________
# import-picard
-TOO_MANY_NO_COVERAGE = 100
-
-def find_picard_files(file_and_dir_names):
- """Search the given paths for 'targetcoverage' CSV files.
-
- Per the convention we use in our Picard applets, the target coverage file
- names end with '.targetcoverage.csv'; anti-target coverages end with
- '.antitargetcoverage.csv'.
- """
- filenames = []
- for tgt in file_and_dir_names:
- if os.path.isdir(tgt):
- # Collect the target coverage files from this directory tree
- fnames = subprocess.check_output(['find', tgt,
- '-name', '*targetcoverage.csv']
- ).splitlines()
- if not fnames:
- raise RuntimeError("Given directory %s does not contain any "
- "'*targetcoverage.csv' files."
- % tgt)
- filenames.extend(fnames)
- elif os.path.isfile(tgt):
- filenames.append(tgt)
- else:
- raise ValueError("Given path is neither a file nor a directory: %s"
- % tgt)
- filenames.sort()
- return filenames
-
-
-def import_picard_pertargetcoverage(fname):
- """Parse a Picard CalculateHsMetrics PER_TARGET_COVERAGE file.
-
- Return a CopyNumArray.
-
- Input column names:
- chrom (str),
- start, end, length (int),
- name (str),
- %gc, mean_coverage, normalized_coverage (float)
- """
- dframe = pd.read_table(fname, na_filter=False)
- coverages = np.asarray(dframe['mean_coverage'])
+def do_import_picard(fname, too_many_no_coverage=100):
+ garr = tabio.read(fname, "picardhs")
+ garr["gene"] = garr["gene"].apply(unpipe_name)
+ # Create log2 column from coverages, avoiding math domain error
+ coverages = garr["ratio"].copy()
no_cvg_idx = (coverages == 0)
- if sum(no_cvg_idx) > TOO_MANY_NO_COVERAGE:
+ if no_cvg_idx.sum() > too_many_no_coverage:
logging.warn("*WARNING* Sample %s has >%d bins with no coverage",
- fname, TOO_MANY_NO_COVERAGE)
- # Avoid math domain error
+ garr.sample_id, too_many_no_coverage)
coverages[no_cvg_idx] = 2**params.NULL_LOG2_COVERAGE
- cnarr = CNA.from_columns({"chromosome": dframe["chrom"],
- "start": dframe["start"] - 1,
- "end": dframe["end"],
- "gene": dframe["name"].apply(unpipe_name),
- "gc": dframe["%gc"],
- "log2": np.log2(coverages)},
- {"sample_id": core.fbase(fname)})
- cnarr.sort()
- return cnarr
+ garr["log2"] = np.log2(coverages)
+ return garr
def unpipe_name(name):
@@ -105,60 +56,26 @@ def unpipe_name(name):
# __________________________________________________________________________
-# import-seg
-
-LOG2_10 = math.log(10, 2) # To convert log10 values to log2
-
-def import_seg(segfname, chrom_names, chrom_prefix, from_log10):
- """Parse a SEG file as an iterable of CopyNumArray instances.
-
- `chrom_names`:
- Map (string) chromosome IDs to names. (Applied before chrom_prefix.)
- e.g. {'23': 'X', '24': 'Y', '25': 'M'}
-
- `chrom_prefix`: prepend this string to chromosome names
- (usually 'chr' or None)
-
- `from_log10`: Convert values from log10 to log2.
- """
- dframe = pd.read_table(segfname, na_filter=False)
- if len(dframe.columns) == 6:
- dframe.columns = ['sample_id', 'chromosome', 'start', 'end', 'nprobes',
- 'mean']
- elif len(dframe.columns) == 5:
- dframe.columns = ['sample_id', 'chromosome', 'start', 'end', 'mean']
- else:
- raise ValueError("SEG format expects 5 or 6 columns; found {}: {}"
- .format(len(dframe.columns), ' '.join(dframe.columns)))
-
- # Calculate values for output columns
- dframe['chromosome'] = dframe['chromosome'].apply(str)
- if chrom_names:
- dframe['chromosome'] = dframe['chromosome'].apply(lambda c:
- chrom_names.get(c, c))
- if chrom_prefix:
- dframe['chromosome'] = dframe['chromosome'].apply(lambda c:
- chrom_prefix + c)
- if from_log10:
- dframe['mean'] *= LOG2_10
- dframe['gene'] = ["G" if mean >= 0 else "L" for mean in dframe['mean']]
-
- for sid in pd.unique(dframe['sample_id']):
- sample = dframe[dframe['sample_id'] == sid]
- cols = {'chromosome': sample['chromosome'],
- 'start': sample['start'],
- 'end': sample['end'],
- 'gene': sample['gene'],
- 'log2': sample['mean']}
- if 'nprobes' in dframe:
- cols['probes'] = sample['nprobes']
- cns = CNA.from_columns(cols, {'sample_id': sid})
- cns.sort()
- yield cns
+# import-theta
+def do_import_theta(segarr, theta_results_fname, ploidy=2):
+ theta = parse_theta_results(theta_results_fname)
+ # THetA doesn't handle sex chromosomes well
+ segarr = segarr.autosomes()
+ for copies in theta['C']:
+ if len(copies) != len(segarr):
+ copies = copies[:len(segarr)]
+ # Drop any segments where the C value is None
+ mask_drop = np.array([c is None for c in copies], dtype='bool')
+ segarr = segarr[~mask_drop].copy()
+ ok_copies = np.asfarray([c for c in copies if c is not None])
+ # Replace remaining segment values with these integers
+ segarr["cn"] = ok_copies.astype('int')
+ ok_copies[ok_copies == 0] = 0.5
+ segarr["log2"] = np.log2(ok_copies / ploidy)
+ segarr.sort_columns()
+ yield segarr
-# __________________________________________________________________________
-# import-theta
def parse_theta_results(fname):
"""Parse THetA results into a data structure.
@@ -176,7 +93,7 @@ def parse_theta_results(fname):
# mu
mu = body[1].split(',')
mu_normal = float(mu[0])
- mu_tumors = map(float, mu[1:])
+ mu_tumors = list(map(float, mu[1:]))
# C
copies = body[2].split(':')
diff --git a/cnvlib/jenks.py b/cnvlib/jenks.py
index b91591f..b9f732b 100644
--- a/cnvlib/jenks.py
+++ b/cnvlib/jenks.py
@@ -9,6 +9,7 @@ See:
- https://www.macwright.org/simple-statistics/docs/simple_statistics.html
"""
from __future__ import division, print_function
+from builtins import range
import numpy as np
@@ -62,7 +63,7 @@ def jenks_matrices(data, n_classes):
# 0 i i i
# 0 i i i
- for l in xrange(2, n_rows):
+ for l in range(2, n_rows):
# Estimate variance for each potential classing of the data, for
# each potential number of classes.
# ENH: lift these out of the loop & apply more array magic
@@ -74,13 +75,13 @@ def jenks_matrices(data, n_classes):
# Record the last variance in column 1
variance_combinations[l][1] = variances[l-1]
- for m in xrange(1, l):
+ for m in range(1, l):
# For each column from index 1 to just before the diagonal
# Or, for each element up to the current l marker again
lower_class_limit = l - m + 1 # >=2, <=l
iv = lower_class_limit - 1 # >=1, <l
variance = variances[m-1]
- for j in xrange(2, n_cols):
+ for j in range(2, n_cols):
# If adding this element to an existing class will increase
# its variance beyond the limit, break the class at this
# point, setting the `lower_class_limit` at this point.
@@ -107,7 +108,7 @@ def jenks_breaks(data, lower_class_limits, n_classes):
breakpoints[n_classes] = data[-1] # Upper bound
# Use the lower_class_limits matrix as indices into itself, iteratively
lower_limit_idx = len(data)
- for j in xrange(n_classes, 0, -1):
+ for j in range(n_classes, 0, -1):
lower_limit_idx = lower_class_limits[lower_limit_idx, j] - 1
breakpoints[j - 1] = data[lower_limit_idx]
return breakpoints
diff --git a/cnvlib/metrics.py b/cnvlib/metrics.py
index 76b790f..019a256 100644
--- a/cnvlib/metrics.py
+++ b/cnvlib/metrics.py
@@ -1,17 +1,56 @@
-"""Robust estimators of central tendency and scale.
-
-For use in evaluating performance of copy number estimation.
-
-See:
- https://en.wikipedia.org/wiki/Robust_measures_of_scale
- https://astropy.readthedocs.org/en/latest/_modules/astropy/stats/funcs.html
-
+"""Robust metrics to evaluate performance of copy number estimates.
"""
-from __future__ import division
+from __future__ import absolute_import, division, print_function
+from builtins import zip
+
+import logging
import numpy as np
+import pandas as pd
from scipy import stats
+from .descriptives import (biweight_midvariance, interquartile_range,
+ median_absolute_deviation)
+
+
+def do_metrics(cnarrs, segments=None, skip_low=False):
+ """Compute coverage deviations and other metrics for self-evaluation."""
+ # Catch if passed args are single CopyNumArrays instead of lists
+ from .cnary import CopyNumArray as CNA
+ if isinstance(cnarrs, CNA):
+ cnarrs = [cnarrs]
+ if isinstance(segments, CNA):
+ segments = [segments]
+ elif segments is None:
+ segments = [None]
+ else:
+ segments = list(segments)
+ if skip_low:
+ cnarrs = (cna.drop_low_coverage() for cna in cnarrs)
+ rows = ((cna.meta.get("filename", cna.sample_id),
+ len(seg) if seg is not None else '-'
+ ) + ests_of_scale(cna.residuals(seg))
+ for cna, seg in zip_repeater(cnarrs, segments))
+ colnames = ["sample", "segments", "stdev", "mad", "iqr", "bivar"]
+ return pd.DataFrame.from_records(rows, columns=colnames)
+
+
+def zip_repeater(iterable, repeatable):
+ """Repeat a single segmentation to match the number of copy ratio inputs"""
+ rpt_len = len(repeatable)
+ if rpt_len == 1:
+ rpt = repeatable[0]
+ for it in iterable:
+ yield it, rpt
+ else:
+ i = -1
+ for i, (it, rpt) in enumerate(zip(iterable, repeatable)):
+ yield it, rpt
+ # Require lengths to match
+ if i + 1 != rpt_len:
+ raise ValueError("""Number of unsegmented and segmented input files
+ did not match (%d vs. %d)""" % (i, rpt_len))
+
def ests_of_scale(deviations):
"""Estimators of scale: standard deviation, MAD, biweight midvariance.
@@ -26,169 +65,102 @@ def ests_of_scale(deviations):
return (std, mad, iqr, biw)
-# M-estimators of central location
-
-def biweight_location(a, initial=None, c=6.0, epsilon=1e-4):
- """Compute the biweight location for an array.
-
- The biweight is a robust statistic for determining the central location of a
- distribution.
- """
- a = np.asarray(a)
- if initial is None:
- initial = np.median(a)
- # Weight the observations by distance from initial estimate
- d = a - initial
- w = d / max(c * median_absolute_deviation(a), epsilon)
- w = (1 - w**2)**2
- # Omit the outlier points
- mask = (w < 1)
- weightsum = w[mask].sum()
- if weightsum == 0:
- # Insufficient variation to improve the initial estimate
- return initial
- return initial + (d[mask] * w[mask]).sum() / weightsum
-
-
-def modal_location(arr):
- """Return the modal value of an array's values.
-
- The "mode" is the location of peak density among the values, estimated using
- a Gaussian kernel density estimator.
-
- `arr` is a 1-D array of floating-point values, e.g. bin log2 ratio values.
- """
- sarr = np.sort(arr)
- kde = stats.gaussian_kde(sarr)
- y = kde.evaluate(sarr)
- peak = sarr[y.argmax()]
- return peak
-
-
def segment_mean(cnarr, skip_low=False):
"""Weighted average of bin log2 values."""
if skip_low:
cnarr = cnarr.drop_low_coverage()
if len(cnarr) == 0:
- return None
+ return np.nan
if 'weight' in cnarr:
return np.average(cnarr['log2'], weights=cnarr['weight'])
return cnarr['log2'].mean()
-# Estimators of scale
-
-def biweight_midvariance(a, initial=None, c=9.0, epsilon=1e-4):
- """Compute the biweight midvariance for an array.
-
- The biweight midvariance is a robust statistic for determining the
- midvariance (i.e. the standard deviation) of a distribution.
-
- See:
- https://en.wikipedia.org/wiki/Robust_measures_of_scale#The_biweight_midvariance
- https://astropy.readthedocs.org/en/latest/_modules/astropy/stats/funcs.html
- """
- a = np.asarray(a)
- if initial is None:
- initial = np.median(a)
- # Difference of observations from initial estimate
- d = a - initial
- # Weighting (avoid dividing by zero)
- w = d / max(c * median_absolute_deviation(a), epsilon)
- w = w**2
- # Omit the outlier points
- mask = np.abs(w) < 1
- n = mask.sum()
- return (n**0.5 * (d[mask] * d[mask] * (1 - w[mask])**4).sum()**0.5
- / np.abs(((1 - w[mask]) * (1 - 5 * w[mask])).sum()))
-
-
-def interquartile_range(a):
- """Compute the difference between the array's first and third quartiles."""
- a = np.asarray(a)
- return np.percentile(a, 75) - np.percentile(a, 25)
-
-
-def median_absolute_deviation(a, scale_to_sd=True):
- """Compute the median absolute deviation (MAD) of array elements.
-
- The MAD is defined as: ``median(abs(a - median(a)))``.
-
- See: https://en.wikipedia.org/wiki/Median_absolute_deviation
- """
- a = np.asarray(a)
- a_median = np.median(a)
- mad = np.median(np.abs(a - a_median))
- if scale_to_sd:
- mad *= 1.4826
- return mad
-
-
-def q_n(a):
- """Rousseeuw & Croux's (1993) Q_n, an alternative to MAD.
-
- ``Qn := Cn first quartile of (|x_i - x_j|: i < j)``
-
- where Cn is a constant depending on n.
-
- Finite-sample correction factors must be used to calibrate the
- scale of Qn for small-to-medium-sized samples.
-
- n E[Qn]
- -- -----
- 10 1.392
- 20 1.193
- 40 1.093
- 60 1.064
- 80 1.048
- 100 1.038
- 200 1.019
-
- """
- a = np.asarray(a)
-
- # First quartile of: (|x_i - x_j|: i < j)
- vals = []
- for i, x_i in enumerate(a):
- for x_j in a[i+1:]:
- vals.append(abs(x_i - x_j))
- quartile = np.percentile(vals, 25)
-
- # Cn: a scaling factor determined by sample size
- n = len(a)
- if n <= 10:
- # ENH: warn when extrapolating beyond the data
- # ENH: simulate for values up to 10
- # (unless the equation below is reliable)
- scale = 1.392
- elif 10 < n < 400:
- # I fitted the simulated values (above) to a power function in Excel:
- # f(x) = 1.0 + 3.9559 * x ^ -1.0086
- # This should be OK for interpolation. (Does it apply generally?)
- scale = 1.0 + (4 / n)
- else:
- scale = 1.0
-
- return quartile / scale
-
-
# Intervals
-def confidence_interval_bootstrap(bins, alpha, bootstraps=100):
+def confidence_interval_bootstrap(bins, alpha, bootstraps=100, smoothed=True):
"""Confidence interval for segment mean log2 value, estimated by bootstrap."""
+ if not 0 < alpha < 1:
+ raise ValueError("alpha must be between 0 and 1; got %s" % alpha)
+ if bootstraps <= 2 / alpha:
+ new_boots = int(np.ceil(2 / alpha))
+ logging.warn("%d bootstraps not enough to estimate CI alpha level %f; "
+ "increasing to %d", bootstraps, alpha, new_boots)
+ bootstraps = new_boots
# Bootstrap for CI
k = len(bins)
- rand_indices = np.random.random_integers(0, k - 1, (bootstraps, k))
- bootstraps = [bins.data.take(idx) for idx in rand_indices]
+ if k < 2:
+ return np.array([bins["log2"][0], bins["log2"][0]])
+
+ np.random.seed(0xA5EED)
+ rand_indices = np.random.randint(0, k, (bootstraps, k))
+ samples = [bins.data.take(idx) for idx in rand_indices]
+ if smoothed:
+ # samples = _smooth_samples(bins, samples, alpha)
+ pass
# Recalculate segment means
- if 'weight' in bins:
- bootstrap_dist = [np.average(boot['log2'], weights=boot['weight'])
- for boot in bootstraps]
+ bootstrap_dist = np.array([segment_mean(samp) for samp in samples])
+ alphas = np.array([alpha / 2, 1 - alpha / 2])
+ if not smoothed:
+ # alphas = _bca_correct_alpha(bins, bootstrap_dist, alphas)
+ pass
+ ci = np.percentile(bootstrap_dist, list(100 * alphas))
+ return ci
+
+
+def _smooth_samples(bins, samples, alpha):
+ k = len(bins)
+ # Essentially, resample from a kernel density estimate of the data
+ # instead of the original data.
+ # Estimate KDE bandwidth (Polansky 1995)
+ resids = bins['log2'] - bins['log2'].mean()
+ s_hat = 1/k * (resids**2).sum() # sigma^2 = E[X-theta]^2
+ y_hat = 1/k * abs((resids**3).sum()) # gamma = E[X-theta]^3
+ z = stats.norm.ppf(alpha / 2) # or alpha?
+ bw = k**(-1/4) * np.sqrt(y_hat*(z**2 + 2) / (3*s_hat*z))
+ # NB: or, Silverman's Rule for KDE bandwidth (roughly):
+ # std = interquartile_range(bins['log2']) / 1.34
+ # bw = std * (k*3/4) ** (-1/5)
+ if bw > 0:
+ samples = [samp.assign(log2=lambda x:
+ x['log2'] + bw * np.random.randn(k))
+ for samp in samples]
+ logging.debug("Smoothing worked for this segment (bw=%s)", bw)
else:
- bootstrap_dist = [boot['log2'].mean() for boot in bootstraps]
- pct_lo = 100 * alpha / 2
- pct_hi = 100 * (1 - alpha / 2)
- return np.percentile(bootstrap_dist, [pct_lo, pct_hi])
+ logging.debug("Smoothing not needed for this segment (bw=%s)", bw)
+ return samples
+
+
+def _bca_correct_alpha(bins, bootstrap_dist, alphas):
+ # BCa correction (Efron 1987, "Better Bootstrap Confidence Intervals")
+ # http://www.tandfonline.com/doi/abs/10.1080/01621459.1987.10478410
+ # Ported from R package "bootstrap" function "bcanon"
+ n_boots = len(bootstrap_dist)
+ orig_mean = segment_mean(bins)
+ logging.warn("boot samples less: %s / %s",
+ (bootstrap_dist < orig_mean).sum(),
+ n_boots)
+ n_boots_below = (bootstrap_dist < orig_mean).sum()
+ if n_boots_below == 0:
+ logging.warn("boots mean %s, orig mean %s",
+ bootstrap_dist.mean(), orig_mean)
+ else:
+ logging.warn("boot samples less: %s / %s",
+ n_boots_below, n_boots)
+ z0 = stats.norm.ppf((bootstrap_dist < orig_mean).sum() / n_boots)
+ zalpha = stats.norm.ppf(alphas)
+ # Jackknife influence values
+ u = np.array([segment_mean(bins.concat([bins[:i], bins[i+1:]]))
+ for i in range(len(bins))])
+ uu = u.mean() - u
+ acc = (u**3).sum() / (6 * (uu**2).sum()**1.5)
+ alphas = stats.norm.cdf(z0 + (z0 + zalpha)
+ / (1 - acc * (z0 + zalpha)))
+ logging.warn("New alphas: %s -- via z0=%s, za=%s, acc=%s",
+ alphas, z0, zalpha, acc)
+ if not 0 < alphas[0] < 1 and 0 < alphas[1] < 1:
+ raise ValueError("CI alphas should be in (0,1); got %s" % alphas)
+ return alphas
def prediction_interval(bins, alpha):
@@ -197,4 +169,3 @@ def prediction_interval(bins, alpha):
pct_hi = 100 * (1 - alpha / 2)
# ENH: weighted percentile
return np.percentile(bins['log2'], [pct_lo, pct_hi])
-
diff --git a/cnvlib/ngfrills/__init__.py b/cnvlib/ngfrills/__init__.py
deleted file mode 100644
index e65d089..0000000
--- a/cnvlib/ngfrills/__init__.py
+++ /dev/null
@@ -1,113 +0,0 @@
-"""NGS utilities."""
-from __future__ import absolute_import, division, print_function
-
-import contextlib
-import logging
-import os
-import subprocess
-import sys
-import tempfile
-
-from Bio._py3k import basestring, map
-
-from .faidx import *
-from .regions import *
-from .samutil import *
-from .shared import *
-
-
-# __________________________________________________________
-# Shell
-
-def call_quiet(*args):
- """Safely run a command and get stdout; print stderr if there's an error.
-
- Like subprocess.check_output, but silent in the normal case where the
- command logs unimportant stuff to stderr. If there is an error, then the
- full error message(s) is shown in the exception message.
- """
- # args = map(str, args)
- if not len(args):
- raise ValueError("Must supply at least one argument (the command name)")
- try:
- proc = subprocess.Popen(args, stdout=subprocess.PIPE,
- stderr=subprocess.PIPE)
- except OSError as exc:
- raise RuntimeError("Could not find the executable %r" % args[0]
- + " -- is it installed correctly?"
- + "\n(Original error: %s)" % exc)
- out, err = proc.communicate()
- if proc.returncode != 0:
- raise RuntimeError("Subprocess command failed:\n$ %s\n\n%s"
- % (' '.join(args), err))
- return out
-
-
-def ensure_path(fname):
- """Create dirs and move an existing file to avoid overwriting, if necessary.
-
- If a file already exists at the given path, it is renamed with an integer
- suffix to clear the way.
- """
- if '/' in os.path.normpath(fname):
- # Ensure the output directory exists
- dname = os.path.dirname(os.path.abspath(fname))
- if dname and not os.path.isdir(dname):
- try:
- os.makedirs(dname)
- except OSError as exc:
- raise OSError("Output path " + fname +
- " contains a directory " + dname +
- " that cannot be created: " + str(exc))
- if os.path.isfile(fname):
- # Add an integer suffix to the existing file name
- cnt = 1
- bak_fname = "%s.%d" % (fname, cnt)
- while os.path.isfile(bak_fname):
- cnt += 1
- bak_fname = "%s.%d" % (fname, cnt)
- os.rename(fname, bak_fname)
- logging.info("Moved existing file %s -> %s", fname, bak_fname)
- return True
-
-
- at contextlib.contextmanager
-def safe_write(outfile, verbose=True):
- """Write to a filename or file-like object with error handling.
-
- If given a file name, open it. If the path includes directories that don't
- exist yet, create them. If given a file-like object, just pass it through.
- """
- if isinstance(outfile, basestring):
- dirname = os.path.dirname(outfile)
- if dirname and not os.path.isdir(dirname):
- os.mkdir(dirname)
- logging.info("Created directory %s", dirname)
- with open(outfile, 'w') as handle:
- yield handle
- else:
- yield outfile
-
- # Log the output path, if possible
- if verbose:
- if isinstance(outfile, basestring):
- outfname = outfile
- elif hasattr(outfile, 'name') and outfile not in (sys.stdout,
- sys.stderr):
- outfname = outfile.name
- else:
- # Probably stdout or stderr -- don't ruin the pipeline
- return
- logging.info("Wrote %s", outfname)
-
-
- at contextlib.contextmanager
-def temp_write_text(text):
- """Save text to a temporary file.
-
- NB: This won't work on Windows b/c the file stays open.
- """
- with tempfile.NamedTemporaryFile() as tmp:
- tmp.write(text)
- tmp.flush()
- yield tmp.name
diff --git a/cnvlib/ngfrills/faidx.py b/cnvlib/ngfrills/faidx.py
deleted file mode 100644
index e2109a2..0000000
--- a/cnvlib/ngfrills/faidx.py
+++ /dev/null
@@ -1,34 +0,0 @@
-"""NGS utilities: Indexed FASTA I/O."""
-from __future__ import absolute_import, division, print_function
-
-import logging
-from itertools import groupby
-from pyfaidx import Fasta
-
-
-def fasta_extract_regions(fa_fname, intervals):
- """Extract an iterable of regions from an indexed FASTA file.
-
- Input: FASTA file name; iterable of (seq_id, start, end) (1-based)
- Output: iterable of string sequences.
- """
- with Fasta(fa_fname, as_raw=True) as fa_file:
- for chrom, rows in groupby(intervals, lambda cse: cse[0]):
- logging.info("Extracting sequences from chromosome %s", chrom)
- for _chrom, start, end in rows:
- yield fa_file[_chrom][start:end]
-
-
-def _fasta_extract_regions_safe(fa_fname, intervals):
- """Simpler, slower version of fasta_extract_regions, for testing it."""
- from Bio import SeqIO
- idx = SeqIO.index(fa_fname, 'fasta')
- for chrom, rows in groupby(intervals, lambda cse: cse[0]):
- logging.info("Extracting sequences from chromosome %s", chrom)
- seq = str(idx[chrom].seq)
- for chrom, start, end in rows:
- subseq = seq[start:end]
- if len(subseq) != end - start:
- logging.info("Short subsequence %s:%d-%d; read %d, wanted %d",
- chrom, start, end, len(subseq), end - start)
- yield subseq
diff --git a/cnvlib/ngfrills/regions.py b/cnvlib/ngfrills/regions.py
deleted file mode 100644
index 9d6b4ba..0000000
--- a/cnvlib/ngfrills/regions.py
+++ /dev/null
@@ -1,248 +0,0 @@
-"""NGS utilities: BED/Interval I/O, genomic regions and ranges."""
-from __future__ import absolute_import, division, print_function
-
-import functools
-import logging
-import re
-import shlex
-
-from Bio.File import as_handle
-
-
-def sniff_num_columns(bed_fname):
- """Detect the number of columns in a BED/interval file.
-
- Guidance:
- 3 cols => coordinates only;
- 5 cols => intervals file (coordinates, strand, name);
- otherwise => Full or extended BED format
- """
- for firstrow in parse_regions(bed_fname):
- return len(firstrow)
-
-
-def sniff_region_format(fname):
- """Guess whether the file format is BED, Picard interval list, or text.
-
- Returns a tuple of the format name (str) or None if the file is empty.
- """
- with open(fname, 'rU') as handle:
- for line in handle:
- if not line.strip():
- continue
- if '\t' not in line and ':' in line and '-' in line:
- return 'text'
- if line.startswith('@') or re.match('\w+\t\d+\t\d+\t(\+|-|\.)\t\S+',
- line):
- return 'interval'
- if line.startswith('track') or line.count('\t') > 1:
- return 'bed'
- raise ValueError("File " + repr(fname) + " does not appear to "
- + "be BED, interval list, or 'chr:start-end' "
- + "text!\nFirst non-blank line: " + repr(line))
-
-
-def parse_regions(fname, coord_only=False, keep_strand=False):
- """Parse regions in any of the expected file formats.
-
- Iterates over tuples of the tabular contents. Header lines are skipped.
-
- Start and end coordinates are base-0, half-open.
-
- If coord_only, yield triplets of (chrom, start, end). Otherwise, yield
- quads of (chrom, start, end, name).
- """
- fmt = sniff_region_format(fname)
- if fmt is None:
- return []
- if fmt == 'bed':
- logging.info("Detected file format: BED")
- elif fmt == 'interval':
- logging.info("Detected file format: interval list")
- parser = {'text': parse_text_coords,
- 'interval': parse_interval_list,
- 'bed': parse_bed,
- }[fmt]
- return parser(fname, coord_only, keep_strand)
-
-
-def report_bad_line(line_parser):
- @functools.wraps(line_parser)
- def wrapper(line):
- try:
- return line_parser(line)
- except ValueError:
- raise ValueError("Bad line: %r" % line)
- return wrapper
-
-
-def parse_text_coords(fname, coord_only, _keep_strand):
- """Parse text coordinates: chrom:start-end
-
- Text coordinates are assumed to be counting from 1.
- """
- if coord_only:
- @report_bad_line
- def _parse_line(line):
- chrom, _rest = line.rstrip().split(':', 1)
- start, end = _rest.split('-')
- if ':' in end:
- end = end.split(':', 1)[0]
- return chrom, int(start) - 1, int(end)
- else:
- @report_bad_line
- def _parse_line(line):
- fields = line.split(':')
- if len(fields) == 3:
- chrom, start_end, name = fields
- elif len(fields) == 2:
- chrom, start_end = fields
- name = '-'
- else:
- raise ValueError
- start, end = start_end.split('-')
- return chrom, int(start) - 1, int(end), name.rstrip()
-
- with as_handle(fname, 'rU') as handle:
- for line in handle:
- yield _parse_line(line)
-
-
-def parse_interval_list(fname, coord_only, keep_strand):
- """Parse a Picard-compatible interval list.
-
- Expected tabular columns:
- chromosome, start position, end position, strand, region name
-
- Counting is from 1.
- """
- if coord_only:
- if keep_strand:
- @report_bad_line
- def _parse_line(line):
- chrom, start, end, strand = line.split('\t')[:4]
- return chrom, int(start) - 1, int(end), strand.rstrip()
- else:
- @report_bad_line
- def _parse_line(line):
- chrom, start, end = line.split('\t')[:3]
- return chrom, int(start) - 1, int(end)
- elif keep_strand:
- @report_bad_line
- def _parse_line(line):
- fields = line.split('\t')
- chrom, start, end, strand = fields[:4]
- if len(fields) > 4:
- name = fields[-1].rstrip()
- else:
- name = '-'
- return chrom, int(start) - 1, int(end), name, strand
- else:
- @report_bad_line
- def _parse_line(line):
- fields = line.split('\t')
- chrom, start, end = fields[:3]
- if len(fields) > 3:
- name = fields[-1].rstrip()
- else:
- name = '-'
- return chrom, int(start) - 1, int(end), name
-
- with as_handle(fname, 'rU') as handle:
- for line in handle:
- if line.startswith('@'):
- # Skip the SAM header
- continue
- yield _parse_line(line)
-
-
-def parse_bed(fname, coord_only, keep_strand):
- """Parse a BED file.
-
- A BED file has these columns:
- chromosome, start position, end position, [name, strand, other stuff...]
-
- Counting is from 0.
-
- Sets of regions are separated by "track" lines. This function stops
- iteration after encountering a track line other than the first one in the
- file.
- """
- if coord_only:
- if keep_strand:
- @report_bad_line
- def _parse_line(line):
- chrom, start, end, _name, _score, strand = line.split('\t', 6)[:6]
- return chrom, int(start), int(end), strand.rstrip()
- else:
- @report_bad_line
- def _parse_line(line):
- chrom, start, end = line.split('\t', 3)[:3]
- return chrom, int(start), int(end)
- elif keep_strand:
- @report_bad_line
- def _parse_line(line):
- fields = line.split('\t', 6)
- chrom, start, end = fields[:3]
- name = (fields[3].rstrip()
- if len(fields) >= 4 else '-')
- strand = (fields[5].rstrip()
- if len(fields) >= 6 else '.')
- return chrom, int(start), int(end), name, strand
- else:
- @report_bad_line
- def _parse_line(line):
- fields = line.split('\t', 4)
- chrom, start, end = fields[:3]
- name = (fields[3].rstrip()
- if len(fields) >= 4 else '-')
- return chrom, int(start), int(end), name
-
- with as_handle(fname, 'rU') as handle:
- firstline = next(handle)
- if firstline.startswith("track"):
- pass
- else:
- yield _parse_line(firstline)
-
- for line in handle:
- if line.startswith('track'):
- raise StopIteration
- yield _parse_line(line)
-
-
-def parse_bed_track(line):
- """Parse the "name" field of a BED track definition line.
-
- Example:
- track name=146793_BastianLabv2_P2_target_region description="146793_BastianLabv2_P2_target_region"
- """
- fields = shlex.split(line) # raises ValueError if line is corrupted
- assert fields[0] == 'track'
- for field in fields[1:]:
- if '=' in field:
- key, val = field.split('=', 1)
- if key == 'name':
- return val
- raise ValueError("No name defined for this track")
-
-
-def group_bed_tracks(bedfile):
- """Group the parsed rows in a BED file by track.
-
- Yields (track_name, iterable_of_lines), much like itertools.groupby.
- """
- # ENH - make this memory-efficient w/ generators or something
- with as_handle(bedfile, 'r') as handle:
- curr_track = 'DEFAULT'
- curr_lines = []
- for line in handle:
- if line.startswith('track'):
- if curr_lines:
- yield curr_track, curr_lines
- curr_lines = []
- curr_track = parse_bed_track(line)
- else:
- curr_lines.append(line)
- yield curr_track, curr_lines
-
diff --git a/cnvlib/ngfrills/shared.py b/cnvlib/ngfrills/shared.py
deleted file mode 100644
index bfde4bb..0000000
--- a/cnvlib/ngfrills/shared.py
+++ /dev/null
@@ -1,10 +0,0 @@
-"""NGS utilities."""
-from __future__ import absolute_import, division, print_function
-
-import os
-
-
-def is_newer_than(target_fname, orig_fname):
- if not os.path.isfile(target_fname):
- return False
- return (os.stat(target_fname).st_mtime >= os.stat(orig_fname).st_mtime)
diff --git a/cnvlib/parallel.py b/cnvlib/parallel.py
index 7a555d0..9f22a21 100644
--- a/cnvlib/parallel.py
+++ b/cnvlib/parallel.py
@@ -1,26 +1,85 @@
"""Utilities for multi-core parallel processing."""
from __future__ import absolute_import, division, print_function
-import multiprocessing
+from builtins import object
+
+import atexit
+import tempfile
+import gzip
+import os
+from contextlib import contextmanager
+from concurrent import futures
+# from concurrent.futures import wait
class SerialPool(object):
- """Mimic the multiprocessing.Pool interface, but run in serial."""
+ """Mimic the concurrent.futures.Executor interface, but run in serial."""
def __init__(self):
pass
- def apply_async(self, func, args):
- """Just call the function."""
- func(*args)
+ def submit(self, func, *args):
+ """Just call the function on the arguments."""
+ return SerialFuture(func(*args))
+
+ def map(self, func, iterable):
+ """Just apply the function to `iterable`."""
+ return map(func, iterable)
+
+ def shutdown(self, wait=True):
+ """Do nothing."""
+ pass
+
+
+
+class SerialFuture(object):
+ """Mimic the concurrent.futures.Future interface."""
+
+ def __init__(self, result):
+ self._result = result
- # No-ops to mimic multiprocessing.Pool
- def close(self): pass
- def join(self): pass
+ def result(self):
+ return self._result
+
+ at contextmanager
def pick_pool(nprocs):
if nprocs == 1:
- return SerialPool()
+ yield SerialPool()
+ raise StopIteration
+
if nprocs < 1:
- nprocs = multiprocessing.cpu_count()
- return multiprocessing.Pool(nprocs)
+ nprocs = None
+ with futures.ProcessPoolExecutor(max_workers=nprocs) as pool:
+ yield pool
+
+
+def rm(path):
+ """Safely remove a file."""
+ try:
+ os.unlink(path)
+ except OSError:
+ pass
+
+
+def to_chunks(bed_fname, chunk_size=5000):
+ """Split the bed-file into chunks for parallelization"""
+ k, chunk = 0, 0
+ fd, name = tempfile.mkstemp(suffix=".bed", prefix="tmp.%s." % chunk)
+ fh = os.fdopen(fd, "w")
+ atexit.register(rm, name)
+ for line in (gzip.open if bed_fname.endswith(".gz") else open)(bed_fname):
+ if line[0] == "#":
+ continue
+ k += 1
+ fh.write(line)
+ if k % chunk_size == 0:
+ fh.close()
+ yield name
+ chunk += 1
+ fd, name = tempfile.mkstemp(suffix=".bed", prefix="tmp.%s." % chunk)
+ fh = os.fdopen(fd, "w")
+ fh.close()
+ if k % chunk_size:
+ fh.close()
+ yield name
diff --git a/cnvlib/params.py b/cnvlib/params.py
index 8f25aa1..00919df 100644
--- a/cnvlib/params.py
+++ b/cnvlib/params.py
@@ -1,15 +1,14 @@
"""Hard-coded parameters for CNVkit. These should not change between runs."""
-# Filters used in constructing the reference
+# Filter thresholds used in constructing the reference (log2 scale)
MIN_REF_COVERAGE = -5.0
MAX_REF_SPREAD = 1.0
NULL_LOG2_COVERAGE = -20.0
-# Sequencing read length (or average, if it varies)
-READ_LEN = 100
-
# Fragment size for paired-end reads
INSERT_SIZE = 250
# Target/bin names that are not meaningful gene names
# (In some UCSF panels, "CGH" probes denote selected intergenic regions)
IGNORE_GENE_NAMES = ("-", ".", "CGH")
+ANTITARGET_NAME = "Antitarget"
+ANTITARGET_ALIASES = (ANTITARGET_NAME, "Background")
diff --git a/cnvlib/plots.py b/cnvlib/plots.py
index 769ac7e..4fde6df 100644
--- a/cnvlib/plots.py
+++ b/cnvlib/plots.py
@@ -1,380 +1,41 @@
"""Plotting utilities."""
from __future__ import absolute_import, division
+from builtins import str
+from past.builtins import basestring
import collections
import logging
import math
-import sys
import numpy as np
-from Bio._py3k import zip
-iteritems = (dict.iteritems if sys.version_info[0] < 3 else dict.items)
+from . import core, params
-from . import core, params, smoothing
-SEG_COLOR = "darkorange"
-POINT_COLOR = '#606060'
-
-# === Chromosome-level scatter plots ===
-
-HIGHLIGHT_COLOR = 'gold'
MB = 1e-6 # To rescale from bases to megabases
-def setup_chromosome(axis, probes=None, segments=None, variants=None,
- y_min=None, y_max=None, y_label=None):
- """Configure axes for plotting a single chromosome's data.
-
- `probes`, `segments`, and `variants` should already be subsetted to the
- region that will be plotted.
- """
- min_x = np.inf
- max_x = 0
- for arr in (probes, segments, variants):
- if arr:
- max_x = max(max_x, arr.end.iat[-1])
- min_x = min(min_x, arr.start.iat[0])
- if not max_x > min_x:
- if any((probes, segments, variants)):
- logging.warn("*WARNING* selection start %s > end %s (%s); did you "
- "correctly sort the input file by genomic location?",
- min_x, max_x, max_x - min_x)
- raise ValueError("No usable data points to plot out of "
- "%d probes, %d segments, %d variants"
- % (len(probes) if probes else 0,
- len(segments) if segments else 0,
- len(variants) if variants else 0))
- axis.set_xlim(min_x * MB, max_x * MB)
- if y_min and y_max:
- axis.set_ylim(y_min, y_max)
- if y_min < 0 < y_max:
- axis.axhline(color='k')
- if y_label:
- axis.set_ylabel(y_label)
- axis.tick_params(which='both', direction='out')
- axis.get_xaxis().tick_bottom()
- axis.get_yaxis().tick_left()
-
-
-def cnv_on_chromosome(axis, probes, segments, genes, background_marker=None,
- do_trend=False, y_min=None, y_max=None):
- """Draw a scatter plot of probe values with CBS calls overlaid.
-
- Argument 'genes' is a list of tuples: (start, end, gene name)
- """
- # Get scatter plot coordinates
- x = 0.5 * (probes['start'] + probes['end']) * MB # bin midpoints
- y = probes['log2']
- if 'weight' in probes:
- w = 46 * probes['weight'] ** 2 + 2
- else:
- w = np.repeat(30, len(x))
- is_bg = (probes['gene'] == 'Background')
-
- # Configure axes
- # TODO - use segment y-values if probes not given
- if not y_min:
- y_min = max(-5.0, min(y.min() - .1, -.3)) if len(y) else -1.1
- if not y_max:
- y_max = max(.3, y.max() + (.25 if genes else .1)) if len(y) else 1.1
- setup_chromosome(axis, probes, segments, None, y_min, y_max,
- "Copy ratio (log2)")
- if genes:
- # Rotate text in proportion to gene density
- ngenes = len(genes)
- text_size = ('small' if ngenes <= 6 else 'x-small')
- if ngenes <= 3:
- text_rot = 'horizontal'
- elif ngenes <= 6:
- text_rot = 30
- elif ngenes <= 10:
- text_rot = 45
- elif ngenes <= 20:
- text_rot = 60
- else:
- text_rot = 'vertical'
- for gene in genes:
- gene_start, gene_end, gene_name = gene
- # Highlight and label gene region
- # (rescale positions from bases to megabases)
- axis.axvspan(gene_start * MB, gene_end * MB,
- alpha=0.5, color=HIGHLIGHT_COLOR, zorder=-1)
- axis.text(0.5 * (gene_start + gene_end) * MB,
- min(2.4, y.max() + .1) if len(y) else .1,
- gene_name,
- horizontalalignment='center',
- rotation=text_rot,
- size=text_size)
- # size='small')
-
- if background_marker in (None, 'o'):
- # Plot targets and antitargets with the same marker
- axis.scatter(x, y, w, color=POINT_COLOR, alpha=0.4, marker='o')
- else:
- # Use the given marker to plot antitargets separately
- x_fg = []
- y_fg = []
- w_fg = []
- x_bg = []
- y_bg = []
- # w_bg = []
- for x_pt, y_pt, w_pt, is_bg_pt in zip(x, y, w, is_bg):
- if is_bg_pt:
- x_bg.append(x_pt)
- y_bg.append(y_pt)
- # w_bg.append(w_pt)
- else:
- x_fg.append(x_pt)
- y_fg.append(y_pt)
- w_fg.append(w_pt)
- axis.scatter(x_fg, y_fg, w_fg, color=POINT_COLOR, alpha=0.4, marker='o')
- axis.scatter(x_bg, y_bg, color=POINT_COLOR, alpha=0.5,
- marker=background_marker)
-
- # Add a local trend line
- if do_trend:
- axis.plot(x, smoothing.smoothed(y, 50),
- color=POINT_COLOR, linewidth=2, zorder=-1)
-
- # Get coordinates for CBS lines & draw them
- if segments:
- for row in segments:
- axis.plot((row.start * MB, row.end * MB),
- (row.log2, row.log2),
- color=SEG_COLOR, linewidth=4, solid_capstyle='round')
-
-
-def snv_on_chromosome(axis, variants, segments, genes,
- do_trend, do_boost=False):
- # XXX only set x-limits if not already done for probes/segments
- # setup_chromosome(axis, None, segments, variants,
- # 0.0, 1.0, "VAF")
- axis.set_ylim(0.0, 1.0)
- axis.set_ylabel("VAF")
- axis.set_xlabel("Position (Mb)")
- axis.get_yaxis().tick_left()
- axis.get_xaxis().tick_top()
- axis.tick_params(which='both', direction='out',
- labelbottom=False, labeltop=False)
-
- x_mb = variants["start"] * MB
- if do_boost:
- y = variants.tumor_boost()
- else:
- y = np.asfarray(variants["alt_freq"])
- axis.scatter(x_mb, y, color=POINT_COLOR, alpha=0.3)
- # TODO - highlight genes/selection
- if segments:
- # Draw average VAF within each segment
- posns = np.asfarray(variants["start"]) # * MB
- y = np.asfarray(y)
- for v_start, v_end, v_freq in group_snvs_by_segments(posns, y,
- segments):
- # ENH: color by segment gain/loss
- axis.plot([v_start * MB, v_end * MB], [v_freq, v_freq],
- color='#C0C0C0', linewidth=2, #zorder=1,
- solid_capstyle='round')
-
-# === Genome-level scatter plots ===
-
-def setup_genome(axis, probes, segments, variants, y_min=None, y_max=None):
- """Configure axes for plotting a whole genomes's data."""
- pass
-
-
-def cnv_on_genome(axis, probes, segments, pad, do_trend=False, y_min=None,
- y_max=None):
- """Plot coverages and CBS calls for all chromosomes on one plot."""
- # Group probes by chromosome (to calculate plotting coordinates)
- if probes:
- chrom_probe_centers = {chrom: 0.5 * (rows['start'] + rows['end'])
- for chrom, rows in probes.by_chromosome()}
- chrom_sizes = chromosome_sizes(probes)
- else:
- chrom_sizes = chromosome_sizes(segments)
-
- # Same for segment calls
- chrom_seg_coords = {chrom: zip(rows['log2'], rows['start'], rows['end'])
- for chrom, rows in segments.by_chromosome()
- } if segments else {}
-
- x_starts = plot_x_dividers(axis, chrom_sizes, pad)
- x = []
- seg_lines = [] # y-val, x-start, x-end
- for chrom, curr_offset in x_starts.items():
- if probes:
- x.extend(chrom_probe_centers[chrom] + curr_offset)
- if chrom in chrom_seg_coords:
- seg_lines.extend((c[0], c[1] + curr_offset, c[2] + curr_offset)
- for c in chrom_seg_coords[chrom])
-
- # Configure axes etc.
- axis.axhline(color='k')
- axis.set_ylabel("Copy ratio (log2)")
- if not (y_min and y_max):
- if segments:
- # Auto-scale y-axis according to segment mean-coverage values
- seg_auto_vals = segments[(segments.chromosome != 'chr6') &
- (segments.chromosome != 'chrY')]['log2']
- if not y_min:
- y_min = min(seg_auto_vals.min() - .2, -1.5)
- if not y_max:
- y_max = max(seg_auto_vals.max() + .2, 1.5)
- else:
- if not y_min:
- y_min = -2.5
- if not y_max:
- y_max = 2.5
- axis.set_ylim(y_min, y_max)
-
- # Plot points
- if probes:
- axis.scatter(x, probes['log2'], color=POINT_COLOR, edgecolor='none',
- alpha=0.2, marker='.')
- # Add a local trend line
- if do_trend:
- axis.plot(x, _smooth_genome_log2(probes, smoothing.smoothed, 150),
- color=POINT_COLOR, linewidth=2, zorder=-1)
- # Plot segments
- for seg_line in seg_lines:
- y1, x1, x2 = seg_line
- axis.plot((x1, x2), (y1, y1),
- color=SEG_COLOR, linewidth=3, solid_capstyle='round')
-
-def _smooth_genome_log2(cnarr, smooth_func, width):
- """Fit a trendline through bin log2 ratios, handling chromosome boundaries.
-
- Returns an array of smoothed log2 values, calculated with `smooth_func`
- and `width`, equal in length to `cnarr`.
- """
- # ENH: also split by centromeres (long internal gaps -- see PSCBS)
- # ENH: use pandas groupby
- out = {chrom: smooth_func(subcna['log2'], width)
- for chrom, subcna in cnarr.by_chromosome()}
- return np.concatenate(
- [out[chrom] for chrom in sorted(out, key=core.sorter_chrom)])
-
-
-def snv_on_genome(axis, variants, chrom_sizes, segments, do_trend, pad,
- do_boost=False):
- """Plot a scatter-plot of SNP chromosomal positions and shifts."""
- axis.set_ylim(0.0, 1.0)
- axis.set_ylabel("VAF")
- x_starts = plot_x_dividers(axis, chrom_sizes, pad)
-
- # Calculate the coordinates of plot components
- chrom_snvs = dict(variants.by_chromosome())
- x_posns_chrom = {}
- y_posns_chrom = {}
- trends = []
- for chrom, curr_offset in iteritems(x_starts):
- snvs = chrom_snvs.get(chrom, [])
- if not len(snvs):
- x_posns_chrom[chrom] = []
- y_posns_chrom[chrom] = []
- continue
- posns = np.asfarray(snvs["start"])
- x_posns = posns + curr_offset
- if do_boost:
- vafs = snvs.tumor_boost()
- else:
- vafs = np.asfarray(snvs["alt_freq"])
- x_posns_chrom[chrom] = x_posns
- y_posns_chrom[chrom] = vafs
- # Trend bars: always calculated, only shown on request
- if segments:
- # Draw average VAF within each segment
- for v_start, v_end, v_freq in group_snvs_by_segments(posns, vafs,
- segments,
- chrom):
- trends.append((v_start + curr_offset, v_end + curr_offset,
- v_freq))
- else:
- # Draw chromosome-wide average VAF
- for mask_vaf in ((vafs > 0.5), (vafs <= 0.5)):
- if sum(mask_vaf) > 1:
- these_posns = x_posns[mask_vaf]
- trends.append((these_posns[0], these_posns[-1],
- np.median(vafs[mask_vaf])))
-
- # Test for significant shifts in VAF
- # ENH - use segments if provided
- # if significant, colorize those points / that median line
- sig_chroms = [] # test_loh(partition_by_chrom(chrom_snvs))
-
- # Render significantly shifted heterozygous regions separately
- x_posns = []
- y_posns = []
- x_posns_sig = []
- y_posns_sig = []
- for chrom in chrom_sizes:
- posns = x_posns_chrom[chrom]
- vafs = y_posns_chrom[chrom]
- if chrom in sig_chroms:
- x_posns_sig.extend(posns)
- y_posns_sig.extend(vafs)
- else:
- x_posns.extend(posns)
- y_posns.extend(vafs)
-
- # Plot the points
- axis.scatter(x_posns, y_posns, color=POINT_COLOR, edgecolor='none',
- alpha=0.2, marker='.')
- axis.scatter(x_posns_sig, y_posns_sig, color='salmon', edgecolor='none',
- alpha=0.3)
- # Add trend lines to each chromosome
- if do_trend or segments:
- # Draw a line across each chromosome at the median shift level
- for x_start, x_end, y_trend in trends:
- # ENH: color by segment gain/loss
- axis.plot([x_start, x_end], [y_trend, y_trend],
- color='#C0C0C0', linewidth=2, zorder=-1,
- solid_capstyle='round')
-
-
-
-# XXX use by_ranges
-def group_snvs_by_segments(snv_posns, snv_freqs, segments, chrom=None):
- """Group SNP allele frequencies by segment.
-
- Return an iterable of: start, end, value.
- """
- if chrom:
- segments = segments.select(chromosome=chrom)
- seg_starts = segments.start
- # Assign a segment number to each variant, basically
- indices = np.maximum(seg_starts.searchsorted(snv_posns), 1) - 1
- for i in sorted(set(indices)):
- mask_in_seg = (indices == i)
- freqs = snv_freqs[mask_in_seg]
- posns = snv_posns[mask_in_seg]
- # Separately emit VAFs above and below .5 for plotting
- mask_above_mid = (freqs > 0.5)
- for mask_vaf in (mask_above_mid, ~mask_above_mid):
- if sum(mask_vaf) > 1:
- these_posns = posns[mask_vaf]
- yield (these_posns[0], these_posns[-1],
- np.median(freqs[mask_vaf]))
-
-
-def plot_x_dividers(axis, chrom_sizes, pad):
+def plot_x_dividers(axis, chrom_sizes, pad=None):
"""Plot vertical dividers and x-axis labels given the chromosome sizes.
- Returns a table of the x-position offsets of each chromosome.
-
Draws vertical black lines between each chromosome, with padding.
Labels each chromosome range with the chromosome name, centered in the
region, under a tick.
Sets the x-axis limits to the covered range.
+
+ Returns
+ -------
+ OrderedDict
+ A table of the x-position offsets of each chromosome.
"""
assert isinstance(chrom_sizes, collections.OrderedDict)
-
+ if pad is None:
+ pad = 0.003 * sum(chrom_sizes.values())
x_dividers = []
x_centers = []
x_starts = collections.OrderedDict()
curr_offset = pad
- for label, size in chrom_sizes.items():
+ for label, size in list(chrom_sizes.items()):
x_starts[label] = curr_offset
x_centers.append(curr_offset + 0.5 * size)
x_dividers.append(curr_offset + size + pad)
@@ -385,7 +46,7 @@ def plot_x_dividers(axis, chrom_sizes, pad):
axis.axvline(x=xposn, color='k')
# Use chromosome names as x-axis labels (instead of base positions)
axis.set_xticks(x_centers)
- axis.set_xticklabels(chrom_sizes.keys(), rotation=60)
+ axis.set_xticklabels(list(chrom_sizes.keys()), rotation=60)
axis.tick_params(labelsize='small')
axis.tick_params(axis='x', length=0)
axis.get_yaxis().tick_left()
@@ -411,7 +72,7 @@ def partition_by_chrom(chrom_snvs):
chromnames = set(chrom_snvs.keys())
bins = {key: {'thisbin': [], 'otherbins': []}
for key in chrom_snvs}
- for thischrom, snvs in iteritems(chrom_snvs):
+ for thischrom, snvs in chrom_snvs.items():
shiftvals = np.array([abs(v[2]) for v in snvs])
bins[thischrom]['thisbin'].extend(shiftvals)
for otherchrom in chromnames:
@@ -428,6 +89,7 @@ def test_loh(bins, alpha=0.0025):
difference in means.
"""
# TODO - this doesn't work right if there are many shifted regions
+ # -> just use cn1!=cn2 if those columns are present
try:
from scipy import stats
except ImportError:
@@ -435,7 +97,7 @@ def test_loh(bins, alpha=0.0025):
return []
significant_chroms = []
- for chrom, partitions in iteritems(bins):
+ for chrom, partitions in bins.items():
these_shifts = np.array(partitions['thisbin'], np.float_)
other_shifts = np.array(partitions['otherbins'], np.float_)
if len(these_shifts) < 20:
@@ -482,7 +144,10 @@ def cvg2rgb(cvg, desaturate):
def gene_coords_by_name(probes, names):
"""Find the chromosomal position of each named gene in probes.
- Returns a dict: {chromosome: [(start, end, gene name), ...]}
+ Returns
+ -------
+ dict
+ Of: {chromosome: [(start, end, gene name), ...]}
"""
# Create an index of gene names
gene_index = collections.defaultdict(set)
@@ -507,9 +172,9 @@ def gene_coords_by_name(probes, names):
all_coords[chrom][start, end].update(orig_names)
# Consolidate each region's gene names into a string
uniq_coords = {}
- for chrom, hits in all_coords.iteritems():
+ for chrom, hits in all_coords.items():
uniq_coords[chrom] = [(start, end, ",".join(sorted(orig_names)))
- for (start, end), orig_names in hits.iteritems()]
+ for (start, end), orig_names in hits.items()]
return uniq_coords
@@ -517,9 +182,12 @@ def gene_coords_by_range(probes, chrom, start, end,
ignore=params.IGNORE_GENE_NAMES):
"""Find the chromosomal position of all genes in a range.
- Returns a dict: {chromosome: [(start, end, gene), ...]}
+ Returns
+ -------
+ dict
+ Of: {chromosome: [(start, end, gene), ...]}
"""
- ignore += ('Background',)
+ ignore += params.ANTITARGET_ALIASES
# Tabulate the genes in the selected region
genes = collections.OrderedDict()
for row in probes.in_range(chrom, start, end):
@@ -532,41 +200,4 @@ def gene_coords_by_range(probes, chrom, start, end,
genes[name] = [row.start, row.end]
# Reorganize the data structure
return {chrom: [(gstart, gend, name)
- for name, (gstart, gend) in genes.items()]}
-
-
-def unpack_range(a_range):
- """Extract chromosome, start, end from a string or tuple.
-
- Examples:
-
- "chr1" -> ("chr1", None, None)
- "chr1:100-123" -> ("chr1", 100, 123)
- ("chr1", 100, 123) -> ("chr1", 100, 123)
- """
- if not a_range:
- return None, None, None
- if isinstance(a_range, basestring):
- if ':' in a_range or '-' in a_range:
- return parse_range_text(a_range)
- return a_range, None, None
- if isinstance(a_range, (list, tuple)) and len(a_range) == 3:
- return tuple(a_range)
- raise ValueError("Not a range: %r" % a_range)
-
-
-def parse_range_text(text):
- """Parse a chromosomal range specification.
-
- Range spec string should look like ``chr1:1234-5678`` or ``chr1:1234-`` or
- ``chr1:-5678``, where missing start becomes 0 and missing end becomes None.
- """
- try:
- chrom, rest = text.split(':')
- start, end = rest.split('-')
- start = int(start) if start else 0
- end = int(end) if end else None
- return chrom, start, end
- except Exception:
- raise ValueError("Invalid range spec: " + text
- + " (should be like: chr1:2333000-2444000)")
+ for name, (gstart, gend) in list(genes.items())]}
diff --git a/cnvlib/rary.py b/cnvlib/rary.py
deleted file mode 100644
index 946a8f7..0000000
--- a/cnvlib/rary.py
+++ /dev/null
@@ -1,176 +0,0 @@
-"""An array of genomic regions or features."""
-from __future__ import absolute_import, division, print_function
-
-import logging
-import sys
-
-import pandas as pd
-from Bio.File import as_handle
-
-from . import core, gary, ngfrills
-
-
-class RegionArray(gary.GenomicArray):
- """An array of genomic intervals."""
- _required_columns = ("chromosome", "start", "end",
- # "name", "strand",
- )
- _required_dtypes = ("string", "int", "int")
-
- def __init__(self, data_table, meta_dict=None):
- gary.GenomicArray.__init__(self, data_table, meta_dict)
-
- @classmethod
- def read(cls, fname, sample_id=None, fmt=None):
- """Read regions in any of the expected file formats.
-
- Iterates over tuples of the tabular contents. Header lines are skipped.
-
- Start and end coordinates are base-0, half-open.
- """
- if sample_id is None:
- if isinstance(fname, basestring):
- sample_id = core.fbase(fname)
- elif fmt is None:
- raise ValueError("To read regions from a stream, the file "
- "format must be specified with the `fmt` "
- "argument.")
- else:
- sample_id = '<unknown>'
-
- if not fmt:
- fmt = ngfrills.sniff_region_format(fname)
- if fmt is None:
- return cls([])
- if fmt == 'bed':
- logging.info("Detected file format: BED")
- elif fmt == 'interval':
- logging.info("Detected file format: interval list")
- parser = {'text': _parse_text_coords,
- 'interval': _parse_interval_list,
- 'bed': _parse_bed,
- }[fmt]
- table = parser(fname)
- return cls(table, {"sample_id": sample_id})
-
- def write(self, outfile=sys.stdout, fmt="bed", verbose=True):
- assert fmt in ("text", "interval") or fmt.startswith("bed")
- if fmt == "text":
- cp = self.copy()
- cp['start'] += 1
- table = cp.labels()
- else:
- table = self.data
- if fmt == "interval":
- table["start"] += 1
- if "name" not in table:
- table["name"] = '-'
- if "strand" not in table:
- table["strand"] = "+"
- table = table.loc[:, ["chromosome", "start", "end", "strand",
- "name"]]
- elif fmt == "bed4":
- if "name" not in table:
- table["name"] = '-'
- table = table.loc[:, ["chromosome", "start", "end", "name"]]
- elif fmt == "bed3":
- table = table.loc[:, ["chromosome", "start", "end"]]
- # Default: bed-like, keep all trailing columns
-
- with ngfrills.safe_write(outfile, False) as outfile:
- table.to_csv(outfile, sep='\t', header=False, index=False)
- if verbose:
- # Log the output path, if possible
- if isinstance(outfile, basestring):
- outfname = outfile
- elif hasattr(outfile, 'name') and outfile not in (sys.stdout,
- sys.stderr):
- outfname = outfile.name
- else:
- # Probably stdout or stderr used in a pipeline -- don't pollute
- return
- logging.info("Wrote %s with %d regions", outfname, len(table))
-
-
-
-def _parse_text_coords(infile):
- """Parse text coordinates: chrom:start-end
-
- Or sometimes: chrom:start-end:name
-
- Text coordinates are assumed to be counting from 1.
- """
- @ngfrills.report_bad_line
- def _parse_line(line):
- fields = line.split(':')
- if len(fields) == 3:
- chrom, start_end, name = fields
- elif len(fields) == 2:
- chrom, start_end = fields
- name = '-'
- else:
- raise ValueError("Bad line: %r" % line)
- start, end = start_end.split('-')
- return chrom, int(start) - 1, int(end), name.rstrip()
-
- with as_handle(infile, 'rU') as handle:
- rows = [_parse_line(line) for line in handle]
- return pd.DataFrame.from_records(rows, columns=["chromosome", "start",
- "end", "name"])
-
-
-def _parse_interval_list(infile):
- """Parse a Picard-compatible interval list.
-
- Expected tabular columns:
- chromosome, start position, end position, strand, region name
-
- Counting is from 1.
- """
- table = pd.read_table(infile,
- comment='@', # Skip the SAM header
- names=["chromosome", "start", "end", "strand", "name",
- ])
- table["name"].fillna('-', inplace=True)
- table["start"] -= 1
- return table
-
-
-def _parse_bed(infile):
- """Parse a BED file.
-
- A BED file has these columns:
- chromosome, start position, end position, [name, strand, other stuff...]
-
- Counting is from 0.
-
- Sets of regions are separated by "track" lines. This function stops reading
- after encountering a track line other than the first one in the file.
- """
- # ENH: just pd.read_table, skip 'track'
- @ngfrills.report_bad_line
- def _parse_line(line):
- fields = line.split('\t', 6)
- chrom, start, end = fields[:3]
- name = (fields[3].rstrip()
- if len(fields) >= 4 else '-')
- strand = (fields[5].rstrip()
- if len(fields) >= 6 else '.')
- return chrom, int(start), int(end), name, strand
-
- def track2track(handle):
- firstline = next(handle)
- if firstline.startswith("track"):
- pass
- else:
- yield firstline
- for line in handle:
- if line.startswith('track'):
- raise StopIteration
- yield line
-
- with as_handle(infile, 'rU') as handle:
- rows = map(_parse_line, track2track(handle))
- return pd.DataFrame.from_records(rows, columns=["chromosome", "start",
- "end", "name", "strand"])
-
diff --git a/cnvlib/reference.py b/cnvlib/reference.py
index 63cb5df..244820a 100644
--- a/cnvlib/reference.py
+++ b/cnvlib/reference.py
@@ -1,46 +1,138 @@
"""Supporting functions for the 'reference' command."""
from __future__ import absolute_import, division, print_function
+from builtins import map, zip
import logging
import numpy as np
-from Bio._py3k import map, zip
+import pyfaidx
+from skgenome import tabio, GenomicArray as GA
-from . import core, fix, metrics, ngfrills, params
+from . import core, fix, descriptives, params
+from .cmdutil import read_cna
from .cnary import CopyNumArray as CNA
-from .rary import RegionArray as RA
+
+
+def do_reference(target_fnames, antitarget_fnames=None, fa_fname=None,
+ male_reference=False, female_samples=None,
+ do_gc=True, do_edge=True, do_rmask=True):
+ """Compile a coverage reference from the given files (normal samples)."""
+ if antitarget_fnames:
+ core.assert_equal("Unequal number of target and antitarget files given",
+ targets=len(target_fnames),
+ antitargets=len(antitarget_fnames))
+ if not fa_fname:
+ logging.info("No FASTA reference genome provided; "
+ "skipping GC, RM calculations")
+
+ if female_samples is None:
+ # NB: Antitargets are usually preferred for inferring sex, but might be
+ # empty files, in which case no inference can be done. Since targets are
+ # guaranteed to exist, infer from those first, then replace those
+ # values where antitargets are suitable.
+ sexes = infer_sexes(target_fnames, male_reference)
+ if antitarget_fnames:
+ sexes.update(infer_sexes(antitarget_fnames, male_reference))
+
+ # Calculate & save probe centers
+ ref_probes = combine_probes(target_fnames, fa_fname,
+ male_reference, sexes, True,
+ do_gc, do_edge, False)
+ if antitarget_fnames:
+ ref_probes.add(combine_probes(antitarget_fnames, fa_fname,
+ male_reference, sexes, False,
+ do_gc, False, do_rmask))
+ ref_probes.center_all(skip_low=True)
+ ref_probes.sort_columns()
+ warn_bad_bins(ref_probes)
+ return ref_probes
+
+
+def do_reference_flat(targets, antitargets=None, fa_fname=None,
+ male_reference=False):
+ """Compile a neutral-coverage reference from the given intervals.
+
+ Combines the intervals, shifts chrX values if requested, and calculates GC
+ and RepeatMasker content from the genome FASTA sequence.
+ """
+ ref_probes = bed2probes(targets)
+ if antitargets:
+ ref_probes.add(bed2probes(antitargets))
+ # Set sex chromosomes by "reference" sex
+ ref_probes['log2'] = ref_probes.expect_flat_log2(male_reference)
+ ref_probes['depth'] = np.exp2(ref_probes['log2']) # Shim
+ # Calculate GC and RepeatMasker content for each probe's genomic region
+ if fa_fname:
+ gc, rmask = get_fasta_stats(ref_probes, fa_fname)
+ ref_probes['gc'] = gc
+ ref_probes['rmask'] = rmask
+ # warn_bad_bins(ref_probes)
+ else:
+ logging.info("No FASTA reference genome provided; "
+ "skipping GC, RM calculations")
+ ref_probes.sort_columns()
+ return ref_probes
def bed2probes(bed_fname):
- """Create neutral-coverage probes from intervals."""
- regions = RA.read(bed_fname)
+ """Create a neutral-coverage CopyNumArray from a file of regions."""
+ regions = tabio.read_auto(bed_fname)
table = regions.data.loc[:, ("chromosome", "start", "end")]
- table["gene"] = (regions.data["name"] if "name" in regions.data else '-')
+ table["gene"] = (regions.data["gene"] if "gene" in regions.data else '-')
table["log2"] = 0.0
table["spread"] = 0.0
return CNA(table, {"sample_id": core.fbase(bed_fname)})
-def combine_probes(filenames, fa_fname, is_male_reference, skip_low,
+def infer_sexes(cnn_fnames, is_male_reference):
+ """Map sample IDs to inferred chromosomal sex, where possible.
+
+ For samples where the source file is empty or does not include either sex
+ chromosome, that sample ID will not be in the returned dictionary.
+ """
+ sexes = {}
+ for fname in cnn_fnames:
+ cnarr = read_cna(fname)
+ if cnarr:
+ is_xx = cnarr.guess_xx(is_male_reference)
+ if is_xx is not None:
+ sexes[cnarr.sample_id] = is_xx
+ return sexes
+
+
+def combine_probes(filenames, fa_fname, is_male_reference, sexes, skip_low,
fix_gc, fix_edge, fix_rmask):
"""Calculate the median coverage of each bin across multiple samples.
- Input:
- List of .cnn files, as generated by 'coverage' or 'import-picard'.
- `fa_fname`: fil columns for GC and RepeatMasker genomic values.
- Returns:
- A single CopyNumArray summarizing the coverages of the input samples,
- including each bin's "average" coverage, "spread" of coverages, and
- genomic GC content.
+ Parameters
+ ----------
+ filenames : list
+ List of string filenames, corresponding to targetcoverage.cnn and
+ antitargetcoverage.cnn files, as generated by 'coverage' or
+ 'import-picard'.
+ fa_fname : str
+ Reference genome sequence in FASTA format, used to extract GC and
+ RepeatMasker content of each genomic bin.
+ is_male_reference : bool
+ skip_low : bool
+ fix_gc : bool
+ fix_edge : bool
+ fix_rmask : bool
+
+ Returns
+ -------
+ CopyNumArray
+ One object summarizing the coverages of the input samples, including
+ each bin's "average" coverage, "spread" of coverages, and GC content.
"""
columns = {}
# Load coverage from target/antitarget files
logging.info("Loading %s", filenames[0])
- cnarr1 = CNA.read(filenames[0])
+ cnarr1 = read_cna(filenames[0])
if not len(cnarr1):
# Just create an empty array with the right columns
- col_names = ['chromosome', 'start', 'end', 'gene', 'log2']
+ col_names = ['chromosome', 'start', 'end', 'gene', 'log2', 'depth']
if 'gc' in cnarr1 or fa_fname:
col_names.append('gc')
if fa_fname:
@@ -63,9 +155,9 @@ def combine_probes(filenames, fa_fname, is_male_reference, skip_low,
# Make the sex-chromosome coverages of male and female samples compatible
is_chr_x = (cnarr1.chromosome == cnarr1._chr_x_label)
is_chr_y = (cnarr1.chromosome == cnarr1._chr_y_label)
- flat_coverage = cnarr1.expect_flat_cvg(is_male_reference)
+ flat_coverage = cnarr1.expect_flat_log2(is_male_reference)
def shift_sex_chroms(cnarr):
- """Shift sample X and Y chromosomes to match the reference gender.
+ """Shift sample X and Y chromosomes to match the reference sex.
Reference values:
XY: chrX -1, chrY -1
@@ -84,12 +176,11 @@ def combine_probes(filenames, fa_fname, is_male_reference, skip_low,
xy sample, xy ref: 0 (from -1) +1
"""
- is_sample_female = cnarr.guess_xx()
+ is_xx = sexes.get(cnarr.sample_id)
cnarr['log2'] += flat_coverage
- if is_sample_female:
- # chrX already OK
- # No chrY; it's all noise, so just match the male
- cnarr[is_chr_y, 'log2'] = -1.0
+ if is_xx:
+ # chrX has same ploidy as autosomes; chrY is just unusable noise
+ cnarr[is_chr_y, 'log2'] = -1.0 # np.nan is worse
else:
# 1/2 #copies of each sex chromosome
cnarr[is_chr_x | is_chr_y, 'log2'] += 1.0
@@ -117,84 +208,93 @@ def combine_probes(filenames, fa_fname, is_male_reference, skip_low,
return cnarr['log2']
# Pseudocount of 1 "flat" sample
+ all_depths = [cnarr1['depth'] if 'depth' in cnarr1
+ else np.exp2(cnarr1['log2'])]
all_coverages = [flat_coverage, bias_correct_coverage(cnarr1)]
for fname in filenames[1:]:
logging.info("Loading target %s", fname)
- cnarrx = CNA.read(fname)
+ cnarrx = read_cna(fname)
# Bin information should match across all files
if not (len(cnarr1) == len(cnarrx)
and (cnarr1.chromosome == cnarrx.chromosome).all()
and (cnarr1.start == cnarrx.start).all()
and (cnarr1.end == cnarrx.end).all()
and (cnarr1['gene'] == cnarrx['gene']).all()):
- raise RuntimeError("%s probes do not match those in %s"
+ raise RuntimeError("%s bins do not match those in %s"
% (fname, filenames[0]))
+ all_depths.append(cnarrx['depth'] if 'depth' in cnarrx
+ else np.exp2(cnarrx['log2']))
all_coverages.append(bias_correct_coverage(cnarrx))
all_coverages = np.vstack(all_coverages)
logging.info("Calculating average bin coverages")
- cvg_centers = np.apply_along_axis(metrics.biweight_location, 0,
+ cvg_centers = np.apply_along_axis(descriptives.biweight_location, 0,
all_coverages)
+ depth_centers = np.apply_along_axis(descriptives.biweight_location, 0,
+ np.vstack(all_depths))
logging.info("Calculating bin spreads")
- spreads = np.apply_along_axis(metrics.biweight_midvariance, 0,
- all_coverages)
- columns['spread'] = spreads
+ spreads = np.asarray([descriptives.biweight_midvariance(a, initial=i)
+ for a, i in zip(all_coverages.T, cvg_centers)])
columns.update({
'chromosome': cnarr1.chromosome,
'start': cnarr1.start,
'end': cnarr1.end,
'gene': cnarr1['gene'],
'log2': cvg_centers,
+ 'depth': depth_centers,
+ 'spread': spreads,
})
return CNA.from_columns(columns, {'sample_id': "reference"})
-def warn_bad_probes(probes):
- """Warn about target probes where coverage is poor.
+def warn_bad_bins(cnarr, max_name_width=50):
+ """Warn about target bins where coverage is poor.
Prints a formatted table to stderr.
"""
- bad_probes = probes[fix.mask_bad_probes(probes)]
- fg_index = (bad_probes['gene'] != 'Background')
- fg_bad_probes = bad_probes[fg_index]
- if len(fg_bad_probes) > 0:
- bad_pct = 100 * len(fg_bad_probes) / sum(probes['gene'] != 'Background')
+ bad_bins = cnarr[fix.mask_bad_bins(cnarr)]
+ fg_index = ~bad_bins['gene'].isin(params.ANTITARGET_ALIASES)
+ fg_bad_bins = bad_bins[fg_index]
+ if len(fg_bad_bins) > 0:
+ bad_pct = (100 * len(fg_bad_bins)
+ / sum(~cnarr['gene'].isin(params.ANTITARGET_ALIASES)))
logging.info("Targets: %d (%s) bins failed filters:",
- len(fg_bad_probes), "%.4f" % bad_pct + '%')
- gene_cols = max(map(len, fg_bad_probes['gene']))
- labels = list(map(CNA.row2label, fg_bad_probes))
- chrom_cols = max(map(len, labels))
+ len(fg_bad_bins), "%.4f" % bad_pct + '%')
+ gene_cols = min(max_name_width, max(map(len, fg_bad_bins['gene'])))
+ labels = fg_bad_bins.labels()
+ chrom_cols = max(labels.apply(len))
last_gene = None
- for label, probe in zip(labels, fg_bad_probes):
+ for label, probe in zip(labels, fg_bad_bins):
if probe.gene == last_gene:
gene = ' "'
else:
gene = probe.gene
last_gene = gene
- if 'rmask' in probes:
- logging.info(" %s %s coverage=%.3f spread=%.3f rmask=%.3f",
+ if len(gene) > max_name_width:
+ gene = gene[:max_name_width-3] + '...'
+ if 'rmask' in cnarr:
+ logging.info(" %s %s log2=%.3f spread=%.3f rmask=%.3f",
gene.ljust(gene_cols), label.ljust(chrom_cols),
probe.log2, probe.spread, probe.rmask)
else:
- logging.info(" %s %s coverage=%.3f spread=%.3f",
+ logging.info(" %s %s log2=%.3f spread=%.3f",
gene.ljust(gene_cols), label.ljust(chrom_cols),
probe.log2, probe.spread)
- # Count the number of BG probes dropped, too (names are all "Background")
- bg_bad_probes = bad_probes[~fg_index]
- if len(bg_bad_probes) > 0:
- bad_pct = 100 * len(bg_bad_probes) / sum(probes['gene'] == 'Background')
+ # Count the number of BG bins dropped, too (names are all "Antitarget")
+ bg_bad_bins = bad_bins[~fg_index]
+ if len(bg_bad_bins) > 0:
+ bad_pct = (100 * len(bg_bad_bins)
+ / sum(cnarr['gene'].isin(params.ANTITARGET_ALIASES)))
logging.info("Antitargets: %d (%s) bins failed filters",
- len(bg_bad_probes), "%.4f" % bad_pct + '%')
+ len(bg_bad_bins), "%.4f" % bad_pct + '%')
-def get_fasta_stats(probes, fa_fname):
+def get_fasta_stats(cnarr, fa_fname):
"""Calculate GC and RepeatMasker content of each bin in the FASTA genome."""
- fa_coords = zip(probes.chromosome, probes.start, probes.end)
logging.info("Calculating GC and RepeatMasker content in %s ...", fa_fname)
gc_rm_vals = [calculate_gc_lo(subseq)
- for subseq in ngfrills.fasta_extract_regions(fa_fname,
- fa_coords)]
+ for subseq in fasta_extract_regions(fa_fname, cnarr)]
gc_vals, rm_vals = zip(*gc_rm_vals)
return np.asfarray(gc_vals), np.asfarray(rm_vals)
@@ -213,28 +313,24 @@ def calculate_gc_lo(subseq):
return frac_gc, frac_lo
-def reference2regions(reference, coord_only=False):
- """Extract iterables of target and antitarget regions from a reference.
+def fasta_extract_regions(fa_fname, intervals):
+ """Extract an iterable of regions from an indexed FASTA file.
- Like loading two BED files with ngfrills.parse_regions.
+ Input: FASTA file name; iterable of (seq_id, start, end) (1-based)
+ Output: iterable of string sequences.
"""
- cna2rows = (_cna2coords if coord_only else _cna2regions)
- return map(cna2rows, _ref_split_targets(reference))
-
-
-def _cna2coords(cnarr):
- """Extract the coordinate columns from a CopyNumberArray"""
- return zip(cnarr['chromosome'], cnarr['start'], cnarr['end'])
-
-
-def _cna2regions(cnarr):
- """Extract the region columns (including genes) from a CopyNumberArray"""
- return zip(cnarr['chromosome'], cnarr['start'], cnarr['end'], cnarr['gene'])
-
-
-def _ref_split_targets(ref_arr):
- """Split reference into 2 sub-arrays of targets/antitargets."""
- is_bg = (ref_arr['gene'] == 'Background')
- targets = ref_arr[~is_bg]
- antitargets = ref_arr[is_bg]
+ with pyfaidx.Fasta(fa_fname, as_raw=True) as fa_file:
+ for chrom, subarr in intervals.by_chromosome():
+ logging.info("Extracting sequences from chromosome %s", chrom)
+ for _chrom, start, end in subarr.coords():
+ yield fa_file[_chrom][start.item():end.item()]
+
+
+def reference2regions(refarr):
+ """Split reference into target and antitarget regions."""
+ is_bg = (refarr['gene'].isin(params.ANTITARGET_ALIASES))
+ regions = GA(refarr.data.loc[:, ('chromosome', 'start', 'end', 'gene')],
+ {'sample_id': 'reference'})
+ targets = regions[~is_bg]
+ antitargets = regions[is_bg]
return targets, antitargets
diff --git a/cnvlib/reports.py b/cnvlib/reports.py
index c8cce1a..c3ba25e 100644
--- a/cnvlib/reports.py
+++ b/cnvlib/reports.py
@@ -3,10 +3,13 @@
Namely: breaks, gainloss.
"""
from __future__ import absolute_import, division
+from builtins import str
import collections
import math
import sys
+import numpy as np
+
from . import metrics, params
iteritems = (dict.iteritems if sys.version_info[0] < 3 else dict.items)
@@ -18,9 +21,12 @@ iteritems = (dict.iteritems if sys.version_info[0] < 3 else dict.items)
def get_gene_intervals(all_probes, ignore=params.IGNORE_GENE_NAMES):
"""Tally genomic locations of each targeted gene.
- Return a dict of chromosomes to a list of tuples: (gene name, start, end).
+ Return a dict of chromosomes to a list of tuples: (gene name, starts, end),
+ where gene name is a string, starts is a sorted list of probe start
+ positions, and end is the last probe's end position as an integer. (The
+ endpoints are redundant since probes are adjacent.)
"""
- ignore += ("Background",)
+ ignore += params.ANTITARGET_ALIASES
# Tally the start & end points for each targeted gene; group by chromosome
gene_probes = collections.defaultdict(lambda: collections.defaultdict(list))
for row in all_probes:
@@ -65,33 +71,38 @@ def get_breakpoints(intervals, segments, min_probes):
# _____________________________________________________________________________
# gainloss
-def gainloss_by_gene(probes, threshold, skip_low=False):
+def gainloss_by_gene(cnarr, threshold, skip_low=False):
"""Identify genes where average bin copy ratio value exceeds `threshold`.
NB: Must shift sex-chromosome values beforehand with shift_xx,
otherwise all chrX/chrY genes may be reported gained/lost.
"""
- for gene, chrom, start, end, coverage, nprobes in group_by_genes(probes,
- skip_low):
- if abs(coverage) >= threshold:
- yield (gene, chrom, start, end, coverage, nprobes)
+ for row in group_by_genes(cnarr, skip_low):
+ if abs(row.log2) >= threshold and row.gene:
+ yield row
-def gainloss_by_segment(probes, segments, threshold, skip_low=False):
+def gainloss_by_segment(cnarr, segments, threshold, skip_low=False):
"""Identify genes where segmented copy ratio exceeds `threshold`.
NB: Must shift sex-chromosome values beforehand with shift_xx,
otherwise all chrX/chrY genes may be reported gained/lost.
"""
- for segment, subprobes in probes.by_ranges(segments):
+ extra_cols = [col for col in segments.data.columns
+ if col not in cnarr.data.columns]
+ for colname in extra_cols:
+ cnarr[colname] = np.nan
+ for segment, subprobes in cnarr.by_ranges(segments):
if abs(segment.log2) >= threshold:
- for (gene, chrom, start, end, _coverage, nprobes
- ) in group_by_genes(subprobes, skip_low):
- yield (gene, chrom, start, end, segment.log2, nprobes)
+ for row in group_by_genes(subprobes, skip_low):
+ row["log2"] = segment.log2
+ for colname in extra_cols:
+ row[colname] = getattr(segment, colname)
+ yield row
# TODO consolidate with CNA.squash_genes
-def group_by_genes(probes, skip_low):
+def group_by_genes(cnarr, skip_low):
"""Group probe and coverage data by gene.
Return an iterable of genes, in chromosomal order, associated with their
@@ -99,13 +110,18 @@ def group_by_genes(probes, skip_low):
[(gene, chrom, start, end, [coverages]), ...]
"""
- for gene, rows in probes.by_gene():
- if gene == 'Background':
+ ignore = ('', np.nan) + params.ANTITARGET_ALIASES
+ for gene, rows in cnarr.by_gene():
+ if not rows or gene in ignore:
+ continue
+ segmean = metrics.segment_mean(rows, skip_low)
+ if segmean is None:
continue
- chrom = rows[0, 'chromosome']
- start = rows[0, 'start']
- end = rows[len(rows)-1, 'end']
- segmean = metrics.segment_mean(rows)
- if segmean is not None:
- nprobes = len(rows)
- yield gene, chrom, start, end, segmean, nprobes
+ outrow = rows[0].copy()
+ outrow["end"] = rows.end.iat[-1]
+ outrow["gene"] = gene
+ outrow["log2"] = segmean
+ outrow["probes"] = len(rows)
+ if "weight" in rows:
+ outrow["weight"] = rows["weight"].sum()
+ yield outrow
diff --git a/cnvlib/ngfrills/samutil.py b/cnvlib/samutil.py
similarity index 50%
rename from cnvlib/ngfrills/samutil.py
rename to cnvlib/samutil.py
index af1ee63..b1df5cd 100644
--- a/cnvlib/ngfrills/samutil.py
+++ b/cnvlib/samutil.py
@@ -1,13 +1,39 @@
"""BAM utilities."""
from __future__ import absolute_import, division, print_function
+# from builtins import str
+from past.builtins import basestring
import logging
import os
from itertools import islice
+import numpy as np
+import pandas as pd
import pysam
+from Bio._py3k import StringIO
-from .shared import is_newer_than
+
+def idxstats(bam_fname, drop_unmapped=False):
+ """Get chromosome names, lengths, and number of mapped/unmapped reads.
+
+ Use the BAM index (.bai) to get the number of reads and size of each
+ chromosome. Contigs with no mapped reads are skipped.
+ """
+ handle = StringIO(pysam.idxstats(bam_fname, split_lines=False))
+ table = pd.read_table(handle, header=None,
+ names=['chromosome', 'length', 'mapped', 'unmapped'])
+ if drop_unmapped:
+ table = table[table.mapped != 0].drop('unmapped', axis=1)
+ return table
+
+
+def bam_total_reads(bam_fname):
+ """Count the total number of mapped reads in a BAM file.
+
+ Uses the BAM index to do this quickly.
+ """
+ table = idxstats(bam_fname, drop_unmapped=True)
+ return table.mapped.sum()
def ensure_bam_index(bam_fname):
@@ -61,4 +87,38 @@ def ensure_bam_sorted(bam_fname, by_name=False, span=50):
if out_of_order(read, last_read):
return False
last_read = read
+ bam.close()
return True
+
+
+def is_newer_than(target_fname, orig_fname):
+ """Compare file modification times."""
+ if not os.path.isfile(target_fname):
+ return False
+ return (os.stat(target_fname).st_mtime >= os.stat(orig_fname).st_mtime)
+
+
+def get_read_length(bam, span=1000):
+ """Get (median) read length from first few reads in a BAM file.
+
+ Illumina reads all have the same length; other sequencers might not.
+
+ Parameters
+ ----------
+ bam : str or pysam.Samfile
+ Filename or pysam-opened BAM file.
+ n : int
+ Number of reads used to calculate median read length.
+ """
+ was_open = False
+ if isinstance(bam, basestring):
+ bam = pysam.Samfile(bam, 'rb')
+ else:
+ was_open = True
+ lengths = [read.query_length for read in islice(bam, span)
+ if read.query_length > 0]
+ if was_open:
+ bam.seek(0)
+ else:
+ bam.close()
+ return np.median(lengths)
diff --git a/cnvlib/scatter.py b/cnvlib/scatter.py
new file mode 100644
index 0000000..bc83a5d
--- /dev/null
+++ b/cnvlib/scatter.py
@@ -0,0 +1,533 @@
+"""Command-line interface and corresponding API for CNVkit."""
+# NB: argparse CLI definitions and API functions are interwoven:
+# "_cmd_*" handles I/O and arguments processing for the command
+# "do_*" runs the command's functionality as an API
+from __future__ import absolute_import, division, print_function
+
+import collections
+import logging
+
+import numpy as np
+from matplotlib import pyplot
+from skgenome.rangelabel import unpack_range
+
+from . import core, params, plots, smoothing
+from .plots import MB
+from .cnary import CopyNumArray as CNA
+
+HIGHLIGHT_COLOR = 'gold'
+POINT_COLOR = '#606060'
+SEG_COLOR = 'darkorange'
+TREND_COLOR = '#C0C0C0'
+
+
+def do_scatter(cnarr, segments=None, variants=None,
+ show_range=None, show_gene=None,
+ antitarget_marker=None, do_trend=False, window_width=1e6,
+ y_min=None, y_max=None, title=None, segment_color=SEG_COLOR,
+ background_marker=None, # DEPRECATED in 0.9.0
+ ):
+ """Plot probe log2 coverages and segmentation calls together."""
+ # Handle the deprecated argument
+ if background_marker is not None:
+ if antitarget_marker is None or antitarget_marker == background_marker:
+ logging.warn("Keyword argument background_marker=%r was given; "
+ "use antitarget_marker instead.", background_marker)
+ antitarget_marker = background_marker
+ elif antitarget_marker != background_marker:
+ raise ValueError(
+ "Deprecated keyword argument background_marker=%r was given, "
+ "but conflicts with its successor antitarget_marker=%r"
+ % (background_marker, antitarget_marker))
+
+ if not show_gene and not show_range:
+ genome_scatter(cnarr, segments, variants, do_trend, y_min, y_max, title,
+ segment_color)
+ else:
+ chromosome_scatter(cnarr, segments, variants, show_range, show_gene,
+ antitarget_marker, do_trend, window_width, y_min,
+ y_max, title, segment_color)
+
+
+# === Genome-level scatter plots ===
+
+def genome_scatter(cnarr, segments=None, variants=None, do_trend=False,
+ y_min=None, y_max=None, title=None, segment_color=SEG_COLOR):
+ """Plot all chromosomes, concatenated on one plot."""
+ if (cnarr or segments) and variants:
+ # Lay out top 3/5 for the CN scatter, bottom 2/5 for SNP plot
+ axgrid = pyplot.GridSpec(5, 1, hspace=.85)
+ axis = pyplot.subplot(axgrid[:3])
+ axis2 = pyplot.subplot(axgrid[3:], sharex=axis)
+ # Place chromosome labels between the CNR and SNP plots
+ axis2.tick_params(labelbottom=False)
+ chrom_sizes = plots.chromosome_sizes(cnarr or segments)
+ snv_on_genome(axis2, variants, chrom_sizes, segments, do_trend)
+ else:
+ _fig, axis = pyplot.subplots()
+ if title is None:
+ title = (cnarr or segments or variants).sample_id
+ if cnarr or segments:
+ axis.set_title(title)
+ cnv_on_genome(axis, cnarr, segments, do_trend, y_min, y_max,
+ segment_color=segment_color)
+ else:
+ axis.set_title("Variant allele frequencies: %s" % title)
+ chrom_sizes = collections.OrderedDict(
+ (chrom, subarr["end"].max())
+ for chrom, subarr in variants.by_chromosome())
+ snv_on_genome(axis, variants, chrom_sizes, segments, do_trend)
+
+
+
+def cnv_on_genome(axis, probes, segments, do_trend=False, y_min=None,
+ y_max=None, segment_color=SEG_COLOR):
+ """Plot coverages and CBS calls for all chromosomes on one plot."""
+ # Group probes by chromosome (to calculate plotting coordinates)
+ if probes:
+ chrom_probe_centers = {chrom: 0.5 * (rows['start'] + rows['end'])
+ for chrom, rows in probes.by_chromosome()}
+ chrom_sizes = plots.chromosome_sizes(probes)
+ else:
+ chrom_sizes = plots.chromosome_sizes(segments)
+
+ # Same for segment calls
+ chrom_seg_coords = {chrom: list(zip(rows['log2'], rows['start'], rows['end']))
+ for chrom, rows in segments.by_chromosome()
+ } if segments else {}
+
+ x_starts = plots.plot_x_dividers(axis, chrom_sizes)
+ x = []
+ seg_lines = [] # y-val, x-start, x-end
+ for chrom, curr_offset in list(x_starts.items()):
+ if probes:
+ x.extend(chrom_probe_centers[chrom] + curr_offset)
+ if chrom in chrom_seg_coords:
+ seg_lines.extend((c[0], c[1] + curr_offset, c[2] + curr_offset)
+ for c in chrom_seg_coords[chrom])
+
+ # Configure axes etc.
+ axis.axhline(color='k')
+ axis.set_ylabel("Copy ratio (log2)")
+ if not (y_min and y_max):
+ if segments:
+ # Auto-scale y-axis according to segment mean-coverage values
+ seg_auto_vals = segments[(segments.chromosome != 'chr6') &
+ (segments.chromosome != 'chrY')]['log2']
+ if not y_min:
+ y_min = min(seg_auto_vals.min() - .2, -1.5)
+ if not y_max:
+ y_max = max(seg_auto_vals.max() + .2, 1.5)
+ else:
+ if not y_min:
+ y_min = -2.5
+ if not y_max:
+ y_max = 2.5
+ axis.set_ylim(y_min, y_max)
+
+ # Plot points
+ if probes:
+ axis.scatter(x, probes['log2'], color=POINT_COLOR, edgecolor='none',
+ alpha=0.2, marker='.')
+ # Add a local trend line
+ if do_trend:
+ axis.plot(x, _smooth_genome_log2(probes, smoothing.smoothed, 150),
+ color=POINT_COLOR, linewidth=2, zorder=-1)
+ # Plot segments
+ for seg_line in seg_lines:
+ y1, x1, x2 = seg_line
+ axis.plot((x1, x2), (y1, y1),
+ color=segment_color, linewidth=3, solid_capstyle='round')
+
+
+def _smooth_genome_log2(cnarr, smooth_func, width):
+ """Fit a trendline through bin log2 ratios, handling chromosome boundaries.
+
+ Returns
+ -------
+ np.array
+ Smoothed log2 values, calculated with `smooth_func` and `width`, equal
+ in length to `cnarr`.
+ """
+ # ENH: also split by centromeres (long internal gaps -- see PSCBS)
+ # ENH: use pandas groupby
+ out = [smooth_func(subcna['log2'], width)
+ for _chrom, subcna in cnarr.by_chromosome()]
+ return np.concatenate(out)
+
+
+def snv_on_genome(axis, variants, chrom_sizes, segments, do_trend):
+ """Plot a scatter-plot of SNP chromosomal positions and shifts."""
+ axis.set_ylim(0.0, 1.0)
+ axis.set_ylabel("VAF")
+ x_starts = plots.plot_x_dividers(axis, chrom_sizes)
+
+ # Calculate the coordinates of plot components
+ chrom_snvs = dict(variants.by_chromosome())
+ x_posns_chrom = {}
+ y_posns_chrom = {}
+ trends = []
+ for chrom, curr_offset in x_starts.items():
+ snvs = chrom_snvs.get(chrom, [])
+ if not len(snvs):
+ x_posns_chrom[chrom] = []
+ y_posns_chrom[chrom] = []
+ continue
+ posns = snvs['start'].values
+ x_posns = posns + curr_offset
+ vafs = snvs['alt_freq'].values
+ x_posns_chrom[chrom] = x_posns
+ y_posns_chrom[chrom] = vafs
+ # Trend bars: always calculated, only shown on request
+ if segments:
+ # Draw average VAF within each segment
+ for v_start, v_end, v_freq in group_snvs_by_segments(posns, vafs,
+ segments,
+ chrom):
+ trends.append((v_start + curr_offset, v_end + curr_offset,
+ v_freq))
+ else:
+ # Draw chromosome-wide average VAF
+ for mask_vaf in ((vafs > 0.5), (vafs <= 0.5)):
+ if sum(mask_vaf) > 1:
+ these_posns = x_posns[mask_vaf]
+ trends.append((these_posns[0], these_posns[-1],
+ np.median(vafs[mask_vaf])))
+
+ # Test for significant shifts in VAF
+ # ENH - use segments if provided
+ # if significant, colorize those points / that median line
+ sig_chroms = [] # test_loh(partition_by_chrom(chrom_snvs))
+
+ # Render significantly shifted heterozygous regions separately
+ x_posns = []
+ y_posns = []
+ x_posns_sig = []
+ y_posns_sig = []
+ for chrom in chrom_sizes:
+ posns = x_posns_chrom[chrom]
+ vafs = y_posns_chrom[chrom]
+ if chrom in sig_chroms:
+ x_posns_sig.extend(posns)
+ y_posns_sig.extend(vafs)
+ else:
+ x_posns.extend(posns)
+ y_posns.extend(vafs)
+
+ # Plot the points
+ axis.scatter(x_posns, y_posns, color=POINT_COLOR, edgecolor='none',
+ alpha=0.2, marker='.')
+ axis.scatter(x_posns_sig, y_posns_sig, color='salmon', edgecolor='none',
+ alpha=0.3)
+ # Add trend lines to each chromosome
+ if do_trend or segments:
+ # Draw a line across each chromosome at the median shift level
+ for x_start, x_end, y_trend in trends:
+ # ENH: color by segment gain/loss
+ axis.plot([x_start, x_end], [y_trend, y_trend],
+ color=TREND_COLOR, linewidth=2, zorder=-1,
+ solid_capstyle='round')
+
+
+# === Chromosome-level scatter plots ===
+
+def chromosome_scatter(cnarr, segments, variants, show_range, show_gene,
+ antitarget_marker, do_trend, window_width, y_min, y_max,
+ title, segment_color):
+ """Plot a specified region on one chromosome.
+
+ Possibilities::
+
+ Options | Shown
+ ------------ | --------
+ -c | -g | Genes | Region
+ ------- | -- | ----- | ------
+ - | + | given | auto: gene(s) + margin
+ chr | - | none | whole chrom
+ chr | + | given | whole chrom
+ chr:s-e | - | all | given
+ chr:s-e | + | given | given
+
+ """
+ chrom, start, end = unpack_range(show_range)
+ window_coords = ()
+ genes = []
+ if show_gene:
+ gene_names = show_gene.split(',')
+ # Scan for probes matching the specified gene
+ gene_coords = plots.gene_coords_by_name(cnarr or segments,
+ gene_names)
+ if len(gene_coords) != 1:
+ raise ValueError("Genes %s are split across chromosomes %s"
+ % (show_gene, list(gene_coords.keys())))
+ g_chrom, genes = gene_coords.popitem()
+ if chrom:
+ # Confirm that the selected chromosomes match
+ core.assert_equal("Chromosome also selected by region (-c) "
+ "does not match",
+ **{"chromosome": chrom,
+ "gene(s)": g_chrom})
+ else:
+ chrom = g_chrom
+ # Set the display window to the selected genes +/- a margin
+ genes.sort()
+ window_coords = (max(0, genes[0][0] - window_width),
+ genes[-1][1] + window_width)
+
+ if start is not None or end is not None:
+ # Default selection endpoint to the maximum chromosome position
+ if not end:
+ end = (cnarr or segments or variants
+ ).filter(chromosome=chrom).end.iat[-1]
+ if window_coords:
+ # Genes were specified, & window was set around them
+ if start > window_coords[0] or end < window_coords[1]:
+ raise ValueError("Selected gene region " + chrom +
+ (":%d-%d" % window_coords) +
+ " is outside specified region " +
+ show_range)
+ window_coords = (max(0, start - window_width), end + window_width)
+ if cnarr and not genes:
+ genes = plots.gene_coords_by_range(cnarr, chrom, start, end)[chrom]
+ if not genes and window_width > (end - start) / 10.0:
+ # No genes in the selected region, so highlight the region
+ # itself (unless the selection is ~entire displayed window)
+ logging.info("No genes found in selection; will show the "
+ "selected region itself instead")
+ genes = [(start, end, "Selection")]
+ elif show_range and window_coords:
+ # Specified range is only chrom, no start-end
+ # Reset window around selected genes to show the whole chromosome
+ window_coords = ()
+
+ # Prune plotted elements to the selected region
+ sel_probes = (cnarr.in_range(chrom, *window_coords)
+ if cnarr else CNA([]))
+ sel_seg = (segments.in_range(chrom, *window_coords, mode='trim')
+ if segments else CNA([]))
+ sel_snvs = (variants.in_range(chrom, *window_coords)
+ if variants else None)
+ logging.info("Showing %d probes and %d selected genes in region %s",
+ len(sel_probes), len(genes),
+ (chrom + ":%d-%d" % window_coords if window_coords else chrom))
+
+ # Create plots
+ if cnarr or segments:
+ # Plot CNVs at chromosome level
+ if variants:
+ # Lay out top 3/5 for the CN scatter, bottom 2/5 for SNP plot
+ axgrid = pyplot.GridSpec(5, 1, hspace=.5)
+ axis = pyplot.subplot(axgrid[:3])
+ axis2 = pyplot.subplot(axgrid[3:], sharex=axis)
+ # Plot allele freqs for only the selected region
+ snv_on_chromosome(axis2, sel_snvs, sel_seg, genes, do_trend)
+ else:
+ _fig, axis = pyplot.subplots()
+ axis.set_xlabel("Position (Mb)")
+ cnv_on_chromosome(axis, sel_probes, sel_seg, genes,
+ antitarget_marker=antitarget_marker,
+ do_trend=do_trend, x_limits=window_coords,
+ y_min=y_min, y_max=y_max, segment_color=segment_color)
+ elif variants:
+ # Only plot SNVs in a single-panel layout
+ _fig, axis = pyplot.subplots()
+ snv_on_chromosome(axis, sel_snvs, sel_seg, genes, do_trend)
+
+ if title is None:
+ title = "%s %s" % ((cnarr or segments or variants).sample_id, chrom)
+ axis.set_title(title)
+
+
+def cnv_on_chromosome(axis, probes, segments, genes, antitarget_marker=None,
+ do_trend=False, x_limits=None, y_min=None, y_max=None,
+ segment_color=SEG_COLOR):
+ """Draw a scatter plot of probe values with CBS calls overlaid.
+
+ Parameters
+ ----------
+ genes : list
+ Of tuples: (start, end, gene name)
+ """
+ # Get scatter plot coordinates
+ x = 0.5 * (probes['start'] + probes['end']) * MB # bin midpoints
+ y = probes['log2']
+ if 'weight' in probes:
+ w = 46 * probes['weight'] ** 2 + 2
+ else:
+ w = np.repeat(30, len(x))
+ is_bg = (probes['gene'] == params.ANTITARGET_NAME)
+
+ # Configure axes
+ # TODO - use segment y-values if probes not given
+ if not y_min:
+ y_min = max(-5.0, min(y.min() - .1, -.3)) if len(y) else -1.1
+ if not y_max:
+ y_max = max(.3, y.max() + (.25 if genes else .1)) if len(y) else 1.1
+ if x_limits:
+ x_min, x_max = x_limits
+ axis.set_xlim(x_min * MB, x_max * MB)
+ else:
+ set_xlim_from(axis, probes, segments)
+ setup_chromosome(axis, y_min, y_max, "Copy ratio (log2)")
+ if genes:
+ # Rotate text in proportion to gene density
+ ngenes = len(genes)
+ text_size = ('small' if ngenes <= 6 else 'x-small')
+ if ngenes <= 3:
+ text_rot = 'horizontal'
+ elif ngenes <= 6:
+ text_rot = 30
+ elif ngenes <= 10:
+ text_rot = 45
+ elif ngenes <= 20:
+ text_rot = 60
+ else:
+ text_rot = 'vertical'
+ for gene in genes:
+ gene_start, gene_end, gene_name = gene
+ # Highlight and label gene region
+ # (rescale positions from bases to megabases)
+ axis.axvspan(gene_start * MB, gene_end * MB,
+ alpha=0.5, color=HIGHLIGHT_COLOR, zorder=-1)
+ axis.text(0.5 * (gene_start + gene_end) * MB,
+ min(2.4, y.max() + .1) if len(y) else .1,
+ gene_name,
+ horizontalalignment='center',
+ rotation=text_rot,
+ size=text_size)
+ # size='small')
+
+ if antitarget_marker in (None, 'o'):
+ # Plot targets and antitargets with the same marker
+ axis.scatter(x, y, w, color=POINT_COLOR, alpha=0.4, marker='o')
+ else:
+ # Use the given marker to plot antitargets separately
+ x_fg = []
+ y_fg = []
+ w_fg = []
+ x_bg = []
+ y_bg = []
+ # w_bg = []
+ for x_pt, y_pt, w_pt, is_bg_pt in zip(x, y, w, is_bg):
+ if is_bg_pt:
+ x_bg.append(x_pt)
+ y_bg.append(y_pt)
+ # w_bg.append(w_pt)
+ else:
+ x_fg.append(x_pt)
+ y_fg.append(y_pt)
+ w_fg.append(w_pt)
+ axis.scatter(x_fg, y_fg, w_fg, color=POINT_COLOR, alpha=0.4, marker='o')
+ axis.scatter(x_bg, y_bg, color=POINT_COLOR, alpha=0.5,
+ marker=antitarget_marker)
+
+ # Add a local trend line
+ if do_trend:
+ axis.plot(x, smoothing.smoothed(y, 50),
+ color=POINT_COLOR, linewidth=2, zorder=-1)
+
+ # Get coordinates for CBS lines & draw them
+ if segments:
+ for row in segments:
+ axis.plot((row.start * MB, row.end * MB),
+ (row.log2, row.log2),
+ color=segment_color, linewidth=4, solid_capstyle='round')
+
+
+def snv_on_chromosome(axis, variants, segments, genes, do_trend):
+ # TODO set x-limits if not already done for probes/segments
+ # set_xlim_from(axis, None, segments, variants)
+ # setup_chromosome(axis, 0.0, 1.0, "VAF")
+ axis.set_ylim(0.0, 1.0)
+ axis.set_ylabel("VAF")
+ axis.set_xlabel("Position (Mb)")
+ axis.get_yaxis().tick_left()
+ axis.get_xaxis().tick_top()
+ axis.tick_params(which='both', direction='out',
+ labelbottom=False, labeltop=False)
+
+ x_mb = variants['start'] * MB
+ y = variants['alt_freq'].values
+ axis.scatter(x_mb, y, color=POINT_COLOR, alpha=0.3)
+ # TODO - highlight genes/selection
+ if segments:
+ # Draw average VAF within each segment
+ # TODO coordinate this w/ do_trend
+ posns = variants['start'].values # * MB
+ for v_start, v_end, v_freq in group_snvs_by_segments(posns, y,
+ segments):
+ # ENH: color by segment gain/loss
+ axis.plot([v_start * MB, v_end * MB], [v_freq, v_freq],
+ color='#C0C0C0', linewidth=2, #zorder=1,
+ solid_capstyle='round')
+
+
+def set_xlim_from(axis, probes=None, segments=None, variants=None):
+ """Configure axes for plotting a single chromosome's data.
+
+ Parameters
+ ----------
+ probes : CopyNumArray
+ segments : CopyNumArray
+ variants : VariantArray
+ All should already be subsetted to the region that will be plotted.
+ """
+ min_x = np.inf
+ max_x = 0
+ for arr in (probes, segments, variants):
+ if arr and len(arr):
+ max_x = max(max_x, arr.end.iat[-1])
+ min_x = min(min_x, arr.start.iat[0])
+ if max_x <= min_x:
+ if min_x != np.inf:
+ logging.warn("*WARNING* selection start %s > end %s; did you "
+ "correctly sort the input file by genomic location?",
+ min_x, max_x)
+ raise ValueError("No usable data points to plot out of "
+ "%d probes, %d segments, %d variants"
+ % (len(probes) if probes else 0,
+ len(segments) if segments else 0,
+ len(variants) if variants else 0))
+ axis.set_xlim(min_x * MB, max_x * MB)
+
+
+def setup_chromosome(axis, y_min=None, y_max=None, y_label=None):
+ """Configure axes for plotting a single chromosome's data."""
+ if y_min and y_max:
+ axis.set_ylim(y_min, y_max)
+ if y_min < 0 < y_max:
+ axis.axhline(color='k')
+ if y_label:
+ axis.set_ylabel(y_label)
+ axis.tick_params(which='both', direction='out')
+ axis.get_xaxis().tick_bottom()
+ axis.get_yaxis().tick_left()
+
+
+# === Shared ===
+
+# XXX use by_ranges
+def group_snvs_by_segments(snv_posns, snv_freqs, segments, chrom=None):
+ """Group SNP allele frequencies by segment.
+
+ Yields
+ ------
+ tuple
+ (start, end, value)
+ """
+ if chrom:
+ segments = segments.filter(chromosome=chrom)
+ seg_starts = segments.start
+ # Assign a segment number to each variant, basically
+ indices = np.maximum(seg_starts.searchsorted(snv_posns), 1) - 1
+ for i in sorted(set(indices)):
+ mask_in_seg = (indices == i)
+ freqs = snv_freqs[mask_in_seg]
+ posns = snv_posns[mask_in_seg]
+ # Separately emit VAFs above and below .5 for plotting
+ mask_above_mid = (freqs > 0.5)
+ for mask_vaf in (mask_above_mid, ~mask_above_mid):
+ if sum(mask_vaf) > 1:
+ these_posns = posns[mask_vaf]
+ yield (these_posns[0], these_posns[-1],
+ np.median(freqs[mask_vaf]))
diff --git a/cnvlib/segfilters.py b/cnvlib/segfilters.py
new file mode 100644
index 0000000..6b20780
--- /dev/null
+++ b/cnvlib/segfilters.py
@@ -0,0 +1,153 @@
+"""Filter copy number segments."""
+from __future__ import absolute_import, division, print_function
+
+import functools
+import logging
+
+import numpy as np
+import pandas as pd
+
+from .descriptives import weighted_median
+
+
+def require_column(*colnames):
+ """Wrapper to coordinate the segment-filtering functions.
+
+ Verify that the given columns are in the CopyNumArray the wrapped function
+ takes. Also log the number of rows in the array before and after filtration.
+ """
+ if len(colnames) == 1:
+ msg = "'{}' filter requires column '{}'"
+ else:
+ msg = "'{}' filter requires columns " + \
+ ", ".join(["'{}'"] * len(colnames))
+ def wrap(func):
+ @functools.wraps(func)
+ def wrapped_f(segarr):
+ filtname = func.__name__
+ if any(c not in segarr for c in colnames):
+ raise ValueError(msg.format(filtname, *colnames))
+ result = func(segarr)
+ logging.info("Filtered by '%s' from %d to %d rows",
+ filtname, len(segarr), len(result))
+ return result
+ return wrapped_f
+ return wrap
+
+
+def squash_by_groups(cnarr, levels):
+ """Reduce CopyNumArray rows to a single row within each given level."""
+ # Enumerate runs of identical values
+ change_levels = enumerate_changes(levels)
+ # Enumerate chromosomes
+ chrom_names = cnarr['chromosome'].unique()
+ change_levels += cnarr['chromosome'].replace(chrom_names,
+ np.arange(len(chrom_names)))
+ data = cnarr.data.assign(_group=change_levels)
+ groupkey = ['_group']
+ if 'cn1' in cnarr:
+ # Keep allele-specific CNAs separate
+ data['_g1'] = enumerate_changes(cnarr['cn1'])
+ data['_g2'] = enumerate_changes(cnarr['cn2'])
+ groupkey.extend(['_g1', '_g2'])
+ data = data.groupby(groupkey, sort=False).apply(squash_region)
+ return cnarr.as_dataframe(data)
+
+
+def enumerate_changes(levels):
+ """Assign a unique integer to each run of identical values.
+
+ Repeated but non-consecutive values will be assigned different integers.
+ """
+ return levels.diff().fillna(0).abs().cumsum().astype(int)
+
+
+def squash_region(cnarr):
+ """Reduce a CopyNumArray to 1 row, keeping fields sensible.
+
+ Most fields added by the `segmetrics` command will be dropped.
+ """
+ assert 'weight' in cnarr and 'probes' in cnarr
+ out = {'chromosome': [cnarr['chromosome'].iat[0]],
+ 'start': cnarr['start'].iat[0],
+ 'end': cnarr['end'].iat[-1],
+ }
+ out['log2'] = np.average(cnarr['log2'], weights=cnarr['weight'])
+ out['gene'] = ','.join(cnarr['gene'].drop_duplicates())
+ out['probes'] = cnarr['probes'].sum()
+ out['weight'] = cnarr['weight'].sum()
+ if 'depth' in cnarr:
+ out['depth'] = np.average(cnarr['depth'], weights=cnarr['weight'])
+ if 'baf' in cnarr:
+ out['baf'] = np.average(cnarr['baf'], weights=cnarr['weight'])
+ if 'cn' in cnarr:
+ out['cn'] = weighted_median(cnarr['cn'], cnarr['weight'])
+ if 'cn1' in cnarr:
+ out['cn1'] = weighted_median(cnarr['cn1'], cnarr['weight'])
+ out['cn2'] = out['cn'] - out['cn1']
+ return pd.DataFrame(out)
+
+
+ at require_column('cn')
+def ampdel(segarr):
+ """Merge segments by amplified/deleted/neutral copy number status.
+
+ Follow the clinical reporting convention:
+
+ - 5+ copies (2.5-fold gain) is amplification
+ - 0 copies is homozygous/deep deletion
+ - CNAs of lesser degree are not reported
+
+ This is recommended only for selecting segments corresponding to
+ actionable, usually focal, CNAs. Any real and potentially informative but
+ lower-level CNAs will be dropped.
+ """
+ levels = pd.Series(np.zeros(len(segarr)))
+ levels[segarr['cn'] == 0] = -1
+ levels[segarr['cn'] >= 5] = 1
+ # or: segarr['log2'] >= np.log2(2.5)
+ cnarr = squash_by_groups(segarr, levels)
+ return cnarr[(cnarr['cn'] == 0) | (cnarr['cn'] >= 5)]
+
+
+ at require_column('depth')
+def bic(segarr):
+ """Merge segments by Bayesian Information Criterion.
+
+ See: BIC-seq (Xi 2011), doi:10.1073/pnas.1110574108
+ """
+ return NotImplemented
+
+
+ at require_column('ci_lo', 'ci_hi')
+def ci(segarr):
+ """Merge segments by confidence interval (overlapping 0).
+
+ Segments with lower CI above 0 are kept as gains, upper CI below 0 as
+ losses, and the rest with CI overlapping zero are collapsed as neutral.
+ """
+ levels = pd.Series(np.zeros(len(segarr)))
+ levels[segarr['ci_lo'] > 0] = 1
+ levels[segarr['ci_hi'] < 0] = -1
+ return squash_by_groups(segarr, levels)
+
+
+ at require_column('cn')
+def cn(segarr):
+ """Merge segments by integer copy number."""
+ return squash_by_groups(segarr, segarr['cn'])
+
+
+ at require_column('sem')
+def sem(segarr, zscore=1.96):
+ """Merge segments by Standard Error of the Mean (SEM).
+
+ Use each segment's SEM value to estimate a 95% confidence interval (via
+ `zscore`). Segments with lower CI above 0 are kept as gains, upper CI below
+ 0 as losses, and the rest with CI overlapping zero are collapsed as neutral.
+ """
+ margin = segarr['sem'] * zscore
+ levels = pd.Series(np.zeros(len(segarr)))
+ levels[segarr['log2'] - margin > 0] = 1
+ levels[segarr['log2'] + margin < 0] = -1
+ return squash_by_groups(segarr, levels)
diff --git a/cnvlib/segmentation/__init__.py b/cnvlib/segmentation/__init__.py
index 0cbda35..da65cae 100644
--- a/cnvlib/segmentation/__init__.py
+++ b/cnvlib/segmentation/__init__.py
@@ -1,49 +1,110 @@
"""Segmentation of copy number values."""
-from __future__ import absolute_import, division
+from __future__ import absolute_import, division, print_function
+from builtins import map
+
+import locale
import logging
import math
import os.path
import tempfile
+from concurrent import futures
import numpy as np
import pandas as pd
+from Bio._py3k import StringIO
+from skgenome import tabio
-from .. import core, ngfrills, params, smoothing, vary
+from .. import core, params, smoothing, vary
from ..cnary import CopyNumArray as CNA
from . import cbs, flasso, haar
-from Bio._py3k import StringIO
-
def do_segmentation(cnarr, method, threshold=None, variants=None,
skip_low=False, skip_outliers=10,
+ save_dataframe=False, rlibpath=None,
+ processes=1):
+ """Infer copy number segments from the given coverage table."""
+ if variants:
+ variants = variants.heterozygous()
+ if not threshold:
+ threshold = {'cbs': 0.0001,
+ 'flasso': 0.005,
+ 'haar': 0.001,
+ }[method]
+ logging.info("Segmenting with method '%s', significance threshold %g",
+ method, threshold)
+
+ # XXX parallel flasso segfaults in R when run on a single chromosome
+ if processes == 1 or method == 'flasso':
+ cna = _do_segmentation(cnarr, method, threshold, variants, skip_low,
+ skip_outliers, save_dataframe, rlibpath)
+ if save_dataframe:
+ cna, rstr = cna
+ rstr = _to_str(rstr)
+
+ else:
+ with futures.ProcessPoolExecutor(processes) as pool:
+ # ENH: run each chrom. arm separately (via knownsegs, see cbs)
+ rets = list(pool.map(_ds, ((ca, method, threshold, variants, skip_low,
+ skip_outliers, save_dataframe, rlibpath)
+ for _, ca in cnarr.by_chromosome())))
+ if save_dataframe:
+ # rets is a list of (CNA, R dataframe string) -- unpack
+ rets, r_dframe_strings = zip(*rets)
+ # Strip the header line from all but the first dataframe, then combine
+ r_dframe_strings = map(_to_str, r_dframe_strings)
+ rstr = [next(r_dframe_strings)]
+ rstr.extend(r[r.index('\n') + 1:] for r in r_dframe_strings)
+ rstr = "".join(rstr)
+ cna = cnarr.concat(rets)
+
+ if save_dataframe:
+ return cna, rstr
+ return cna
+
+
+def _to_str(s, enc=locale.getpreferredencoding()):
+ if isinstance(s, bytes):
+ return s.decode(enc)
+ return s
+
+
+def _ds(args):
+ """Wrapper for parallel map"""
+ return _do_segmentation(*args)
+
+
+def _do_segmentation(cnarr, method, threshold, variants=None,
+ skip_low=False, skip_outliers=10,
save_dataframe=False, rlibpath=None):
"""Infer copy number segments from the given coverage table."""
- filtered_cn = cnarr
+ if not len(cnarr):
+ return cnarr
+
+ filtered_cn = cnarr.copy()
if skip_low:
- before = len(filtered_cn)
- filtered_cn = filtered_cn.drop_low_coverage()
- logging.info("Dropped %d low-coverage bins", before - len(filtered_cn))
+ filtered_cn = filtered_cn.drop_low_coverage(verbose=True)
if skip_outliers:
filtered_cn = drop_outliers(filtered_cn, 50, skip_outliers)
+ if not len(filtered_cn):
+ return filtered_cn
+ seg_out = ""
if method == 'haar':
- threshold = threshold or 0.001
segarr = haar.segment_haar(filtered_cn, threshold)
- segarr['gene'], segarr['weight'] = transfer_names_weights(segarr, cnarr)
+ segarr['gene'], segarr['weight'], segarr['depth'] = \
+ transfer_fields(segarr, cnarr)
elif method in ('cbs', 'flasso'):
# Run R scripts to calculate copy number segments
- if method == 'cbs':
- rscript = cbs.CBS_RSCRIPT
- threshold = threshold or 0.0001
- elif method == 'flasso':
- rscript = flasso.FLASSO_RSCRIPT
- threshold = threshold or 0.005
-
- with tempfile.NamedTemporaryFile(suffix='.cnr') as tmp:
+ rscript = {'cbs': cbs.CBS_RSCRIPT,
+ 'flasso': flasso.FLASSO_RSCRIPT,
+ }[method]
+
+ filtered_cn['start'] += 1 # Convert to 1-indexed coordinates for R
+ with tempfile.NamedTemporaryFile(suffix='.cnr', mode="w+t") as tmp:
filtered_cn.data.to_csv(tmp, index=False, sep='\t',
- float_format='%.6g')
+ float_format='%.6g', mode="w+t")
tmp.flush()
script_strings = {
'probes_fname': tmp.name,
@@ -51,33 +112,30 @@ def do_segmentation(cnarr, method, threshold=None, variants=None,
'threshold': threshold,
'rlibpath': ('.libPaths(c("%s"))' % rlibpath if rlibpath else ''),
}
- with ngfrills.temp_write_text(rscript % script_strings) as script_fname:
- seg_out = ngfrills.call_quiet('Rscript', script_fname)
- # ENH: run each chromosome separately
- # ENH: run each chrom. arm separately (via knownsegs)
- segarr = cnarr.as_dataframe(seg2cns(seg_out))
- segarr.sort_columns()
-
+ with core.temp_write_text(rscript % script_strings,
+ mode='w+t') as script_fname:
+ seg_out = core.call_quiet('Rscript', '--vanilla', script_fname)
+ # Convert R dataframe contents (SEG) to a proper CopyNumArray
+ # NB: Automatically shifts 'start' back from 1- to 0-indexed
+ segarr = tabio.read(StringIO(seg_out.decode()), "seg", into=CNA)
if method == 'flasso':
segarr = squash_segments(segarr)
-
segarr = repair_segments(segarr, cnarr)
else:
raise ValueError("Unknown method %r" % method)
+ segarr.meta = cnarr.meta.copy()
if variants:
# Re-segment the variant allele freqs within each segment
newsegs = [haar.variants_in_segment(subvarr, segment, 0.01 * threshold)
for segment, subvarr in variants.by_ranges(segarr)]
segarr = segarr.as_dataframe(pd.concat(newsegs))
- segarr.sort_columns()
- # TODO fix ploidy on allosomes
- allelics = vary._allele_specific_copy_numbers(segarr, variants)
- segarr.data = pd.concat([segarr.data, allelics], axis=1, copy=False)
-
- segarr['gene'], segarr['weight'] = transfer_names_weights(segarr, cnarr)
+ segarr['baf'] = variants.baf_by_ranges(segarr)
+ segarr['gene'], segarr['weight'], segarr['depth'] = \
+ transfer_fields(segarr, cnarr)
+ segarr.sort_columns()
if save_dataframe:
return segarr, seg_out
else:
@@ -94,6 +152,8 @@ def drop_outliers(cnarr, width, factor):
deviations from the rolling mean. For a window size of 50, the breakdown
point is 2.5 outliers within a window, which is plenty robust for our needs.
"""
+ if not len(cnarr):
+ return cnarr
outlier_mask = np.concatenate([
smoothing.rolling_outlier_quantile(subarr['log2'], width, .95, factor)
for _chrom, subarr in cnarr.by_chromosome()])
@@ -103,94 +163,83 @@ def drop_outliers(cnarr, width, factor):
n_outliers,
cnarr[outlier_mask].data.head(20),
"\n..." if n_outliers > 20 else "")
- else:
- logging.info("No outlier bins")
return cnarr[~outlier_mask]
-def transfer_names_weights(segments, cnarr, ignore=params.IGNORE_GENE_NAMES):
- """Copy gene names from `cnarr` to the segmented `segarr`.
+def transfer_fields(segments, cnarr, ignore=params.IGNORE_GENE_NAMES):
+ """Map gene names, weights, depths from `cnarr` bins to `segarr` segments.
- Segment name is the comma-separated list of bin gene names.
+ Segment gene name is the comma-separated list of bin gene names. Segment
+ weight is the sum of bin weights, and depth is the (weighted) mean of bin
+ depths.
"""
- ignore += ("Background",)
- segnames = ['-'] * len(segments)
+ if not len(cnarr):
+ return [], [], []
+
+ ignore += params.ANTITARGET_ALIASES
+ if 'weight' not in cnarr:
+ cnarr['weight'] = 1
+ if 'depth' not in cnarr:
+ cnarr['depth'] = np.exp2(cnarr['log2'])
+ seggenes = ['-'] * len(segments)
segweights = np.zeros(len(segments))
+ segdepths = np.zeros(len(segments))
for i, (_seg, subprobes) in enumerate(cnarr.by_ranges(segments)):
+ if not len(subprobes):
+ continue
segweights[i] = subprobes['weight'].sum()
+ if subprobes['weight'].sum() > 0:
+ segdepths[i] = np.average(subprobes['depth'], weights=subprobes['weight'])
subgenes = [g for g in pd.unique(subprobes['gene']) if g not in ignore]
if subgenes:
- segnames[i] = ",".join(subgenes)
- return segnames, segweights
-
-
-def seg2cns(seg_text):
- """Convert R dataframe contents (SEG) to our native tabular format.
-
- Return a pandas.Dataframe with CNA columns.
- """
- try:
- table = pd.read_table(StringIO(seg_text), comment='[')
- except pd.parser.CParserError:
- raise ValueError("Unexpected dataframe contents:\n%s" % (seg_text))
- if len(table.columns) == 6:
- table.columns = ["sample_id", "chromosome", "start", "end", "probes",
- "log2"]
- elif len(table.columns) == 5:
- table.columns = ["sample_id", "chromosome", "start", "end", "log2"]
- else:
- raise ValueError("Segmentation output is not valid SEG format:\n"
- + seg_text)
- del table["sample_id"]
- table["start"] = [int(math.ceil(float(val))) for val in table["start"]]
- table["end"] = [int(math.ceil(float(val))) for val in table["end"]]
- table["gene"] = '-'
- return table
+ seggenes[i] = ",".join(subgenes)
+ return seggenes, segweights, segdepths
-def squash_segments(seg_pset):
+def squash_segments(segments):
"""Combine contiguous segments."""
curr_chrom = None
curr_start = None
curr_end = None
curr_genes = []
- curr_val = None
- curr_cnt = 0
+ curr_log2 = None
+ curr_probes = 0
squashed_rows = []
- for row in seg_pset:
- if row.chromosome == curr_chrom and row.log2 == curr_val:
+ for row in segments:
+ if row.chromosome == curr_chrom and row.log2 == curr_log2:
# Continue the current segment
curr_end = row.end
curr_genes.append(row.gene)
- curr_cnt += 1
+ curr_probes += 1
else:
# Segment break
# Finish the current segment
- if curr_cnt:
+ if curr_probes:
squashed_rows.append((curr_chrom, curr_start, curr_end,
",".join(pd.unique(curr_genes)),
- curr_val, curr_cnt))
+ curr_log2, curr_probes))
# Start a new segment
curr_chrom = row.chromosome
curr_start = row.start
curr_end = row.end
curr_genes = []
- curr_val = row.log2
- curr_cnt = 1
+ curr_log2 = row.log2
+ curr_probes = 1
# Remainder
squashed_rows.append((curr_chrom, curr_start, curr_end,
",".join(pd.unique(curr_genes)),
- curr_val, curr_cnt))
- return seg_pset.as_rows(squashed_rows)
+ curr_log2, curr_probes))
+ return segments.as_rows(squashed_rows)
+# TODO/ENH combine with transfer_fields
+# Recalculate segment means, weights, depths here instead of in R
def repair_segments(segments, orig_probes):
"""Post-process segmentation output.
1. Ensure every chromosome has at least one segment.
2. Ensure first and last segment ends match 1st/last bin ends
(but keep log2 as-is).
- 3. Store probe-level gene names, comma-separated, as the segment name.
"""
segments = segments.copy()
extra_segments = []
@@ -207,5 +256,4 @@ def repair_segments(segments, orig_probes):
extra_segments.append(null_segment)
if extra_segments:
segments.add(segments.as_rows(extra_segments))
- # ENH: Recalculate segment means here instead of in R
return segments
diff --git a/cnvlib/segmentation/cbs.py b/cnvlib/segmentation/cbs.py
index 5e70d97..c6b1625 100644
--- a/cnvlib/segmentation/cbs.py
+++ b/cnvlib/segmentation/cbs.py
@@ -2,8 +2,8 @@ CBS_RSCRIPT = """\
#!/usr/bin/env Rscript
# Calculate copy number segmentation by CBS.
-# Input: log2 coverage data in Nexus 'basic' format
-# Output: the CBS data table
+# Input: log2 coverage data in CNVkit's tabular format
+# Output: the CBS data table (SEG)
%(rlibpath)s
library('PSCBS') # Requires: R.utils, R.oo, R.methodsS3
diff --git a/cnvlib/segmentation/flasso.py b/cnvlib/segmentation/flasso.py
index 610cf2a..f04f8b6 100644
--- a/cnvlib/segmentation/flasso.py
+++ b/cnvlib/segmentation/flasso.py
@@ -1,18 +1,16 @@
FLASSO_RSCRIPT = """\
#!/usr/bin/env Rscript
-# Calculate copy number segmentation by CBS.
-# Input: log2 coverage data in Nexus 'basic' format
-# Output: the CBS data table
+# Calculate copy number segmentation by Fused Lasso.
+# Input: log2 coverage data in CNVkit's tabular format
+# Output: the CBS-style SEG data table
%(rlibpath)s
library('cghFLasso')
tbl <- read.delim("%(probes_fname)s")
-# Ignore low-coverage probes
-positions <- (tbl$start + tbl$end) * 0.5
-write("Segmenting the probe data", stderr())
+write(paste("Segmenting", levels(tbl$chromosome)), stderr())
fit <- cghFLasso(tbl$log2, FDR=%(threshold)g)
# Reformat the output table as SEG
diff --git a/cnvlib/segmentation/haar.py b/cnvlib/segmentation/haar.py
index c7bd5ac..8bad79a 100644
--- a/cnvlib/segmentation/haar.py
+++ b/cnvlib/segmentation/haar.py
@@ -23,6 +23,7 @@ segmentation result.
"""
from __future__ import absolute_import, division, print_function
+from builtins import range, zip
import logging
import math
@@ -31,17 +32,24 @@ import numpy as np
import pandas as pd
from scipy import stats
-# from .. import params
-
def segment_haar(cnarr, fdr_q):
"""Do segmentation for CNVkit.
Calculate copy number segmentation by HaarSeg
(http://haarseg.r-forge.r-project.org/)
- Input: log2 coverage data in Nexus 'basic' format
- Output: the CBS data table
+ Parameters
+ ----------
+ cnarr : CopyNumArray
+ Binned, normalized copy ratios.
+ fdr_q : float
+ False discovery rate q-value.
+
+ Returns
+ -------
+ CopyNumArray
+ The CBS data table as a CNVkit object.
"""
# Segment each chromosome individually
# ENH - skip large gaps (segment chrom. arms separately)
@@ -72,14 +80,14 @@ def one_chrom(cnarr, fdr_q, chrom):
def variants_in_segment(varr, segment, fdr_q):
if len(varr):
- values = varr.mirrored_baf()
+ values = varr.mirrored_baf(above_half=True, tumor_boost=True)
segtable = haarSeg(values,
fdr_q,
W=None) # weight by sqrt(DP)?
else:
- values = []
- segtable = []
- if segtable and len(segtable['start']) > 1:
+ values = pd.Series()
+ segtable = None
+ if segtable is not None and len(segtable['start']) > 1:
logging.info("Segmented on allele freqs in %s:%d-%d",
segment.chromosome, segment.start, segment.end)
# Ensure breakpoint locations make sense
@@ -96,18 +104,19 @@ def variants_in_segment(varr, segment, fdr_q):
'start': starts,
'end': ends,
# 'baf': segtable['mean'],
- 'gene': '-', #segment.gene,
+ 'gene': segment.gene, # '-'
'log2': segment.log2,
'probes': segtable['size'],
- # 'weight': segment.weight * segtable['size'] / segment.size,
+ # 'weight': (segment.weight * segtable['size']
+ # / (segment.end - segment.start)),
})
else:
table = pd.DataFrame({
'chromosome': segment.chromosome,
'start': segment.start,
'end': segment.end,
- # 'baf': np.median(values),
- 'gene': '-', #segment.gene,
+ # 'baf': values.median(),
+ 'gene': segment.gene, #'-',
'log2': segment.log2,
'probes': segment.probes,
# 'weight': segment.weight,
@@ -126,43 +135,43 @@ def haarSeg(I, breaksFdrQ,
haarEndLevel=5):
r"""Perform segmentation according to the HaarSeg algorithm.
- Arguments:
-
- I
+ Parameters
+ ----------
+ I : array
A 1D array of log-ratio values, sorted according to their genomic
location.
- W
+ W : array
Weight matrix, corresponding to quality of measurement, with values
:math:`1/(\sigma^2)`. Must have the same size as I.
- rawI
+ rawI : array
The minimum between the raw test-sample and control-sample coverages
(before applying log ratio, but after any background reduction and/or
normalization). These raw red / green measurments are used to detect
low-value probes, which are more sensitive to noise.
Used for the non-stationary variance compensation.
Must have the same size as I.
- breaksFdrQ
+ breaksFdrQ : float
The FDR q parameter. This value should lie between 0 and 0.5. The
smaller this value is, the less sensitive the segmentation result will
be.
For example, we will detect fewer segmentation breaks when using Q =
1e-4, compared to when using Q = 1e-3.
Common used values are 1e-2, 1e-3, 1e-4.
- haarStartLevel
+ haarStartLevel : int
The detail subband from which we start to detect peaks. The higher this
value is, the less sensitive we are to short segments. The default is
value is 1, corresponding to segments of 2 probes.
- haarEndLevel
+ haarEndLevel : int
The detail subband until which we use to detect peaks. The higher this
value is, the more sensitive we are to large trends in the data. This
value DOES NOT indicate the largest possible segment that can be
detected. The default is value is 5, corresponding to step of 32 probes
in each direction.
-
- Returns:
-
- A tuple of two elements:
+ Returns
+ -------
+ tuple
+ Two elements:
1. Segments result table, a list of tuples:
(segment start index, segment size, segment value)
2. Segmented signal array (same size as I)
@@ -173,9 +182,9 @@ def haarSeg(I, breaksFdrQ,
"""Median absolute deviation, with deviations given."""
if len(diff_vals) == 0:
return 0.
- return np.median(np.abs(diff_vals)) * 1.4826
+ return diff_vals.abs().median() * 1.4826
- diffI = HaarConv(I, None, 1)
+ diffI = pd.Series(HaarConv(I, None, 1))
if rawI:
# Non-stationary variance empirical threshold set to 50
NSV_TH = 50
@@ -241,8 +250,12 @@ def FDRThres(x, q, stdev):
def SegmentByPeaks(data, peaks, weights=None):
"""Average the values of the probes within each segment.
- `data` : the probe array values
- `peaks` : array of copy number breakpoints
+ Parameters
+ ----------
+ data : array
+ the probe array values
+ peaks : array
+ Positions of copy number breakpoints in the original array
Source: SegmentByPeaks.R
"""
@@ -270,14 +283,16 @@ def HaarConv(signal, #const double * signal,
):
"""Convolve haar wavelet function with a signal, applying circular padding.
- Params:
-
- signal: const array of floats
- weight: const array of floats (optional)
- stepHalfSize: int
+ Parameters
+ ----------
+ signal : const array of floats
+ weight : const array of floats (optional)
+ stepHalfSize : int
- Output:
- result: array of floats
+ Returns
+ -------
+ array
+ Of floats, representing the convolved signal.
Source: HaarSeg.c
"""
@@ -336,12 +351,14 @@ def FindLocalPeaks(signal, #const double * signal,
First and last index are never considered extramum.
- Parameters:
+ Parameters
+ ----------
+ signal : const array of floats
- signal: const array of floats
-
- Output:
- peakLoc: array of ints
+ Returns
+ -------
+ peakLoc : array of ints
+ Locations of extrema in `signal`
Source: HaarSeg.c
"""
@@ -390,15 +407,15 @@ def UnifyLevels(baseLevel, #const int * baseLevel,
Merge the two lists of breakpoints, but drop addonLevel values that are too
close to baseLevel values.
- Parameters:
-
- baseLevel: const array of ints
- addonLevel: const array of ints
- windowSize: int
-
- Output:
+ Parameters
+ ----------
+ baseLevel : const array of ints
+ addonLevel : const array of ints
+ windowSize : int
- joinedLevel: array of ints
+ Returns
+ -------
+ joinedLevel : array of ints
Source: HaarSeg.c
"""
@@ -443,13 +460,14 @@ def PulseConv(signal, #const double * signal,
Used for non-stationary variance compensation.
- Parameters:
+ Parameters
+ ----------
+ signal: const array of floats
+ pulseSize: int
- signal: const array of floats
- pulseSize: int
-
- Output:
- result: modifiable array of floats
+ Returns
+ -------
+ array of floats
Source: HaarSeg.c
"""
@@ -492,10 +510,10 @@ def AdjustBreaks(signal, #const double * signal,
We try to move each break 1 sample left/right, choosing the offset which
leads to minimum data error.
- Parameters:
-
- signal: const array of floats
- peakLoc: const array of ints
+ Parameters
+ ----------
+ signal: const array of floats
+ peakLoc: const array of ints
Source: HaarSeg.c
"""
diff --git a/cnvlib/smoothing.py b/cnvlib/smoothing.py
index 2f28621..b7cfd6a 100644
--- a/cnvlib/smoothing.py
+++ b/cnvlib/smoothing.py
@@ -2,7 +2,6 @@
from __future__ import absolute_import, division
import math
-import warnings
import numpy as np
import pandas as pd
@@ -23,48 +22,37 @@ def check_inputs(x, width):
elif width >= 2 and int(width) == width:
wing = width // 2
else:
- raise ValueError("width must be between 0 and 1 (got %s)" % width)
- if wing > len(x):
- wing = len(x) - 1
+ raise ValueError("width fraction must be between 0 and 1 (got %s)"
+ % width)
+ wing = max(wing, 5)
+ wing = min(wing, len(x) - 1)
assert wing > 0, "Wing must be greater than 0 (got %s)" % wing
- return x, wing
+ # Pad the edges of the original array with mirror copies
+ signal = pd.Series(np.concatenate((x[wing-1::-1], x, x[:-wing-1:-1])))
+ return x, wing, signal
def rolling_median(x, width):
"""Rolling median with mirrored edges."""
- x, wing = check_inputs(x, width)
- # Pad the edges of the original array with mirror copies
- signal = np.concatenate((x[wing-1::-1], x, x[:-wing-1:-1]))
- with warnings.catch_warnings():
- # NB: in pandas 0.18+ this function is deprecated
- warnings.simplefilter("ignore", FutureWarning)
- rolled = pd.rolling_median(signal, 2 * wing + 1, center=True)
- return rolled[wing:-wing]
+ x, wing, signal = check_inputs(x, width)
+ rolled = signal.rolling(2 * wing + 1, 1, center=True).median()
+ # if rolled.hasnans:
+ # rolled = rolled.interpolate()
+ return np.asfarray(rolled[wing:-wing])
def rolling_quantile(x, width, quantile):
"""Rolling quantile (0--1) with mirrored edges."""
- x, wing = check_inputs(x, width)
- # Pad the edges of the original array with mirror copies
- signal = np.concatenate((x[wing-1::-1], x, x[:-wing-1:-1]))
- with warnings.catch_warnings():
- # NB: in pandas 0.18+ this function is deprecated
- warnings.simplefilter("ignore", FutureWarning)
- rolled = pd.rolling_quantile(signal, 2 * wing + 1, quantile,
- center=True)
- return rolled[wing:-wing]
+ x, wing, signal = check_inputs(x, width)
+ rolled = signal.rolling(2 * wing + 1, 2, center=True).quantile(quantile)
+ return np.asfarray(rolled[wing:-wing])
def rolling_std(x, width):
"""Rolling quantile (0--1) with mirrored edges."""
- x, wing = check_inputs(x, width)
- # Pad the edges of the original array with mirror copies
- signal = np.concatenate((x[wing-1::-1], x, x[:-wing-1:-1]))
- with warnings.catch_warnings():
- # NB: in pandas 0.18+ this function is deprecated
- warnings.simplefilter("ignore", FutureWarning)
- rolled = pd.rolling_std(signal, 2 * wing + 1, center=True)
- return rolled[wing:-wing]
+ x, wing, signal = check_inputs(x, width)
+ rolled = signal.rolling(2 * wing + 1, 2, center=True).std()
+ return np.asfarray(rolled[wing:-wing])
def smoothed(x, width, do_fit_edges=False):
@@ -72,17 +60,15 @@ def smoothed(x, width, do_fit_edges=False):
See: https://en.wikipedia.org/wiki/Kaiser_window
- Parameters:
-
+ Parameters
+ ----------
x : array-like
1-dimensional numeric data set.
width : float
Fraction of x's total length to include in the rolling window (i.e. the
proportional window width), or the integer size of the window.
"""
- x, wing = check_inputs(x, width)
- # Pad the edges with mirror-image copies of the array
- signal = np.concatenate((x[wing-1::-1], x, x[:-wing-1:-1]))
+ x, wing, signal = check_inputs(x, width)
# Apply signal smoothing
window = np.kaiser(2 * wing + 1, 14)
y = np.convolve(window / window.sum(), signal, mode='same')
@@ -146,8 +132,6 @@ def outlier_iqr(a, c=3.0):
def outlier_mad_median(a):
"""MAD-Median rule for detecting outliers.
- Returns: a boolean array of the same size, where outlier indices are True.
-
X_i is an outlier if::
| X_i - M |
@@ -161,8 +145,13 @@ def outlier_mad_median(a):
This is a very robust rule with the highest possible breakdown point of 0.5.
- See:
+ Returns
+ -------
+ np.array
+ A boolean array of the same size as `a`, where outlier indices are True.
+ References
+ ----------
- Davies & Gather (1993) The Identification of Multiple Outliers.
- Rand R. Wilcox (2012) Introduction to robust estimation and hypothesis
testing. Ch.3: Estimating measures of location and scale.
@@ -193,7 +182,7 @@ def rolling_outlier_iqr(x, width, c=3.0):
def rolling_outlier_quantile(x, width, q, m):
- """Return a boolean mask of outliers by multiples of a quantile in a window.
+ """Detect outliers by multiples of a quantile in a window.
Outliers are the array elements outside `m` times the `q`'th
quantile of deviations from the smoothed trend line, as calculated from
@@ -203,6 +192,11 @@ def rolling_outlier_quantile(x, width, q, m):
This is the smoothing method used in BIC-seq (doi:10.1073/pnas.1110574108)
with the parameters width=200, q=.95, m=5 for WGS.
+
+ Returns
+ -------
+ np.array
+ A boolean array of the same size as `x`, where outlier indices are True.
"""
if len(x) <= width:
return np.zeros(len(x), dtype=np.bool_)
@@ -213,10 +207,15 @@ def rolling_outlier_quantile(x, width, q, m):
def rolling_outlier_std(x, width, stdevs):
- """Return a boolean mask of outliers by stdev within a rolling window.
+ """Detect outliers by stdev within a rolling window.
Outliers are the array elements outside `stdevs` standard deviations from
the smoothed trend line, as calculated from the trend line residuals.
+
+ Returns
+ -------
+ np.array
+ A boolean array of the same size as `x`, where outlier indices are True.
"""
if len(x) <= width:
return np.zeros(len(x), dtype=np.bool_)
diff --git a/cnvlib/target.py b/cnvlib/target.py
index b23010e..55c2b6b 100644
--- a/cnvlib/target.py
+++ b/cnvlib/target.py
@@ -2,186 +2,33 @@
from __future__ import division, absolute_import
import logging
-import collections
-from itertools import groupby
+from skgenome import tabio
-# _____________________________________________________________________________
-# Assign refFlat gene names to target intervals
-# ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/
+from . import antitarget
-def add_refflat_names(region_rows, refflat_fname):
- """Apply RefSeq gene names to a list of targeted regions."""
- return assign_names(region_rows, refflat_fname)
-
-def assign_names(region_rows, refflat_fname, default_name='-'):
- """Replace the interval gene names with those at the same loc in refFlat.txt
- """
- ref_genes = read_refflat_genes(refflat_fname)
- for (chrom, strand), chr_rows in groupby(sorted(region_rows,
- key=lambda row: (
- row[0], # chromosome
- row[4], # strand
- row[1], # start
- row[2])), # end
- lambda row: (row[0], row[4])):
- if strand == '.':
- strand = "+|-"
- if (chrom, strand) in ref_genes:
- genes_in_chrom = iter(ref_genes[(chrom, strand)])
- elif '|' in strand:
- strands_with_genes = []
- for std in strand.split('|'):
- if (chrom, std) in ref_genes:
- strands_with_genes.extend(ref_genes[(chrom, std)])
- if strands_with_genes:
- genes_in_chrom = iter(sorted(strands_with_genes))
- else:
- logging.info("Chromosome %s %s not in annotations",
- chrom, strand)
- continue
- else:
- logging.info("Chromosome %s %s not in annotations",
- chrom, strand)
- continue
-
- ex_start, ex_end, ex_name = next(genes_in_chrom)
- for row in chr_rows:
- start, end = row[1:3]
- if ex_end < start:
- # Burn through genes until hitting or passing the interval
- while ex_end < start:
- try:
- ex_start, ex_end, ex_name = next(genes_in_chrom)
- except StopIteration:
- # Interval is past the last annotated gene in chromosome
- # Fake it...
- ex_start, ex_end = end + 1, end + 2
- ex_name = default_name
-
- if ex_start > end:
- # Interval is an unannotated intergenic region (we skipped it)
- yield (chrom, start, end, default_name)
- else:
- assert ex_end > start or ex_start < end
- # Overlap: Use this gene's name and emit the interval
- yield (chrom, start, end, ex_name)
-
-
-def read_refflat_genes(fname):
- """Parse genes; merge those with same name and overlapping regions.
-
- Returns a dict of: {(chrom, strand): [(gene start, gene end, gene name), ...]}
- """
- genedict = collections.defaultdict(list)
- with open(fname) as genefile:
- for line in genefile:
- name, _rx, chrom, strand, start, end, _ex = parse_refflat_line(line)
- # Skip antisense RNA annotations
- if name.endswith('-AS1'):
- continue
- assert strand in '+-'
- genedict[name].append((chrom, strand, start, end))
-
- chromdict = collections.defaultdict(list)
- for name, locs in genedict.iteritems():
- locs = list(set(locs))
- if len(locs) == 1:
- chrom, strand, start, end = locs[0]
- chromdict[(chrom, strand)].append((start, end, name))
- else:
- # Check locs for overlap; merge if so
- locs.sort()
- curr_chrom, curr_strand, curr_start, curr_end = locs[0]
- curr_start, curr_end = int(curr_start), int(curr_end)
- for chrom, strand, start, end in locs[1:]:
- start, end = int(start), int(end)
- if (chrom != curr_chrom or
- strand != curr_strand or
- start > curr_end + 1 or
- end < curr_start - 1):
- chromdict[(curr_chrom, curr_strand)].append(
- (curr_start, curr_end, name))
- curr_chrom, curr_start, curr_end = chrom, start, end
- else:
- curr_start = min(start, curr_start)
- curr_end = max(end, curr_end)
- # Emit the final interval in this group
- chromdict[(curr_chrom, curr_strand)].append(
- (curr_start, curr_end, name))
-
- # Finally, sort the keys, and return the results
- for key in list(chromdict):
- chromdict[key].sort()
- return chromdict
-
-
-def parse_refflat_line(line):
- """Parse one line of refFlat.txt; return relevant info.
-
- Pair up the exon start and end positions. Add strand direction to each
- chromosome as a "+"/"-" suffix (it will be stripped off later).
- """
- fields = line.split('\t')
- name, refseq, chrom, strand = fields[:4]
- start, end = fields[4:6]
- # start, end = fields[6:8]
- exon_count, exon_starts, exon_ends = fields[8:11]
- exons = zip(exon_starts.rstrip(',').split(','),
- exon_ends.rstrip(',').split(','))
- assert len(exons) == int(exon_count), (
- "Exon count mismatch at %s: file says %s, but counted %d intervals"
- % (name, exon_count, len(exons)))
- return name, refseq, chrom, strand, int(start), int(end), exons
+def do_target(bait_arr, annotate=None, do_short_names=False, do_split=False,
+ avg_size=200/.75):
+ """Transform bait intervals into targets more suitable for CNVkit."""
+ tgt_arr = bait_arr.copy()
+ # Drop zero-width regions
+ tgt_arr = tgt_arr[tgt_arr.start != tgt_arr.end]
+ if do_split:
+ logging.info("Splitting large targets")
+ tgt_arr = tgt_arr.subdivide(avg_size, 0)
+ if annotate:
+ logging.info("Applying annotations as target names")
+ annotation = tabio.read_auto(annotate)
+ antitarget.compare_chrom_names(tgt_arr, annotation)
+ tgt_arr['gene'] = annotation.into_ranges(tgt_arr, 'gene', '-')
+ if do_short_names:
+ logging.info("Shortening target interval labels")
+ tgt_arr['gene'] = list(shorten_labels(tgt_arr['gene']))
+ return tgt_arr
-# def cover_introns(regions):
-# """Apply the name of the surrounding gene to intronic targets.
-
-# If an unnamed target is surrounded by targets that have the same name,
-# consider it an intron and apply that gene name to the unnamed target.
-# Otherwise, leave it unnamed ("-").
-# """
-# last_gene = None
-# last_chrom = None
-# queue = []
-# for chrom, start, end, name in regions:
-# if chrom != last_chrom:
-# # Queue was not intronic (3'-terminal of last chrom)
-# for row in queue:
-# yield row
-# queue = []
-# last_chrom = chrom
-# last_gene = name if name != '-' else None
-# # Track genes; smooth over intronic '-' regions
-# if name == '-':
-# # Not sure if intronic -- enqueue
-# queue.append((chrom, start, end, name))
-# else:
-# if name == last_gene:
-# # Queued row(s) were intronic
-# if queue:
-# for cm, st, ed, _nm in queue:
-# yield cm, st, ed, name
-# queue = []
-# else:
-# # Queued row(s) were intergenic
-# for row in queue:
-# yield row
-# queue = []
-# last_gene = name
-# yield chrom, start, end, name
-# # Remainder
-# for row in queue:
-# yield row
-
-
-
-# _____________________________________________________________________________
-# Clean/shorten interval names
-
-def shorten_labels(interval_rows):
+def shorten_labels(gene_labels):
"""Reduce multi-accession interval labels to the minimum consistent.
So: BED or interval_list files have a label for every region. We want this
@@ -190,46 +37,47 @@ def shorten_labels(interval_rows):
sub-regions of the gene, we can extract a single accession that covers the
maximum number of consecutive regions that share this accession.
- e.g.
+ e.g.::
- ...
- chr1 879125 879593 + mRNA|JX093079,ens|ENST00000342066,mRNA|JX093077,ref|SAMD11,mRNA|AF161376,mRNA|JX093104
- chr1 880158 880279 + ens|ENST00000483767,mRNA|AF161376,ccds|CCDS3.1,ref|NOC2L
- ...
+ ...
+ mRNA|JX093079,ens|ENST00000342066,mRNA|JX093077,ref|SAMD11,mRNA|AF161376,mRNA|JX093104
+ ens|ENST00000483767,mRNA|AF161376,ccds|CCDS3.1,ref|NOC2L
+ ...
- becomes:
+ becomes::
- chr1 879125 879593 + mRNA|AF161376
- chr1 880158 880279 + mRNA|AF161376
+ ...
+ mRNA|AF161376
+ mRNA|AF161376
+ ...
"""
longest_name_len = 0
curr_names = set()
- curr_gene_coords = []
+ curr_gene_count = 0
- for row in interval_rows:
- next_coords = row[:-1]
- next_names = set(row[-1].rstrip().split(','))
+ for label in gene_labels:
+ next_names = set(label.rstrip().split(','))
assert len(next_names)
overlap = curr_names.intersection(next_names)
if overlap:
# Continuing the same gene; update shared accessions
curr_names = filter_names(overlap)
- curr_gene_coords.append(next_coords)
+ curr_gene_count += 1
else:
- # End of the old gene -- emit coords + shared name(s)
- for coords in curr_gene_coords:
- out_row = emit(coords, curr_names)
- yield out_row
- longest_name_len = max(longest_name_len, len(out_row[-1]))
+ # End of the old gene -- emit shared name(s)
+ for _i in range(curr_gene_count):
+ out_name = shortest_name(curr_names)
+ yield out_name
+ longest_name_len = max(longest_name_len, len(out_name))
# Start of a new gene
- curr_gene_coords = [next_coords]
+ curr_gene_count = 1
curr_names = next_names
# Final emission
- for coords in curr_gene_coords:
- out_row = emit(coords, curr_names)
- yield out_row
- longest_name_len = max(longest_name_len, len(out_row[-1]))
+ for _i in range(curr_gene_count):
+ out_name = shortest_name(curr_names)
+ yield out_name
+ longest_name_len = max(longest_name_len, len(out_name))
logging.info("Longest name length: %d", longest_name_len)
@@ -245,79 +93,10 @@ def filter_names(names, exclude=('mRNA',)):
return names
-def emit(coords, names):
- """Try filtering names again. Format the row for yielding."""
- try:
- final_name = shortest_name(filter_names(names))
- out_row = list(coords) + [final_name]
- except ValueError:
- raise ValueError(coords)
- return out_row
-
-
def shortest_name(names):
"""Return the shortest trimmed name from the given set."""
- name = min(names, key=len)
+ name = min(filter_names(names), key=len)
if len(name) > 2 and '|' in name[1:-1]:
# Split 'DB|accession' and extract the accession sans-DB
name = name.split('|')[-1]
return name
-
-
-# _____________________________________________________________________________
-# Split targets
-
-# ENH - fix overlapping bins at midpoint of overlap? try to equalize bin size?
-# - or just concatenate the bins & divide evenly?
-# - do this for adjacent bins too?
-# e.g. --balance-adjacent
-def split_targets(region_rows, avg_size):
- """Split large tiled intervals into smaller, consecutive targets.
-
- For each of the tiled regions:
-
- - Divide into equal-size (tile_size/avg_size) portions
- - Emit the (chrom, start, end) coords of each portion
-
- Bin the regions according to avg_size.
- """
- prev_chrom = None
- prev_start = None
- prev_end = -1
- for chrom, start, end, name in region_rows:
- if (chrom, start, end) == (prev_chrom, prev_start, prev_end):
- # Skip duplicate regions, even if names differ
- # ENH - Update the name?
- logging.info("Duplicate row %s %s:%d-%d", name, chrom, start, end)
- continue
- if chrom == prev_chrom and start <= prev_end:
- if end > prev_end:
- # Partial overlap: already handled the initial part of this bin
- start = prev_end
- else:
- # Complete overlap: nothing to do on this bin
- logging.info("Bin %s %s:%s-%s fully covered by previous bin"
- "%s:%s-%s",
- name, chrom, start, end,
- prev_chrom, prev_start, prev_end)
- continue
- prev_chrom = chrom
- prev_start = start
- span = end - start
- if span >= avg_size * 1.5:
- logging.info("Splitting: %s %s",
- name.ljust(15), str(end - start + 1).rjust(6))
- # Divide the background region into equal-sized bins
- nbins = round(span / avg_size) or 1
- bin_size = span / nbins
- # Locate & emit background bins
- bin_start = start
- while bin_start < (end - 2):
- bin_end = bin_start + bin_size
- yield (chrom, int(bin_start), int(bin_end), name)
- prev_end = int(bin_end)
- bin_start = bin_end
- else:
- yield (chrom, start, end, name)
- prev_end = end
-
diff --git a/cnvlib/vary.py b/cnvlib/vary.py
index 932f8bc..d5921f1 100644
--- a/cnvlib/vary.py
+++ b/cnvlib/vary.py
@@ -1,308 +1,160 @@
"""An array of genomic intervals, treated as variant loci."""
from __future__ import absolute_import, division, print_function
-
+from builtins import str
import logging
import numpy as np
import pandas as pd
-import vcf
-
-from . import gary
+from skgenome import GenomicArray
-class VariantArray(gary.GenomicArray):
+class VariantArray(GenomicArray):
"""An array of genomic intervals, treated as variant loci.
Required columns: chromosome, start, end, ref, alt
"""
_required_columns = ("chromosome", "start", "end", "ref", "alt")
- _required_dtypes = ("string", "int", "int", "string", "string")
+ _required_dtypes = (str, int, int, str, str)
# Extra: somatic, zygosity, depth, alt_count, alt_freq
def __init__(self, data_table, meta_dict=None):
- gary.GenomicArray.__init__(self, data_table, meta_dict)
-
- def mirrored_baf(self, above_half=True, tumor_boost=True):
+ GenomicArray.__init__(self, data_table, meta_dict)
+
+ def baf_by_ranges(self, ranges, summary_func=np.nanmedian, above_half=None,
+ tumor_boost=False):
+ """Aggregate variant (b-allele) frequencies in each given bin.
+
+ Get the average BAF in each of the bins of another genomic array:
+ BAFs are mirrored above/below 0.5 (per `above_half`), grouped in each
+ bin of `ranges`, and summarized into one value per bin with
+ `summary_func` (default median).
+
+ Parameters
+ ----------
+ ranges : GenomicArray or subclass
+ Bins for grouping the variants in `self`.
+ above_half : bool
+ The same as in `mirrored_baf`.
+ tumor_boost : bool
+ The same as in `mirrored_baf`.
+
+ Returns
+ -------
+ float array
+ Average b-allele frequency in each range; same length as `ranges`.
+ May contain NaN values where no variants overlap a range.
+ """
+ if 'alt_freq' not in self:
+ logging.warn("VCF has no allele frequencies for BAF calculation")
+ return pd.Series(np.repeat(np.nan, len(ranges)))
+
+ def summarize(vals):
+ return summary_func(_mirrored_baf(vals, above_half))
+
+ if tumor_boost and 'n_alt_freq' in self:
+ self = self.copy()
+ self['alt_freq'] = self.tumor_boost()
+ return self.into_ranges(ranges, 'alt_freq', np.nan, summarize)
+
+ def zygosity_from_freq(self, het_freq=0.0, hom_freq=1.0):
+ """Set zygosity (genotype) according to allele frequencies.
+
+ Creates or replaces 'zygosity' column if 'alt_freq' column is present,
+ and 'n_zygosity' if 'n_alt_freq' is present.
+
+ Parameters
+ ----------
+ het_freq : float
+ Assign zygosity 0.5 (heterozygous), otherwise 0.0 (i.e. reference
+ genotype), to variants with alt allele frequency of at least this
+ value.
+ hom_freq : float
+ Assign zygosity 1.0 (homozygous) to variants with alt allele
+ frequency of at least this value.
+ """
+ assert 0.0 <= het_freq <= hom_freq <= 1.0
+ self = self.copy() # Don't modify the original
+ for freq_key, zyg_key in (('alt_freq', 'zygosity'),
+ ('n_alt_freq', 'n_zygosity')):
+ if zyg_key in self:
+ zyg = np.repeat(0.5, len(self))
+ vals = self[freq_key].values
+ zyg[vals >= hom_freq] = 1.0
+ zyg[vals < het_freq] = 0.0
+ self[zyg_key] = zyg
+ return self
+
+ def heterozygous(self):
+ """Subset to only heterozygous variants.
+
+ Use 'zygosity' or 'n_zygosity' genotype values (if present) to exclude
+ variants with value 0.0 or 1.0.
+ If these columns are missing, or there are no heterozygous variants,
+ then return the full (input) set of variants.
+
+ Returns
+ -------
+ VariantArray
+ The subset of `self` with heterozygous genotype, or allele frequency
+ between the specified thresholds.
+ """
+ if 'zygosity' in self:
+ # Use existing genotype/zygosity info
+ zygosity = self['n_zygosity' if 'n_zygosity' in self
+ else 'zygosity']
+ het_idx = (zygosity != 0.0) & (zygosity != 1.0)
+ if het_idx.any():
+ # Only take het. subset if the subset is not empty
+ self = self[het_idx]
+ return self
+
+ def mirrored_baf(self, above_half=None, tumor_boost=False):
"""Mirrored B-allele frequencies (BAFs).
- Flip BAFs to be all above 0.5 (if `above_half`) or below 0.5, for
- consistency.
-
- With `tumor_boost`, normalize tumor-sample allele frequencies to the
- matched normal allele frequencies.
+ Parameters
+ ----------
+ above_half : bool or None
+ If specified, flip BAFs to be all above 0.5 (True) or below 0.5
+ (False), respectively, for consistency. Otherwise, if None, mirror
+ in the direction of the majority of BAFs.
+ tumor_boost : bool
+ Normalize tumor-sample allele frequencies to the matched normal
+ sample's allele frequencies.
+
+ Returns
+ -------
+ float array
+ Mirrored b-allele frequencies, the same length as `self`. May
+ contain NaN values.
"""
if tumor_boost and "n_alt_freq" in self:
- alt_freqs = self.tumor_boost()
- else:
- alt_freqs = self["alt_freq"]
- fromhalf = np.abs(alt_freqs - 0.5)
- if above_half:
- return fromhalf + 0.5
+ alt_freq = self.tumor_boost()
else:
- return 0.5 - fromhalf
+ alt_freq = self["alt_freq"]
+ return _mirrored_baf(alt_freq, above_half)
def tumor_boost(self):
"""TumorBoost normalization of tumor-sample allele frequencies.
De-noises the signal for detecting LOH.
- """
- if "n_alt_freq" in self:
- n_freqs = self["n_alt_freq"]
- else:
- raise ValueError("TumorBoost requires a paired normal sample in "
- "the VCF.")
- t_freqs = self["alt_freq"]
- return _tumor_boost(t_freqs, n_freqs)
-
- # I/O
-
- @classmethod
- def read_vcf(cls, infile, sample_id=None, normal_id=None, min_depth=None,
- skip_hom=False, skip_reject=False, skip_somatic=False):
- """Parse SNV coordinates from a VCF file into a VariantArray."""
- if isinstance(infile, basestring):
- vcf_reader = vcf.Reader(filename=infile)
- else:
- vcf_reader = vcf.Reader(infile)
- if not vcf_reader.samples:
- logging.warn("VCF file %s has no samples; parsing minimal info",
- infile)
- return cls._read_vcf_nosample(infile, sample_id, skip_reject)
-
- columns = [
- "chromosome", "start", "end", "ref", "alt",
- "somatic", "zygosity", "depth", "alt_count"]
- sample_id, normal_id = _select_sample(vcf_reader, sample_id, normal_id)
- if normal_id:
- columns.extend(["n_zygosity", "n_depth", "n_alt_count"])
- rows = _parse_records(vcf_reader, sample_id, normal_id, skip_reject)
- table = pd.DataFrame.from_records(rows, columns=columns)
- table["alt_freq"] = table["alt_count"] / table["depth"]
- if normal_id:
- table["n_alt_freq"] = table["n_alt_count"] / table["n_depth"]
- # Filter out records as requested
- cnt_depth = cnt_hom = cnt_som = 0
- if min_depth:
- dkey = "n_depth" if "n_depth" in table else "depth"
- idx_depth = table[dkey] >= min_depth
- cnt_depth = (~idx_depth).sum()
- table = table[idx_depth]
- if skip_hom:
- zkey = "n_zygosity" if "n_zygosity" in table else "zygosity"
- idx_het = (table[zkey] != 0.0) & (table[zkey] != 1.0)
- cnt_hom = (~idx_het).sum()
- table = table[idx_het]
- if skip_somatic:
- idx_som = table["somatic"]
- cnt_som = idx_som.sum()
- table = table[~idx_som]
- logging.info("Skipped records: %d somatic, %d depth, %d homozygous",
- cnt_som, cnt_depth, cnt_hom)
-
- return cls(table, {"sample_id": sample_id})
-
- @classmethod
- def _read_vcf_nosample(cls, vcf_file, sample_id=None, skip_reject=False):
- table = pd.read_table(vcf_file,
- comment="#",
- header=None,
- na_filter=False,
- names=["chromosome", "start", "_ID", "ref", "alt",
- "_QUAL", "filter", "info"],
- usecols=cls._required_columns,
- # usecols=["chromosome", "start", "ref", "alt",
- # # "filter", "info",
- # ],
- # ENH: converters=func -> to parse each col
- dtype=dict(zip(cls._required_columns,
- cls._required_dtypes)),
- )
- # ENH: do things with filter, info
- # if skip_reject and record.FILTER and len(record.FILTER) > 0:
- table['end'] = table['start'] # TODO: _get_end
- table['start'] -= 1
- table = table.loc[:, cls._required_columns]
- return cls(table, {"sample_id": sample_id})
-
-
- # def write_vcf(self, outfile=sys.stdout):
- # """Write data to a file or handle in VCF format."""
- # # grab from export.export_vcf()
-
-
-def _select_sample(vcf_reader, sample_id, normal_id):
- """Select a sample ID in the VCF; ensure it's valid."""
- peds = list(_parse_pedigrees(vcf_reader))
- if sample_id is None and normal_id is None and peds:
- # Use the VCF header to select the tumor sample
- # Take the first entry, if any
- sample_id, normal_id = peds[0]
- elif sample_id and normal_id:
- # Take the given IDs at face value, just verify below
- pass
- elif sample_id:
- if peds:
- for sid, nid in peds:
- if sid == sample_id:
- normal_id = nid
- break
- # if normal_id is None and len(vcf_reader.samples == 2):
- # normal_id = next(s for s in vcf_reader.samples if s != sample_id)
- elif normal_id:
- if peds:
- for sid, nid in peds:
- if nid == normal_id:
- sample_id = sid
- break
- else:
- try:
- sample_id = next(s for s in vcf_reader.samples if s != normal_id)
- except StopIteration:
- raise ValueError(
- "No other sample in VCF besides the specified normal " +
- normal_id + "; did you mean to use this as the sample_id "
- "instead?")
- else:
- sample_id = vcf_reader.samples[0]
- _confirm_unique(sample_id, vcf_reader.samples)
- if normal_id:
- _confirm_unique(normal_id, vcf_reader.samples)
- logging.info("Selected test sample " + sample_id +
- (" and control sample %s" % normal_id if normal_id else ''))
- return sample_id, normal_id
+ See: TumorBoost, Bengtsson et al. 2010
+ """
+ if not ("alt_freq" in self and "n_alt_freq" in self):
+ raise ValueError("TumorBoost requires a matched tumor and normal "
+ "pair of samples in the VCF.")
+ return _tumor_boost(self["alt_freq"], self["n_alt_freq"])
-def _parse_pedigrees(vcf_reader):
- """Extract tumor/normal pair sample IDs from the VCF header.
- Return an iterable of (tumor sample ID, normal sample ID).
- """
- if "PEDIGREE" in vcf_reader.metadata:
- for tag in vcf_reader.metadata["PEDIGREE"]:
- if "Derived" in tag:
- sample_id = tag["Derived"]
- normal_id = tag["Original"]
- logging.debug("Found tumor sample %s and normal sample %s "
- "in the VCF header PEDIGREE tag",
- sample_id, normal_id)
- yield sample_id, normal_id
-
- elif "GATKCommandLine" in vcf_reader.metadata:
- for tag in vcf_reader.metadata["GATKCommandLine"]:
- if tag.get("ID") == "MuTect": # any others OK?
- options = dict(kv.split("=", 1)
- for kv in tag["CommandLineOptions"].split()
- if '=' in kv)
- sample_id = options.get('tumor_sample_name')
- normal_id = options['normal_sample_name']
- logging.debug("Found tumor sample %s and normal sample "
- "%s in the MuTect VCF header",
- sample_id, normal_id)
- yield sample_id, normal_id
-
-
-def _confirm_unique(sample_id, samples):
- occurrences = [s for s in samples if s == sample_id]
- if len(occurrences) != 1:
- raise ValueError(
- "Did not find a single sample ID '%s' in: %s"
- % (sample_id, samples))
-
-
-def _parse_records(vcf_reader, sample_id, normal_id, skip_reject):
- """Parse VCF records into DataFrame rows.
-
- Apply filters to skip records with low depth, homozygosity, the REJECT
- flag, or the SOMATIC info field.
- """
- cnt_reject = 0 # For logging
- for record in vcf_reader:
- is_som = False
- if skip_reject and record.FILTER and len(record.FILTER) > 0:
- cnt_reject += 1
- continue
- if record.INFO.get("SOMATIC"):
- is_som = True
-
- sample = record.genotype(sample_id)
- depth, zygosity, alt_count = _extract_genotype(sample)
- if normal_id:
- normal = record.genotype(normal_id)
- n_depth, n_zygosity, n_alt_count = _extract_genotype(normal)
- if n_zygosity == 0:
- is_som = True
-
- # Split multiallelics?
- # XXX Ensure sample genotypes are handled properly
- for alt in record.ALT:
- posn = record.POS - 1
- end = _get_end(posn, alt, record.INFO)
- row = (record.CHROM, posn, end, record.REF, str(alt),
- is_som,
- zygosity,
- depth,
- alt_count,
- )
- if normal_id:
- row += (n_zygosity, n_depth, n_alt_count)
- yield row
-
- if cnt_reject:
- logging.info('Filtered out %d records', cnt_reject)
-
-
-def _extract_genotype(sample):
- if "DP" in sample.data._fields:
- depth = sample.data.DP
- else:
- # SV, probably
- depth = alt_count = None
- if sample.is_het:
- zygosity = 0.5
- elif sample.gt_type == 0:
- zygosity = 0.0
+def _mirrored_baf(vals, above_half=None):
+ shift = (vals - .5).abs()
+ if above_half is None:
+ above_half = (vals.median() > .5)
+ if above_half:
+ return .5 + shift
else:
- zygosity = 1.0
- alt_count = (_get_alt_count(sample) if sample.gt_type else 0.0)
- return depth, zygosity, alt_count
-
-
-def _get_alt_count(sample):
- """Get the alternative allele count from a sample in a VCF record."""
- if "AD" in sample.data._fields and sample.data.AD is not None:
- # GATK and other callers
- if isinstance(sample.data.AD, (list, tuple)):
- alt_count = float(sample.data.AD[1])
- # VarScan
- else:
- alt_count = float(sample.data.AD)
- elif "CLCAD2" in sample.data._fields and sample.data.CLCAD2 is not None:
- # Qiagen CLC Genomics Server -- similar to GATK's AD
- alt_count = float(sample.data.CLCAD2[1])
- elif "AO" in sample.data._fields:
- if sample.data.AO:
- if isinstance(sample.data.AO, (list, tuple)):
- alt_count = sum(map(float, sample.data.AO))
- else:
- alt_count = float(sample.data.AO)
- else:
- alt_count = 0.0
- else:
- logging.warn("Skipping %s:%d %s; "
- "unsure how to get alternative allele count: %s",
- sample.site.CHROM, sample.site.POS, sample.site.REF,
- sample.data)
- alt_count = None # or 0 or "missing data"?
- return alt_count
-
-
-def _get_end(posn, alt, info):
- """Get record end position."""
- if "END" in info:
- # Structural variant
- return info['END']
- return posn + len(alt)
+ return .5 - shift
def _tumor_boost(t_freqs, n_freqs):
@@ -316,7 +168,7 @@ def _tumor_boost(t_freqs, n_freqs):
lt_mask = (t_freqs < n_freqs)
lt_idx = np.nonzero(lt_mask)[0]
gt_idx = np.nonzero(~lt_mask)[0]
- out = np.zeros_like(t_freqs)
+ out = pd.Series(np.zeros_like(t_freqs))
out[lt_idx] = 0.5 * t_freqs.take(lt_idx) / n_freqs.take(lt_idx)
out[gt_idx] = 1 - 0.5 * (1 - t_freqs.take(gt_idx)
) / (1 - n_freqs.take(gt_idx))
@@ -328,13 +180,12 @@ def _allele_specific_copy_numbers(segarr, varr, ploidy=2):
See: PSCBS, Bentsson et al. 2011
"""
+ # TODO fix ploidy on allosomes
seg_depths = ploidy * np.exp2(segarr["log2"])
- seg_bafs = np.asarray([(np.median(subvarr.mirrored_baf())
- if len(subvarr) else np.nan)
- for _seg, subvarr in varr.by_ranges(segarr)])
+ seg_bafs = varr.baf_by_ranges(segarr, above_half=True)
cn1 = 0.5 * (1 - seg_bafs) * seg_depths
cn2 = seg_depths - cn1
# segout = segarr.copy()
# segout.update({"baf": seg_bafs, "CN1": cn1, "CN2": cn2})
# return segout
- return pd.DataFrame({"baf": seg_bafs, "CN1": cn1, "CN2": cn2})
+ return pd.DataFrame({"baf": seg_bafs, "cn1": cn1, "cn2": cn2})
diff --git a/devtools/conda-recipe/build.sh b/devtools/conda-recipe/build.sh
new file mode 100644
index 0000000..8948114
--- /dev/null
+++ b/devtools/conda-recipe/build.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+$PYTHON setup.py install --single-version-externally-managed --record=record.txt
diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml
new file mode 100644
index 0000000..1f6b4b8
--- /dev/null
+++ b/devtools/conda-recipe/meta.yaml
@@ -0,0 +1,43 @@
+package:
+ name: cnvkit
+ version: "dev"
+
+source:
+ path: ../../
+
+build:
+ number: 0
+ skip: False
+
+requirements:
+ build:
+ - python
+ - setuptools
+
+ run:
+ - python
+ - atlas # [not osx]
+ - numpy >=1.9
+ - scipy >=0.9
+ - pandas >=0.18.1
+ - matplotlib >=1.1
+ - biopython >=1.62
+ - reportlab >=3.0
+ - pysam >=0.10.0
+ - r-pscbs
+ - r-cghflasso
+ - pyfaidx >=0.4.7
+ - future >=0.15.2
+ - futures
+
+test:
+ imports:
+ - cnvlib
+ - skgenome
+ commands:
+ - cnvkit.py -h
+
+about:
+ home: https://github.com/etal/cnvkit
+ license: Apache License 2.0
+ summary: Copy number variant detection from targeted DNA sequencing
diff --git a/devtools/travis-ci/install_miniconda.sh b/devtools/travis-ci/install_miniconda.sh
new file mode 100755
index 0000000..7848c9f
--- /dev/null
+++ b/devtools/travis-ci/install_miniconda.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then MINICONDA=Miniconda3-latest-MacOSX-x86_64.sh; fi
+if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then MINICONDA=Miniconda3-latest-Linux-x86_64.sh; fi
+
+MINICONDA_MD5=$(curl -s http://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *<td>\(.*\)<\/td> */\1/p')
+wget http://repo.continuum.io/miniconda/$MINICONDA
+if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then
+ echo "Miniconda MD5 mismatch"
+ # XXX This MD5 check failing since late Oct. 2015
+ # exit 1
+fi
+bash $MINICONDA -b
+rm -f $MINICONDA
+
+export PATH=$HOME/miniconda3/bin:$PATH
+
+conda update -yq conda
+conda install -yq conda-build jinja2
diff --git a/doc/baf.rst b/doc/baf.rst
new file mode 100644
index 0000000..c0cf2fb
--- /dev/null
+++ b/doc/baf.rst
@@ -0,0 +1,45 @@
+Allele frequencies and copy number
+==================================
+
+What is BAF?
+------------
+
+In this context, the "B" allele is the non-reference allele observed in a germline
+heterozygous SNP, i.e. in the normal/control sample. Since the tumor cells' DNA
+originally derived from normal cells' DNA, most of these SNPs will also be
+present in the tumor sample. But due to allele-specific copy number alterations,
+loss of heterozygosity or allelic imbalance, the allelic frequency of these SNPs
+may be different in the tumor, and that's evidence that one (or both) of the
+germline copies was gained or lost during tumor evolution.
+
+The shift in b-allele frequency is calculated relative to the expected
+heterozygous frequency 0.5, and minor allele frequencies are "mirrored" above
+and below 0.5 so that it does not matter which allele is considered the
+reference -- the relative shift from 0.5 will be the same either way. (Multiple
+alternate alleles are not considered here.)
+
+
+How does it work?
+-----------------
+
+Estimation from a SNP b-allele frequencies works by comparing the shift in
+allele frequency of heterozygous, germline SNPs in the tumor sample from the
+expected ~50% -- e.g. a 3-copy segment in a diploid genome would have log2
+ratio of +0.58 and heterozygous SNPs would have an average BAF of 67% or 33% if
+the tumor sample is fully clonal, and closer to log2 0.0 and BAF 0.5 if there
+is normal-cell contamination and/or :doc:`tumor heterogeneity <heterogeneity>`.
+
+Typically you would use a properly formatted :ref:`vcfformat` from joint
+tumor-normal SNV calling, e.g. the output of MuTect, VarDict, or FreeBayes,
+having already flagged somatic mutations so they can be skipped in this
+analysis. If you have no matched normal sample for a given tumor, you can use
+1000 Genomes common SNP sites to extract the likely germline SNVs from a
+tumor-only VCF, and use just those sites with THetA2 (or another tool like
+PyClone or BubbleTree).
+
+Use SNP b-allele frequencies from a VCF in these commands:
+
+- :ref:`call`
+- :ref:`scatter`
+- :ref:`export` ``nexus-ogt`` and ``theta``
+
diff --git a/doc/calling.rst b/doc/calling.rst
index c796928..82105f5 100644
--- a/doc/calling.rst
+++ b/doc/calling.rst
@@ -1,12 +1,12 @@
-Calling absolute copy number
-============================
+Calling copy number gains and losses
+====================================
The relationship between the observed copy ratio and the true underlying copy
number depends on tumor cell fraction (purity), genome ploidy (which may be
heterogeneous in a tissue sample), and the size of the subclonal population
-containing the CNA. Because of these ambiguities, CNVkit only reports the
-estimated log2 copy ratio, and does not currently attempt a formal statistical
-test for estimating integer copy number.
+containing the CNA. Because of these ambiguities, CNVkit initially reports only
+the estimated log2 copy ratio, and supports several approaches to deriving
+absolute integer copy number or evaluating copy number gains and losses.
In a diploid genome, a single-copy gain in a perfectly pure, homogeneous sample
has a copy ratio of 3/2. In log2 scale, this is log2(3/2) = 0.585, and a
@@ -15,20 +15,28 @@ single-copy loss is log2(1/2) = -1.0.
In the :ref:`diagram` plot, for the sake of providing a clean visualization of
confidently called CNAs, the default threshold to label genes is 0.5. This
threshold will tend to display gene amplifications, fully clonal single-copy
-gains in fairly pure samples, most single-copy losses, and complete deletions.
+gains in fairly pure samples, most single-copy losses, and total (homozygous)
+deletions.
When using the :ref:`gainloss` command, choose a threshold to suit your needs
depending on your knowledge of the sample's purity, heterogeneity, and likely
features of interest. As a starting point, try 0.1 or 0.2 if you are going to
do your own filtering downstream, or 0.3 if not.
+To evaluate the level of support for each segment, use the :ref:`segmetrics`
+command. In particular, the `--ci` option estimates the confidence interval of
+the segment mean: the difference between the upper and lower limits suggests the
+reliability of the estimate, and the value of the upper or lower limit suggests
+the minimum loss or gain value, respectively, supported by the bin-level log2
+ratios in that segment.
+
The :ref:`call` command implements two simple methods to convert the log2
-ratios in a segmented .cns file to absolute integer copy number values. The
-:ref:`segmetrics` command computes segment-level summary statistics that can be
-used to evaluate the reliability of each segment. Future releases of CNVkit
-will integrate further statistical testing to help make meaningful variant
-calls from the log2 copy ratio data.
+ratios in a segmented .cns file to absolute integer copy number values. Given
+known or estimated tumor purity and ploidy values, this command can also adjust
+for :doc:`tumor heterogeneity <heterogeneity>`.
-After using :ref:`call`, the adjusted .cns file can then be converted to BED or
-VCF format using the :ref:`export` command. These output styles display the
-inferred absolute integer copy number value of each segment.
+A .cns file can be converted to BED or VCF format using the :ref:`export`
+command. These output styles display the inferred absolute integer copy number
+value of each segment. To first adjust for known purity and ploidy of the
+sample, or apply log2 thresholds for integer calls, use :ref:`call` before
+exporting.
diff --git a/doc/cnvlib.rst b/doc/cnvlib.rst
index 9d184fc..a303473 100644
--- a/doc/cnvlib.rst
+++ b/doc/cnvlib.rst
@@ -1,5 +1,5 @@
-Python API (cnvlib package)
-===========================
+cnvlib package
+==============
Module ``cnvlib`` contents
--------------------------
@@ -9,28 +9,26 @@ Module ``cnvlib`` contents
:undoc-members:
:show-inheritance:
-The one function exposed at the top level, read, loads a file in CNVkit's native
-format and returns a CopyNumArray instance. For your own scripting, you can
-usually accomplish what you need using the CopyNumArray and GenomicArray methods
-available on this returned object.
+The one function exposed at the top level, `read`, loads a file in CNVkit's
+BED-like tabular format and returns a CopyNumArray instance. For your own
+scripting, you can usually accomplish what you need using just the CopyNumArray
+and GenomicArray methods available on this returned object (see
+:ref:`api_classes`).
+To load other file formats, see :ref:`api_tabio`. To run functions equivalent to
+CNVkit commands within Python, see :ref:`api_commands`.
-Core classes
-------------
-
-The core objects used throughout CNVkit. The base class is GenomicArray. All
-of these classes wrap a `pandas <http://pandas.pydata.org/>`_ DataFrame instance
-accessible through the ``.data`` attribute which can be used for any
-manipulations that aren't already provided by methods in the wrapper class.
-``gary``
-~~~~~~~~~
+.. _api_classes:
-.. automodule:: cnvlib.gary
- :members:
- :undoc-members:
- :show-inheritance:
+Core classes
+------------
+The core objects used throughout CNVkit. The base class is GenomicArray from
+:doc:`skgenome`. All of these classes wrap a `pandas
+<http://pandas.pydata.org/>`_ DataFrame instance, which is accessible through
+the ``.data`` attribute and can be used for any manipulations that aren't
+already provided by methods in the wrapper class.
``cnary``
~~~~~~~~~
@@ -40,16 +38,8 @@ manipulations that aren't already provided by methods in the wrapper class.
:undoc-members:
:show-inheritance:
-``rary``
-~~~~~~~~~
-
-.. automodule:: cnvlib.rary
- :members:
- :undoc-members:
- :show-inheritance:
-
``vary``
-~~~~~~~~~
+~~~~~~~~
.. automodule:: cnvlib.vary
:members:
@@ -57,6 +47,8 @@ manipulations that aren't already provided by methods in the wrapper class.
:show-inheritance:
+.. _api_commands:
+
Interface to CNVkit sub-commands
--------------------------------
@@ -74,6 +66,14 @@ The public API for each of the commands defined in the CNVkit workflow.
The following modules implement lower-level functionality specific to each of
the CNVkit sub-commands.
+``access``
+~~~~~~~~~~
+
+.. automodule:: cnvlib.access
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
``antitarget``
~~~~~~~~~~~~~~
@@ -82,8 +82,25 @@ the CNVkit sub-commands.
:undoc-members:
:show-inheritance:
+``autobin``
+~~~~~~~~~~~
+
+.. automodule:: cnvlib.autobin
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+``batch``
+~~~~~~~~~
+
+.. automodule:: cnvlib.batch
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
``call``
-~~~~~~~~~~~~
+~~~~~~~~
.. automodule:: cnvlib.call
:members:
@@ -122,6 +139,14 @@ the CNVkit sub-commands.
:undoc-members:
:show-inheritance:
+``heatmap``
+~~~~~~~~~~~
+
+.. automodule:: cnvlib.heatmap
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
``importers``
~~~~~~~~~~~~~
@@ -130,8 +155,16 @@ the CNVkit sub-commands.
:undoc-members:
:show-inheritance:
+``metrics``
+~~~~~~~~~~~
+
+.. automodule:: cnvlib.metrics
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
``reference``
-~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~
.. automodule:: cnvlib.reference
:members:
@@ -139,7 +172,7 @@ the CNVkit sub-commands.
:show-inheritance:
``reports``
-~~~~~~~~~~~~~~~~
+~~~~~~~~~~~
Supports the sub-commands :ref:`breaks` and :ref:`gainloss`.
@@ -148,6 +181,14 @@ Supports the sub-commands :ref:`breaks` and :ref:`gainloss`.
:undoc-members:
:show-inheritance:
+``scatter``
+~~~~~~~~~~~
+
+.. automodule:: cnvlib.scatter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
``segmentation``
~~~~~~~~~~~~~~~~
@@ -157,7 +198,7 @@ Supports the sub-commands :ref:`breaks` and :ref:`gainloss`.
:show-inheritance:
``target``
-~~~~~~~~~~~~~~
+~~~~~~~~~~
.. automodule:: cnvlib.target
:members:
@@ -165,29 +206,31 @@ Supports the sub-commands :ref:`breaks` and :ref:`gainloss`.
:show-inheritance:
+.. _api_helpers:
+
Helper modules
--------------
-``core``
-~~~~~~~~
+``cmdutil``
+~~~~~~~~~~~
-.. automodule:: cnvlib.core
+.. automodule:: cnvlib.cmdutil
:members:
:undoc-members:
:show-inheritance:
-``metrics``
-~~~~~~~~~~~
+``core``
+~~~~~~~~
-.. automodule:: cnvlib.metrics
+.. automodule:: cnvlib.core
:members:
:undoc-members:
:show-inheritance:
-``ngfrills``
-~~~~~~~~~~~~
+``descriptives``
+~~~~~~~~~~~~~~~~
-.. automodule:: cnvlib.ngfrills
+.. automodule:: cnvlib.descriptives
:members:
:undoc-members:
:show-inheritance:
@@ -218,6 +261,22 @@ Defines several constants used in the pipeline.
:undoc-members:
:show-inheritance:
+``samutil``
+~~~~~~~~~~~
+
+.. automodule:: cnvlib.samutil
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+``segfilters``
+~~~~~~~~~~~~~~
+
+.. automodule:: cnvlib.segfilters
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
``smoothing``
~~~~~~~~~~~~~
diff --git a/doc/conf.py b/doc/conf.py
index c37c9c7..337b34c 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -33,12 +33,25 @@ from cnvlib import __version__
# ones.
extensions = [
'sphinx.ext.autodoc',
- 'sphinx.ext.todo',
- 'sphinx.ext.mathjax',
'sphinx.ext.ifconfig',
+ 'sphinx.ext.mathjax',
+ 'sphinx.ext.napoleon',
+ 'sphinx.ext.todo',
'sphinx.ext.viewcode',
]
+# Napoleon settings
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+# napoleon_include_private_with_doc = False
+# napoleon_include_special_with_doc = True
+# napoleon_use_admonition_for_examples = False
+# napoleon_use_admonition_for_notes = False
+# napoleon_use_admonition_for_references = False
+# napoleon_use_ivar = False
+# napoleon_use_param = True
+# napoleon_use_rtype = True
+
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
@@ -53,7 +66,7 @@ master_doc = 'index'
# General information about the project.
project = u'CNVkit'
-copyright = u'2014-2015, Eric Talevich'
+copyright = u'2014-2016, Eric Talevich'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
diff --git a/doc/fileformats.rst b/doc/fileformats.rst
index 4597a13..d6c6916 100644
--- a/doc/fileformats.rst
+++ b/doc/fileformats.rst
@@ -39,27 +39,48 @@ See the `VCF specifications <https://github.com/samtools/hts-specs>`_.
CNVkit currently uses VCF files in two ways:
+- To extract single-nucleotide variant (SNV) allele frequencies, which can be
+ plotted in the :ref:`scatter` command, used to assign allele-specific copy
+ number in the :ref:`call` command, or exported along with bin-level copy
+ ratios to the "nexus-ogt" format.
- To :ref:`export` CNVs, describing/encoding each CNV segment as a structural
variant (SV).
-- To plot single-nucleotide variant (SNV) allele frequencies in the
- :ref:`scatter` and :ref:`loh` commands, or export these allele frequencies to
- the "nexus-ogt" format.
+
+For the former -- investigating allelic imbalance and loss of heterozygosity
+(LOH) -- it's most useful to perform paired calling on matched tumor/normal
+samples. You can use a separate SNV caller such as FreeBayes, VarDict, or MuTect
+to do this. For best results, ensure that:
+
+- Both the tumor and normal samples are present in the same VCF file.
+- Include both germline and somatic variants (if any) in the VCF file.
+ (For MuTect, this means keeping the "REJECT" records.)
+ Mark somatic variants with the "SOMATIC" flag in the INFO column.
+- Add a PEDIGREE tag to the VCF header declaring the tumor sample(s) as
+ "Derived" and the normal as "Original". Without this tag, you'll need to tell
+ CNVkit which sample is which using the `-i` and `-n` options in each command.
+
+An `example VCF
+<https://github.com/etal/cnvkit/blob/master/test/formats/na12878_na12882_mix.vcf?raw=true>`_
+constructed from the 1000 Genomes samples NA12878 and NA12882 is included in
+CNVkit's test suite.
Target and antitarget bin-level coverages (.cnn)
------------------------------------------------
-Coverage of binned regions is saved in a tabular format similar to BED but with
-additional columns. Each row in the file indicates an on-target or off-target
-(antitarget, background) bin. Genomic coordinates are 0-indexed, like BED.
+CNVkit saves its information in a tabular format similar to BED, but with
+additional columns. Each row in the file indicates an on-target or off-target
+(a.k.a. "antitarget") bin. Genomic coordinates are 0-indexed, like BED.
+Column names are shown as the first line of the file.
-Column names are shown as the first line of the file:
+In the output of the :ref:`coverage` command, the columns are:
* Chromosome or reference sequence name (``chromosome``)
* Start position (``start``)
* End position (``end``)
* Gene name (``gene``)
* Log2 mean coverage depth (``log2``)
+* Absolute-scale mean coverage depth (``depth``)
Essentially the same tabular file format is used for coverages (.cnn), ratios
(.cnr) and segments (.cns) emitted by CNVkit.
@@ -75,14 +96,16 @@ the reference .cnn file has the columns:
* RepeatMasker-masked proportion of the sequence region (``rmask``)
* Statistical spread or dispersion (``spread``)
-The log2 coverage depth is the weighted average of coverage depths, excluding
-extreme outliers, observed at the corresponding bin in each the sample .cnn
-files used to construct the reference. The spread is a similarly weighted
-estimate of the standard deviation of normalized coverages in the bin.
+The **log2** coverage depth is the robust average of coverage depths,
+excluding extreme outliers, observed at the corresponding bin in each the sample
+.cnn files used to construct the :ref:`reference`. The **spread** is a similarly
+robust estimate of the standard deviation of normalized log2 coverages in the
+bin. The **depth** column is the robust average of absolute-scale coverage
+depths from the input .cnn files, but without any bias corrections.
-To manually review potentially problematic genes in the built reference, you can
-sort the file by the "spread" column; bins with higher values are the noisy
-ones.
+To manually review potentially problematic targets in the built reference, you
+can sort the file by the **spread** column; bins with higher values are the
+noisy ones.
It is important to keep the copy number reference file consistent for the
duration of a project, reusing the same reference for bias correction of all
@@ -95,13 +118,11 @@ new protocol.
Bin-level log2 ratios (.cnr)
----------------------------
-In addition to the BED-like ``chromosome``, ``start``, ``end`` and ``gene``
-columns present in .cnn files, the .cnr file has the columns:
+In addition to the ``chromosome``, ``start``, ``end``, ``gene``, ``log2`` and
+``depth`` columns present in .cnn files, the .cnr file includes each bin's
+proportional weight or reliability (``weight``).
-* Log2 ratio (``log2``)
-* Proportional weight to be used for segmentation (``weight``)
-
-The weight value is derived from several sources:
+The **weight** value is derived from several sources:
- The size of the bin relative to the average bin size (for targets or
antitargets, separately)
@@ -121,10 +142,12 @@ small point indicates a less reliable bin.
Segmented log2 ratios (.cns)
----------------------------
-In addition to the ``chromosome``, ``start``, ``end``, ``gene`` and ``log2``
-columns present in .cnr files, the .cns file format has the additional column
-``probes``, indicating the number of bins covered by the segment.
-
-The ``gene`` column concatenates the gene names of all the bins that the segment
-covers. The ``weight`` column sums the bin-level weights.
+In addition to the ``chromosome``, ``start``, ``end``, ``gene``, ``log2``,
+``depth`` and ``weight`` columns present in .cnr files, the .cns file format has
+the additional column ``probes``, indicating the number of bins covered by the
+segment.
+The **gene** column concatenates the gene names of all the bins that the segment
+covers. The **weight** column sums the bin-level weights, and the **depth** and
+**log2** is the weighted mean of the input bin-level values corresponding to
+the segment.
diff --git a/doc/germline.rst b/doc/germline.rst
new file mode 100644
index 0000000..c4094a0
--- /dev/null
+++ b/doc/germline.rst
@@ -0,0 +1,33 @@
+Germline analysis
+=================
+
+CNVkit can be used with exome sequencing of constitutional (non-tumor) samples,
+for example to detect germline copy number alterations associated with heritable
+conditions. However, note that CNVkit is less accurate in detecting CNVs
+smaller than 1 Mbp, typically only detecting variants that span multiple exons
+or captured regions. When used on exome or target panel datasets, CNVkit will
+not detect the small CNVs that are more common in populations.
+
+To use CNVkit to detect medium-to-large CNVs or unbalanced SVs in constitutional
+samples:
+
+- The :ref:`call` command can be used directly without specifying the
+ ``--purity`` and ``--ploidy`` values, as the defaults will be correct for
+ mammalian cells. (For non-diploid species, use the correct ``--ploidy``, of
+ course.) The default ``--method threshold`` assigns integer copy number
+ similarly to ``--method clonal``, but with smaller thresholds for calling
+ single-copy changes. The default thresholds allow for mosaicism in CNVs, which
+ have smaller log2 value than a single-copy CNV would indicate. (They're more
+ common than often thought.)
+
+- The ``--filter`` option in :ref:`call` can be used to reduce the number of
+ false-positive segments returned. To use the ``ci`` (recommended) or ``sem``
+ filters, first run each sample's segmented .cns file through :ref:`segmetrics`
+ with the ``--ci`` option, which adds upper and lower confidence limits to the
+ .cns output that ``call --filter ci`` can then use.
+
+- The ``--drop-low-coverage`` option (see :doc:`tumor`) should not be used; it
+ will typically remove germline deep deletions altogether, which is not
+ desirable.
+
+- For using CNVkit with whole-genome sequencing datasets, see :doc:`nonhybrid`.
diff --git a/doc/heterogeneity.rst b/doc/heterogeneity.rst
index 5df5d5a..dd298af 100644
--- a/doc/heterogeneity.rst
+++ b/doc/heterogeneity.rst
@@ -59,8 +59,8 @@ integer copy number of tumor subclones in a sample.
Using CNVkit with THetA2
````````````````````````
-CNVkit provides wrappers for exporting segments to THetA2's input format and
-importing THetA2's result file as CNVkit's segmented .cns files.
+CNVkit provides wrappers for exporting .cns segments to THetA2's input format
+and importing THetA2's result file as CNVkit's segmented .cns files.
See the commands :ref:`export_theta` and :ref:`import-theta` for usage
instructions.
@@ -78,8 +78,8 @@ Then, run THetA2 (assuming the program was unpacked at ``/path/to/theta2/``)::
# Generates Sample_T.BEST.results:
/path/to/theta2/bin/RunTHetA Sample_T.interval_count \
- --TUMOR_SNP Sample_T.tumor.snp_formatted.txt \
- --NORMAL_SNP Sample_T.normal.snp_formatted.txt \
+ --TUMOR_FILE Sample_T.tumor.snp_formatted.txt \
+ --NORMAL_FILE Sample_T.normal.snp_formatted.txt \
--BAF --NUM_PROCESSES `nproc` --FORCE
Finally, import THetA2's results back into CNVkit's .cns format, matching the
@@ -100,33 +100,33 @@ convenience in plotting etc. with CNVkit. These files are also easily converted
to other formats using the :ref:`export` command.
-
Adjusting copy ratios and segments for normal cell contamination
----------------------------------------------------------------
-CNVkit's :ref:`rescale` command uses an estimate of tumor fraction (from
-any source) to directly rescale segment log2 ratio values to the value that
-would be seen a completely pure, uncontaminated sample. Example with tumor
-purity of 60% and a male reference::
+CNVkit's :ref:`call` command uses an estimate of tumor fraction (from
+any source) to directly rescale segment log2 ratio values, and SNV b-allele
+frequencies if present, to the value that would be seen a completely pure,
+uncontaminated sample. Example with tumor purity of 60% and a male reference::
+
+ cnvkit.py call -m none Sample.cns --purity 0.6 -y -o Sample.call.cns
- cnvkit.py rescale Sample.cns --purity 0.6 -y -o Sample.rescale.cns
+The :ref:`call` command can also convert the segmented log2 ratio estimates to
+absolute integer copy numbers. If the tumor cell fraction is known confidently,
+use the ``-m clonal`` method to round the log2 ratios to the nearest integer
+copy number. Alternatively, the ``-m threshold`` method to applies hard
+thresholds. Note that rescaling for purity is optional; either way, integer copy
+numbers are emitted unless the ``-m none`` option is used to skip it.
-CNVkit's :ref:`call` command then converts the segmented log2 ratio estimates to
-absolute integer copy numbers. Note that the rescaling step is optional; either
-way, hard thresholds can be used::
+::
+ cnvkit.py call -m clonal Sample.cns -y --purity 0.65 -o Sample.call.cns
+ # Or, if already rescaled
+ cnvkit.py call -m clonal Sample.call.cns -y -o Sample.call.cns
# With CNVkit's default cutoffs
cnvkit.py call -m threshold Sample.cns -y -o Sample.call.cns
# Or, using a custom set of cutoffs
cnvkit.py call -t=-1.1,-0.4,0.3,0.7 Sample.cns -y -o Sample.call.cns
-Alternatively, if the tumor cell fraction is known confidently, then these can
-be done in one step with ``call``, using the ``clonal`` method to simply round
-the log2 ratios to the nearest integer copy number::
-
- cnvkit.py call -m clonal Sample.cns -y --purity 0.65 -o Sample.call.cns
- # Or, if already rescaled
- cnvkit.py call -m clonal Sample.rescale.cns -y -o Sample.call.cns
Export integer copy numbers as BED or VCF
-----------------------------------------
@@ -137,5 +137,5 @@ the standard BED or VCF formats::
cnvkit.py export bed Sample.call.cns -y -o Sample.bed
cnvkit.py export vcf Sample.call.cns -y -o Sample.vcf
-The rounding of the .cns file's log2 ratios to integer copy numbers here is the
-same as in the :ref:`call` command with the ``clonal`` method.
+If the `.call.cns` files were generated by the :ref:`call` command, the
+integer copy numbers calculated in that step will be exported as well.
diff --git a/doc/importexport.rst b/doc/importexport.rst
index 91f5ed7..b0b533d 100644
--- a/doc/importexport.rst
+++ b/doc/importexport.rst
@@ -58,7 +58,7 @@ Procedure:
import-seg
----------
-Convert a file in the `SEG format <https://www.broadinstitute.org/igv/SEG>`_
+Convert a file in the `SEG format <https://software.broadinstitute.org/software/igv/SEG>`_
(e.g. the output of standard CBS or the GenePattern server) into one or more
CNVkit .cns files.
@@ -86,7 +86,7 @@ representing subclones with integer absolute copy number in each segment.
cnvkit.py import-theta Sample.cns Sample.BEST.results
-See the page on tumor :ref:`heterogeneity` for more guidance on performing this
+See the page on tumor :doc:`heterogeneity` for more guidance on performing this
analysis.
.. _export:
@@ -101,9 +101,16 @@ bed
```
Segments can be exported to BED format to support a variety of other uses, such
-as viewing in a genome browser. The log2 ratio value of each segment is
-converted and rounded to an integer value, as required by the BED format. To get
-accurate copy number values, see the commands :ref:`rescale` and :ref:`call`.
+as viewing in a genome browser.
+By default only regions with copy number different from the given ploidy
+(default 2) are output. (Notice what this means for allosomes.)
+To output all segments, use the ``--show all`` option.
+
+The BED format represents integer copy numbers in absolute scale, not log2
+ratios. If the input .cns file contains a "cn" column with integer copy number
+values, as generated by the :ref:`call` command, `export bed` will use those
+values. Otherwise the log2 ratio value of each input segment is converted and
+rounded to an integer value, similar to the `call -m clonal` method.
::
@@ -112,31 +119,27 @@ accurate copy number values, see the commands :ref:`rescale` and :ref:`call`.
# Show estimated integer copy number of all regions
cnvkit.py export bed Sample.call.cns --show all -y -o Sample.bed
-The same format can also specify CNV regions to the FreeBayes variant caller
+The same BED format can also specify CNV regions to the FreeBayes variant caller
with FreeBayes's ``--cnv-map`` option::
# Show only CNV regions
cnvkit.py export bed Sample.call.cns -o all-samples.cnv-map.bed
-By default only regions with copy number different from the given ploidy
-(default 2) are output. (Notice what this means for allosomes.)
-To output all segments, use the ``--show all`` option.
-
vcf
```
-Convert segments, ideally already adjusted by the :ref:`rescale` and/or
-:ref:`call` commands, to a :ref:`vcfformat` file. Copy ratios are converted to
-absolute integers, as with BED export, and VCF records are created for the
-segments where the copy number is different from the expected ploidy (e.g. 2 on
-autosomes, 1 on haploid sex chromosomes, depending on sample gender).
+Convert segments, ideally already adjusted by the :ref:`call` command, to a
+:ref:`vcfformat` file. Copy ratios are converted to absolute integers, as with
+BED export, and VCF records are created for the segments where the copy number
+is different from the expected ploidy (e.g. 2 on autosomes, 1 on haploid sex
+chromosomes, depending on sample sex).
-Gender can be specified with the ``-g``/``--gender`` option, or will be guessed
-automatically. If a male reference is used, use ``-y``/``--male-reference`` to
-say so. Note that these are different: If a female sample is run with a male
-reference, segments on chromosome X with log2-ratio +1 will be skipped, because
-that's the expected copy number, while an X-chromosome segment with log2-ratio 0
-will be printed as a hemizygous loss.
+Chromosomal sex can be specified with the ``-x``/``--sample-sex`` option, or
+will be guessed automatically. If a male reference is used, use
+``-y``/``--male-reference`` to say so. Note that these are different: If a
+female sample is run with a male reference, segments on chromosome X with
+log2-ratio +1 will be skipped, because that's the expected copy number, while an
+X-chromosome segment with log2-ratio 0 will be printed as a hemizygous loss.
::
@@ -210,7 +213,7 @@ theta
`THetA2 <http://compbio.cs.brown.edu/projects/theta/>`_ is a program for
estimating normal-cell contamination and tumor subclone population fractions
based on a tumor sample's copy number profile and, optionally, SNP allele
-frequencies. (See the page on tumor :ref:`heterogeneity` for more guidance.)
+frequencies. (See the page on tumor :doc:`heterogeneity` for more guidance.)
THetA2's input file is a BED-like file, typically with the extension
``.interval_count``, listing the read counts within each copy-number segment in
diff --git a/doc/index.rst b/doc/index.rst
index 898f03e..82536eb 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -3,10 +3,12 @@ CNVkit: Genome-wide copy number from targeted DNA sequencing
:Author: Eric Talevich
:Contact: eric.talevich at ucsf.edu
-:License: `Apache License 2.0 <http://www.apache.org/licenses/LICENSE-2.0>`_
:Source code: `GitHub <https://github.com/etal/cnvkit>`_
+:License: `Apache License 2.0 <http://www.apache.org/licenses/LICENSE-2.0>`_
:Packages: `PyPI <https://pypi.python.org/pypi/CNVkit>`_ | `Docker <https://hub.docker.com/r/etal/cnvkit/>`_ | `Galaxy <https://testtoolshed.g2.bx.psu.edu/view/etal/cnvkit>`_ | `DNAnexus <https://platform.dnanexus.com/app/cnvkit_batch>`_
-:Q&A: `Biostars <https://www.biostars.org/t/CNVkit/>`_ | `SeqAnswers <http://seqanswers.com/forums/showthread.php?t=47910>`_
+:Article: `PLOS Computational Biology <http://dx.doi.org/10.1371/journal.pcbi.1004873>`_
+:Q&A: `Biostars <https://www.biostars.org/t/CNVkit/>`_
+
CNVkit is a Python library and command-line software toolkit to infer and
visualize copy number from targeted DNA sequencing data. It is designed for use
@@ -37,13 +39,17 @@ FAQ & How To
------------
.. toctree::
- :maxdepth: 3
+ :maxdepth: 2
- fileformats
- bias
calling
+ baf
+ tumor
heterogeneity
+ germline
nonhybrid
+ sex
+ bias
+ fileformats
Python API
@@ -53,35 +59,54 @@ Python API
:maxdepth: 2
cnvlib
+ skgenome
Citation
========
-We are in the process of publishing a manuscript describing CNVkit.
-If you use this software in a publication, for now, please cite our preprint
-manuscript by DOI, like so:
+If you use this software in a publication, please cite our paper describing CNVkit:
Talevich, E., Shain, A.H., Botton, T., & Bastian, B.C. (2014).
- CNVkit: Copy number detection and visualization for targeted sequencing using off-target reads.
- *bioRxiv* doi: http://dx.doi.org/10.1101/010876
-
-A poster presentation can be viewed at `F1000 Research
-<http://f1000research.com/posters/1096236>`_.
-
-Who is using CNVkit?
---------------------
+ `CNVkit: Genome-wide copy number detection and visualization from targeted sequencing.
+ <http://dx.doi.org/10.1371/journal.pcbi.1004873>`_
+ *PLOS Computational Biology* 12(4):e1004873
+
+Also please cite the supporting paper for the segmentation method you use:
+
+PSCBS (``cbs``, the default):
+ - Olshen, A.B., Bengtsson, H., Neuvial, P., Spellman, P.T., Olshen, R.A., & Seshan, V.E. (2011).
+ `Parent-specific copy number in paired tumor-normal studies using circular binary segmentation.
+ <http://doi.org/10.1093/bioinformatics/btr329>`_
+ *Bioinformatics* 27(15):2038–46.
+ - Venkatraman, E.S., & Olshen, A.B. (2007).
+ `A faster circular binary segmentation algorithm for the analysis of array CGH data.
+ <http://doi.org/10.1093/bioinformatics/btl646>`_
+ *Bioinformatics* 23(6):657–63
+HaarSeg (``haar``):
+ Ben-Yaacov, E., & Eldar, Y.C. (2008).
+ `A fast and flexible method for the segmentation of aCGH data.
+ <http://doi.org/10.1093/bioinformatics/btn272>`_
+ *Bioinformatics* 24(16):i139-45.
+CGH Fused Lasso (``flasso``):
+ Tibshirani, R., & Wang, P. (2008).
+ `Spatial smoothing and hot spot detection for CGH data using the fused lasso.
+ <http://doi.org/10.1093/biostatistics/kxm013>`_
+ *Biostatistics* 9(1):18–29
+
+
+Who else is using CNVkit?
+-------------------------
`Google Scholar
<https://scholar.google.com/scholar?cites=4696125388809243311&as_sdt=2005&sciodt=0,5&hl=en>`_
-lists some of the references where CNVkit has been used by other researchers.
-
+lists some of the studies where CNVkit has been used by other researchers.
We'd like to highlight:
* McCreery, M.Q. *et al.* (2015).
`Evolution of metastasis revealed by mutational landscapes of chemically
induced skin cancers. <http://dx.doi.org/10.1038/nm.3979>`_
- *Nature Medicine*
+ *Nature Medicine* 21, 1514–1520
* Shain, A.H. *et al.* (2015).
`Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE
promoter mutations and diverse activating mutations in the MAPK pathway.
@@ -92,12 +117,19 @@ We'd like to highlight:
<http://dx.doi.org/10.1056/NEJMoa1502583>`_
*New England Journal of Medicine*, 373(20), 1926-1936
-Specific support for CNVkit is included in `bcbio-nextgen
-<https://bcbio-nextgen.readthedocs.org/>`_, `THetA2
-<http://compbio.cs.brown.edu/projects/theta/>`_, and `MetaSV
-<http://bioinform.github.io/metasv/>`_;
-CNVkit can also :ref:`export` files to several standard formats that can be used
-with many other software packages.
+Specific support for CNVkit is included in
+`bcbio-nextgen <https://bcbio-nextgen.readthedocs.io/>`_,
+`THetA2 <http://compbio.cs.brown.edu/projects/theta/>`_,
+and `MetaSV <http://bioinform.github.io/metasv/>`_.
+CNVkit is also available on the commercial platforms
+`DNAnexus <http://www.dnanexus.com/>`_,
+`Bina RAVE <http://www.bina.com/rave>`_, and
+`Diploid InHelix <http://www.diploid.com/inhelix>`_.
+
+Finally, CNVkit can :ref:`export` files to several standard formats that can be
+used with many other software packages, including `BioDiscovery Nexus Copy
+Number <http://www.biodiscovery.com/nexus-copy-number/>`_ and `Integrative
+Genomics Viewer (IGV) <http://software.broadinstitute.org/software/igv/>`_.
Indices and tables
diff --git a/doc/nonhybrid.rst b/doc/nonhybrid.rst
index 7a16b3a..f4845e6 100644
--- a/doc/nonhybrid.rst
+++ b/doc/nonhybrid.rst
@@ -1,39 +1,106 @@
Whole-genome sequencing and targeted amplicon capture
=====================================================
-CNVkit is designed for use on **hybrid capture** sequencing data, where
-off-target reads are present and can be used improve copy number estimates.
+CNVkit is primarily designed for use on **hybrid capture** sequencing data,
+where off-target reads are present and can be used improve copy number
+estimates. However, CNVkit can also be used on **whole-genome sequencing** (WGS)
+and **targeted amplicon sequencing** (TAS) datasets by using alternative
+command-line options.
-If necessary, CNVkit can be used on **whole-genome sequencing** (WGS) datasets
-by specifying the genome's sequencing-accessible regions as the "targets",
-avoiding "antitargets", and using a gene annotation database to label genes in
-the resulting BED file::
+The :ref:`batch` command supports these workflows through the
+``-m``/``--method`` option.
- cnvkit.py batch ... -t data/access-5kb-mappable.hg19.bed -g data/access-5kb-mappable.hg19.bed --split --annotate refFlat.txt
-Or::
+.. _wgs:
- cnvkit.py target data/access-5kb-mappable.hg19.bed --split --annotate refFlat.txt -o Targets.bed
- cnvkit.py antitarget data/access-5kb-mappable.hg19.bed -g data/access-5kb-mappable.hg19.bed -o Background.bed
+Whole-Genome Sequencing (WGS)
+-----------------------------
-This produces a "target" binning of the entire sequencing-accessible area of the
-genome, and empty "antitarget" files which CNVkit will handle safely from
-version 0.3.4 onward.
+CNVkit treats WGS data as a capture of all of the genome's sequencing-accessible
+regions, with no off-target regions.
+The ``batch --method wgs`` option uses the given reference genome's
+sequencing-accessible regions ("access" BED) as the "targets" -- these will be
+calculated on the fly if not provided. No "antitarget" regions are used.
+Since the input does not contain useful per-target gene labels, a gene
+annotation database is required and used to label genes in the outputs::
-Similarly, to use CNVkit on **targeted amplicon sequencing** data instead --
-although this is not recommended -- you can exclude all off-target regions from
-the analysis by passing the target BED file as the "access" file as well::
+ cnvkit.py batch -m wgs -g data/access-5kb-mappable.hg19.bed --annotate refFlat.txt *.bam
- cnvkit.py batch ... -t Targeted.bed -g Targeted.bed ...
+Equivalently::
-Or::
+ cnvkit.py target data/access-5kb-mappable.hg19.bed --split --short-names --annotate refFlat.txt -o targets.bed
+ # Create a blank file to substitute for antitargets
+ touch MT
+ # For each sample
+ cnvkit.py coverage Sample.bam targets.bed -p 0 -o Sample.targetcoverage.cnn
+ cnvkit.py reference *.targetcoverage.cnn --no-edge -o ref-wgs.cnn
+ cnvkit.py fix Sample.targetcoverage.cnn MT ref-wgs.cnn --no-edge
- cnvkit.py antitarget Targeted.bed -g Targeted.bed -o Background.bed
+To speed up and/or improve the accuracy of WGS analyses, try any or all of the
+following:
-However, this approach does not collect any copy number information between
-targeted regions, so it should only be used if you have in fact prepared your
-samples with a targeted amplicon sequencing protocol. It also does not attempt
-to normalize each amplicon at the gene level, though this may be addressed in a
-future version of CNVkit.
+- Instead of analyzing the whole genome, use the "target" BED file
+ to limit the analysis to just the genic regions. You can get such a BED file
+ from the [UCSC Genome Browser](https://genome.ucsc.edu/cgi-bin/hgTables), for
+ example.
+- Increase the "target" average bin size, e.g. to at least 1000 bases for 30x
+ coverage, or proportionally more for lower-coverage sequencing.
+- Specify a smaller p-value threshold (``segment -t``). For the CBS method,
+ ``1e-6`` may work well. Or, try the ``haar`` segmentation method.
+- Use the ``-p/--processes`` option in the :ref:`batch`, :ref:`coverage` and
+ :ref:`segment` commands to ensure all available CPUs are used.
+- Ensure you are using the most recent version of CNVkit. Each release includes
+ some performance improvements.
+- Turn off the "edge" bias correction in the :ref:`reference` and :ref:`fix`
+ commands (`--no-edge`).
+The ``batch -m wgs`` option does all of these except the first automatically.
+
+
+.. _tas:
+
+Targeted Amplicon Sequencing (TAS)
+----------------------------------
+
+When amplicon sequencing is used as a targeted capture method, no off-target
+reads are sequenced. While this limits the copy number information available in
+the sequencing data versus hybrid capture, CNVkit can analyze TAS data using
+only on-target coverages and excluding all off-target regions from the analysis.
+
+The ``batch -m amplicon`` option uses the given targets to infer coverage,
+ignoring off-target regions::
+
+ cnvkit.py batch -m amplicon -t targets.bed *.bam
+
+Equivalently::
+
+ cnvkit.py target targets.bed --split -o targets.split.bed
+ # Create a blank file to substitute for antitargets
+ touch MT
+ # For each sample
+ cnvkit.py coverage Sample.bam targets.split.bed -p 0 -o Sample.targetcoverage.cnn
+ cnvkit.py reference *.targetcoverage.cnn --no-edge -o ref-tas.cnn
+ cnvkit.py fix Sample.targetcoverage.cnn MT ref-tas.cnn --no-edge
+
+This approach does not collect any copy number information between targeted
+regions, so it should only be used if you have in fact prepared your samples
+with a targeted amplicon sequencing protocol. It also does not attempt to
+further normalize each amplicon at the gene level, though this may be addressed
+in a future version of CNVkit.
+
+.. note::
+ **Do not mark duplicates** in the BAM files for samples sequenced by this
+ method.
+
+ Picard MarkDuplicates, samtools rmdup, *et al.* are designed to flag
+ possible PCR duplicates (originally for WGS datasets, but also useful for
+ hybrid capture). Variant callers like GATK and CNVkit will ignore those
+ reads in their internal calculations, considering these reads to be
+ non-independent measurements. (`This SeqAnswers thread
+ <http://seqanswers.com/forums/showthread.php?t=6854>`_ has details and
+ background).
+
+ In targeted amplicon sequencing, all of the amplified reads are in fact PCR
+ duplicates by design. By marking and thus omitting these reads, the
+ remaining coverage will be low, as if no amplification were performed.
diff --git a/doc/pipeline.rst b/doc/pipeline.rst
index 742dede..f96e612 100644
--- a/doc/pipeline.rst
+++ b/doc/pipeline.rst
@@ -27,7 +27,7 @@ Run the CNVkit pipeline on one or more BAM files::
# From baits and tumor/normal BAMs
cnvkit.py batch *Tumor.bam --normal *Normal.bam \
- --targets my_baits.bed --split --annotate refFlat.txt \
+ --targets my_baits.bed --annotate refFlat.txt \
--fasta hg19.fasta --access data/access-5kb-mappable.hg19.bed \
--output-reference my_reference.cnn --output-dir results/ \
--diagram --scatter
@@ -51,16 +51,16 @@ complete sooner.
The pipeline executed by the ``batch`` command is equivalent to::
- cnvkit.py target baits.bed [--split --annotate --short-names] -o my_targets.bed
- cnvkit.py antitarget my_targets.bed [--access] -o my_antitargets.bed
+ cnvkit.py target baits.bed --split [--annotate refFlat.txt --short-names] -o my_targets.bed
+ cnvkit.py access baits.bed --fasta hg19.fa -o access.hg19.bed
+ cnvkit.py antitarget my_targets.bed --access access.hg19.bed -o my_antitargets.bed
# For each sample...
cnvkit.py coverage Sample.bam my_targets.bed -o Sample.targetcoverage.cnn
cnvkit.py coverage Sample.bam my_antitargets.bed -o Sample.antitargetcoverage.cnn
# With all normal samples...
- cnvkit.py reference *Normal.bam -t my_targets.bed -a my_antitargets.bed \
- [--fasta hg19.fa --male-reference] -o my_reference.cnn
+ cnvkit.py reference *Normal.{,anti}targetcoverage.cnn --fasta hg19.fa [--male-reference] -o my_reference.cnn
# For each tumor sample...
cnvkit.py fix Sample.targetcoverage.cnn Sample.antitargetcoverage.cnn my_reference.cnn -o Sample.cnr
@@ -70,6 +70,11 @@ The pipeline executed by the ``batch`` command is equivalent to::
cnvkit.py scatter Sample.cnr -s Sample.cns -o Sample-scatter.pdf
cnvkit.py diagram Sample.cnr -s Sample.cns [--male-reference] -o Sample-diagram.pdf
+This is for hybrid capture protocols in which both on- and off-target reads can
+be used for copy number detection. To run alternative pipelines for targeted
+amplicon sequencing or whole genome sequencing, use the ``--method`` option with
+value ``amplicon`` or ``wgs``, respectively. The default is ``hybrid``.
+
See the rest of the commands below to learn about each of these steps and other
functionality in CNVkit.
@@ -188,7 +193,7 @@ antitarget
Given a "target" BED file that lists the chromosomal coordinates of the tiled
regions used for targeted resequencing, derive a BED file
-off-target/"antitarget"/"background" regions.
+off-target/"antitarget" regions.
::
@@ -221,6 +226,10 @@ CalculateHsMetrics in the Picard suite (http://picard.sourceforge.net/), or from
the console output of the CNVkit :ref:`coverage` command when run on the target
regions.
+.. note::
+ The generated off-target bins are given the label "Antitarget" in CNVkit
+ versions 0.9.0 and later. In earlier versions, the label "Background" was
+ used -- CNVkit will still accept this label for compatibility.
.. _coverage:
@@ -237,8 +246,8 @@ interval size.
::
- cnvkit.py coverage Sample.bam Tiled.bed -o Sample.targetcoverage.cnn
- cnvkit.py coverage Sample.bam Background.bed -o Sample.antitargetcoverage.cnn
+ cnvkit.py coverage Sample.bam targets.bed -o Sample.targetcoverage.cnn
+ cnvkit.py coverage Sample.bam antitargets.bed -o Sample.antitargetcoverage.cnn
Summary statistics of read counts and their binning are printed to standard
error when CNVkit finishes calculating the coverage of each sample (through
@@ -293,10 +302,18 @@ Compile a copy-number reference from the given files or directory (containing
normal samples). If given a reference genome (-f option), also calculate the GC
content and repeat-masked proportion of each region.
-The reference can be constructed from zero, one or multiple control samples.
-A reference should be constructed specifically for each target capture panel
-(i.e. set of baits) and, ideally, match the type of sample (e.g. FFPE-extracted
-or fresh DNA) and library preparation protocol or kit used.
+The reference can be constructed from zero, one or multiple control samples (see
+below).
+
+A reference should be constructed specifically for each target capture panel,
+using a BED file listing the genomic coordinates of the baited regions.
+Ideally, the control or "normal" samples used to build the reference should
+match the type of sample (e.g. FFPE-extracted or fresh DNA) and library
+preparation protocol or kit used for the test (e.g. tumor) samples.
+
+For :doc:`target amplicon or whole-genome sequencing <nonhybrid>` protocols, the
+"antitarget" BED and .cnn files can be omitted.
+
Paired or pooled normals
````````````````````````
@@ -346,7 +363,7 @@ still computes the GC content of each region if the reference genome is given.
::
- cnvkit.py reference -o FlatReference.cnn -f ucsc.hg19.fa -t Tiled.bed -a Background.bed
+ cnvkit.py reference -o FlatReference.cnn -f ucsc.hg19.fa -t targets.bed -a antitargets.bed
Possible uses for a flat reference include:
@@ -483,42 +500,9 @@ methods use R internally.
Fused Lasso additionally performs significance testing to distinguish CNAs from
regions of neutral copy number, whereas CBS and HaarSeg by themselves only
-identify the supported segmentation breakpoints.
-
-.. _rescale:
-
-rescale
--------
-
-(Deprecated in favor of ``call -m none``, see below.)
-
-If there is a known level of normal-cell DNA contamination in the analyzed tumor
-sample (see the page on :doc:`tumor heterogeneity <heterogeneity>`), you can
-opt to rescale the log2 copy ratio estimates in your .cnr or .cns file to remove
-the impact of this contamination, so the resulting log2 ratio values in the file
-match what would be observed in a completely pure tumor sample.
-
-The calculation of new log2 values for the sex chromosomes depends on the
-chromosomal gender of the sample and whether a male reference was used, while
-for autosomes the specified ploidy (default 2, diploid) is used. For example,
-with tumor purity of 60% and a male reference, letting CNVkit guess the sample's
-chromosomal gender::
-
- cnvkit.py rescale Sample.cns --purity 0.6 -y -o Sample.rescaled.cns
-
-This can be done before or after segmentation, using a .cnr or .cns file; the
-resulting .cns file should be essentially the same.
-
-The ``rescale`` command can also optionally re-center the log2 values, though
-this will typically not be needed since the .cnr files are automatically
-median-centered by the :ref:`fix` command when normalizing to a reference and
-correcting biases. However, if the analyzed genome is highly aneuploid and
-contains widespread copy number losses or gains unequally, median centering may
-place copy-number-neutral regions slightly off-center from the expected log2
-value of 0.0. To address such cases, alternative centering approaches can be
-specified with the ``--center`` option::
-
- cnvkit.py rescale Sample.cns --center mode
+identify the supported segmentation breakpoints. Fused Lasso has been reported
+to work well on whole-exome and whole-genome data, while HaarSeg is less suited
+to those larger datasets and better on target panels.
.. _call:
@@ -530,10 +514,8 @@ Given segmented log2 ratio estimates (.cns), derive each segment's absolute
integer copy number using either:
- A list of threshold log2 values for each copy number state (``-m threshold``),
- or
-- :ref:`Rescaling <rescale>` for a given known tumor cell fraction and normal
- ploidy, then simple rounding to the nearest integer copy number
- (``-m clonal``).
+ or rescaling - for a given known tumor cell fraction and normal ploidy, then
+ simple rounding to the nearest integer copy number (``-m clonal``).
::
@@ -567,18 +549,36 @@ extracting b-allele frequencies from a VCF (if requested), but does not add a
Transformations
```````````````
-With the ``--purity`` option, log2 ratios are rescaled using the same
-calculation as the :ref:`rescale` command. The observed log2 ratios in the input
-.cns file are treated as a mix of some fraction of tumor cells (specified by
-``--purity``), possibly with altered copy number, and a remainder of normal
-cells with neutral copy number (specified by ``--ploidy`` for autosomes; by
-default, diploid autosomes, haploid Y or X/Y depending on reference gender).
-This equation is rearranged to find the absolute copy number of the tumor cells
-alone, rounded to the nearest integer. The expected and observed ploidy of the
-sex chromosomes (X and Y) is different, so it's important to specify
-``-y``/``--male-reference`` if a male reference was used; the sample gender can
-be specified if known, otherwise it will be guessed from the average log2 ratio
-of chromosome X.
+If there is a known level of normal-cell DNA contamination in the analyzed tumor
+sample (see the page on :doc:`tumor heterogeneity <heterogeneity>`), you can
+opt to rescale the log2 copy ratio estimates in your .cnr or .cns file to remove
+the impact of this contamination, so the resulting log2 ratio values in the file
+match what would be observed in a completely pure tumor sample.
+
+With the ``--purity`` option, log2 ratios are rescaled to the value that would
+be seen a completely pure, uncontaminated sample. The observed log2 ratios in
+the input .cns file are treated as a mix of some fraction of tumor cells
+(specified by ``--purity``), possibly with altered copy number, and a remainder
+of normal cells with neutral copy number (specified by ``--ploidy`` for
+autosomes; by default, diploid autosomes, haploid Y or X/Y depending on
+reference sex). This equation is rearranged to find the absolute copy number
+of the tumor cells alone, rounded to the nearest integer.
+
+The expected and observed ploidy of the sex chromosomes (X and Y) is different,
+so it's important to specify ``-y``/``--male-reference`` if a male reference was
+used; the sample sex can be specified if known, otherwise it will be guessed
+from the average log2 ratio of chromosome X.
+
+.. The calculation of new log2 values for the sex chromosomes depends on the
+.. chromosomal sex of the sample and whether a male reference was used, while
+.. for autosomes the specified ploidy (default 2, diploid) is used. For example,
+.. with tumor purity of 60% and a male reference, letting CNVkit guess the sample's
+.. chromosomal sex::
+
+.. cnvkit.py call -m none Sample.cns --purity 0.6 -y -o Sample.rescaled.cns
+
+.. This can be done before or after segmentation, using a .cnr or .cns file; the
+.. resulting .cns file should be essentially the same.
When a VCF file containing SNV calls for the same tumor sample (and optionally a
matched normal) is given using the ``-v``/``--vcf`` option, the b-allele
@@ -587,6 +587,17 @@ segment are mirrored, averaged, and listed in the output .cns file as an
additional "baf" column (using the same logic as ``export nexus-ogt``).
If ``--purity`` was specified, then the BAF values are also rescaled.
+The ``call`` command can also optionally re-center the log2 values, though
+this will typically not be needed since the .cnr files are automatically
+median-centered by the :ref:`fix` command when normalizing to a reference and
+correcting biases. However, if the analyzed genome is highly aneuploid and
+contains widespread copy number losses or gains unequally, the default median
+centering may place copy-number-neutral regions slightly above or below the
+expected log2 value of 0.0. To address such cases, alternative centering
+approaches can be specified with the ``--center`` option::
+
+ cnvkit.py call -m none Sample.cns --center mode
+
Calling methods
```````````````
@@ -661,11 +672,34 @@ Allele frequencies and counts
`````````````````````````````
If a VCF file is given using the ``-v``/``--vcf`` option, then for each segment
-with a BAF value (i.e. where SNVs were available), allele-specific integer copy
-number values are inferred from the total copy number and BAF, and output in
-columns "cn1" and "cn2". This calculation uses the same method as `PSCBS
+containing SNVs in the VCF, an average b-allele frequency (BAF) within that
+segment is calculated, and output in the "baf" column.
+Allele-specific integer copy number values are then inferred from the total copy
+number and BAF, and output in columns "cn1" and "cn2".
+This calculation uses the same method as `PSCBS
<http://bioinformatics.oxfordjournals.org/content/27/15/2038.short>`_:
total copy number is multiplied by the BAF, and rounded to the nearest integer.
Allelic imbalance, including copy-number-neutral loss of heterozygosity (LOH),
is then apparent when a segment's "cn1" and "cn2" fields have different values.
+
+Filtering segments
+``````````````````
+
+*New in version 0.8.0.*
+
+Finally, segments can be filtered according to several criteria, which may be
+combined:
+
+- Integer copy number (``cn``), merging adjacent with the same called value.
+- Keeping only high-level amplifications (5 copies or more) and homozygous
+ deletions (0 copies) (``ampdel``).
+- Confidence interval overlapping zero (``ci``).
+- Standard error of the mean (``sem``), a parametric estimate of confidence
+ intervals which behaves similarly.
+
+In each case, adjacent segments with the same value according to the given
+criteria are merged together and the column values are recalculated
+appropriately. Segments on different chromosomes or with different
+allele-specific copy number values will not be merged, even if the total copy
+number is the same.
diff --git a/doc/plots.rst b/doc/plots.rst
index 47bc1fd..d2a274c 100644
--- a/doc/plots.rst
+++ b/doc/plots.rst
@@ -60,15 +60,6 @@ listed in a separate file and passed to the ``scattter`` command with the
separately with the ``-c`` option and then combining the plots into a single
multi-page PDF.
-Loss of heterozygosity (LOH) can be viewed alongside copy number by passing
-variants as a VCF file with the ``-v`` option. Heterozygous SNP allelic
-frequencies are shown in a subplot below the CNV scatter plot. (Also see the
-:ref:`loh` command.)
-
-::
-
- cnvkit.py scatter Sample.cnr -s Sample.cns -v Sample.vcf
-
The bin-level log2 ratios or coverages can also be plotted without segmentation
calls::
@@ -83,20 +74,28 @@ fairly superfluous if a valid segment file is given, but could be helpful if the
CBS dependency is not available, or if you're skeptical of the segmentation in a
region.
+SNV b-allele frequencies
+````````````````````````
-.. _loh:
+Loss of heterozygosity (LOH) can be viewed alongside copy number by passing
+variants as a VCF file with the ``-v`` option. Heterozygous SNP allelic
+frequencies are shown in a subplot below the CNV scatter plot.
+
+::
-loh
----
+ cnvkit.py scatter Sample.cnr -s Sample.cns -v Sample.vcf
-Plot allelic frequencies at each variant position in a VCF file. Given segments,
-show the mean b-allele frequency values above and below 0.5 of SNVs falling
-within each segment. Divergence from 0.5 indicates LOH in the tumor sample.
+If only the VCF file is given by itself, just plot the allelic frequencies::
+
+ cnvkit.py scatter -v Sample.vcf
+
+Given segments, show the mean b-allele frequency values above and below 0.5 of
+SNVs falling within each segment. Divergence from 0.5 indicates LOH in the tumor
+sample.
::
- cnvkit.py loh Sample.vcf
- cnvkit.py loh Sample.vcf -s Sample.cns -i Sample_Tumor -n Sample_Normal
+ cnvkit.py scatter -s Sample.cns -v Sample.vcf -i TumorID -n NormalID
Regions with LOH are reflected in heterozygous germline SNPs in the tumor sample
with allele frequencies shifted away from the expected 0.5 value.
@@ -149,6 +148,15 @@ If only segments are provided (``-s``), gene labels are not shown. This plot is
then equivalent to the ``heatmap`` command, which effectively summarizes the
segmented values from many samples.
+By default, the sex chromosomes X and Y are colorized relative to the expected
+ploidy, i.e. for female samples analyzed with a male reference, while the X
+chromosome has a copy ratio near +1.0 in the input .cnr and .cns files, in the
+output diagram it will be shown as neutral copy number (white or faint colors)
+rather than a gain (red), because the diploid X is expected. The sample sex can
+be specified with the ``-x``/``--sample-sex`` option, or will otherwise be
+guessed automatically (see :doc:`sex`). This correction is done by default, but
+can be disabled with the option ``--no-shift-xy``.
+
.. _heatmap:
@@ -185,3 +193,57 @@ or chromosomal region at a time, using the ``-c`` option::
If an output file name is not specified with the ``-o`` option, an interactive
matplotlib window will open, allowing you to select smaller regions, zoom in,
and save the image as a PDF or PNG file.
+
+The samples are shown in the order there's given on the command line.
+If you use "\*.cns" then the filenames might always be fetched
+alphabetically (depending on your operating system), but if you type
+them out in the order you like, it should keep that order. You can use
+the Unix shell to pull the names out of a file on the fly, e.g.::
+
+ cnvkit.py heatmap `cat filenames.txt`
+
+
+As with :ref:`diagram`, the sex chromosomes X and Y are colorized relative to
+the expected ploidy, based on the sample and reference sex (see :doc:`sex`).
+This correction can be disabled with the option ``--no-shift-xy``.
+
+
+.. _plotcustom:
+
+Customizing plots
+-----------------
+
+The plots generated with the :ref:`scatter` and :ref:`heatmap` commands use the
+Python plotting library matplotlib.
+
+To quickly adjust the displayed area of the genome in a plot, run either
+plotting command without the `-o` option to generate an interactive plot in a
+new window. You can then resize that plot up to the full size of your screen,
+use the plot window's selection mode to select a smaller area of the genome, and
+use the plot window's save button to save the plot in your preferred format.
+
+You can customize font sizes and other aspects of the plots by `configuring
+matplotlib <http://matplotlib.org/users/customizing.html>`_.
+If you're running CNVkit on the command line and not using it as a Python
+library, then you can just create a file in your home directory (or the same
+directory as ``cnvkit.py``) called ``.matplotlibrc``. For example, to shrink
+the font size of the x- and y-axis labels, put this line in the configuration
+file::
+
+ axes.labelsize : small
+
+For more control, in the Python intepreter (or a script, or a Jupyter notebook),
+import the :doc:`cnvlib` module and call the `do_scatter` or `do_heatmap`
+function to create a plot. Then you can use matplotlib.pyplot to get the current
+axis and modify the plot elements, change font sizes, or anything else you
+like::
+
+ from glob import glob
+ from matplotlib import pyplot as plt
+ import cnvlib
+
+ segments = map(cnvlib.read, glob("*.cns"))
+ ax = cnvlib.do_heatmap(segments)
+ ax.set_title("All my samples")
+ plt.rcParams["font.size"] = 9.0
+ plt.show()
diff --git a/doc/quickstart.rst b/doc/quickstart.rst
index b1b0cc4..fa8faca 100644
--- a/doc/quickstart.rst
+++ b/doc/quickstart.rst
@@ -102,7 +102,7 @@ command could be::
cnvkit.py batch *Tumor.bam --normal *Normal.bam \
--targets my_baits.bed --fasta hg19.fasta \
- --split --access data/access-5kb-mappable.hg19.bed \
+ --access data/access-5kb-mappable.hg19.bed \
--output-reference my_reference.cnn --output-dir example/
See the built-in help message to see what these options do, and for additional
@@ -115,7 +115,7 @@ reference which assumes equal coverage in all bins by using the ``--normal/-n``
flag without specifying any additional BAM files::
cnvkit.py batch *Tumor.bam -n -t my_baits.bed -f hg19.fasta \
- --split --access data/access-5kb-mappable.hg19.bed \
+ --access data/access-5kb-mappable.hg19.bed \
--output-reference my_flat_reference.cnn -d example2/
In either case, you should run this command with the reference genome sequence
@@ -127,12 +127,26 @@ If your targets are missing gene names, you can add them here with the
``--annotate`` argument::
cnvkit.py batch *Tumor.bam -n *Normal.bam -t my_baits.bed -f hg19.fasta \
- --annotate refFlat.txt --split --access data/access-5kb-mappable.hg19.bed \
+ --annotate refFlat.txt --access data/access-5kb-mappable.hg19.bed \
--output-reference my_flat_reference.cnn -d example3/
+.. note:: **Which BED file should I use?**
-Process more tumor samples
---------------------------
+ - *target* vs. *bait* BED files: For hybrid capture, the targeted regions
+ (or "primary targets") are the genomic regions your capture kit attempts
+ to ensure are well covered, e.g. exons of genes of interest. The baited
+ regions (or "capture targets") are the genomic regions your kit actually
+ captures, usually including about 50bp flanking either side of each
+ target. Give CNVkit the bait/capture BED file, not the primary targets.
+ - For :ref:`wgs`, use the ``batch --method wgs`` option and optionally give
+ the genome's "access" file -- if not given, it will be calculated from the
+ genome sequence FASTA file.
+ - For :ref:`tas`, use the ``batch --method amplicon`` option and give the
+ target BED file.
+
+
+Next steps
+----------
You can reuse the reference file you've previously constructed to extract copy
number information from additional tumor sample BAM files, without repeating the
@@ -147,7 +161,33 @@ The coordinates of the target and antitarget bins, the gene names for the
targets, and the GC and RepeatMasker information for bias corrections are
automatically extracted from the reference .cnn file you've built.
+Now, starting a project from scratch, you could follow any of these approaches:
+
+- Run ``batch`` as above with all tumor/test and normal/control samples
+ specified as they are, and hope for the best. (This should usually work fine.)
+- *For the careful:* Run ``batch`` with just the normal samples specified as
+ normal, yielding coverage .cnn files and a **pooled reference**. Inspect the
+ coverages of all samples with the :ref:`metrics` command, eliminating any
+ poor-quality samples and choosing a larger or smaller antitarget bin size if
+ necessary. Build an updated pooled reference using :ref:`batch` or
+ :ref:`coverage` and :ref:`reference` (see :doc:`pipeline`), coordinating your
+ work in a `Makefile <https://en.wikipedia.org/wiki/Makefile>`_, Rakefile, or
+ similar build tool.
+
+ - See also: `Ten Simple Rules for Reproducible Computational Research
+ <http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003285>`_
+
+- *For the power user:* Run ``batch`` with all samples specified as tumor
+ samples, using ``-n`` by itself to build a **flat reference**, yielding
+ coverages, copy ratios, segments and optionally plots for all samples, both
+ tumor and normal. Inspect the "rough draft" outputs and determine an
+ appropriate strategy to build and use a **pooled reference** to re-analyze the
+ samples -- ideally coordinated with a build tool as above.
+- Use a framework like `bcbio-nextgen <https://bcbio-nextgen.readthedocs.io/>`_
+ to coordinate the complete sequencing data analysis pipeline.
+
See the command-line usage pages for additional
:doc:`visualization <plots>`,
:doc:`reporting <reports>` and
:doc:`import/export <importexport>` commands in CNVkit.
+
diff --git a/doc/reports.rst b/doc/reports.rst
index 5741c6f..5b44ff6 100644
--- a/doc/reports.rst
+++ b/doc/reports.rst
@@ -20,6 +20,17 @@ The output is a text table of tab-separated values, which is amenable to further
processing by scripts and standard Unix tools such as ``grep``, ``sort``,
``cut`` and ``awk``.
+Columns:
+
+- `gene`, `chromosome` -- as in .cns (see :doc:`fileformats`), the gene where
+ the breakpoint occurs and the chromosome it lies on.
+- `location` -- the `end` of the segment to the left of the breakpoint, and
+ `start` of the segment to the right.
+- `change` -- the difference in `log2` values between the adjacent segments.
+- `probes_left`, `probes_right` -- the number of probes on each side of the
+ breakpoint within the gene. (Not the same as the number of probes supporting
+ each segment; just the portion within the gene.)
+
For example, to get a list of the names of genes that contain a possible copy
number breakpoint::
@@ -58,7 +69,7 @@ Some likely false positives can be eliminated by dropping CNVs that cover a
small number of bins (e.g. with ``-m 3``, genes where only 1 or 2 bins show copy
number change will not be reported), at the risk of missing some true positives.
-Specify the reference gender (``-y`` if male) to ensure CNVs on the X and Y
+Specify the reference sex (``-y`` if male) to ensure CNVs on the X and Y
chromosomes are reported correctly; otherwise, a large number of spurious gains
or losses on the sex chromosomes may be reported.
@@ -78,37 +89,36 @@ visualize each of them with :ref:`scatter`::
(The point is that it's possible.)
-.. _gender:
+.. _sex:
-gender
-------
+sex
+---
-Guess samples' gender from the relative coverage of chromoxsome X.
-A table of the sample name (derived from the filename), guessed chromosomal
-gender (string "Female" or "Male"), and log2 ratio value of chromosome X is
-printed.
+Guess samples' chromosomal sex from the relative coverage of chromosomes X and Y.
+A table of the sample name (derived from the filename), inferred sex (string
+"Female" or "Male"), and log2 ratio value of chromosomes X and Y is printed.
::
- cnvkit.py gender *.cnn *.cnr *.cns
- cnvkit.py gender -y *.cnn *.cnr *.cns
+ cnvkit.py sex *.cnn *.cnr *.cns
+ cnvkit.py sex -y *.cnn *.cnr *.cns
-If there is any confusion in specifying either the gender of the sample or the
+If there is any confusion in specifying either the sex of the sample or the
construction of the reference copy number profile, you can check what happened
-using the "gender" command.
+using the ``sex`` command.
If the reference and intermediate .cnn files are available (.targetcoverage.cnn
and .antitargetcoverage.cnn, which are created before most of CNVkit's
-corrections), CNVkit can report the reference gender and the apparent chromosome
-X copy number that appears in the sample::
+corrections), CNVkit can report the reference sex and the sample's relative coverage of
+the X and Y chromosomes::
- cnvkit.py gender reference.cnn Sample.targetcoverage.cnn Sample.antitargetcoverage.cnn
+ cnvkit.py sex reference.cnn Sample.targetcoverage.cnn Sample.antitargetcoverage.cnn
-The output looks like this, where columns are filename, apparent gender, and
-log2 ratio of chrX::
+The output looks like this, where columns are filename, inferred sex, and
+ratio of chromosome X and Y log2 coverages relative to autosomes::
- cnv_reference.cnn Female -0.176
- Sample.targetcoverage.cnn Female -0.0818
- Sample.antitargetcoverage.cnn Female -0.265
+ cnv_reference.cnn Female -0.176 -1.061
+ Sample.targetcoverage.cnn Female -0.0818 -12.471
+ Sample.antitargetcoverage.cnn Female -0.265 -15.139
If the ``-y`` option was not specified when constructing the reference (e.g.
``cnvkit.py batch ...``), then you have a female reference, and in the final
@@ -182,7 +192,7 @@ segments are spurious. One possible heuristic for judging the overall noisiness
of each sample in a table is to multiply the number of segments by the biweight
midvariance -- the value will tend to be higher for unreliable samples.
Check questionable samples for poor coverage (using e.g. `bedtools
-<http://bedtools.readthedocs.org/>`_, `chanjo <http://www.chanjo.co/>`_,
+<http://bedtools.readthedocs.io/>`_, `chanjo <http://www.chanjo.co/>`_,
`IGV <http://www.broadinstitute.org/igv/>`_ or `Picard CalculateHsMetrics
<http://broadinstitute.github.io/picard/command-line-overview.html#CalculateHsMetrics>`_).
@@ -196,7 +206,6 @@ be trusted.
segmetrics
----------
-
Calculate summary statistics of the residual bin-level log2 ratio estimates
from the segment means, similar to the existing :ref:`metrics` command, but for each
segment individually.
@@ -211,12 +220,23 @@ with the stat names and calculated values printed in additional columns.
Supported stats:
+- Alternative estimators of segment mean, which ignore bin weights: ``--mean``,
+ ``-median``, ``--mode``.
+
- As in :ref:`metrics`: standard deviation (``--std``), median absolute
deviation (``--mad``), inter-quartile range (``--iqr``), Tukey's biweight
midvariance (``--bivar``)
-- confidence interval (``--ci``), estimated by bootstrap (100 resamples)
+- Additionally: mean squared error (``--mse``), standard error of the mean
+ (``-sem``).
+
+- Confidence interval of the segment mean (``--ci``), estimated by bootstrap
+ (100 resamplings) of the bin-level log2 ratio values within the segment. The
+ upper and lower bounds are output as separate columns ``ci_lo`` and ``ci_hi``.
-- prediction interval (``--pi``), estimated by the range between the 2.5-97.5
- percentiles of bin-level log2 ratio values within the segment.
+- Prediction interval (``--pi``), estimated by the range between the 2.5-97.5
+ percentiles of the segment's bin-level log2 ratios. The upper and lower bounds
+ are output as columns ``pi_lo`` and ``pi_hi``.
+The ``--ci`` and ``--sem`` values obtained here can also be used in the
+:ref:`call` command for filtering segments.
diff --git a/doc/scripts.rst b/doc/scripts.rst
index fcf36b7..29bfced 100644
--- a/doc/scripts.rst
+++ b/doc/scripts.rst
@@ -1,16 +1,46 @@
Additional scripts
==================
-refFlat2bed.py
- Generate a BED file of the genes or exons in the reference genome given in
- UCSC refFlat.txt format. (Download the input file from `UCSC Genome
- Bioinformatics <http://hgdownload.soe.ucsc.edu/downloads.html>`_).
+cnn_annotate.py
+ Update gene names (the 'gene' column) in CNVkit .cnn/.cnr files,
+ using gene annotations from another UCSC RefFlat, BED, or GFF file (e.g.
+ refFlat.txt). This may be useful if you notice at the end of an analysis
+ that vendor-annotated targets are not the desired gene names, and want to
+ change the labeling without repeating the analysis with an updated target
+ BED file.
+cnn_updater.py
+ Update .cnn, .cnr and .cns files previously generated by earlier versions of
+ CNVkit to add a "depth" column used in CNVkit version 0.8.0 and later. The
+ script reads each input file, calculates absolute-scale depth from the
+ file's existing "log2" column value in each row, and creates a corresponding
+ output file with a modified name -- the input files are not modified
+ in-place.
+
+ Running this script is not necesssary for new analyses, but may help ease
+ the transition for analyses that have already begun.
+
+guess_baits.py
+ Use the read depths in one or more given BAM files to infer which regions
+ were targeted in a hybrid capture or targeted amplicon capture sequencing
+ protocol.
This script can be used in case the original BED file of targeted intervals
- is unavailable. Subsequent steps of the pipeline will remove probes that
- did not receive sufficient coverage, including those exons or genes that
- were not targeted by the sequencing library. However, CNVkit will give much
- better results if the true targeted intervals can be provided.
+ is unavailable. (However, CNVkit will give much better results if the true
+ targeted intervals can be provided.)
+ It works in 2 modes, guided and unguided:
+
+ - **Guided:** Given candidate targets, such as all known exons in the reference
+ genome, test the mean coverage depth in each candidate target and drop
+ those that did not receive sufficient coverage, presumed to be those exons
+ or genes that were not targeted by the sequencing library. ::
+
+ guess_baits.py Sample1.bam Sample2.bam -t ucsc-exons.bed -o baits.bed
+
+ - **Unguided:** Scan every base in the sample BAM(s), inferring likely
+ boundaries for enriched regions. (This is usually much slower then the
+ guided approach.) ::
+
+ guess_baits.py -g access.hg19.bed Sample1.bam Sample2.bam -o baits.bed
reference2targets.py
Extract target and antitarget BED files from a CNVkit reference file.
@@ -24,3 +54,13 @@ reference2targets.py
antitarget BED files (and subsequently built references) to avoid
unnecessarily calculating coverage in those bins during future runs.
+refFlat2bed.py
+ (Deprecated in favor of `skg_convert.py`)
+
+ Generate a BED file of the genes or exons in the reference genome given in
+ UCSC refFlat.txt format. (Download the input file from `UCSC Genome
+ Bioinformatics <http://hgdownload.soe.ucsc.edu/downloads.html>`_).
+
+skg_convert.py
+ Convert between any of the tabular data formats supported by skgenome.tabio,
+ including BED and UCSC RefFlat.
diff --git a/doc/sex.rst b/doc/sex.rst
new file mode 100644
index 0000000..03823aa
--- /dev/null
+++ b/doc/sex.rst
@@ -0,0 +1,73 @@
+Chromosomal sex
+===============
+
+CNVkit attempts to handle chromosomal sex correctly throughout the analysis
+pipelines. Several commands automatically infer a given sample's chromosomal
+sex from the relative copy number of the autosomes and chromosomes X and Y; the
+status log messages will indicate when this is happening. In most cases the
+inference can be skipped or overridden by using the ``-x``/``--sample-sex``
+option.
+
+The :ref:`sex` command runs and report's CNVkit's inference for one or more
+given samples, and can be used on .cnn, .cnr or .cns files at any stage of
+processing.
+
+Reference sex
+-------------
+
+See :ref:`reference`
+
+If you want copy number calls to be relative to a male reference with a single X
+chromosome but dipoid autosomes, use the ``-y`` option everywhere.
+Otherwise, X and all autosomes will be considered normally diploid. Chromosome Y
+will be considered haploid in either case.
+
+
+Chromosomal sex in calling absolute copy number
+-----------------------------------------------
+
+See :ref:`call`
+
+Plots and sex chromosomes
+-------------------------
+
+:ref:`diagram` adjusts the sex chromosomes for sample and reference sex so
+that gains and losses on chromosomes X and Y are highlighted and labeled
+appropriately.
+
+:ref:`scatter` and :ref:`heatmap` do not adjust the sex chromosomes for sample
+or reference sex.
+
+FAQ
+---
+
+Why does chromosome X/Y show a gain/loss?
+`````````````````````````````````````````
+
+The copy number status of sex chromosomes may be surprising if you are unsure
+about the sex of the samples and reference used:
+
+- Female samples normalized to a male reference will show a doubling of
+ chromosome X (log2 value about +1.0) and complete loss of chromosome Y (log2
+ value below -3.0, usually far below).
+- Male samples normalized to a female reference will show a single-copy loss of
+ chromosome X (log2 value about -1.0). The chromosome Y value should be near
+ 0.0, but the log2 values may be noisier and less reliable than on autosomes.
+
+In the output of the :ref:`diagram`, :ref:`call`, and :ref:`export` commands,
+the X or Y copy number may be wrong if the sex of the reference
+(``-y``/``--male-reference``) or sample (``-x``) was not specified correctly. If
+sample sex was not specified on the command line, check the command's logged
+status messages to see if the sample's sex was guessed incorrectly.
+
+After you've verified the above, the CNV might be real.
+
+CNVkit is not detecting my sample's sex correctly. What can I do?
+`````````````````````````````````````````````````````````````````
+
+In lower-quality samples, particularly tumor samples analyzed without a robust
+reference (see :doc:`tumor`), there may be many bins with no coverage which bias
+the segment means. Try repeating the :ref:`segment` command with the
+``--drop-low-coverage`` option if you did not do so originally.
+
+See also: https://www.biostars.org/p/210080/
diff --git a/doc/skgenome.rst b/doc/skgenome.rst
new file mode 100644
index 0000000..b0bccbe
--- /dev/null
+++ b/doc/skgenome.rst
@@ -0,0 +1,112 @@
+scikit-genome package
+=====================
+
+Module ``skgenome`` contents
+----------------------------
+
+.. automodule:: skgenome
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
+.. _api_tabio:
+
+Tabular file I/O (tabio)
+------------------------
+
+``tabio``
+~~~~~~~~~
+
+.. automodule:: skgenome.tabio
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
+.. _api_sk_gary:
+
+Base class: GenomicArray
+------------------------
+
+The base class of the core objects used throughout CNVkit and scikit-genome is
+GenomicArray. It wraps a `pandas <http://pandas.pydata.org/>`_ DataFrame
+instance, which is accessible through the ``.data`` attribute and can be used
+for any manipulations that aren't already provided by methods in the wrapper
+class.
+
+``gary``
+~~~~~~~~
+
+.. automodule:: skgenome.gary
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
+.. _api_sk_interval:
+
+Genomic interval arithmetic
+---------------------------
+
+``intersect``
+~~~~~~~~~~~~~
+
+.. automodule:: skgenome.intersect
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+``merge``
+~~~~~~~~~
+
+.. automodule:: skgenome.merge
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+``subdivide``
+~~~~~~~~~~~~~
+
+.. automodule:: skgenome.subdivide
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+``subtract``
+~~~~~~~~~~~~
+
+.. automodule:: skgenome.subtract
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
+.. _api_sk_helpers:
+
+Helper modules
+--------------
+
+``chromsort``
+~~~~~~~~~~~~~
+
+.. automodule:: skgenome.chromsort
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+``combiners``
+~~~~~~~~~~~~~
+
+.. automodule:: skgenome.combiners
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+``rangelabel``
+~~~~~~~~~~~~~~
+
+.. automodule:: skgenome.rangelabel
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/tumor.rst b/doc/tumor.rst
new file mode 100644
index 0000000..a69f891
--- /dev/null
+++ b/doc/tumor.rst
@@ -0,0 +1,42 @@
+Tumor analysis
+==============
+
+CNVkit has been used most extensively on solid tumor samples sequenced with a
+target panel or whole-exome sequencing protocol. Several options and approaches
+are available to support this use case:
+
+- If you have unpaired tumor samples, or no normal samples sequenced on the same
+ platform, see the :ref:`reference` command for strategies.
+
+- Use ``--drop-low-coverage`` to ignore bins with log2 normalized coverage
+ values below -15. Virtually all tumor samples, even cancer cell lines, are
+ not completely homogeneous. Even in regions of homozygous deletion in the
+ largest tumor-cell clonal population, some sequencing reads will be obtained
+ from contaminating normal cells without the deletion. Therefore, extremely low
+ log2 copy ratio values do not indicate homozygous deletions but failed
+ sequencing or mapping in all cells regardless of copy number status at that
+ site, which are not informative for copy number. This option in the
+ :ref:`batch` command applies to segmentation; the option is also available in
+ the :ref:`segment`, :ref:`metrics`, :ref:`segmetrics`, :ref:`gainloss` and
+ :doc:`heterogeneity` commands.
+
+ - Why -15? The null log2 value substituted for bins with zero coverage is
+ -20 (about 1 millionth the average bin's coverage), and the maximum
+ positive shift that can be introduced by normalizing to the reference is 5
+ (for bins with 1/32 the average coverage; bins below this are masked out
+ by the reference). In a .cnr file, any bins with log2 value below -15 are
+ probably based on dummy values corresponding to zero-coverage (perhaps
+ unmappable) bins, and not real observations.
+
+- The :ref:`batch` command does not directly output integer copy number calls
+ (see :doc:`heterogeneity`). Instead, use the ``--ploidy`` and ``--purity``
+ options in :ref:`call` to calculate copy number for each sample individually
+ using known or estimated tumor-cell fractions. Also consider using ``--center
+ median`` in highly aneuploid samples to shift the log2 value of true neutral
+ regions closer to zero, as it may be slightly off initially.
+
+- If SNV calls are available in VCF format, use the ``-v``/``--vcf`` option in
+ the :ref:`call` and :ref:`scatter` commands to calculate or plot b-allele
+ frequencies alongside each segment's total copy number or log2 ratio. These
+ values reveal allelic imbalance and loss of heterozygosity (LOH), supporting
+ and extending the inferred CNVs.
diff --git a/doc/workflow.svg b/doc/workflow.svg
index 832c2ed..57a7e00 100644
--- a/doc/workflow.svg
+++ b/doc/workflow.svg
@@ -328,10 +328,10 @@
fit-margin-left="3"
fit-margin-right="3"
fit-margin-bottom="3"
- inkscape:window-width="1855"
+ inkscape:window-width="1920"
inkscape:window-height="1056"
- inkscape:window-x="65"
- inkscape:window-y="24"
+ inkscape:window-x="1920"
+ inkscape:window-y="37"
inkscape:window-maximized="1"
showguides="true"
inkscape:guide-bbox="true">
@@ -372,7 +372,7 @@
<dc:format>image/svg+xml</dc:format>
<dc:type
rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
- <dc:title></dc:title>
+ <dc:title />
</cc:Work>
</rdf:RDF>
</metadata>
@@ -1055,7 +1055,8 @@
height="93.220268"
width="266.10168"
id="rect19342" /></flowRegion><flowPara
- id="flowPara19344">Circular binary segmentation</flowPara></flowRoot> <text
+ id="flowPara19344">Find CNV</flowPara><flowPara
+ id="flowPara3204"> breakpoints</flowPara></flowRoot> <text
sodipodi:linespacing="125%"
id="text85158"
y="262.52502"
@@ -1116,7 +1117,7 @@
height="83.066666"
width="212.11784"
id="rect85239" /></flowRegion><flowPara
- id="flowPara85247">scatter, diagram, heatmap, loh</flowPara></flowRoot> </g>
+ id="flowPara85247">scatter, diagram, heatmap</flowPara></flowRoot> </g>
<g
id="g86823"
transform="translate(-157.38334,27.079956)">
@@ -1145,7 +1146,7 @@
width="215.85146"
id="rect85259" /></flowRegion><flowPara
style="font-size:20px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;text-align:center;text-anchor:middle;font-family:DejaVu Sans Mono;-inkscape-font-specification:DejaVu Sans Mono"
- id="flowPara85261">breaks, gainloss, gender, metrics</flowPara></flowRoot> </g>
+ id="flowPara85261">breaks, gainloss, sex, metrics</flowPara></flowRoot> </g>
<g
id="g86795"
transform="translate(-109.16488,-75.798883)">
@@ -1174,7 +1175,7 @@
width="248.9796"
id="rect85267" /></flowRegion><flowPara
style="font-size:20px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;text-align:center;text-anchor:middle;font-family:DejaVu Sans;-inkscape-font-specification:DejaVu Sans"
- id="flowPara85269">CDT, SEG, JTV</flowPara></flowRoot> </g>
+ id="flowPara85269">BED, SEG, VCF</flowPara></flowRoot> </g>
<g
id="g85404"
transform="translate(14.429685,73.856892)">
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 18c65f6..bfea9d4 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,24 +1,26 @@
-FROM ubuntu:15.10
+FROM ubuntu:latest
MAINTAINER Eric Talevich <eric.talevich at ucsf.edu>
ENV DEBIAN_FRONTEND noninteractive
-RUN apt-get update && apt-get install -y \
- cython \
- libfreetype6-dev \
+RUN apt-get update && apt-get install -y r-base-core
+RUN Rscript -e "source('http://bioconductor.org/biocLite.R'); biocLite('PSCBS', 'cghFLasso')"
+
+RUN apt-get install -y \
python-biopython \
python-dev \
+ python-future \
python-matplotlib \
python-numpy \
python-pip \
python-reportlab \
python-scipy \
python-tk \
- r-base-core \
zlib1g-dev
-RUN pip install pandas pysam pyvcf
-RUN Rscript -e "source('http://bioconductor.org/biocLite.R'); biocLite('PSCBS', 'cghFLasso')"
-RUN pip install cnvkit==0.7.5
+RUN pip install -U futures pandas pyfaidx pysam
+RUN pip install cnvkit==0.8.5
+# Let matplotlib build its font cache
+RUN cnvkit.py version
-ENTRYPOINT ["cnvkit.py"]
-CMD ["--help"]
-# CMD ["bash"]
+# ENTRYPOINT ["cnvkit.py"]
+# CMD ["--help"]
+CMD ["bash"]
diff --git a/scripts/cnn_annotate.py b/scripts/cnn_annotate.py
new file mode 100755
index 0000000..ce462a9
--- /dev/null
+++ b/scripts/cnn_annotate.py
@@ -0,0 +1,35 @@
+#!/usr/bin/env python
+
+"""Update gene names in CNVkit .cnn/.cnr files.
+"""
+from __future__ import absolute_import, division, print_function
+import argparse
+import logging
+import sys
+
+from skgenome import tabio
+from cnvlib.cmdutil import read_cna
+
+logging.basicConfig(level=logging.INFO, format="%(message)s")
+
+
+def main(args):
+ annot = tabio.read_auto(args.annotate)
+ cnarr = read_cna(args.cn_file)
+ cnarr['gene'] = annot.into_ranges(cnarr, 'gene', '-')
+ tabio.write(cnarr, args.output or sys.stdout)
+ # ENH:
+ # .cns: join gene names with commas
+ # cut antitargets & insert untargeted gene names
+ # some math for how to update probes, weight
+ # --short-names
+ # annotation: --merge, --flatten, --exons, ...
+
+
+
+if __name__ == '__main__':
+ AP = argparse.ArgumentParser(description=__doc__)
+ AP.add_argument('annotate', help="Genome annotations.")
+ AP.add_argument('cn_file', help="CNVkit .cnn or .cnr file.")
+ AP.add_argument('-o', '--output', help="Output filename.")
+ main(AP.parse_args())
diff --git a/scripts/cnn_updater.py b/scripts/cnn_updater.py
new file mode 100755
index 0000000..0338281
--- /dev/null
+++ b/scripts/cnn_updater.py
@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+
+"""Update CNVkit .cnn files to include 'depth' column.
+
+CNVkit v0.8.0 and later uses a 'depth' column in the *.targetcoverage.cnn and
+*.antitargetcoverage.cnn files produced by the 'coverage' command.
+To use .cnn files created by CNVkit v0.7.11 or earlier with the current version,
+run this script on the old .cnn files to convert them to the new format,
+calculating 'depth' from 'log2'.
+
+"""
+from __future__ import absolute_import, division, print_function
+
+import argparse
+import logging
+import os.path
+
+import numpy as np
+
+import cnvlib
+from skgenome import tabio
+
+logging.basicConfig(level=logging.INFO, format="%(message)s")
+
+
+AP = argparse.ArgumentParser(description=__doc__)
+AP.add_argument("cnn_files", nargs='+',
+ help="""CNVkit coverage files to update (*.targetcoverage.cnn,
+ *.antitargetcoverage.cnn).""")
+AP.add_argument("-d", "--output-dir", default=".",
+ help="""Directory to write output .cnn files.""")
+AP.add_argument("-s", "--suffix", default=".updated",
+ help="""Filename suffix to add before the '.cnn' extension in output
+ files. [Default: %(default)s]""")
+args = AP.parse_args()
+
+for fname in args.cnn_files:
+ cnarr = cnvlib.read(fname)
+ # Convert coverage depths from log2 scale to absolute scale.
+ # NB: The log2 values are un-centered in CNVkit v0.7.0(?) through v0.7.11;
+ # earlier than that, the average 'depth' will be about 1.0.
+ cnarr['depth'] = np.exp2(cnarr['log2'])
+ # Construct the output filename
+ base, ext = os.path.basename(fname).rsplit('.', 1)
+ if '.' in base:
+ base, zone = base.rsplit('.', 1)
+ out_fname = '.'.join((base + args.suffix, zone, ext))
+ else:
+ # e.g. reference.cnn or .cnr file, no "*.targetcoverage.*" in name
+ out_fname = '.'.join((base + args.suffix, ext))
+ tabio.write(cnarr, os.path.join(args.output_dir, out_fname))
diff --git a/scripts/genome2access.py b/scripts/genome2access.py
deleted file mode 100755
index b065b8b..0000000
--- a/scripts/genome2access.py
+++ /dev/null
@@ -1,46 +0,0 @@
-#!/usr/bin/env python
-
-"""List the locations of accessible sequence regions in a FASTA file.
-
-Inaccessible regions, e.g. telomeres and centromeres, are masked out with N in
-the reference genome sequence; this script scans those to identify the
-coordinates of the accessible regions (those between the long spans of N's).
-
-DEPRECATED -- use "cnvkit.py access" instead.
-"""
-
-import argparse
-import sys
-
-import logging
-logging.basicConfig(level=logging.INFO, format="%(message)s")
-
-from cnvlib import access
-
-
-AP = argparse.ArgumentParser(description=__doc__)
-AP.add_argument("fa_fname",
- help="Genome FASTA file name")
-AP.add_argument("-s", "--min-gap-size", type=int, default=5000,
- help="""Minimum gap size between accessible sequence
- regions. Regions separated by less than this distance will
- be joined together. [Default: %(default)s]""")
-AP.add_argument("-x", "--exclude", action="append", default=[],
- help="""Additional regions to exclude, in BED format. Can be
- used multiple times.""")
-AP.add_argument("-o", "--output",
- type=argparse.FileType('w'), default=sys.stdout,
- help="Output file name")
-args = AP.parse_args()
-
-# Closes over args.output
-def write_row(chrom, run_start, run_end):
- args.output.write("%s\t%s\t%s\n" % (chrom, run_start, run_end))
- args.output.flush()
-
-access_regions = access.get_regions(args.fa_fname)
-for ex_fname in args.exclude:
- access_regions = access.exclude_regions(ex_fname, access_regions)
-for row in access.join_regions(access_regions, args.min_gap_size):
- write_row(*row)
-
diff --git a/scripts/guess_baits.py b/scripts/guess_baits.py
new file mode 100755
index 0000000..7ce7ed5
--- /dev/null
+++ b/scripts/guess_baits.py
@@ -0,0 +1,238 @@
+#!/usr/bin/env python
+"""Guess the coordinates of captured regions from sample read depths.
+
+Two approaches available:
+
+- (Faster) Scan a given list of exons and/or other potentially targeted regions.
+ The script checks each region and drops those with very low coverage
+ indicating they were not captured.
+- (Slower) Scan the entire genome, or the given sequencing-accessible regions,
+ for regions with elevated coverage. Choose reasonable boundaries for each
+ apparently captured region.
+
+Use multiple BAMs for greater robustness in detecting targeted regions, as a
+single sample may have poor coverage are some targets by chance.
+Still, this script does not guarantee correctly detecting all targets.
+
+See also: https://github.com/brentp/goleft
+"""
+from __future__ import absolute_import, division, print_function
+
+import argparse
+import collections
+import logging
+import subprocess
+import sys
+
+import numpy as np
+import pandas as pd
+
+import cnvlib
+from cnvlib import parallel
+from cnvlib.descriptives import modal_location
+from skgenome import tabio, GenomicArray as GA
+
+logging.basicConfig(level=logging.INFO, format="%(message)s")
+
+
+# ___________________________________________
+# Guided method: guess from potential targets
+
+def filter_targets(target_bed, sample_bams, procs):
+ """Check if each potential target has significant coverage."""
+ baits = tabio.read_auto(target_bed)
+ # Loop over BAMs to calculate weighted averages of bin coverage depths
+ total_depths = np.zeros(len(baits), dtype=np.float_)
+ for bam_fname in sample_bams:
+ logging.info("Evaluating targets in %s", bam_fname)
+ sample = cnvlib.do_coverage(target_bed, bam_fname, processes=procs)
+ total_depths += sample['depth'].values
+ baits['depth'] = total_depths / len(sample_bams)
+ return baits
+
+
+# _________________________________________
+# Unguided method: guess from raw depths
+
+def scan_targets(access_bed, sample_bams, min_depth, min_gap, min_length,
+ procs):
+ """Estimate baited regions from a genome-wide, per-base depth profile."""
+ bait_chunks = []
+ # ENH: context manager to call rm on bed chunks? with to_chunks as pool, ck?
+ logging.info("Scanning for enriched regions in:\n %s",
+ '\n '.join(sample_bams))
+ # with futures.ProcessPoolExecutor(procs) as pool:
+ with parallel.pick_pool(procs) as pool:
+ args_iter = ((bed_chunk, sample_bams,
+ min_depth, min_gap, min_length)
+ for bed_chunk in parallel.to_chunks(access_bed))
+ for bed_chunk_fname, bait_chunk in pool.map(_scan_depth, args_iter):
+ bait_chunks.append(bait_chunk)
+ parallel.rm(bed_chunk_fname)
+ baits = GA(pd.concat(bait_chunks))
+ baits['depth'] /= len(sample_bams)
+ return baits
+
+
+def _scan_depth(args):
+ """Wrapper for parallel map"""
+ bed_fname, bam_fnames, min_depth, min_gap, min_length = args
+ regions = list(drop_small(merge_gaps(scan_depth(bed_fname, bam_fnames,
+ min_depth),
+ min_gap),
+ min_length))
+ result = pd.DataFrame.from_records(list(regions),
+ columns=regions[0]._fields)
+ return bed_fname, result
+
+
+def scan_depth(bed_fname, bam_fnames, min_depth):
+ """Locate sub-regions with enriched read depth in the given regions.
+
+ Yields
+ ------
+ tuple
+ Region coordinates (0-indexed, half-open): chromosome name, start, end
+ """
+ Region = collections.namedtuple('Region', 'chromosome start end depth')
+
+ nsamples = len(bam_fnames)
+ if nsamples == 1:
+ def get_depth(depths):
+ return int(depths[0])
+ else:
+ min_depth *= nsamples
+ # NB: samtools emits additional BAMs' depths as trailing columns
+ def get_depth(depths):
+ return sum(map(int, depths))
+
+ proc = subprocess.Popen(['samtools', 'depth',
+ '-Q', '1', # Skip pseudogenes
+ '-b', bed_fname,
+ ] + bam_fnames,
+ stdout=subprocess.PIPE,
+ shell=False)
+
+ # Detect runs of >= min_depth; emit their coordinates
+ chrom = start = depths = None
+ for line in proc.stdout:
+ fields = line.split('\t')
+ depth = get_depth(fields[2:])
+ is_enriched = (depth >= min_depth)
+ if start is None:
+ if is_enriched:
+ # Entering a new captured region
+ chrom = fields[0]
+ start = int(fields[1]) - 1
+ depths = [depth]
+ else:
+ # Still not in a captured region
+ continue
+ elif is_enriched and fields[0] == chrom:
+ # Still in a captured region -- extend it
+ depths.append(depth)
+ else:
+ # Exiting a captured region
+ # Update target region boundaries
+ darr = np.asarray(depths)
+ half_depth = 0.5 * darr.max()
+ ok_dp_idx = np.nonzero(darr >= half_depth)[0]
+ start_idx = ok_dp_idx[0]
+ end_idx = ok_dp_idx[-1] + 1
+ yield Region(chrom,
+ start + start_idx,
+ start + end_idx,
+ darr[start_idx:end_idx].mean())
+ chrom = start = depths = None
+
+
+def merge_gaps(regions, min_gap):
+ """Merge regions across small gaps."""
+ prev = next(regions)
+ for reg in regions:
+ if reg.start - prev.end < min_gap:
+ # Merge
+ prev = prev._replace(end=reg.end)
+ else:
+ # Done merging; move on
+ yield prev
+ prev = reg
+ # Residual
+ yield prev
+
+
+def drop_small(regions, min_length):
+ """Merge small gaps and filter by minimum length."""
+ return (reg for reg in regions
+ if reg.end - reg.start >= min_length)
+
+
+# ___________________________________________
+# Shared
+
+def normalize_depth_log2_filter(baits, min_depth, enrich_ratio=0.1):
+ """Calculate normalized depth, add log2 column, filter by enrich_ratio."""
+ # Normalize depths to a neutral value of 1.0
+ dp_mode = modal_location(baits.data.loc[baits['depth'] > min_depth,
+ 'depth'].values)
+ norm_depth = baits['depth'] / dp_mode
+ # Drop low-coverage targets
+ keep_idx = (norm_depth >= enrich_ratio)
+ logging.info("Keeping %d/%d bins with coverage depth >= %f, modal depth %f",
+ keep_idx.sum(), len(keep_idx), dp_mode * enrich_ratio, dp_mode)
+ return baits[keep_idx]
+
+
+
+if __name__ == '__main__':
+ AP = argparse.ArgumentParser(description=__doc__)
+ AP.add_argument('sample_bams', nargs='+',
+ help="""Sample BAM file(s) to test for target coverage""")
+ AP.add_argument('-o', '--output', metavar='FILENAME',
+ help="""The inferred targets, in BED format.""")
+ AP.add_argument('-c', '--coverage', metavar='FILENAME',
+ help="""Filename to output average coverage depths in .cnn
+ format.""")
+ AP.add_argument('-p', '--processes',
+ metavar='CPU', nargs='?', type=int, const=0, default=1,
+ help="""Number of subprocesses to segment in parallel.
+ If given without an argument, use the maximum number
+ of available CPUs. [Default: use 1 process]""")
+
+ AP_x = AP.add_mutually_exclusive_group(required=True)
+ AP_x.add_argument('-t', '--targets', metavar='TARGET_BED',
+ help="""Potentially targeted genomic regions, e.g. all
+ possible exons for the reference genome. (Faster
+ method)""")
+ AP_x.add_argument('-a', '--access', metavar='ACCESS_BED',
+ # default="../data/access-5k-mappable.grch37.bed",
+ help="""Sequencing-accessible genomic regions, or exons to
+ use as possible targets, e.g. output of refFlat2bed.py.
+ (Slower method)""")
+
+ AP.add_argument('-d', '--min-depth', metavar='DEPTH', type=int, default=5,
+ help="Minimum sequencing read depth to accept as captured.")
+ # Just for --access
+ AP.add_argument('-g', '--min-gap', metavar='GAP_SIZE', type=int, default=25,
+ help="Merge regions separated by gaps smaller than this.")
+ AP.add_argument('-l', '--min-length',
+ metavar='TARGET_SIZE', type=int, default=50,
+ help="Minimum region length to accept as captured.")
+
+ args = AP.parse_args()
+
+ # ENH: can we reserve multiple cores for htslib?
+ if args.processes < 1:
+ args.processes = None
+
+ if args.targets:
+ baits = filter_targets(args.targets, args.sample_bams, args.processes)
+ else:
+ baits = scan_targets(args.access, args.sample_bams,
+ 0.5 * args.min_depth, # More sensitive 1st pass
+ args.min_gap, args.min_length, args.processes)
+ baits = normalize_depth_log2_filter(baits, args.min_depth)
+ tabio.write(baits, args.output or sys.stdout, 'bed')
+ if args.coverage:
+ baits['log2'] = np.log2(baits['depth'] / baits['depth'].median())
+ tabio.write(baits, args.coverage, 'tab')
diff --git a/scripts/refFlat2bed.py b/scripts/refFlat2bed.py
index f854112..26f3a04 100755
--- a/scripts/refFlat2bed.py
+++ b/scripts/refFlat2bed.py
@@ -1,135 +1,43 @@
#!/usr/bin/env python
-"""Extract canonical gene coordinates from UCSC's refFlat.txt.
+"""[DEPRECATED; use skg_convert.py]
+
+Extract canonical gene coordinates from UCSC's refFlat.txt.
Usage:
- refFlat2bed.py /path/to/refFlat.txt > genes.bed
- refFlat2bed.py -e /path/to/refFlat.txt > exons.bed
+ refFlat2bed.py /path/to/refFlat.txt -f > genes.bed
+ refFlat2bed.py /path/to/refFlat.txt -e -m > exons.bed
"""
-# XXX what about overlapping genes w/ different names?
-from __future__ import print_function
-
-from collections import defaultdict
-
-from cnvlib.core import sorter_chrom
-
-
-def parse_refflat_line(line):
- """Parse one line of refFlat.txt; return relevant info.
-
- Pair up the exon start and end positions. Add strand direction to each
- chromosome as a "+"/"-" suffix (it will be stripped off later).
- """
- fields = line.split('\t')
- name, refseq, chrom, strand = fields[:4]
- start, end = fields[4:6]
- # start, end = fields[6:8]
- exon_count, exon_starts, exon_ends = fields[8:11]
- exons = zip(map(int, exon_starts.rstrip(',').split(',')),
- map(int, exon_ends.rstrip('\n,').split(',')))
- assert len(exons) == int(exon_count), (
- "Exon count mismatch at %s: file says %s, but counted %d intervals"
- % (name, exon_count, len(exons)))
- return name, refseq, chrom + strand, int(start), int(end), exons
-
-
-def load_genes(fname):
- genedict = defaultdict(list)
- with open(fname) as genefile:
- for line in genefile:
- name, _refseq, chrom, start, end, _exons = parse_refflat_line(line)
- genedict[name].append((chrom, start, end))
- return genedict
-
-
-def load_exons(fname):
- exondict = defaultdict(list)
- with open(fname) as genefile:
- for line in genefile:
- name, _refseq, chrom, _start, _end, exons = parse_refflat_line(line)
- for start, end in exons:
- exondict[name].append((chrom, start, end))
- return exondict
-
-
-def dedupe_regions(regions):
- """Merge genes/exons with the same name and overlapping regions."""
- for name, locs in regions.iteritems():
- locs = list(set(locs))
- if len(locs) == 1:
- chrom, start, end = locs[0]
- # Strip the strand indicator off the end of the chromosome name
- yield (chrom[:-1], start, end, name)
- else:
- # Check locs for overlap; merge if so
- locs.sort()
- chroms, starts, ends = zip(*locs)
- curr_chrom, curr_start, curr_end = chroms[0], starts[0], ends[0]
- for chrom, start, end in zip(chroms[1:], starts[1:], ends[1:]):
- if (chrom != curr_chrom or
- start > curr_end + 1 or
- end < curr_start - 1):
- yield (curr_chrom[:-1], curr_start, curr_end, name)
- curr_chrom, curr_start, curr_end = chrom, start, end
- else:
- curr_start = min(start, curr_start)
- curr_end = max(end, curr_end)
- # Emit the final gene/exon in this group
- yield (curr_chrom[:-1], curr_start, curr_end, name)
-
-def merge_rows(rows):
- """Where rows overlap, merge the regions and gene names."""
- rows = iter(rows)
- prev_chrom, prev_start, prev_end, prev_name = next(rows)
-
- for chrom, start, end, name in rows:
- # No overlap.
- if (chrom != prev_chrom) or (start >= prev_end):
- yield (prev_chrom, prev_start, prev_end, prev_name)
- # out_row = (chrom, start, end, name)
- prev_chrom, prev_start, prev_end, prev_name = \
- (chrom, start, end, name)
- continue
-
- # Some overlap. Adjust prev_ values accordingly.
- # Known: chrom == prev_chrom; start <= prev_end
- assert prev_start <= start, (
- "Botched overlap: %s %s:%s-%s vs. prev. %s %s:%s-%d"
- % (name, chrom, start, end,
- prev_name, prev_chrom, prev_start, prev_end))
- prev_end = max(prev_end, end)
- if name not in prev_name.split('|'):
- prev_name += '|' + name
-
- # Remainder
- yield (prev_chrom, prev_start, prev_end, prev_name)
-
-
-def key_genomic_position(row):
- """Turn genomic position into a sort key: (chrom_key, end_posn)
-
- Input rows are BED-like: (chrom, start, end, name)
- """
- return sorter_chrom(row[0]), row[1]
-
-
-if __name__ == '__main__':
- import argparse
- AP = argparse.ArgumentParser(description=__doc__)
- AP.add_argument('genes', help="refFlat.txt")
- AP.add_argument('-e', '--exons', action='store_true',
- help="Emit each exon, not just the genes.")
- AP.add_argument('-m', '--merge', action='store_true',
- help="Merge overlapping regions with different names.")
- args = AP.parse_args()
-
- if args.exons:
- regions = load_exons(args.genes)
- else:
- regions = load_genes(args.genes)
- out_rows = sorted(dedupe_regions(regions), key=key_genomic_position)
- if args.merge:
- out_rows = merge_rows(out_rows)
- for row in out_rows:
- print('\t'.join(map(str, row)))
-
+from __future__ import absolute_import, division, print_function
+
+import argparse
+import logging
+
+from skgenome import tabio
+
+logging.basicConfig(level=logging.INFO, format="%(message)s")
+
+AP = argparse.ArgumentParser(description=__doc__)
+AP.add_argument('refflat',
+ help="UCSC refFlat.txt for the reference genome.")
+AP.add_argument('-e', '--exons', action='store_true',
+ help="""Emit each exon instead of the whole gene regions.""")
+AP.add_argument('-f', '--flatten', action='store_true',
+ help="""Flatten overlapping regions, keeping original
+ boundaries. Not recommended with --exons.""")
+AP.add_argument('-m', '--merge',
+ metavar='BASEPAIRS', nargs='?', type=int, const=1,
+ help="""Merge overlapping regions with different names.
+ Recommended with --exons. Optional argument value is the
+ number of overlapping bases between two regions to trigger a
+ merge. [Default: %(const)s]""")
+AP.add_argument('-o', '--output',
+ help="Output filename.")
+args = AP.parse_args()
+
+regions = tabio.read(args.refflat, 'refflat', exons=args.exons)
+if args.flatten:
+ regions = regions.flatten()
+elif args.merge:
+ regions = regions.merge(bp=args.merge)
+tabio.write(regions, args.output, 'bed4')
diff --git a/scripts/reference2targets.py b/scripts/reference2targets.py
index 9a6eb45..fe86c9c 100755
--- a/scripts/reference2targets.py
+++ b/scripts/reference2targets.py
@@ -10,37 +10,24 @@ This script is also useful to recover the target and antitarget BED files that
match the reference if those BED files are missing or you're not sure which ones
are correct.
"""
+from __future__ import absolute_import, division, print_function
+import argparse
import logging
-logging.basicConfig(level=logging.INFO, format="%(message)s")
import cnvlib
-from cnvlib import ngfrills, reference
-
-
-def write_bed(rows, fname):
- """Write region coordinates to `fname` in BED format."""
- with ngfrills.safe_write(fname, False) as outfile:
- i = 0
- for i, row in enumerate(rows):
- outfile.write("\t".join(map(str, row)) + '\n')
- logging.info("Wrote %s with %d bins", fname, i + 1)
-
+from cnvlib import reference
+from skgenome import tabio
-def main(args):
- """Run the script."""
- ref = cnvlib.read(args.reference)
- targets, antitargets = reference.reference2regions(ref)
- name = args.output or ref.sample_id
- write_bed(targets, name + '.target.bed')
- write_bed(antitargets, name + '.antitarget.bed')
-
-
-if __name__ == '__main__':
- import argparse
- AP = argparse.ArgumentParser(description=__doc__)
- AP.add_argument("reference", help="Reference file.")
- AP.add_argument("-o", "--output",
- help="Output base name (extensions added automatically).")
- main(AP.parse_args())
+logging.basicConfig(level=logging.INFO, format="%(message)s")
+AP = argparse.ArgumentParser(description=__doc__)
+AP.add_argument("reference", help="Reference file.")
+AP.add_argument("-o", "--output",
+ help="Output base name (extensions added automatically).")
+args = AP.parse_args()
+ref = cnvlib.read(args.reference)
+targets, antitargets = reference.reference2regions(ref)
+name = args.output or ref.sample_id
+tabio.write(targets, name + '.target.bed', 'bed4')
+tabio.write(antitargets, name + '.antitarget.bed', 'bed4')
diff --git a/scripts/skg_convert.py b/scripts/skg_convert.py
new file mode 100755
index 0000000..aaa60fc
--- /dev/null
+++ b/scripts/skg_convert.py
@@ -0,0 +1,35 @@
+#!/usr/bin/env python
+
+"""Convert between tabular formats using scikit-genome I/O."""
+from __future__ import absolute_import, division, print_function
+import argparse
+import logging
+import sys
+
+from skgenome import tabio
+
+logging.basicConfig(level=logging.INFO, format="%(message)s")
+
+
+def main(args):
+ logging.info("Converting %s%s to %s",
+ "input" if args.infile is sys.stdin else args.infile,
+ "from "+ args.in_fmt if args.in_fmt != 'auto' else '',
+ args.out_fmt)
+
+ table = tabio.read(args.infile, args.in_fmt)
+ tabio.write(table, args.output, args.out_fmt)
+
+
+
+if __name__ == '__main__':
+ AP = argparse.ArgumentParser(description=__doc__)
+ AP.add_argument('infile', nargs='?', default=sys.stdin,
+ help="Input filename.")
+ AP.add_argument('-f', '--from', dest='in_fmt', default='auto',
+ help="Input format.")
+ AP.add_argument('-t', '--to', dest='out_fmt', required=True,
+ help="Output format.")
+ AP.add_argument('-o', '--output',
+ help="Output filename.")
+ main(AP.parse_args())
diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 0000000..2a9acf1
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,2 @@
+[bdist_wheel]
+universal = 1
diff --git a/setup.py b/setup.py
index a11fd43..a16b437 100755
--- a/setup.py
+++ b/setup.py
@@ -12,15 +12,16 @@ try:
# Dependencies for easy_install and pip:
setup_args.update(
install_requires=[
- 'numpy >= 1.6',
- 'scipy >= 0.9',
- 'matplotlib >= 1.1',
- 'pandas >= 0.17.1',
- 'pysam >= 0.8',
- 'pyvcf >= 0.5',
- 'reportlab >= 3.0',
'biopython >= 1.62',
- 'pyfaidx >= 0.4.7'
+ 'future >= 0.15.2',
+ 'futures >= 3.0',
+ 'matplotlib >= 1.3.1',
+ 'numpy >= 1.9',
+ 'pandas >= 0.18.1',
+ 'pyfaidx >= 0.4.7',
+ 'pysam >= 0.10.0',
+ 'reportlab >= 3.0',
+ 'scipy >= 0.15.0',
])
except ImportError:
from distutils.core import setup
@@ -38,8 +39,9 @@ setup_args.update(
url='http://github.com/etal/cnvkit',
packages=[
'cnvlib',
- 'cnvlib.ngfrills',
'cnvlib.segmentation',
+ 'skgenome',
+ 'skgenome.tabio',
],
scripts=[join(DIR, 'cnvkit.py')] + glob(join(DIR, 'scripts/*.py')),
classifiers=[
@@ -53,6 +55,8 @@ setup_args.update(
"Operating System :: POSIX :: Linux",
"Operating System :: Unix",
"Programming Language :: Python",
+ "Programming Language :: Python :: 3",
+ "Programming Language :: Python :: 3.4",
"Programming Language :: Python :: 2",
"Programming Language :: Python :: 2.7",
"Topic :: Scientific/Engineering",
diff --git a/skgenome/__init__.py b/skgenome/__init__.py
new file mode 100644
index 0000000..f813e51
--- /dev/null
+++ b/skgenome/__init__.py
@@ -0,0 +1,2 @@
+from . import tabio
+from .gary import GenomicArray
diff --git a/skgenome/chromsort.py b/skgenome/chromsort.py
new file mode 100644
index 0000000..e81db06
--- /dev/null
+++ b/skgenome/chromsort.py
@@ -0,0 +1,61 @@
+"""Operations on chromosome/contig/sequence names."""
+from __future__ import absolute_import, division, print_function
+
+from itertools import takewhile
+
+import numpy as np
+import pandas as pd
+
+
+def detect_big_chroms(sizes):
+ """Determine the number of "big" chromosomes from their lengths.
+
+ In the human genome, this returns 24, where the canonical chromosomes 1-22,
+ X, and Y are considered "big", while mitochrondria and the alternative
+ contigs are not. This allows us to exclude the non-canonical chromosomes
+ from an analysis where they're not relevant.
+
+ Returns
+ -------
+ n_big : int
+ Number of "big" chromosomes in the genome.
+ thresh : int
+ Length of the smallest "big" chromosomes.
+ """
+ sizes = pd.Series(sizes).sort_values(ascending=False)
+ reldiff = sizes.diff().abs().values[1:] / sizes.values[:-1]
+ changepoints = np.nonzero(reldiff > .5)[0]
+ if changepoints.any():
+ n_big = changepoints[0] + 1
+ thresh = sizes.iat[n_big - 1]
+ else:
+ n_big = len(sizes)
+ thresh = sizes[-1]
+ return n_big, thresh
+
+
+def sorter_chrom(label):
+ """Create a sorting key from chromosome label.
+
+ Sort by integers first, then letters or strings. The prefix "chr"
+ (case-insensitive), if present, is stripped automatically for sorting.
+
+ E.g. chr1 < chr2 < chr10 < chrX < chrY < chrM
+ """
+ # Strip "chr" prefix
+ chrom = (label[3:] if label.lower().startswith('chr')
+ else label)
+ if chrom in ('X', 'Y'):
+ key = (1000, chrom)
+ else:
+ # Separate numeric and special chromosomes
+ nums = ''.join(takewhile(str.isdigit, chrom))
+ chars = chrom[len(nums):]
+ nums = int(nums) if nums else 0
+ if not chars:
+ key = (nums, '')
+ elif len(chars) == 1:
+ key = (2000 + nums, chars)
+ else:
+ key = (3000 + nums, chars)
+ return key
diff --git a/skgenome/combiners.py b/skgenome/combiners.py
new file mode 100644
index 0000000..384f377
--- /dev/null
+++ b/skgenome/combiners.py
@@ -0,0 +1,67 @@
+"""Combiner functions for Python list-like input."""
+from __future__ import print_function, absolute_import, division
+
+import pandas as pd
+
+
+def get_combiners(table, stranded=False, combine=None):
+ """Get a `combine` lookup suitable for `table`.
+
+ Parameters
+ ----------
+ table : DataFrame
+ stranded : bool
+ combine : dict or None
+ Column names to their value-combining functions, replacing or in
+ addition to the defaults.
+
+ Returns
+ -------
+ dict:
+ Column names to their value-combining functions.
+ """
+ cmb = {
+ 'chromosome': first_of,
+ 'start': first_of,
+ 'end': max_of,
+ 'gene': join_strings,
+ 'accession': join_strings,
+ }
+ if combine:
+ cmb.update(combine)
+ if 'strand' not in cmb:
+ cmb['strand'] = first_of if stranded else merge_strands
+ return {k: v for k, v in cmb.items() if k in table.columns}
+
+
+def first_of(elems):
+ """Return the first element of the input."""
+ return elems[0]
+
+
+def last_of(elems):
+ """Return the last element of the input."""
+ return elems[-1]
+
+
+def max_of(elems):
+ return max(elems)
+
+
+def join_strings(elems, sep=','):
+ """Join a Series of strings by commas."""
+ # ENH if elements are also comma-separated, split+uniq those too
+ return sep.join(pd.unique(elems))
+
+
+def merge_strands(elems):
+ strands = set(elems)
+ if len(strands) > 1:
+ return '.'
+ return elems[0]
+
+
+def make_const(val):
+ def const(_elems):
+ return val
+ return const
diff --git a/skgenome/gary.py b/skgenome/gary.py
new file mode 100644
index 0000000..142a43c
--- /dev/null
+++ b/skgenome/gary.py
@@ -0,0 +1,615 @@
+"""Base class for an array of annotated genomic regions."""
+from __future__ import print_function, absolute_import, division
+from builtins import next, object, zip
+from past.builtins import basestring
+
+import logging
+import warnings
+from collections import OrderedDict
+
+import numpy as np
+import pandas as pd
+
+from .chromsort import sorter_chrom
+from .intersect import by_ranges, into_ranges, iter_ranges
+from .merge import flatten, merge
+from .rangelabel import to_label
+from .subtract import subtract
+from .subdivide import subdivide
+
+
+class GenomicArray(object):
+ """An array of genomic intervals. Base class for genomic data structures.
+
+ Can represent most BED-like tabular formats with arbitrary additional
+ columns.
+ """
+ _required_columns = ("chromosome", "start", "end")
+ _required_dtypes = (str, int, int)
+
+ def __init__(self, data_table, meta_dict=None):
+ # Validation
+ if (data_table is None or
+ (isinstance(data_table, (list, tuple)) and not len(data_table)) or
+ (isinstance(data_table, pd.DataFrame) and not len(data_table.columns))
+ ):
+ data_table = self._make_blank()
+ else:
+ if not isinstance(data_table, pd.DataFrame):
+ # Rarely if ever needed -- prefer from_rows, from_columns, etc.
+ data_table = pd.DataFrame(data_table)
+ if not all(c in data_table.columns for c in self._required_columns):
+ raise ValueError("data table must have at least columns %r; "
+ "got %r" % (self._required_columns,
+ tuple(data_table.columns)))
+ # Ensure columns are the right type
+ # (in case they've been automatically converted to the wrong type,
+ # e.g. chromosome names as integers; genome coordinates as floats)
+ if len(data_table):
+ def ok_dtype(col, dt):
+ return isinstance(data_table[col].iat[0], dt)
+ else:
+ def ok_dtype(col, dt):
+ return data_table[col].dtype == np.dtype(dt)
+ for col, dtype in zip(self._required_columns, self._required_dtypes):
+ if not ok_dtype(col, dtype):
+ data_table[col] = data_table[col].astype(dtype)
+
+ self.data = data_table
+ self.meta = (dict(meta_dict)
+ if meta_dict is not None and len(meta_dict)
+ else {})
+
+ @classmethod
+ def _make_blank(cls):
+ """Create an empty dataframe with the columns required by this class."""
+ spec = list(zip(cls._required_columns, cls._required_dtypes))
+ try:
+ arr = np.zeros(0, dtype=spec)
+ return pd.DataFrame(arr)
+ except TypeError as exc:
+ raise TypeError("{}: {}".format(exc, spec))
+
+ @classmethod
+ def from_columns(cls, columns, meta_dict=None):
+ """Create a new instance from column arrays, given as a dict."""
+ table = pd.DataFrame.from_dict(columns)
+ ary = cls(table, meta_dict)
+ ary.sort_columns()
+ return ary
+
+ @classmethod
+ def from_rows(cls, rows, columns=None, meta_dict=None):
+ """Create a new instance from a list of rows, as tuples or arrays."""
+ if columns is None:
+ columns = cls._required_columns
+ table = pd.DataFrame.from_records(rows, columns=columns)
+ return cls(table, meta_dict)
+
+ def as_columns(self, **columns):
+ """Wrap the named columns in this instance's metadata."""
+ return self.__class__.from_columns(columns, self.meta)
+ # return self.__class__(self.data.loc[:, columns], self.meta.copy())
+
+ def as_dataframe(self, dframe):
+ """Wrap the given pandas dataframe in this instance's metadata."""
+ return self.__class__(dframe.reset_index(drop=True), self.meta.copy())
+
+ # def as_index(self, index):
+ # """Subset with fancy/boolean indexing; reuse this instance's metadata."""
+ # """Extract rows by indices, reusing this instance's metadata."""
+ # if isinstance(index, (int, slice)):
+ # return self.__class__(self.data.iloc[index], self.meta.copy())
+ # else:
+ # return self.__class__(self.data[index], self.meta.copy())
+
+ def as_rows(self, rows):
+ """Wrap the given rows in this instance's metadata."""
+ return self.from_rows(rows,
+ columns=self.data.columns,
+ meta_dict=self.meta)
+
+ # Container behaviour
+
+ def __eq__(self, other):
+ return (isinstance(other, self.__class__) and
+ self.data.equals(other.data))
+
+ def __len__(self):
+ return len(self.data)
+
+ def __contains__(self, key):
+ return key in self.data.columns
+
+ def __getitem__(self, index):
+ """Access a portion of the data.
+
+ Cases:
+
+ - single integer: a row, as pd.Series
+ - string row name: a column, as pd.Series
+ - a boolean array: masked rows, as_dataframe
+ - tuple of integers: selected rows, as_dataframe
+ """
+ if isinstance(index, int):
+ # A single row
+ return self.data.iloc[index]
+ # return self.as_dataframe(self.data.iloc[index:index+1])
+ elif isinstance(index, basestring):
+ # A column, by name
+ return self.data[index]
+ elif (isinstance(index, tuple) and
+ len(index) == 2 and
+ index[1] in self.data.columns):
+ # Row index, column index -> cell value
+ return self.data.loc[index]
+ elif isinstance(index, slice):
+ # return self.as_dataframe(self.data.take(index))
+ return self.as_dataframe(self.data[index])
+ else:
+ # Iterable -- selected row indices or boolean array, probably
+ try:
+ if isinstance(index, type(None)) or len(index) == 0:
+ empty = pd.DataFrame(columns=self.data.columns)
+ return self.as_dataframe(empty)
+ except TypeError:
+ raise TypeError("object of type %r " % type(index) +
+ "cannot be used as an index into a " +
+ self.__class__.__name__)
+ return self.as_dataframe(self.data[index])
+ # return self.as_dataframe(self.data.take(index))
+
+ def __setitem__(self, index, value):
+ """Assign to a portion of the data."""
+ if isinstance(index, int):
+ self.data.iloc[index] = value
+ elif isinstance(index, basestring):
+ self.data[index] = value
+ elif (isinstance(index, tuple) and
+ len(index) == 2 and
+ index[1] in self.data.columns):
+ self.data.loc[index] = value
+ else:
+ assert isinstance(index, slice) or len(index) > 0
+ self.data[index] = value
+
+ def __delitem__(self, index):
+ return NotImplemented
+
+ def __iter__(self):
+ return self.data.itertuples(index=False)
+
+ __next__ = next
+
+ @property
+ def chromosome(self):
+ return self.data['chromosome']
+
+ @property
+ def start(self):
+ return self.data['start']
+
+ @property
+ def end(self):
+ return self.data['end']
+
+ @property
+ def sample_id(self):
+ return self.meta.get('sample_id')
+
+ # Traversal
+
+ def autosomes(self, also=()):
+ """Select chromosomes w/ integer names, ignoring any 'chr' prefixes."""
+ with warnings.catch_warnings():
+ # NB: We're not using the deprecated part of this pandas method
+ # (as_indexer introduced before 0.18.1, deprecated 0.20.1)
+ warnings.simplefilter("ignore", UserWarning)
+ kwargs = dict(na=False)
+ if pd.__version__ < "0.20.1":
+ kwargs["as_indexer"] = True
+ is_auto = self.chromosome.str.match(r"(chr)?\d+$", **kwargs)
+ if not is_auto.any():
+ # The autosomes, if any, are not named with plain integers
+ return self
+ if also:
+ if isinstance(also, basestring):
+ also = [also]
+ for a_chrom in also:
+ is_auto |= (self.chromosome == a_chrom)
+ return self[is_auto]
+
+ def by_chromosome(self):
+ """Iterate over bins grouped by chromosome name."""
+ # Workaround for pandas 0.18.0 bug:
+ # https://github.com/pydata/pandas/issues/13179
+ self.data.chromosome = self.data.chromosome.astype(str)
+ for chrom, subtable in self.data.groupby("chromosome", sort=False):
+ yield chrom, self.as_dataframe(subtable)
+
+ def by_ranges(self, other, mode='inner', keep_empty=True):
+ """Group rows by another GenomicArray's bin coordinate ranges.
+
+ For example, this can be used to group SNVs by CNV segments.
+
+ Bins in this array that fall outside the other array's bins are skipped.
+
+ Parameters
+ ----------
+ other : GenomicArray
+ Another GA instance.
+ mode : string
+ Determines what to do with bins that overlap a boundary of the
+ selection. Possible values are:
+
+ - ``inner``: Drop the bins on the selection boundary, don't emit them.
+ - ``outer``: Keep/emit those bins as they are.
+ - ``trim``: Emit those bins but alter their boundaries to match the
+ selection; the bin start or end position is replaced with the
+ selection boundary position.
+ keep_empty : bool
+ Whether to also yield `other` bins with no overlapping bins in
+ `self`, or to skip them when iterating.
+
+ Yields
+ ------
+ tuple
+ (other bin, GenomicArray of overlapping rows in self)
+ """
+ for bin_row, subrange in by_ranges(self.data, other.data,
+ mode, keep_empty):
+ if len(subrange):
+ yield bin_row, self.as_dataframe(subrange)
+ elif keep_empty:
+ yield bin_row, self.as_rows(subrange)
+
+ def coords(self, also=()):
+ """Iterate over plain coordinates of each bin: chromosome, start, end.
+
+ Parameters
+ ----------
+ also : str, or iterable of strings
+ Also include these columns from `self`, in addition to chromosome,
+ start, and end.
+
+ Example, yielding rows in BED format:
+
+ >>> probes.coords(also=["gene", "strand"])
+ """
+ cols = list(GenomicArray._required_columns)
+ if also:
+ if isinstance(also, basestring):
+ cols.append(also)
+ else:
+ cols.extend(also)
+ coordframe = self.data.loc[:, cols]
+ return coordframe.itertuples(index=False)
+
+ def labels(self):
+ return self.data.apply(to_label, axis=1)
+
+ def in_range(self, chrom=None, start=None, end=None, mode='inner'):
+ """Get the GenomicArray portion within the given genomic range.
+
+ Parameters
+ ----------
+ chrom : str or None
+ Chromosome name to select. Use None if `self` has only one
+ chromosome.
+ start : int or None
+ Start coordinate of range to select, in 0-based coordinates.
+ If None, start from 0.
+ end : int or None
+ End coordinate of range to select. If None, select to the end of the
+ chromosome.
+ mode : str
+ As in `by_ranges`: ``outer`` includes bins straddling the range
+ boundaries, ``trim`` additionally alters the straddling bins'
+ endpoints to match the range boundaries, and ``inner`` excludes
+ those bins.
+
+ Returns
+ -------
+ GenomicArray
+ The subset of `self` enclosed by the specified range.
+ """
+ if isinstance(start, (int, np.int64, float, np.float64)):
+ start = [int(start)]
+ if isinstance(end, (int, np.int64, float, np.float64)):
+ end = [int(end)]
+ results = iter_ranges(self.data, chrom, start, end, mode)
+ return self.as_dataframe(next(results))
+
+ def in_ranges(self, chrom=None, starts=None, ends=None, mode='inner'):
+ """Get the GenomicArray portion within the specified ranges.
+
+ Similar to `in_ranges`, but concatenating the selections of all the
+ regions specified by the `starts` and `ends` arrays.
+
+ Parameters
+ ----------
+ chrom : str or None
+ Chromosome name to select. Use None if `self` has only one
+ chromosome.
+ starts : int array, or None
+ Start coordinates of ranges to select, in 0-based coordinates.
+ If None, start from 0.
+ ends : int array, or None
+ End coordinates of ranges to select. If None, select to the end of the
+ chromosome. If `starts` and `ends` are both specified, they must be
+ arrays of equal length.
+ mode : str
+ As in `by_ranges`: ``outer`` includes bins straddling the range
+ boundaries, ``trim`` additionally alters the straddling bins'
+ endpoints to match the range boundaries, and ``inner`` excludes
+ those bins.
+
+ Returns
+ -------
+ GenomicArray
+ Concatenation of all the subsets of `self` enclosed by the specified
+ ranges.
+ """
+ table = pd.concat(iter_ranges(self.data, chrom, starts, ends, mode))
+ return self.as_dataframe(table)
+
+ def into_ranges(self, other, column, default, summary_func=None):
+ """Re-bin values from `column` into the corresponding ranges in `other`.
+
+ Match overlapping/intersecting rows from `other` to each row in `self`.
+ Then, within each range in `other`, extract the value(s) from `column`
+ in `self`, using the function `summary_func` to produce a single value
+ if multiple bins in `self` map to a single range in `other`.
+
+ For example, group SNVs (self) by CNV segments (other) and calculate the
+ median (summary_func) of each SNV group's allele frequencies.
+
+ Parameters
+ ----------
+ other : GenomicArray
+ Bins to
+ column : string
+ Column name in `self` to extract values from.
+ default
+ Value to assign to indices in `other` that do not overlap any bins in
+ `self`. Type should be the same as or compatible with the output
+ field specified by `column`, or the output of `summary_func`.
+ summary_func : callable, dict of string-to-callable, or None
+ Specify how to reduce 1 or more `other` rows into a single value for
+ the corresponding row in `self`.
+
+ - If callable, apply to the `column` field each group of rows in
+ `other` column.
+ - If a single-element dict of column name to callable, apply to that
+ field in `other` instead of `column`.
+ - If None, use an appropriate summarizing function for the datatype
+ of the `column` column in `other` (e.g. median of numbers,
+ concatenation of strings).
+ - If some other value, assign that value to `self` wherever there is
+ an overlap.
+
+ Returns
+ -------
+ pd.Series
+ The extracted and summarized values from `self` corresponding to
+ other's genomic ranges, the same length as `other`.
+ """
+ if column not in self:
+ logging.warn("No '%s' column available for summary calculation",
+ column)
+ return pd.Series(np.repeat(default, len(other)))
+ return into_ranges(self.data, other.data, column, default, summary_func)
+
+ # Modification
+
+ def add(self, other):
+ """Combine this array's data with another GenomicArray (in-place).
+
+ Any optional columns must match between both arrays.
+ """
+ if not isinstance(other, self.__class__):
+ raise ValueError("Argument (type %s) is not a %s instance"
+ % (type(other), self.__class__))
+ if not len(other.data):
+ return self.copy()
+ self.data = self.data.append(other.data, ignore_index=True)
+ self.sort()
+
+ def concat(self, others):
+ """Concatenate several GenomicArrays, keeping this array's metadata.
+
+ This array's data table is not implicitly included in the result.
+ """
+ table = pd.concat([otr.data for otr in others], ignore_index=True)
+ result = self.as_dataframe(table)
+ result.sort()
+ return result
+
+ def copy(self):
+ """Create an independent copy of this object."""
+ return self.as_dataframe(self.data.copy())
+
+ def add_columns(self, **columns):
+ """Add the given columns to a copy of this GenomicArray.
+
+ Parameters
+ ----------
+ **columns : array
+ Keyword arguments where the key is the new column's name and the
+ value is an array of the same length as `self` which will be the new
+ column's values.
+
+ Returns
+ -------
+ GenomicArray or subclass
+ A new instance of `self` with the given columns included in the
+ underlying dataframe.
+ """
+ # return self.as_dataframe(self.data.assign(**columns))
+ result = self.copy()
+ for key, values in columns.items():
+ result[key] = values
+ return result
+
+ def keep_columns(self, columns):
+ """Extract a subset of columns, reusing this instance's metadata."""
+ return self.__class__(self.data.loc[:, columns], self.meta.copy())
+
+ def drop_extra_columns(self):
+ """Remove any optional columns from this GenomicArray.
+
+ Returns
+ -------
+ GenomicArray or subclass
+ A new copy with only the minimal set of columns required by the
+ class (e.g. chromosome, start, end for GenomicArray; may be more for
+ subclasses).
+ """
+ table = self.data.loc[:, self._required_columns]
+ return self.as_dataframe(table)
+
+ def filter(self, func=None, **kwargs):
+ """Take a subset of rows where the given condition is true.
+
+ Parameters
+ ----------
+ func : callable
+ A boolean function which will be applied to each row to keep rows
+ where the result is True.
+ **kwargs : string
+ Keyword arguments like ``chromosome="chr7"`` or
+ ``gene="Antitarget"``, which will keep rows where the keyed field
+ equals the specified value.
+
+ Return
+ ------
+ GenomicArray
+ Subset of `self` where the specified condition is True.
+ """
+ table = self.data
+ if func is not None:
+ table = table[table.apply(func, axis=1)]
+ for key, val in list(kwargs.items()):
+ assert key in self
+ table = table[table[key] == val]
+ return self.as_dataframe(table)
+
+ def shuffle(self):
+ """Randomize the order of bins in this array (in-place)."""
+ order = np.arange(len(self.data))
+ np.random.seed(0xA5EED)
+ np.random.shuffle(order)
+ self.data = self.data.iloc[order]
+ return order
+
+ def sort(self):
+ """Sort this array's bins in-place, with smart chromosome ordering."""
+ sort_key = self.data.chromosome.apply(sorter_chrom)
+ self.data = (self.data.assign(_sort_key_=sort_key)
+ .sort_values(by=['_sort_key_', 'start', 'end'],
+ kind='mergesort')
+ .drop('_sort_key_', axis=1)
+ .reset_index(drop=True))
+
+ def sort_columns(self):
+ """Sort this array's columns in-place, per class definition."""
+ extra_cols = []
+ for col in self.data.columns:
+ if col not in self._required_columns:
+ extra_cols.append(col)
+ sorted_colnames = list(self._required_columns) + sorted(extra_cols)
+ assert len(sorted_colnames) == len(self.data.columns)
+ self.data = self.data.reindex(columns=sorted_colnames)
+
+ # Genome arithmetic
+
+ def cut(self, other, combine=None):
+ """Split this array's regions at the boundaries in `other`."""
+ # TODO
+ return NotImplemented
+
+ def flatten(self, combine=None):
+ """Split this array's regions where they overlap."""
+ return self.as_dataframe(flatten(self.data, combine=combine))
+
+ def merge(self, bp=0, stranded=False, combine=None):
+ """Merge adjacent or overlapping regions into single rows.
+
+ Similar to 'bedtools merge'.
+ """
+ return self.as_dataframe(merge(self.data, bp, stranded, combine))
+
+ def resize_ranges(self, bp, chrom_sizes=None):
+ """Resize each genomic bin by a fixed number of bases at each end.
+
+ Bin 'start' values have a minimum of 0, and `chrom_sizes` can
+ specify each chromosome's maximum 'end' value.
+
+ Similar to 'bedtools slop'.
+
+ Parameters
+ ----------
+ bp : int
+ Number of bases in each direction to expand or shrink each bin.
+ Applies to 'start' and 'end' values symmetrically, and may be
+ positive (expand) or negative (shrink).
+ chrom_sizes : dict of string-to-int
+ Chromosome name to length in base pairs. If given, all chromosomes
+ in `self` must be included.
+ """
+ table = self.data
+ limits = dict(lower=0)
+ if chrom_sizes:
+ limits['upper'] = self.chromosome.replace(chrom_sizes)
+ table = table.assign(start=(table['start'] - bp).clip(**limits),
+ end=(table['end'] + bp).clip(**limits))
+ if bp < 0:
+ # Drop any bins that now have zero or negative size
+ ok_size = table['end'] - table['start'] > 0
+ logging.debug("Dropping %d bins with size <= 0", (~ok_size).sum())
+ table = table[ok_size]
+ # Don't modify the original
+ return self.as_dataframe(table.copy())
+
+ def squash(self, combine=None):
+ """Combine some groups of rows, by some criteria, into single rows."""
+ # TODO
+ return NotImplemented
+
+ def subdivide(self, avg_size, min_size=0, verbose=False):
+ """Split this array's regions into roughly equal-sized sub-regions."""
+ return self.as_dataframe(subdivide(self.data, avg_size, min_size,
+ verbose))
+
+ def subtract(self, other):
+ """Remove the overlapping regions in `other` from this array."""
+ return self.as_dataframe(subtract(self.data, other.data))
+
+ def total_range_size(self):
+ """Total number of bases covered by all (merged) regions."""
+ if not len(self):
+ return 0
+ regions = merge(self.data, bp=1)
+ return regions.end.sum() - regions.start.sum()
+
+ def _get_gene_map(self):
+ """Map unique gene names to their indices in this array.
+
+ Returns
+ -------
+ OrderedDict
+ An (ordered) dictionary of unique gene names and the data indices of
+ their segments in the order of occurrence (genomic order).
+ """
+ if 'gene' not in self.data:
+ return OrderedDict()
+
+ genes = OrderedDict()
+ for idx, genestr in self.data['gene'].iteritems():
+ if pd.isnull(genestr):
+ continue
+ for gene in genestr.split(','):
+ if gene not in genes:
+ genes[gene] = []
+ genes[gene].append(idx)
+ return genes
diff --git a/skgenome/intersect.py b/skgenome/intersect.py
new file mode 100644
index 0000000..59f89c1
--- /dev/null
+++ b/skgenome/intersect.py
@@ -0,0 +1,181 @@
+"""DataFrame-level intersection operations.
+
+Calculate overlapping regions, similar to bedtools intersect.
+
+The functions here operate on pandas DataFrame and Series instances, not
+GenomicArray types.
+
+"""
+from __future__ import print_function, absolute_import, division
+from builtins import zip
+from past.builtins import basestring
+
+import numpy as np
+import pandas as pd
+
+from .combiners import first_of, join_strings, make_const
+
+
+def by_ranges(table, other, mode, keep_empty):
+ """Group rows by another GenomicArray's bin coordinate ranges."""
+ for _chrom, bin_rows, src_rows in by_shared_chroms(other, table,
+ keep_empty):
+ if src_rows is not None:
+ subranges = iter_ranges(src_rows, None, bin_rows['start'],
+ bin_rows['end'], mode)
+ for bin_row, subrange in zip(bin_rows.itertuples(index=False),
+ subranges):
+ yield bin_row, subrange
+ elif keep_empty:
+ for bin_row in bin_rows.itertuples(index=False):
+ yield bin_row, [] # ENH: empty dframe matching table
+
+
+def by_shared_chroms(table, other, keep_empty=True):
+ other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)}
+ for chrom, ctable in table.groupby(['chromosome'], sort=False):
+ if chrom in other_chroms:
+ otable = other_chroms[chrom]
+ yield chrom, ctable, otable
+ elif keep_empty:
+ yield chrom, ctable, None
+
+
+def into_ranges(source, dest, src_col, default, summary_func):
+ """Group a column in `source` by regions in `dest` and summarize."""
+ if not len(source) or not len(dest):
+ return dest
+
+ if summary_func is None:
+ # Choose a type-appropriate summary function
+ elem = source[src_col].iat[0]
+ if isinstance(elem, (basestring, np.string_)):
+ summary_func = join_strings
+ elif isinstance(elem, (float, np.float_)):
+ summary_func = np.nanmedian
+ else:
+ summary_func = first_of
+ elif not callable(summary_func):
+ # Just fill in the given value, I suppose.
+ summary_func = make_const(summary_func)
+
+ def series2value(ser):
+ if len(ser) == 1:
+ return ser.iat[0]
+ return summary_func(ser)
+
+ return pd.Series([(series2value(src_rows[src_col])
+ if len(src_rows) else default)
+ for _bin, src_rows in by_ranges(source, dest, 'outer',
+ True)])
+
+
+def iter_ranges(table, chrom, starts, ends, mode):
+ """Iterate through sub-ranges."""
+ assert mode in ('inner', 'outer', 'trim')
+ # Optional if we've already subsetted by chromosome (not checked!)
+ if chrom:
+ assert isinstance(chrom, basestring) # ENH: accept array?
+ try:
+ table = table[table['chromosome'] == chrom]
+ except KeyError:
+ raise KeyError("Chromosome %s is not in this probe set" % chrom)
+ # Edge cases
+ if not len(table) or (starts is None and ends is None):
+ yield table
+ raise StopIteration
+ # Don't be fooled by nested bins
+ if ((ends is not None and len(ends)) and
+ (starts is not None and len(starts))
+ ) and not _monotonic(table.end):
+ # At least one bin is fully nested -- account for it
+ irange_func = _irange_nested
+ else:
+ irange_func = _irange_simple
+ for region_idx, start_val, end_val in irange_func(table, starts, ends, mode):
+ subtable = table.iloc[region_idx]
+ if mode == 'trim':
+ subtable = subtable.copy()
+ # Update 5' endpoints to the boundary
+ if start_val:
+ subtable.start = subtable.start.clip_lower(start_val)
+ # Update 3' endpoints to the boundary
+ if end_val:
+ subtable.end = subtable.end.clip_upper(end_val)
+ yield subtable
+
+
+def _irange_simple(table, starts, ends, mode):
+ """Slice subsets of table when regions are not nested."""
+ if starts is not None and len(starts):
+ if mode == 'inner':
+ # Only rows entirely after the start point
+ start_idxs = table.start.searchsorted(starts)
+ else:
+ # Include all rows overlapping the start point
+ start_idxs = table.end.searchsorted(starts, 'right')
+ else:
+ starts = np.zeros(len(ends) if ends is not None else 1,
+ dtype=np.int_)
+ start_idxs = starts.copy()
+
+ if ends is not None and len(ends):
+ if mode == 'inner':
+ end_idxs = table.end.searchsorted(ends, 'right')
+ else:
+ end_idxs = table.start.searchsorted(ends)
+ else:
+ end_idxs = np.repeat(len(table), len(starts))
+ ends = [None] * len(starts)
+
+ for start_idx, start_val, end_idx, end_val in zip(start_idxs, starts,
+ end_idxs, ends):
+ yield (slice(start_idx, end_idx), start_val, end_val)
+
+
+def _irange_nested(table, starts, ends, mode):
+ """Slice subsets of table when regions are nested."""
+ # ENH: Binary Interval Search (BITS) or Layer&Quinlan(2015)
+ assert len(starts) == len(ends) > 0
+ for start_val, end_val in zip(starts, ends):
+ # Mask of table rows to keep for this query region
+ region_mask = np.ones(len(table), dtype=np.bool_)
+ if start_val:
+ if mode == 'inner':
+ # Only rows entirely after the start point
+ start_idx = table.start.searchsorted(start_val)
+ region_mask[:start_idx.item()] = 0
+ else:
+ # Include all rows overlapping the start point
+ region_mask = (table.end.values > start_val)
+ if end_val is not None:
+ if mode == 'inner':
+ # Only rows up to the end point
+ region_mask &= (table.end.values <= end_val)
+ else:
+ # Include all rows overlapping the end point
+ end_idx = table.start.searchsorted(end_val)
+ region_mask[end_idx.item():] = 0
+
+ yield region_mask, start_val, end_val
+
+
+def venn(table, other, mode):
+ # TODO -- implement 'venn' via fjoin algorithm
+ # 'cut' table at all 'other' boundaries
+ # -> extra column '_venn_':int (0, 1, 2)
+ # 0=self only, 1=both, 2=other only
+ # -> 'cut' just drops the '_venn_' column
+ # -> 'subtract' drops 1 and 2?
+ # (is that faster? prolly not)
+ # -> 'jaccard' does math with it...
+ return table
+
+
+# Shim for pandas 0.18.1 (chapmanb/bcbio-nextgen#1836)
+if hasattr(pd.Series, 'is_monotonic_increasing'):
+ def _monotonic(ser):
+ return ser.is_monotonic_increasing
+else:
+ def _monotonic(ser):
+ return (np.diff(ser) >= 0).all()
diff --git a/skgenome/merge.py b/skgenome/merge.py
new file mode 100644
index 0000000..b54d502
--- /dev/null
+++ b/skgenome/merge.py
@@ -0,0 +1,178 @@
+"""DataFrame-level merging operations.
+
+Merge overlapping regions into single rows, similar to bedtools merge.
+
+The functions here operate on pandas DataFrame and Series instances, not
+GenomicArray types.
+
+"""
+from __future__ import print_function, absolute_import, division
+from builtins import zip
+
+import itertools
+
+import numpy as np
+import pandas as pd
+
+from .chromsort import sorter_chrom
+from .combiners import get_combiners, first_of
+
+
+def flatten(table, combine=None):
+ if not len(table):
+ return table
+ if (table.start.values[1:] >= table.end.cummax().values[:-1]).all():
+ return table
+ # NB: Input rows and columns should already be sorted like this
+ table = table.sort_values(['chromosome', 'start', 'end'])
+ cmb = get_combiners(table, False, combine)
+ out = (table.groupby(by='chromosome',
+ as_index=False, group_keys=False, sort=False)
+ .apply(_flatten_overlapping, cmb)
+ .reset_index(drop=True))
+ return out.reindex(out.chromosome.apply(sorter_chrom)
+ .sort_values(kind='mergesort').index)
+
+
+def _flatten_overlapping(table, combine):
+ """Merge overlapping regions within a chromosome/strand.
+
+ Assume chromosome and (if relevant) strand are already identical, so only
+ start and end coordinates are considered.
+ """
+ # flat_rows = itertools.chain(
+ # *(_flatten_tuples(row_group, combine)
+ # for _key, row_group in itertools.groupby(keyed_groups, first_of)))
+ # out = pd.DataFrame.from_records(list(flat_rows),
+ # columns=table.columns)
+ # # columns=flat_rows[0]._fields)
+ bits = [pd.DataFrame.from_records(list(_flatten_tuples(row_group, combine)),
+ columns=table.columns)
+ for row_group in _nonoverlapping_groups(table, 0)]
+ out = pd.concat(bits)
+ return out
+
+
+def _flatten_tuples(keyed_rows, combine):
+ """Divide multiple rows where they overlap.
+
+ Parameters
+ ----------
+ keyed_rows : iterable
+ pairs of (non-overlapping-group index, overlapping rows)
+ combine : dict
+
+ Returns
+ -------
+ DataFrame
+ """
+ # TODO speed this up!
+ rows = [kr[1] for kr in keyed_rows]
+ first_row = rows[0]
+ if len(rows) == 1:
+ yield first_row
+ raise StopIteration
+
+ extra_cols = first_row._fields[3:]
+ breaks = sorted(set(itertools.chain(*[(r.start, r.end) for r in rows])))
+ for bp_start, bp_end in zip(breaks[:-1], breaks[1:]):
+ # Find the row(s) overlapping this region
+ # i.e. any not already seen and not already passed
+ rows_in_play = []
+ for row in rows:
+ if row.start <= bp_start and row.end >= bp_end:
+ rows_in_play.append(row)
+
+ # Combine the extra fields of the overlapping regions
+ extra_fields = {key: combine[key]([getattr(r, key)
+ for r in rows_in_play])
+ for key in extra_cols}
+ yield first_row._replace(start=bp_start, end=bp_end,
+ **extra_fields)
+
+
+def merge(table, bp=0, stranded=False, combine=None):
+ """Merge overlapping rows in a DataFrame."""
+ if not len(table):
+ return table
+ gap_sizes = table.start.values[1:] - table.end.cummax().values[:-1]
+ if (gap_sizes > -bp).all():
+ return table
+ if stranded:
+ groupkey = ['chromosome', 'strand']
+ else:
+ # NB: same gene name can appear on alt. contigs
+ groupkey = ['chromosome']
+ table = table.sort_values(groupkey + ['start', 'end'])
+ cmb = get_combiners(table, stranded, combine)
+ out = (table.groupby(by=groupkey,
+ as_index=False, group_keys=False, sort=False)
+ .apply(_merge_overlapping, bp, cmb)
+ .reset_index(drop=True))
+ # Re-sort chromosomes cleverly instead of lexicographically
+ return out.reindex(out.chromosome.apply(sorter_chrom)
+ .sort_values(kind='mergesort').index)
+
+
+def _merge_overlapping(table, bp, combine):
+ """Merge overlapping regions within a chromosome/strand.
+
+ Assume chromosome and (if relevant) strand are already identical, so only
+ start and end coordinates are considered.
+ """
+ merged_rows = [_squash_tuples(row_group, combine)
+ for row_group in _nonoverlapping_groups(table, bp)]
+ return pd.DataFrame.from_records(merged_rows,
+ columns=merged_rows[0]._fields)
+
+
+def _nonoverlapping_groups(table, bp):
+ """Identify and enumerate groups of overlapping rows.
+
+ That is, increment the group ID after each non-negative gap between
+ intervals. Intervals (rows) will be merged if any bases overlap by at least
+ `bp`.
+ """
+ # Examples:
+ #
+ # gap? F T F F T T T F
+ # group 0 1 1 2 3 3 3 3 4
+ #
+ # gap? T F T T F F F T
+ # group 0 0 1 1 1 2 3 4 4
+ gap_sizes = table.start.values[1:] - table.end.cummax().values[:-1]
+ group_keys = np.r_[False, gap_sizes > (-bp)].cumsum()
+ # NB: pandas groupby seems like the obvious choice over itertools, but it is
+ # very slow -- probably because it traverses the whole table (i.e.
+ # chromosome) again to select groups, redoing the various inferences that
+ # would be worthwhile outside this inner loop. With itertools, we take
+ # advantage of the grouping and sorting already done, and don't repeat
+ # pandas' traversal and inferences.
+ # ENH: Find & use a lower-level, 1-pass pandas function
+ keyed_groups = zip(group_keys, table.itertuples(index=False))
+ return (row_group
+ for _key, row_group in itertools.groupby(keyed_groups, first_of))
+
+
+# Squash rows according to a given grouping criterion
+# XXX see also segfilter.py
+def _squash_tuples(keyed_rows, combine):
+ """Combine multiple rows into one NamedTuple.
+
+ Parameters
+ ----------
+ keyed_rows : iterable
+ pairs of (non-overlapping-group index, overlapping rows)
+ combine : dict
+
+ Returns
+ -------
+ namedtuple
+ """
+ rows = [kr[1] for kr in keyed_rows] #list(rows)
+ firsttup = rows[0]
+ if len(rows) == 1:
+ return firsttup
+ newfields = {key: combiner([getattr(r, key) for r in rows])
+ for key, combiner in combine.items()}
+ return firsttup._replace(**newfields)
diff --git a/skgenome/rangelabel.py b/skgenome/rangelabel.py
new file mode 100644
index 0000000..b6df24e
--- /dev/null
+++ b/skgenome/rangelabel.py
@@ -0,0 +1,69 @@
+"""Handle text genomic ranges as named tuples.
+
+A range specification should look like ``chromosome:start-end``, e.g.
+``chr1:1234-5678``, with 1-indexed integer coordinates. We also allow
+``chr1:1234-`` or ``chr1:-5678``, where missing start becomes 0 and missing end
+becomes None.
+"""
+from __future__ import absolute_import, division, print_function
+from past.builtins import basestring
+import collections
+import re
+
+Region = collections.namedtuple('Region', 'chromosome start end')
+NamedRegion = collections.namedtuple('NamedRegion', 'chromosome start end gene')
+
+re_label = re.compile(r'(\w+)?:(\d+)?-(\d+)?\s*(\S+)?')
+
+
+def from_label(text, keep_gene=True):
+ """Parse a chromosomal range specification.
+
+ Parameters
+ ----------
+ text : string
+ Range specification, which should look like ``chr1:1234-5678`` or
+ ``chr1:1234-`` or ``chr1:-5678``, where missing start becomes 0 and
+ missing end becomes None.
+ """
+ match = re_label.match(text)
+ if match:
+ chrom, start, end, gene = match.groups()
+ start = int(start) - 1 if start else None
+ end = int(end) if end else None
+ if keep_gene:
+ gene = gene or ''
+ return NamedRegion(chrom, start, end, gene)
+ else:
+ return Region(chrom, start, end)
+ else:
+ raise ValueError("Invalid range spec: " + text
+ + " (should be like: chr1:2333000-2444000)")
+
+
+def to_label(row):
+ """Convert a Region or (chrom, start, end) tuple to a region label."""
+ return "{}:{}-{}".format(row.chromosome, row.start + 1, row.end)
+
+
+def unpack_range(a_range):
+ """Extract chromosome, start, end from a string or tuple.
+
+ Examples::
+
+ "chr1" -> ("chr1", None, None)
+ "chr1:100-123" -> ("chr1", 99, 123)
+ ("chr1", 100, 123) -> ("chr1", 100, 123)
+ """
+ if not a_range:
+ return Region(None, None, None)
+ if isinstance(a_range, basestring):
+ if ':' in a_range and '-' in a_range:
+ return from_label(a_range, keep_gene=False)
+ return Region(a_range, None, None)
+ if isinstance(a_range, (list, tuple)):
+ if len(a_range) == 3:
+ return Region(*a_range)
+ elif len(a_range) == 4:
+ return Region(*a_range[:3])
+ raise ValueError("Not a range: %r" % a_range)
diff --git a/skgenome/subdivide.py b/skgenome/subdivide.py
new file mode 100644
index 0000000..130d18e
--- /dev/null
+++ b/skgenome/subdivide.py
@@ -0,0 +1,62 @@
+"""DataFrame-level subdivide operation.
+
+Split each region into similar-sized sub-regions.
+
+The functions here operate on pandas DataFrame and Series instances, not
+GenomicArray types.
+
+"""
+from __future__ import print_function, absolute_import, division
+from builtins import range
+
+import logging
+
+import pandas as pd
+
+from .merge import merge
+
+
+def subdivide(table, avg_size, min_size=0, verbose=False):
+ return pd.DataFrame.from_records(
+ _split_targets(table, avg_size, min_size, verbose),
+ columns=table.columns)
+
+
+def _split_targets(regions, avg_size, min_size, verbose):
+ """Split large regions into smaller, consecutive regions.
+
+ Output bin metadata and additional columns match the input dataframe.
+
+ Parameters
+ ----------
+ avg_size : int
+ Split regions into equal-sized subregions of about this size.
+ Specifically, subregions are no larger than 150% of this size, no
+ smaller than 75% this size, and the average will approach this size when
+ subdividing a large region.
+ min_size : int
+ Drop any regions smaller than this size.
+ verbose : bool
+ Print a log message when subdividing a region.
+
+ """
+ for row in merge(regions).itertuples(index=False):
+ span = row.end - row.start
+ if span >= min_size:
+ nbins = int(round(span / avg_size)) or 1
+ if nbins == 1:
+ yield row
+ else:
+ # Divide the region into equal-sized bins
+ bin_size = span / nbins
+ bin_start = row.start
+ if verbose:
+ label = (row.gene if 'gene' in regions else
+ "%s:%d-%d" % (row.chromosome, row.start, row.end))
+ logging.info("Splitting: {:30} {:7} / {} = {:.2f}"
+ .format(label, span, nbins, bin_size))
+ for i in range(1, nbins):
+ bin_end = row.start + int(i * bin_size)
+ yield row._replace(start=bin_start, end=bin_end)
+ bin_start = bin_end
+ yield row._replace(start=bin_start)
diff --git a/skgenome/subtract.py b/skgenome/subtract.py
new file mode 100644
index 0000000..0a14ef3
--- /dev/null
+++ b/skgenome/subtract.py
@@ -0,0 +1,72 @@
+"""DataFrame-level subtraction operations.
+
+Subtract one set of regions from another, returning the one-way difference.
+
+The functions here operate on pandas DataFrame and Series instances, not
+GenomicArray types.
+
+"""
+from __future__ import print_function, absolute_import, division
+
+import logging
+
+import numpy as np
+import pandas as pd
+
+from .intersect import by_ranges
+
+
+def subtract(table, other):
+ if not len(other):
+ return table
+ return pd.DataFrame.from_records(_subtraction(table, other),
+ columns=table.columns)
+
+
+def _subtraction(table, other):
+ for keeper, rows_to_exclude in by_ranges(other, table, 'outer', True):
+ if len(rows_to_exclude):
+ logging.debug(" %s:%d-%d : Subtracting %d excluded regions",
+ keeper.chromosome, keeper.start, keeper.end,
+ len(rows_to_exclude))
+
+ keep_left = (keeper.start < rows_to_exclude.start.iat[0])
+ keep_right = (keeper.end > rows_to_exclude.end.iat[-1])
+ if keep_left and keep_right:
+ # Keep both original edges of the source region
+ # =========
+ # -- --
+ starts = np.r_[keeper.start, rows_to_exclude.end.values]
+ ends = np.r_[rows_to_exclude.start.values, keeper.end]
+ elif keep_left:
+ # Exclusion overlaps only the right side
+ # =======
+ # -- ---
+ starts = np.r_[keeper.start, rows_to_exclude.end.values[:-1]]
+ ends = rows_to_exclude.start.values
+ elif keep_right:
+ # Exclusion overlaps only the left side
+ # ========
+ # --- --
+ starts = rows_to_exclude.end.values
+ ends = np.r_[rows_to_exclude.start.values[1:], keeper.end]
+ elif len(rows_to_exclude) > 1:
+ # Exclusions overlap both edges
+ # ======
+ # -- -- ---
+ starts = rows_to_exclude.end.values[:-1]
+ ends = rows_to_exclude.start.values[1:]
+ else:
+ # Exclusion covers the whole region
+ continue
+
+ for start, end in zip(starts, ends):
+ if end > start:
+ yield keeper._replace(start=start, end=end)
+ else:
+ logging.debug("Discarding pair: (%d, %d)", start, end)
+
+ else:
+ logging.debug(" %s:%d-%d : No excluded regions",
+ keeper.chromosome, keeper.start, keeper.end)
+ yield keeper
diff --git a/skgenome/tabio/__init__.py b/skgenome/tabio/__init__.py
new file mode 100644
index 0000000..e9e82d6
--- /dev/null
+++ b/skgenome/tabio/__init__.py
@@ -0,0 +1,267 @@
+"""I/O for tabular formats of genomic data (regions or features).
+"""
+from __future__ import absolute_import, division, print_function
+from past.builtins import basestring
+
+import collections
+import contextlib
+import logging
+import os
+import re
+import sys
+
+import pandas as pd
+from Bio.File import as_handle
+
+from ..gary import GenomicArray as GA
+from . import bedio, genepred, gff, picard, seg, tab, textcoord, vcfio
+
+
+def read(infile, fmt="tab", into=None, sample_id=None, meta=None, **kwargs):
+ """Read tabular data from a file or stream into a genome object.
+
+ Supported formats: see `READERS`
+
+ If a format supports multiple samples, return the sample specified by
+ `sample_id`, or if unspecified, return the first sample and warn if there
+ were other samples present in the file.
+
+ Parameters
+ ----------
+ infile : handle or string
+ Filename or opened file-like object to read.
+ fmt : string
+ File format.
+ into : class
+ GenomicArray class or subclass to instantiate, overriding the
+ default for the target file format.
+ sample_id : string
+ Sample identifier.
+ meta : dict
+ Metadata, as arbitrary key-value pairs.
+ **kwargs :
+ Additional keyword arguments to the format-specific reader function.
+
+ Returns
+ -------
+ GenomicArray or subclass
+ The data from the given file instantiated as `into`, if specified, or
+ the default base class for the given file format (usually GenomicArray).
+ """
+ from cnvlib.core import fbase
+ if fmt == 'auto':
+ return read_auto(infile)
+ elif fmt in READERS:
+ reader, suggest_into = READERS[fmt]
+ else:
+ raise ValueError("Unknown format: %s" % fmt)
+
+ if meta is None:
+ meta = {}
+ if "sample_id" not in meta:
+ if sample_id:
+ meta["sample_id"] = sample_id
+ elif isinstance(infile, basestring):
+ meta["sample_id"] = fbase(infile)
+ elif hasattr(infile, "name"):
+ meta["sample_id"] = fbase(infile.name)
+ else:
+ # meta["sample_id"] = "<unknown>"
+ pass
+ if "filename" not in meta:
+ if isinstance(infile, basestring):
+ meta["filename"] = infile
+ elif hasattr(infile, "name"):
+ meta["filename"] = infile.name
+ if fmt in ("seg", "vcf") and sample_id is not None:
+ # Multi-sample formats: choose one sample
+ kwargs["sample_id"] = sample_id
+ try:
+ dframe = reader(infile, **kwargs)
+ except pd.io.common.EmptyDataError:
+ # File is blank/empty, most likely
+ logging.info("Blank %s file?: %s", fmt, infile)
+ dframe = []
+ if fmt == "vcf":
+ from cnvlib.vary import VariantArray as VA
+ suggest_into = VA
+ result = (into or suggest_into)(dframe, meta)
+ result.sort_columns()
+ result.sort()
+ return result
+ # ENH CategoricalIndex ---
+ # if dframe:
+ # dframe['chromosome'] = pd.Categorical(dframe['chromosome'],
+ # dframe.chromosome.drop_duplicates(),
+ # ordered=True)
+ # Create a multi-index of genomic coordinates (like GRanges)
+ # dframe.set_index(['chromosome', 'start'], inplace=True)
+
+
+def read_auto(infile):
+ """Auto-detect a file's format and use an appropriate parser to read it."""
+ if not isinstance(infile, basestring) and not hasattr(infile, "seek"):
+ raise ValueError("Can only auto-detect format from filename or "
+ "seekable (local, on-disk) files, which %s is not"
+ % infile)
+
+ fmt = sniff_region_format(infile)
+ if hasattr(infile, "seek"):
+ infile.seek(0)
+ if fmt:
+ logging.info("Detected file format: " + fmt)
+ else:
+ # File is blank -- simple BED will handle this OK
+ fmt = "bed3"
+ return read(infile, fmt or 'tab')
+
+
+READERS = {
+ # Format name, formatter, default target class
+ "auto": (read_auto, GA),
+ "bed": (bedio.read_bed, GA),
+ "bed3": (bedio.read_bed3, GA),
+ "bed4": (bedio.read_bed4, GA),
+ "bed6": (bedio.read_bed6, GA),
+ "gff": (gff.read_gff, GA),
+ "interval": (picard.read_interval, GA),
+ "refflat": (genepred.read_refflat, GA),
+ "picardhs": (picard.read_picard_hs, GA),
+ "seg": (seg.read_seg, GA),
+ "tab": (tab.read_tab, GA),
+ "text": (textcoord.read_text, GA),
+ "vcf": (vcfio.read_vcf, GA),
+}
+
+
+# _____________________________________________________________________
+
+def write(garr, outfile=None, fmt="tab", verbose=True, **kwargs):
+ """Write a genome object to a file or stream."""
+ formatter, show_header = WRITERS[fmt]
+ if fmt in ("seg", "vcf"):
+ kwargs["sample_id"] = garr.sample_id
+ dframe = formatter(garr.data, **kwargs)
+ with safe_write(outfile or sys.stdout, verbose=False) as handle:
+ dframe.to_csv(handle, header=show_header, index=False, sep='\t',
+ float_format='%.6g')
+ if verbose:
+ # Log the output path, if possible
+ if isinstance(outfile, basestring):
+ outfname = outfile
+ elif hasattr(outfile, 'name') and outfile not in (sys.stdout,
+ sys.stderr):
+ outfname = outfile.name
+ else:
+ # Probably stdout or stderr used in a pipeline -- don't pollute
+ return
+ logging.info("Wrote %s with %d regions", outfname, len(dframe))
+
+
+WRITERS = {
+ # Format name, formatter, show header
+ "bed": (bedio.write_bed, False),
+ "bed3": (bedio.write_bed3, False),
+ "bed4": (bedio.write_bed4, False),
+ # "gff": (gff.write_gff, False),
+ "interval": (picard.write_interval, False),
+ "picardhs": (picard.write_picard_hs, True),
+ "seg": (seg.write_seg, True),
+ "tab": (tab.write_tab, True),
+ "text": (textcoord.write_text, False),
+ "vcf": (vcfio.write_vcf, True),
+}
+
+
+# _____________________________________________________________________
+
+ at contextlib.contextmanager
+def safe_write(outfile, verbose=True):
+ """Write to a filename or file-like object with error handling.
+
+ If given a file name, open it. If the path includes directories that don't
+ exist yet, create them. If given a file-like object, just pass it through.
+ """
+ if isinstance(outfile, basestring):
+ dirname = os.path.dirname(outfile)
+ if dirname and not os.path.isdir(dirname):
+ os.mkdir(dirname)
+ logging.info("Created directory %s", dirname)
+ with open(outfile, 'w') as handle:
+ yield handle
+ else:
+ yield outfile
+
+ # Log the output path, if possible
+ if verbose:
+ if isinstance(outfile, basestring):
+ outfname = outfile
+ elif hasattr(outfile, 'name') and outfile not in (sys.stdout,
+ sys.stderr):
+ outfname = outfile.name
+ else:
+ # Probably stdout or stderr -- don't ruin the pipeline
+ return
+ logging.info("Wrote %s", outfname)
+
+
+def sniff_region_format(fname):
+ """Guess the format of the given file by reading the first line.
+
+ Returns
+ -------
+ str or None
+ The detected format name, or None if the file is empty.
+ """
+ # has_track = False
+ with as_handle(fname, 'rU') as handle:
+ for line in handle:
+ if not line.strip():
+ # Skip blank lines
+ continue
+ if line.startswith('track'):
+ # NB: Could be UCSC BED or Ensembl GFF
+ # has_track = True
+ continue
+ # Formats that (may) declare themselves in an initial '#' comment
+ if (line.startswith('##gff-version') or
+ format_patterns['gff'].match(line)):
+ return 'gff'
+ if line.startswith(('##fileformat=VCF', '#CHROM\tPOS\tID')):
+ return 'vcf'
+ if line.startswith('#'):
+ continue
+ # Formats that need to be guessed solely by regex
+ if format_patterns['text'].match(line):
+ return 'text'
+ if format_patterns['tab'].match(line):
+ return 'tab'
+ if line.startswith('@') or format_patterns['interval'].match(line):
+ return 'interval'
+ if format_patterns['refflat'].match(line):
+ return 'refflat'
+ if format_patterns['bed'].match(line):
+ return 'bed'
+
+ raise ValueError("File %r does not appear to be a recognized "
+ "format! (Any of: %s)\n"
+ "First non-blank line:\n%s"
+ % (fname, ', '.join(format_patterns.keys()), line))
+
+
+format_patterns = collections.OrderedDict([
+ # ('genepred', re.compile()),
+ # ('genepredext', re.compile()),
+ ('text', re.compile(r'\w+:\d*-\d*.*')),
+ ('tab', re.compile('\t'.join(('chromosome', 'start', 'end')))),
+ ('interval', re.compile('\t'.join((
+ r'\w+', r'\d+', r'\d+', r'[.+-]', r'\S+$')))),
+ ('refflat', re.compile('\t'.join((
+ r'\S+', r'\S+', r'\w+', r'[+-]',
+ r'\d+', r'\d+', r'\d+', r'\d+', r'\d+',
+ r'(\d+,)+', r'(\d+,)+$')))),
+ ('gff', re.compile('\t'.join((
+ r'\w+', r'\S+', r'\w+', r'\d+', r'\d+',
+ r'\S+', r'[.?+-]', r'[012.]', r'.*')))),
+ ('bed', re.compile('\t'.join((r'\w+', r'\d+', r'\d+')))),
+])
diff --git a/skgenome/tabio/bedio.py b/skgenome/tabio/bedio.py
new file mode 100644
index 0000000..e0e26de
--- /dev/null
+++ b/skgenome/tabio/bedio.py
@@ -0,0 +1,125 @@
+"""I/O for UCSC Browser Extensible Data (BED)."""
+from __future__ import absolute_import, division, print_function
+from builtins import map, next
+
+import shlex
+
+import pandas as pd
+from Bio.File import as_handle
+
+from .util import report_bad_line
+
+
+def read_bed(infile):
+ """UCSC Browser Extensible Data (BED) format.
+
+ A BED file has these columns:
+ chromosome, start position, end position, [gene, strand, other stuff...]
+
+ Coordinate indexing is from 0.
+
+ Sets of regions are separated by "track" lines. This function stops reading
+ after encountering a track line other than the first one in the file.
+ """
+ # ENH: just pd.read_table, skip 'track'
+ @report_bad_line
+ def _parse_line(line):
+ fields = line.split('\t', 6)
+ chrom, start, end = fields[:3]
+ gene = (fields[3].rstrip()
+ if len(fields) >= 4 else '-')
+ strand = (fields[5].rstrip()
+ if len(fields) >= 6 else '.')
+ return chrom, int(start), int(end), gene, strand
+
+ def track2track(handle):
+ firstline = next(handle)
+ if firstline.startswith("track"):
+ pass
+ else:
+ yield firstline
+ for line in handle:
+ if line.startswith('track'):
+ raise StopIteration
+ yield line
+
+ with as_handle(infile, 'rU') as handle:
+ rows = map(_parse_line, track2track(handle))
+ return pd.DataFrame.from_records(rows, columns=["chromosome", "start",
+ "end", "gene", "strand"])
+
+
+def read_bed3(infile):
+ """3-column BED format: chromosome, start, end."""
+ table = read_bed(infile)
+ return table.loc[:, ['chromosome', 'start', 'end']]
+
+
+def read_bed4(infile):
+ """4-column BED format: chromosome, start, end, name."""
+ table = read_bed(infile)
+ return table.loc[:, ['chromosome', 'start', 'end', 'gene']]
+
+
+def read_bed6(infile):
+ """6-column BED format: chromosome, start, end, name, score, strand."""
+ return NotImplemented
+
+
+def parse_bed_track(line):
+ """Parse the "name" field of a BED track definition line.
+
+ Example:
+ track name=146793_BastianLabv2_P2_target_region description="146793_BastianLabv2_P2_target_region"
+ """
+ fields = shlex.split(line) # raises ValueError if line is corrupted
+ assert fields[0] == 'track'
+ for field in fields[1:]:
+ if '=' in field:
+ key, val = field.split('=', 1)
+ if key == 'name':
+ return val
+ raise ValueError("No name defined for this track")
+
+
+def group_bed_tracks(bedfile):
+ """Group the parsed rows in a BED file by track.
+
+ Yields (track_name, iterable_of_lines), much like itertools.groupby.
+ """
+ # ENH - make this memory-efficient w/ generators or something
+ with as_handle(bedfile, 'r') as handle:
+ curr_track = 'DEFAULT'
+ curr_lines = []
+ for line in handle:
+ if line.startswith('track'):
+ if curr_lines:
+ yield curr_track, curr_lines
+ curr_lines = []
+ curr_track = parse_bed_track(line)
+ else:
+ curr_lines.append(line)
+ yield curr_track, curr_lines
+
+
+# _____________________________________________________________________
+
+def write_bed(dframe):
+ if len(dframe.columns) == 3:
+ return write_bed3(dframe)
+ elif len(dframe.columns) == 3:
+ return write_bed4(dframe)
+ else:
+ # Default: BED-like, keep all trailing columns
+ return dframe
+
+
+def write_bed3(dframe):
+ return dframe.loc[:, ["chromosome", "start", "end"]]
+
+
+def write_bed4(dframe):
+ dframe = dframe.copy()
+ if "gene" not in dframe:
+ dframe["gene"] = '-'
+ return dframe.loc[:, ["chromosome", "start", "end", "gene"]]
diff --git a/skgenome/tabio/genepred.py b/skgenome/tabio/genepred.py
new file mode 100644
index 0000000..7c26226
--- /dev/null
+++ b/skgenome/tabio/genepred.py
@@ -0,0 +1,163 @@
+"""I/O for UCSC 'genePred' formats.
+
+The formats are tabular, with no header row, and columns defined by the SQL
+table definitions shown with each function. In alternative-splicing situations,
+each transcript has a row in these tables.
+
+Note: The parsers here load the gene information in each row and deduplicate
+identical rows, but do not merge non-identical rows.
+
+Generally the more-standard GFF or GTF would be used for this information; these
+formats are essentially UCSC Genome Browser database dumps.
+
+See:
+
+- https://genome.ucsc.edu/FAQ/FAQformat.html#format9
+- ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/
+"""
+from __future__ import absolute_import, division, print_function
+
+import pandas as pd
+
+
+def read_genepred(infile, exons=False):
+ """Gene Predictions.
+
+ ::
+
+ table genePred
+ "A gene prediction."
+ (
+ string name; "Name of gene"
+ string chrom; "Chromosome name"
+ char[1] strand; "+ or - for strand"
+ uint txStart; "Transcription start position"
+ uint txEnd; "Transcription end position"
+ uint cdsStart; "Coding region start"
+ uint cdsEnd; "Coding region end"
+ uint exonCount; "Number of exons"
+ uint[exonCount] exonStarts; "Exon start positions"
+ uint[exonCount] exonEnds; "Exon end positions"
+ )
+
+ """
+ raise NotImplementedError
+
+
+def read_genepred_ext(infile, exons=False):
+ """Gene Predictions (Extended).
+
+ The refGene table is an example of the genePredExt format.
+
+ ::
+
+ table genePredExt
+ "A gene prediction with some additional info."
+ (
+ string name; "Name of gene (usually transcript_id from GTF)"
+ string chrom; "Chromosome name"
+ char[1] strand; "+ or - for strand"
+ uint txStart; "Transcription start position"
+ uint txEnd; "Transcription end position"
+ uint cdsStart; "Coding region start"
+ uint cdsEnd; "Coding region end"
+ uint exonCount; "Number of exons"
+ uint[exonCount] exonStarts; "Exon start positions"
+ uint[exonCount] exonEnds; "Exon end positions"
+ int score; "Score"
+ string name2; "Alternate name (e.g. gene_id from GTF)"
+ string cdsStartStat; "enum('none','unk','incmpl','cmpl')"
+ string cdsEndStat; "enum('none','unk','incmpl','cmpl')"
+ lstring exonFrames; "Exon frame offsets {0,1,2}"
+ )
+
+ """
+ raise NotImplementedError
+
+
+def read_refflat(infile, cds=False, exons=False):
+ """Gene predictions and RefSeq genes with gene names (e.g. refFlat.txt).
+
+ This version of genePred associates the gene name with the gene prediction
+ information. For example, the UCSC "refFlat" database lists HGNC gene names
+ and RefSeq accessions for each gene, alongside the gene model coordinates
+ for transcription region, coding region, and exons.
+
+ ::
+
+ table refFlat
+ "A gene prediction with additional geneName field."
+ (
+ string geneName; "Name of gene as it appears in Genome Browser."
+ string name; "Name of gene"
+ string chrom; "Chromosome name"
+ char[1] strand; "+ or - for strand"
+ uint txStart; "Transcription start position"
+ uint txEnd; "Transcription end position"
+ uint cdsStart; "Coding region start"
+ uint cdsEnd; "Coding region end"
+ uint exonCount; "Number of exons"
+ uint[exonCount] exonStarts; "Exon start positions"
+ uint[exonCount] exonEnds; "Exon end positions"
+ )
+
+ Parameters
+ ----------
+ cds : bool
+ Emit each gene's CDS region (coding and introns, but not UTRs) instead
+ of the full transcript region (default).
+ exons : bool
+ Emit individual exonic regions for each gene instead of the full
+ transcribed genomic region (default). Mutually exclusive with `cds`.
+
+ """
+ # ENH: choice of regions=('transcript', 'cds', 'exons') instead of flags?
+ if cds and exons:
+ raise ValueError("Arguments 'cds' and 'exons' are mutually exclusive")
+
+ cols_shared = ['gene', 'accession', 'chromosome', 'strand']
+ converters = None
+ if exons:
+ cols_rest = ['_start_tx', '_end_tx', # Transcription
+ '_start_cds', '_end_cds', # Coding region
+ '_exon_count', 'exon_starts', 'exon_ends']
+ converters = {'exon_starts': _split_commas, 'exon_ends': _split_commas}
+ elif cds:
+ # Use CDS instead of transcription region
+ cols_rest = ['_start_tx', '_end_tx',
+ 'start', 'end',
+ '_exon_count', '_exon_starts', '_exon_ends']
+ else:
+ cols_rest = ['start', 'end',
+ '_start_cds', '_end_cds',
+ '_exon_count', '_exon_starts', '_exon_ends']
+ colnames = cols_shared + cols_rest
+ usecols = [c for c in colnames if not c.startswith('_')]
+ # Parse the file contents
+ dframe = pd.read_table(infile, header=None, na_filter=False,
+ names=colnames, usecols=usecols,
+ dtype={c: str for c in cols_shared},
+ converters=converters)
+
+ # Calculate values for output columns
+ if exons:
+ dframe = pd.DataFrame.from_records(_split_exons(dframe),
+ columns=cols_shared + ['start', 'end'])
+ dframe['start'] = dframe['start'].astype('int')
+ dframe['end'] = dframe['end'].astype('int')
+
+ return (dframe.assign(start=dframe.start - 1)
+ .sort_values(['chromosome', 'start', 'end'])
+ .reset_index(drop=True))
+
+
+def _split_commas(field):
+ return field.rstrip(',').split(',')
+
+
+def _split_exons(dframe):
+ """Split exons into individual rows."""
+ for row in dframe.itertuples(index=False):
+ shared = row[:4]
+ for start, end in zip(row.exon_starts, row.exon_ends):
+ yield shared + (start, end)
diff --git a/skgenome/tabio/gff.py b/skgenome/tabio/gff.py
new file mode 100644
index 0000000..f3fb16f
--- /dev/null
+++ b/skgenome/tabio/gff.py
@@ -0,0 +1,55 @@
+"""I/O for Generic Feature Format (GFF).
+
+Columns:
+
+1. seqid/reference/seqname/chromosome
+2. source
+3. type/method/feature
+4. start: in 1-based integer coordinates
+5. end: in 1-based integer coordinates
+6. score: float or '.' (for NA)
+7. strand: [+-.?]
+8. phase/frame: [012.]
+9. attribute/group: string
+
+Specs:
+
+- http://www.ensembl.org/info/website/upload/gff.html
+- http://gmod.org/wiki/GFF3
+# http://gmod.org/wiki/GFF2
+"""
+from __future__ import absolute_import, division, print_function
+
+import pandas as pd
+
+
+def read_gff(infile):
+ """Works for GFF2/GTF/GFF3 because we don't parse inside column 9."""
+ colnames = ['chromosome', 'source', 'type', 'start', 'end',
+ 'score', 'strand', 'phase', 'attribute']
+ coltypes = ['str', 'str', 'str', 'int', 'int',
+ 'str', 'str', 'str', 'str']
+ dframe = pd.read_table(infile, comment='#', header=None, na_filter=False,
+ names=colnames, dtype=dict(zip(colnames, coltypes)))
+ return (dframe
+ .assign(start=dframe.start - 1,
+ score=dframe.score.replace('.', 'nan').astype('float'),
+ gene=dframe.attribute.apply(_parse_name))
+ .sort_values(['chromosome', 'start', 'end'])
+ .reset_index(drop=True))
+
+
+def _parse_name(text, default='-'):
+ """Extract name from the 'attributes' field, if present.
+
+ e.g. 'ID=mrna0001;Name=sonichedgehog' -> 'sonichedgehog'
+ """
+ tag = 'Name='
+ idx = text.find(tag)
+ if idx == -1:
+ return default
+ text = text[idx + len(tag):]
+ idx = text.find(';')
+ if idx != -1:
+ text = text[:idx]
+ return text
diff --git a/skgenome/tabio/picard.py b/skgenome/tabio/picard.py
new file mode 100644
index 0000000..d5de717
--- /dev/null
+++ b/skgenome/tabio/picard.py
@@ -0,0 +1,90 @@
+"""I/O for formats used by Picard tools.
+
+- Interval list (also used in GATK)
+- CalculateHsMetrics PER_TARGET_COVERAGE output
+
+"""
+from __future__ import absolute_import, division, print_function
+
+import numpy as np
+import pandas as pd
+
+
+def read_interval(infile):
+ """GATK/Picard-compatible interval list format.
+
+ Expected tabular columns:
+ chromosome, start position, end position, strand, gene
+
+ Coordinate indexing is from 1.
+ """
+ dframe = pd.read_table(infile,
+ comment='@', # Skip the SAM header
+ names=["chromosome", "start", "end", "strand", "gene",
+ ])
+ dframe["gene"].fillna('-', inplace=True)
+ dframe["start"] -= 1
+ return dframe
+
+
+def read_picard_hs(infile):
+ """Picard CalculateHsMetrics PER_TARGET_COVERAGE.
+
+ The format is BED-like, but with a header row and the columns::
+
+ chrom (str),
+ start, end, length (int),
+ name (str),
+ %gc, mean_coverage, normalized_coverage (float)
+
+ """
+ dframe = pd.read_table(infile, na_filter=False, dtype={
+ "chrom": "str",
+ "start": "int",
+ "end": "int",
+ "length": "int",
+ "name": "str",
+ "%gc": "float",
+ "mean_coverage": "float",
+ "normalized_coverage": "float",
+ })
+ dframe.columns = ["chromosome", # chrom
+ "start", "end", "length",
+ "gene", # name
+ "gc", # %gc
+ "depth", "ratio"]
+ del dframe["length"]
+ dframe["start"] -= 1
+ return dframe
+
+
+# _____________________________________________________________________
+
+def write_interval(dframe):
+ dframe = dframe.copy()
+ dframe["start"] += 1
+ if "gene" not in dframe:
+ dframe["gene"] = '-'
+ if "strand" not in dframe:
+ dframe["strand"] = "+"
+ return dframe.loc[:, ["chromosome", "start", "end", "strand", "gene"]]
+
+
+def write_picard_hs(dframe):
+ if "depth" in dframe.columns:
+ coverage = dframe["depth"]
+ norm = coverage / coverage.mean()
+ else:
+ coverage = np.exp2(dframe["log2"])
+ norm = coverage
+ return pd.DataFrame.from_items([
+ ("chrom", dframe["chromosome"]),
+ ("start", dframe["start"] + 1),
+ ("end", dframe["end"]),
+ ("length", dframe["end"] - dframe["start"]),
+ ("name", dframe["gene"]),
+ ("%gc", dframe["gc"]),
+ ("mean_coverage", coverage),
+ ("normalized_coverage", norm),
+ ])
+
diff --git a/skgenome/tabio/seg.py b/skgenome/tabio/seg.py
new file mode 100644
index 0000000..81312bb
--- /dev/null
+++ b/skgenome/tabio/seg.py
@@ -0,0 +1,228 @@
+"""I/O for SEG format.
+
+This is the output of DNAcopy segmentation, widely used to serialize segment
+data.
+
+The format is BED-like, but with a header row included and the
+columns:
+
+ - ID, "sampleName"
+ - chrom, "chromosome"
+ - loc.start, "start"
+ - loc.end, "end"
+ - num.mark, "nbrOfLoci" (optional)
+ - seg.mean, "mean"
+
+See: https://software.broadinstitute.org/software/igv/SEG
+"""
+from __future__ import absolute_import, division, print_function
+from builtins import next
+from past.builtins import basestring
+# from itertools import zip_longest
+from future.moves.itertools import zip_longest
+
+import collections
+import csv
+import logging
+import math
+
+import pandas as pd
+from Bio.File import as_handle
+
+LOG2_10 = math.log(10, 2) # To convert log10 values to log2
+
+# To catch exceptions from pandas versions 0.18 -- 0.20
+CSV_ERRORS = (
+ # Raised by the pandas 'python' CSV parser, at some point, I think
+ csv.Error,
+ # Deprecated in pandas 0.20
+ # Same as pandas.parser.CParserError in <0.20
+ pd.io.common.CParserError,
+)
+if hasattr(pd, 'errors'):
+ # New in pandas 0.20
+ CSV_ERRORS += (pd.errors.ParserError,)
+
+
+def read_seg(infile, sample_id=None,
+ chrom_names=None, chrom_prefix=None, from_log10=False):
+ """Read one sample from a SEG file.
+
+ Parameters
+ ----------
+ sample_id : string, int or None
+ If a string identifier, return the sample matching that ID. If a
+ positive integer, return the sample at that index position, counting
+ from 0. If None (default), return the first sample in the file.
+ chrom_names : dict
+ Map (string) chromosome IDs to names. (Applied before chrom_prefix.)
+ e.g. {'23': 'X', '24': 'Y', '25': 'M'}
+ chrom_prefix : str
+ Prepend this string to chromosome names. (Usually 'chr' or None)
+ from_log10 : bool
+ Convert values from log10 to log2.
+
+ Returns
+ -------
+ DataFrame of the selected sample's segments.
+ """
+ results = parse_seg(infile, chrom_names, chrom_prefix, from_log10)
+ if isinstance(sample_id, int):
+ # Select sample by index number
+ for i, (_sid, dframe) in enumerate(results):
+ if i == sample_id:
+ return dframe
+ else:
+ raise IndexError("No sample index %d found in SEG file" % sample_id)
+
+ elif isinstance(sample_id, basestring):
+ # Select sample by name
+ for sid, dframe in results:
+ if sid == sample_id:
+ return dframe
+ else:
+ raise IndexError("No sample ID '%s' found in SEG file" % sample_id)
+ else:
+ # Select the first sample
+ sid, dframe = next(results)
+ try:
+ next(results)
+ except StopIteration:
+ pass
+ else:
+ logging.warn("WARNING: SEG file contains multiple samples; "
+ "returning the first sample '%s'", sid)
+ return dframe
+
+
+def parse_seg(infile, chrom_names=None, chrom_prefix=None, from_log10=False):
+ """Parse a SEG file as an iterable of samples.
+
+ Coordinates are automatically converted from 1-indexed to half-open
+ 0-indexed (Python-style indexing).
+
+ Parameters
+ ----------
+ chrom_names : dict
+ Map (string) chromosome IDs to names. (Applied before chrom_prefix.)
+ e.g. {'23': 'X', '24': 'Y', '25': 'M'}
+ chrom_prefix : str
+ Prepend this string to chromosome names. (Usually 'chr' or None)
+ from_log10 : bool
+ Convert values from log10 to log2.
+
+ Yields
+ ------
+ Tuple of (string sample ID, DataFrame of segments)
+ """
+ # Scan through any leading garbage to find the header
+ with as_handle(infile) as handle:
+ n_tabs = None
+ for line in handle:
+ n_tabs = line.count('\t')
+ if n_tabs == 0:
+ # Skip misc. R output (e.g. "WARNING...") before the header
+ continue
+ if n_tabs == 5:
+ col_names = ["sample_id", "chromosome", "start", "end", "probes",
+ "log2"]
+ elif n_tabs == 4:
+ col_names = ["sample_id", "chromosome", "start", "end", "log2"]
+ else:
+ raise ValueError("SEG format expects 5 or 6 columns; found {}: {}"
+ .format(n_tabs + 1, line))
+ break
+ else:
+ raise ValueError("SEG file contains no data")
+ # Parse the SEG file contents
+ try:
+ dframe = pd.read_table(handle, names=col_names, header=None,
+ # * pandas.io.common.CParserError: Error
+ # tokenizing data. C error: Calling
+ # read(nbytes) on source failed. Try
+ # engine='python'.
+ engine='python',
+ # * engine='c' only:
+ # na_filter=False,
+ # dtype={
+ # 'sample_id': 'str',
+ # 'chromosome': 'str',
+ # 'start': 'int',
+ # 'end': 'int',
+ # 'log2': 'float'
+ # },
+ )
+ dframe['sample_id'] = dframe['sample_id'].astype("str")
+ dframe['chromosome'] = dframe['chromosome'].astype("str")
+ except CSV_ERRORS as err:
+ raise ValueError("Unexpected dataframe contents:\n%s\n%s" %
+ (err, next(handle)))
+
+ # Calculate values for output columns
+ if chrom_names:
+ dframe['chromosome'] = dframe['chromosome'].replace(chrom_names)
+ if chrom_prefix:
+ dframe['chromosome'] = dframe['chromosome'].apply(lambda c:
+ chrom_prefix + c)
+ if from_log10:
+ dframe['log2'] *= LOG2_10
+ dframe['gene'] = "-"
+ dframe['start'] -= 1
+ keep_columns = dframe.columns.drop(['sample_id'])
+ for sid, sample in dframe.groupby(by='sample_id', sort=False):
+ yield sid, sample.loc[:, keep_columns]
+
+
+def write_seg(dframe, sample_id=None, chrom_ids=None):
+ """Format a dataframe or list of dataframes as SEG.
+
+ To put multiple samples into one SEG table, pass `dframe` and `sample_id` as
+ equal-length lists of data tables and sample IDs in matching order.
+ """
+ assert sample_id is not None
+ if isinstance(dframe, pd.DataFrame):
+ first = dframe
+ first_sid = sample_id
+ sids = dframes = None
+ else:
+ assert not isinstance(sample_id, basestring)
+ dframes = iter(dframe)
+ sids = iter(sample_id)
+ first = next(dframes)
+ first_sid = next(sids)
+
+ if chrom_ids is None:
+ chrom_ids = create_chrom_ids(first)
+ results = [format_seg(first, first_sid, chrom_ids)]
+ if dframes is not None:
+ # Unpack matching lists of data and sample IDs
+ results.extend(
+ format_seg(subframe, sid, chrom_ids)
+ for subframe, sid in zip_longest(dframes, sids))
+ return pd.concat(results)
+
+
+def format_seg(dframe, sample_id, chrom_ids):
+ assert dframe is not None
+ assert sample_id is not None
+ # assert chrom_ids is not None
+ rename_cols = {"log2": "mean"}
+ # NB: in some programs the "sampleName" column is labeled "ID"
+ reindex_cols = ["sampleName", "chromosome", "start", "end", "mean"]
+ if "probes" in dframe:
+ rename_cols["probes"] = "nbrOfLoci" # or num_probes
+ reindex_cols.insert(-1, "nbrOfLoci")
+ return (dframe.assign(sampleName=sample_id,
+ chromosome=dframe.chromosome.replace(chrom_ids),
+ start=dframe.start + 1)
+ .rename(columns=rename_cols)
+ .reindex(columns=reindex_cols))
+
+
+def create_chrom_ids(segments):
+ """Map chromosome names to integers in the order encountered."""
+ mapping = collections.OrderedDict(
+ (chrom, i+1)
+ for i, chrom in enumerate(segments.chromosome.drop_duplicates())
+ if str(i + 1) != chrom)
+ return mapping
diff --git a/skgenome/tabio/simplevcf.py b/skgenome/tabio/simplevcf.py
new file mode 100644
index 0000000..b654cdd
--- /dev/null
+++ b/skgenome/tabio/simplevcf.py
@@ -0,0 +1,41 @@
+"""Simple VCF I/O.
+
+Read only coordinate info & store the remaining columns as unparsed strings.
+Just enough functionality to extract a subset of samples and/or perform
+bedtools-like operations on VCF records.
+"""
+from __future__ import absolute_import, division, print_function
+
+import logging
+
+import pandas as pd
+
+# TODO
+# save VCF header (as string, the whole text block) in meta{header=}
+# ENH:
+# splode the INFO column
+# 1st just as strings?
+# Then parse according to VCF 4.3 spec (floats, tuples, flags, etc.)
+# matching pysam as much as possible (using pysam reader?)
+def read_vcf(infile, skip_reject=False):
+ """Read VCF file w/o samples."""
+ columns = ['chromosome', 'start', 'ref', 'alt', # 'filter', 'info',
+ ]
+ dtypes = [str, int, str, str, # str, str
+ ]
+ table = pd.read_table(infile,
+ comment="#",
+ header=None,
+ na_filter=False,
+ names=["chromosome", "start", "id", "ref", "alt",
+ "qual", "filter", "info"],
+ usecols=columns,
+ # ENH: converters={'info': func to parse it}
+ dtype=dict(zip(columns, dtypes)),
+ )
+ # ENH: do things with filter, info
+ # if skip_reject and record.FILTER and len(record.FILTER) > 0:
+ table['end'] = table['start'] + table["alt"].str.len() # ENH: INFO["END"]
+ table['start'] -= 1
+ logging.info("Loaded %d plain records", len(table))
+ return table
diff --git a/skgenome/tabio/tab.py b/skgenome/tabio/tab.py
new file mode 100644
index 0000000..3a9203d
--- /dev/null
+++ b/skgenome/tabio/tab.py
@@ -0,0 +1,33 @@
+"""I/O for tab-delimited format with an initial header row.
+
+Column names match the target class attributes. At least "chromosome", "start",
+and "end" are required.
+"""
+from __future__ import absolute_import, division, print_function
+
+import logging
+
+import pandas as pd
+
+
+def read_tab(infile):
+ """Read tab-separated data with column names in the first row.
+
+ The format is BED-like, but with a header row included and with
+ arbitrary extra columns.
+ """
+ dframe = pd.read_table(infile, dtype={'chromosome': 'str'})
+ if "log2" in dframe.columns:
+ # Every bin needs a log2 value; the others can be NaN
+ d2 = dframe.dropna(subset=["log2"])
+ if len(d2) < len(dframe):
+ logging.warn("Dropped %d rows with missing log2 values",
+ len(dframe) - len(d2))
+ dframe = d2.copy()
+ return dframe
+
+
+def write_tab(dframe):
+ """Write tab-separated data with column names in the first row."""
+ return dframe
+
diff --git a/skgenome/tabio/textcoord.py b/skgenome/tabio/textcoord.py
new file mode 100644
index 0000000..999d324
--- /dev/null
+++ b/skgenome/tabio/textcoord.py
@@ -0,0 +1,30 @@
+from __future__ import absolute_import, division, print_function
+
+import pandas as pd
+from Bio.File import as_handle
+
+from skgenome.rangelabel import from_label, to_label
+from .util import report_bad_line
+
+
+def read_text(infile):
+ """Text coordinate format: "chr:start-end", one per line.
+
+ Or sometimes: "chrom:start-end gene" or "chrom:start-end REF>ALT"
+
+ Coordinate indexing is assumed to be from 1.
+ """
+ parse_line = report_bad_line(from_label)
+ with as_handle(infile, 'rU') as handle:
+ rows = [parse_line(line) for line in handle]
+ table = pd.DataFrame.from_records(rows, columns=["chromosome", "start",
+ "end", "gene"])
+ table['gene'] = table['gene'].replace('', '-')
+ return table
+
+
+def write_text(dframe):
+ """Text coordinate format: "chr:start-end", one per line."""
+ dframe = dframe.copy()
+ dframe['start'] += 1
+ return dframe.apply(to_label, axis=1)
diff --git a/skgenome/tabio/util.py b/skgenome/tabio/util.py
new file mode 100644
index 0000000..7dc5be3
--- /dev/null
+++ b/skgenome/tabio/util.py
@@ -0,0 +1,14 @@
+"""Utilities."""
+from __future__ import absolute_import, division, print_function
+
+import functools
+
+
+def report_bad_line(line_parser):
+ @functools.wraps(line_parser)
+ def wrapper(line):
+ try:
+ return line_parser(line)
+ except ValueError:
+ raise ValueError("Bad line: %r" % line)
+ return wrapper
diff --git a/skgenome/tabio/vcfio.py b/skgenome/tabio/vcfio.py
new file mode 100644
index 0000000..8ede0f3
--- /dev/null
+++ b/skgenome/tabio/vcfio.py
@@ -0,0 +1,305 @@
+"""Variant Call Format (VCF) for SNV loci."""
+from __future__ import absolute_import, division, print_function
+# from past.builtins import basestring
+
+import collections
+import logging
+from itertools import chain
+
+import pandas as pd
+import numpy as np
+import pysam
+
+
+def read_vcf(infile, sample_id=None, normal_id=None,
+ min_depth=None, skip_reject=False, skip_somatic=False):
+ """Read one tumor-normal pair or unmatched sample from a VCF file.
+
+ By default, return the first tumor-normal pair or unmatched sample in the
+ file. If `sample_id` is a string identifier, return the (paired or single)
+ sample matching that ID. If `sample_id` is a positive integer, return the
+ sample or pair at that index position, counting from 0.
+ """
+ try:
+ vcf_reader = pysam.VariantFile(infile)
+ except Exception as exc:
+ raise ValueError("Must give a VCF filename, not open file handle: %s"
+ % exc)
+ if vcf_reader.header.samples:
+ sid, nid = _choose_samples(vcf_reader, sample_id, normal_id)
+ logging.info("Selected test sample " + str(sid) +
+ (" and control sample %s" % nid if nid else ''))
+ # NB: in-place
+ vcf_reader.subset_samples(list(filter(None, (sid, nid))))
+ else:
+ logging.warn("VCF file %s has no sample genotypes", infile)
+ sid = sample_id
+ nid = None
+
+ columns = ['chromosome', 'start', 'end', 'ref', 'alt', 'somatic',
+ 'zygosity', 'depth', 'alt_count']
+ if nid:
+ columns.extend(['n_zygosity', 'n_depth', 'n_alt_count'])
+
+ rows = _parse_records(vcf_reader, sid, nid, skip_reject)
+ table = pd.DataFrame.from_records(rows, columns=columns)
+ table['alt_freq'] = table['alt_count'] / table['depth']
+ if nid:
+ table['n_alt_freq'] = table['n_alt_count'] / table['n_depth']
+ table = table.fillna({col: 0.0 for col in table.columns[6:]})
+ # Filter out records as requested
+ cnt_depth = cnt_som = 0
+ if min_depth:
+ if table['depth'].any():
+ dkey = 'n_depth' if 'n_depth' in table else 'depth'
+ idx_depth = table[dkey] >= min_depth
+ cnt_depth = (~idx_depth).sum()
+ table = table[idx_depth]
+ else:
+ logging.warn("Depth info not available for filtering")
+ if skip_somatic:
+ idx_som = table['somatic']
+ cnt_som = idx_som.sum()
+ table = table[~idx_som]
+ logging.info("Loaded %d records; skipped: %d somatic, %d depth",
+ len(table), cnt_som, cnt_depth)
+ # return sid, nid, table
+ return table
+
+
+def _choose_samples(vcf_reader, sample_id, normal_id):
+ """Emit the sample IDs of all samples or tumor-normal pairs in the VCF.
+
+ Determine tumor-normal pairs from the PEDIGREE tag(s). If no PEDIGREE tag is
+ present, use the specified sample_id and normal_id as the pair, or if
+ unspecified, emit all samples as unpaired tumors.
+ """
+ vcf_samples = list(vcf_reader.header.samples)
+ if isinstance(sample_id, int):
+ sample_id = vcf_samples[sample_id]
+ if isinstance(normal_id, int):
+ normal_id = vcf_samples[normal_id]
+ for sid in (sample_id, normal_id):
+ if sid and sid not in vcf_samples:
+ raise IndexError("Specified sample %s not in VCF file"
+ % sid)
+ pairs = None
+ peds = list(_parse_pedigrees(vcf_reader))
+ if peds:
+ # Trust the PEDIGREE tag
+ pairs = peds
+ elif normal_id:
+ # All/any other samples are tumors paired with this normal
+ try:
+ other_ids = [s for s in vcf_samples if s != normal_id]
+ except StopIteration:
+ raise IndexError(
+ "No other sample in VCF besides the specified normal " +
+ normal_id + "; did you mean to use this as the sample_id "
+ "instead?")
+ pairs = [(oid, normal_id) for oid in other_ids]
+ else:
+ # All samples are unpaired tumors
+ pairs = [(sid, None) for sid in vcf_samples]
+ if sample_id:
+ # Keep only the specified tumor/test sample
+ pairs = [(s, n) for s, n in pairs if s == sample_id]
+ if not pairs:
+ # sample_id refers to a normal/control sample -- salvage it
+ pairs = [(sample_id, None)]
+ for sid in set(chain(*pairs)) - {None}:
+ _confirm_unique(sid, vcf_samples)
+
+ sid, nid = pairs[0]
+ if len(pairs) > 1:
+ if nid :
+ logging.warn("WARNING: VCF file contains multiple tumor-normal "
+ "pairs; returning the first pair '%s' / '%s'",
+ sid, nid)
+ else:
+ logging.warn("WARNING: VCF file contains multiple samples; "
+ "returning the first sample '%s'", sid)
+
+ return sid, nid
+
+
+def _parse_pedigrees(vcf_reader):
+ """Extract tumor/normal pair sample IDs from the VCF header.
+
+ Return an iterable of (tumor sample ID, normal sample ID).
+ """
+ meta = collections.defaultdict(list)
+ for hr in vcf_reader.header.records:
+ if hr.key and hr.key not in ('ALT', 'FILTER', 'FORMAT', 'INFO', 'contig'):
+ meta[hr.key].append(dict(hr.items()))
+ # Prefer the standard tag
+ if "PEDIGREE" in meta:
+ for tag in meta["PEDIGREE"]:
+ if "Derived" in tag:
+ sample_id = tag["Derived"]
+ normal_id = tag["Original"]
+ logging.debug("Found tumor sample %s and normal sample %s "
+ "in the VCF header PEDIGREE tag",
+ sample_id, normal_id)
+ yield sample_id, normal_id
+ # GATK Mutect and Mutect2 imply paired tumor & normal IDs
+ elif "GATKCommandLine" in meta:
+ # GATK 3.0(?) and earlier
+ for tag in meta["GATKCommandLine"]:
+ if tag.get("ID") == "MuTect": # any others OK?
+ options = dict(kv.split("=", 1)
+ for kv in (tag["CommandLineOptions"]
+ .strip('"').split())
+ if '=' in kv)
+ sample_id = options.get('tumor_sample_name')
+ normal_id = options['normal_sample_name']
+ logging.debug("Found tumor sample %s and normal sample "
+ "%s in the MuTect VCF header",
+ sample_id, normal_id)
+ yield sample_id, normal_id
+ elif "GATKCommandLine.MuTect2" in meta:
+ # GATK 3+ metadata is suboptimal.
+ # Apparent T/N convention: The samples are just renamed TUMOR and
+ # NORMAL, listed in arbitrary order. Metadata is data! We have always
+ # been at war with metadata! (#195)
+ # Mutect2 can also run in tumor-only mode (safe fallback)
+ if len(vcf_reader.header.samples) == 2:
+ sample_ids = tuple(vcf_reader.header.samples)
+ if sample_ids == ("NORMAL", "TUMOR"):
+ yield ("TUMOR", "NORMAL")
+ else:
+ yield sample_ids
+
+
+def _confirm_unique(sample_id, samples):
+ occurrences = [s for s in samples if s == sample_id]
+ if len(occurrences) != 1:
+ raise IndexError(
+ "Did not find a single sample ID '%s' in: %s"
+ % (sample_id, samples))
+
+
+def _parse_records(records, sample_id, normal_id, skip_reject):
+ """Parse VCF records into DataFrame rows.
+
+ Apply filters to skip records with low depth, homozygosity, the REJECT
+ flag, or the SOMATIC info field.
+ """
+ cnt_reject = 0 # For logging
+ for record in records:
+ if (skip_reject and record.filter and len(record.filter) > 0
+ and len(set(record.filter) - {'.', 'PASS', 'KEEP'})):
+ cnt_reject += 1
+ continue
+
+ if record.samples:
+ sample = record.samples[sample_id]
+ try:
+ depth, zygosity, alt_count = _extract_genotype(sample, record)
+ if normal_id:
+ normal = record.samples[normal_id]
+ n_depth, n_zygosity, n_alt_count = _extract_genotype(normal,
+ record)
+ except Exception as exc:
+ logging.error("Skipping %s:%d %s @ %s; %s",
+ record.chrom, record.pos, record.ref, sample_id,
+ exc)
+ raise
+ else:
+ # Assume unpaired tumor; take DP, AF from INFO (e.g. LoFreq)
+ depth = record.info.get('DP', 0.0) if "DP" in record.info else 0.0
+ if 'AF' in record.info:
+ alt_freq = record.info['AF']
+ alt_count = int(round(alt_freq * depth))
+ # NB: No genotype, so crudely guess from allele frequency
+ if alt_freq < 0.25:
+ zygosity = 0.0
+ elif alt_freq < 0.75:
+ zygosity = 0.5
+ else:
+ zygosity = 1.0
+ else:
+ alt_count = 0
+ zygosity = 0.0
+
+ is_som = "SOMATIC" in record.info and bool(record.info.get("SOMATIC"))
+ # Split multiallelics?
+ # XXX Ensure sample genotypes are handled properly
+ start = record.start
+ for alt in record.alts:
+ if alt == '<NON_REF>':
+ # gVCF placeholder -- not a real allele
+ continue
+ end = _get_end(start, alt, record.info)
+ row = (record.chrom, start, end, record.ref, alt,
+ is_som, zygosity, depth, alt_count)
+ if normal_id:
+ row += (n_zygosity, n_depth, n_alt_count)
+ yield row
+
+ if cnt_reject:
+ logging.info('Filtered out %d records', cnt_reject)
+
+
+def _extract_genotype(sample, record):
+ if 'DP' in sample:
+ depth = sample['DP']
+ elif 'AD' in sample and isinstance(sample['AD'], tuple):
+ depth = _safesum(sample['AD'])
+ elif 'DP' in record.info:
+ depth = record.info['DP']
+ else:
+ # SV or not called, probably
+ depth = np.nan #0.0
+ gts = set(sample['GT'])
+ if len(gts) > 1:
+ zygosity = 0.5
+ elif gts.pop() == 0:
+ zygosity = 0.0
+ else:
+ zygosity = 1.0
+ alt_count = _get_alt_count(sample)
+ return depth, zygosity, alt_count
+
+
+def _get_alt_count(sample):
+ """Get the alternative allele count from a sample in a VCF record."""
+ if sample.get('AD') not in (None, (None,)):
+ # GATK and other callers: (ref depth, alt depth)
+ if isinstance(sample['AD'], tuple):
+ alt_count = sample['AD'][1]
+ # VarScan
+ else:
+ alt_count = sample['AD']
+ elif sample.get('CLCAD2') not in (None, (None,)):
+ # Qiagen CLC Genomics Server -- similar to GATK's AD
+ alt_count = sample['CLCAD2'][1]
+ elif 'AO' in sample:
+ if isinstance(sample['AO'], tuple):
+ alt_count = _safesum(sample['AO'])
+ elif sample['AO']:
+ alt_count = sample['AO']
+ else:
+ alt_count = 0.0
+ else:
+ alt_count = np.nan
+ return alt_count
+
+
+def _safesum(tup):
+ return sum(filter(None, tup))
+
+
+def _get_end(posn, alt, info):
+ """Get record end position."""
+ if "END" in info:
+ # Structural variant
+ return info['END']
+ return posn + len(alt)
+
+# _____________________________________________________________________
+
+def write_vcf(dframe):
+ """Variant Call Format (VCF) for SV loci."""
+ return NotImplemented
+ # See export.export_vcf()
diff --git a/test/.coveragerc b/test/.coveragerc
index 23652dc..02e97ec 100644
--- a/test/.coveragerc
+++ b/test/.coveragerc
@@ -1,6 +1,8 @@
[run]
branch = True
-source = cnvlib
+source =
+ cnvlib
+ skgenome
[report]
exclude_lines =
diff --git a/test/Makefile b/test/Makefile
index 477b4eb..364fa75 100644
--- a/test/Makefile
+++ b/test/Makefile
@@ -17,13 +17,13 @@ picard_segs=$(picard_cnrs:.cnr=.cns)
picard_targets= build/reference-picard.cnn $(picard_cnrs) $(picard_segs) \
all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf \
p2-9_2-breaks.txt p2-9_2-gainloss.txt gender-picard.txt \
- p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus \
+ p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt \
p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns
# ------------------------------------------------------------------------------
# Action!
-all: $(picard_targets) p2-5_5-metrics.txt p2-9_2-metrics.txt p2-20-metrics.csv
+all: $(picard_targets) p2-5_5-metrics.tsv p2-9_2-metrics.tsv p2-20-metrics.tsv
.PHONY: clean
@@ -33,6 +33,8 @@ clean:
.PHONY: test
test:
+ python test_io.py
+ python test_genome.py
python test_cnvlib.py
python test_r.py
@@ -59,7 +61,7 @@ $(picard_cnrs): %.cnr: %.targetcoverage.cnn %.antitargetcoverage.cnn build/refer
$(cnvkit) fix $^ -o $@
$(picard_segs): %.cns: %.cnr
- $(cnvkit) segment -t .01 $< -o $@
+ $(cnvkit) segment -p 2 --drop-low-coverage -t .01 $< -o $@
$(picard_segs:.cns=.call.cns): build/%.call.cns: build/%.cns
$(cnvkit) call $^ -y -m clonal --purity 0.65 -o $@
@@ -69,7 +71,7 @@ $(picard_segs:.cns=.call.cns): build/%.call.cns: build/%.cns
# Demo other features with Picard outputs
heatmap-picard.pdf: $(picard_segs)
- $(cnvkit) heatmap $^ -o $@
+ $(cnvkit) heatmap $^ -y -o $@
# == Plot coverages with segmentation calls
@@ -77,7 +79,7 @@ all-scatters.pdf: p2-5_5-scatter.pdf p2-9_2-scatter.pdf p2-9_2-chr1-scatter.pdf
which pdfunite && pdfunite $^ $@ || touch $@
p2-5_5-scatter.pdf p2-9_2-scatter.pdf: %-scatter.pdf: build/%.cns build/%.cnr
- $(cnvkit) scatter -s $^ -t -o $@
+ $(cnvkit) scatter -s $^ -t --y-min=-2.5 -o $@
p2-9_2-chr1-scatter.pdf: build/p2-9_2.cns build/p2-9_2.cnr
$(cnvkit) scatter -s $^ -c chr1 -t -o $@
@@ -114,17 +116,19 @@ p2-9_2-gainloss.txt: build/p2-9_2.cns build/p2-9_2.cnr
$(cnvkit) gainloss -y -m 2 -s $^ -o $@
gender-picard.txt: build/p2-5_5.cnr build/p2-5_5.cns build/p2-9_2.cnr build/p2-9_2.cns build/p2-20_5.cnr build/p2-20_5.cns
- $(cnvkit) gender -y $^ -o $@
+ $(cnvkit) sex -y $^ -o $@
-p2-5_5-metrics.txt p2-9_2-metrics.txt: %-metrics.txt: build/%.cnr build/%.cns
+p2-5_5-metrics.tsv p2-9_2-metrics.tsv: %-metrics.tsv: build/%.cnr build/%.cns
$(cnvkit) metrics $< -s $(lastword $^) -o $@
-p2-20-metrics.csv: $(addprefix build/p2-20_,$(addsuffix .cns,1 2 3 4 5))
+p2-20-metrics.tsv: $(addprefix build/p2-20_,$(addsuffix .cns,1 2 3 4 5))
$(cnvkit) metrics $(^:.cns=.cnr) -s $^ -o $@
p2-9_2-segmetrics.cns: build/p2-9_2.cns build/p2-9_2.cnr
- $(cnvkit) segmetrics -s $^ -o $@ --stdev --mad --iqr --bivar --ci --pi
-
+ $(cnvkit) segmetrics -s $^ -o $@ \
+ --mean --median --mode \
+ --stdev --mad --mse --iqr --bivar \
+ --ci --pi --sem
# == Export to other formats
@@ -134,15 +138,18 @@ p2-all.seg: $(picard_segs)
p2-all.bed: $(picard_segs:.cns=.call.cns)
$(cnvkit) export bed $^ -y --show variant -o $@
-p2-9_2.vcf: build/p2-9_2.call.cns
- $(cnvkit) export vcf $^ -y -o $@
+p2-9_2.vcf: build/p2-9_2.cnr build/p2-9_2.call.cns
+ $(cnvkit) export vcf -o $@ -y --cnr $^ -y -o $@
p2-9_2.theta2.input: build/p2-9_2.cns build/reference-picard.cnn
- $(cnvkit) export theta $^ -o $@
+ $(cnvkit) export theta $< -r $(lastword $^) -o $@
p2-9_2.nexus: build/p2-9_2.cnr
$(cnvkit) export nexus-basic $^ -o $@
+p2-9_2.nexus-ogt: build/p2-9_2.cnr formats/na12878_na12882_mix.vcf
+ $(cnvkit) export nexus-ogt $^ -o $@
+
p2-all.cdt: $(picard_cnrs)
$(cnvkit) export cdt $^ -o $@
diff --git a/test/formats/amplicon.cnr b/test/formats/amplicon.cnr
index 0787b1f..93fa695 100644
--- a/test/formats/amplicon.cnr
+++ b/test/formats/amplicon.cnr
@@ -1,1434 +1,1434 @@
-chromosome start end gene log2 weight
-chr1 160786623 160786747 LY9 -1.87949 0.310777
-chr2 29415994 29416295 ALK -2.08816 0.754386
-chr2 29416295 29416596 ALK -2.12646 0.754386
-chr2 29416596 29416897 ALK -3.71354 0.754386
-chr2 29419567 29419830 ALK 0.837094 0.659148
-chr2 29420327 29420675 ALK -1.46015 0.87218
-chr2 29429995 29430239 ALK -0.37488 0.611529
-chr2 29432543 29432864 ALK -1.55798 0.804511
-chr2 29436737 29437014 ALK -1.19306 0.694236
-chr2 29443528 29443751 ALK 0.0884886 0.558897
-chr2 29445133 29445527 ALK -2.2403 0.987469
-chr2 29446146 29446478 ALK 1.30778 0.83208
-chr2 29448254 29448472 ALK 2.06833 0.546366
-chr2 29449734 29450024 ALK -0.778137 0.726817
-chr2 29450393 29450639 ALK 0.127206 0.616541
-chr2 29451691 29451992 ALK -6.83711 0.754386
-chr2 29455073 29455408 ALK -1.12009 0.839599
-chr2 29456391 29456633 ALK -1.98773 0.606516
-chr2 29462459 29462797 ALK -0.524991 0.847118
-chr2 29473913 29474250 ALK -0.646302 0.844612
-chr2 29497883 29498144 ALK -1.2367 0.654135
-chr2 29498172 29498437 ALK -0.628051 0.66416
-chr2 29519706 29520012 ALK -2.03725 0.766917
-chr2 29541109 29541350 ALK -0.184643 0.60401
-chr2 29543564 29543795 ALK -1.14312 0.578947
-chr2 29551118 29551460 ALK -0.985134 0.857143
-chr2 29606540 29606805 ALK -1.27817 0.66416
-chr2 29754720 29755076 ALK -1.55854 0.892231
-chr2 29917613 29917939 ALK -0.482538 0.817043
-chr2 29940352 29940605 ALK -1.04701 0.634085
-chr2 30142795 30143159 ALK -3.40587 0.912281
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+chr19 9065684 9065951 MUC16 -0.335876 0.792303 0.669173
+chr19 9065951 9066219 MUC16 -0.551325 0.682393 0.671679
+chr19 9066219 9066486 MUC16 1.22079 2.33074 0.669173
+chr19 9066486 9066753 MUC16 -0.605515 0.657237 0.669173
+chr19 9066753 9067021 MUC16 -0.58072 0.66863 0.671679
+chr19 9067021 9067288 MUC16 1.47397 2.77785 0.669173
+chr19 9067288 9067555 MUC16 0.295274 1.22712 0.669173
+chr19 9067555 9067822 MUC16 -0.251959 0.839755 0.669173
+chr19 9067822 9068090 MUC16 -0.482878 0.715549 0.671679
+chr19 9068090 9068357 MUC16 -0.552073 0.682039 0.669173
+chr19 9068357 9068624 MUC16 -0.0533476 0.963698 0.669173
+chr19 9068624 9068892 MUC16 1.23567 2.35491 0.671679
+chr19 9068892 9069159 MUC16 1.01664 2.0232 0.669173
+chr19 9069159 9069426 MUC16 0.710333 1.63618 0.669173
+chr19 9069426 9069693 MUC16 -0.301662 0.811317 0.669173
+chr19 9069693 9069961 MUC16 0.559755 1.47402 0.671679
+chr19 9069961 9070228 MUC16 -0.781147 0.581904 0.669173
+chr19 9070228 9070495 MUC16 0.433984 1.35096 0.669173
+chr19 9070495 9070763 MUC16 0.388622 1.30914 0.671679
+chr19 9070763 9071030 MUC16 0.866693 1.82348 0.669173
+chr19 9071030 9071297 MUC16 0.682045 1.60441 0.669173
+chr19 9071297 9071564 MUC16 0.0398283 1.02799 0.669173
+chr19 9071564 9071832 MUC16 -0.714261 0.609517 0.671679
+chr19 9071832 9072099 MUC16 0.325843 1.2534 0.669173
+chr19 9072099 9072366 MUC16 0.0378065 1.02655 0.669173
+chr19 9072366 9072634 MUC16 -0.211555 0.863606 0.671679
+chr19 9072634 9072901 MUC16 0.186033 1.13763 0.669173
+chr19 9072901 9073168 MUC16 0.450125 1.36616 0.669173
+chr19 9073168 9073436 MUC16 -0.438156 0.738077 0.671679
+chr19 9073436 9073703 MUC16 0.15389 1.11257 0.669173
+chr19 9073703 9073970 MUC16 -0.562957 0.676913 0.669173
+chr19 9073970 9074237 MUC16 0.182437 1.1348 0.669173
+chr19 9074237 9074505 MUC16 -0.140574 0.907158 0.671679
+chr19 9074505 9074772 MUC16 0.561556 1.47586 0.669173
+chr19 9074772 9075039 MUC16 -0.381599 0.767586 0.669173
+chr19 9075039 9075307 MUC16 0.128059 1.09282 0.671679
+chr19 9075307 9075574 MUC16 0.605437 1.52144 0.669173
+chr19 9075574 9075841 MUC16 -0.780452 0.582184 0.669173
+chr19 9075841 9076108 MUC16 -1.3456 0.39349 0.669173
+chr19 9076108 9076376 MUC16 0.629105 1.54661 0.671679
+chr19 9076376 9076643 MUC16 0.215031 1.16073 0.669173
+chr19 9076643 9076910 MUC16 -0.638291 0.642474 0.669173
+chr19 9076910 9077178 MUC16 -0.189297 0.877033 0.671679
+chr19 9077178 9077445 MUC16 0.520918 1.43487 0.669173
+chr19 9077445 9077712 MUC16 0.166825 1.12259 0.669173
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+chr19 9082546 9082812 MUC16 0.944288 1.92424 0.666667
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+chr19 9083344 9083610 MUC16 0.470735 1.38582 0.666667
+chr19 9083610 9083876 MUC16 0.293619 1.22571 0.666667
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+chr19 9084142 9084408 MUC16 0.336548 1.26273 0.666667
+chr19 9084408 9084674 MUC16 0.73452 1.66384 0.666667
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+chr19 9085738 9086004 MUC16 0.311153 1.2407 0.666667
+chr19 9086004 9086270 MUC16 -0.5741 0.671705 0.666667
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+chr19 9086536 9086802 MUC16 0.974751 1.9653 0.666667
+chr19 9086802 9087068 MUC16 0.039854 1.02801 0.666667
+chr19 9087068 9087334 MUC16 0.107411 1.07729 0.666667
+chr19 9087334 9087600 MUC16 0.143126 1.1043 0.666667
+chr19 9087600 9087866 MUC16 -0.00836849 0.994216 0.666667
+chr19 9087866 9088132 MUC16 -0.282535 0.822145 0.666667
+chr19 9088132 9088398 MUC16 0.468019 1.38321 0.666667
+chr19 9088398 9088664 MUC16 1.01676 2.02337 0.666667
+chr19 9088664 9088930 MUC16 1.89369 3.71584 0.666667
+chr19 9088930 9089196 MUC16 0.280088 1.21427 0.666667
+chr19 9089196 9089462 MUC16 -0.566661 0.675178 0.666667
+chr19 9089462 9089728 MUC16 1.25387 2.3848 0.666667
+chr19 9089728 9089994 MUC16 0.100456 1.07211 0.666667
+chr19 9089994 9090260 MUC16 -0.246219 0.843103 0.666667
+chr19 9090260 9090526 MUC16 -0.164215 0.892414 0.666667
+chr19 9090526 9090792 MUC16 -0.021102 0.98548 0.666667
+chr19 9090792 9091058 MUC16 -0.864263 0.549327 0.666667
+chr19 9091058 9091324 MUC16 -0.28605 0.820144 0.666667
+chr19 9091324 9091590 MUC16 -1.88539 0.270671 0.666667
+chr19 9091590 9091855 MUC16 -1.56568 0.337818 0.66416
+chr19 10597276 10597593 KEAP1 -0.316381 0.803082 0.794486
+chr19 10599814 10600122 KEAP1 -2.8388 0.139777 0.77193
+chr19 10600257 10600583 KEAP1 -2.40526 0.188775 0.817043
+chr19 10602172 10602405 KEAP1 1.1748 2.25762 0.58396
+chr19 10602558 10602805 KEAP1 0.76085 1.69449 0.619048
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+chr19 11096763 11097037 SMARCA4 -0.260192 0.834977 0.686717
+chr19 11097037 11097312 SMARCA4 0.305186 1.23558 0.689223
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+chr19 11098586 11098744 SMARCA4 -4.02225 0.0615435 0.39599
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+chr19 11106832 11107092 SMARCA4 0.933856 1.91038 0.651629
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+chr19 11113631 11113886 SMARCA4 1.8247 3.54233 0.639098
+chr19 11113968 11114112 SMARCA4 -2.77925 0.145667 0.360902
+chr19 11118496 11118807 SMARCA4 0.177238 1.13072 0.779449
+chr19 11121009 11121322 SMARCA4 0.68726 1.61022 0.784461
+chr19 11123535 11123859 CTC-215O4.4,SMARCA4 0.613626 1.5301 0.81203
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+chr19 11134891 11135224 SMARCA4 0.499044 1.41328 0.834586
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+chr19 11143905 11144116 SMARCA4 1.18465 2.27308 0.528822
+chr19 11144116 11144328 SMARCA4 -0.502709 0.70578 0.531328
+chr19 11144695 11144920 SMARCA4 -3.04019 0.121566 0.56391
+chr19 11145544 11145925 SMARCA4 -0.584464 0.666897 0.954887
+chr19 11150177 11150332 SMARCA4 -0.118386 0.921218 0.388471
+chr19 11151845 11152098 SMARCA4 3.04116 8.23153 0.634085
+chr19 11152098 11152352 SMARCA4 1.79973 3.48155 0.636591
+chr19 11168814 11169157 SMARCA4 -4.06943 0.0595634 0.859649
+chr19 11169341 11169658 SMARCA4 -0.237855 0.848005 0.794486
+chr19 11170411 11170706 SMARCA4 -0.414359 0.750353 0.739348
+chr19 11170706 11171002 SMARCA4 0.603008 1.51888 0.741855
+chr19 11172370 11172549 SMARCA4 2.58955 6.01911 0.448622
+chr20 51296082 51296237 RP4-715N11.2 -0.353978 0.782424 0.388471
+chr22 41558670 41558820 EP300 0.620682 1.5376 0.37594
+chrX 11314993 11315106 AMELX,ARHGAP6 0.37563 1.29741 0.283208
diff --git a/test/formats/blank.vcf b/test/formats/blank.vcf
new file mode 100644
index 0000000..48d1d9f
--- /dev/null
+++ b/test/formats/blank.vcf
@@ -0,0 +1,140 @@
+##fileformat=VCFv4.2
+##fileDate=20150729
+##source=SNV-Unifier
+##reference=file:///home/dnanexus/genome.fa
+##phasing=none
+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic event">
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
+##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
+##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
+##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
+##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
+##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
+##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
+##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
+##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
+##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
+##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
+##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without.">
+##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
+##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
+##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
+##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
+##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
+##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
+##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
+##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
+##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
+##INFO=<ID=technology.ILLUMINA,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from ILLUMINA">
+##INFO=<ID=SPLITMULTIALLELIC,Number=0,Type=Flag,Description="Variant represents one alternate allele from a multiallelic variant call.">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=VT,Number=1,Type=String,Description="Variant type, can be SNP, MNP, INS or DEL">
+##INFO=<ID=JOINED,Number=0,Type=Flag,Description="Variant is the result of joining adjacent SNPs/MNPs. Please use caution when interpreting sample-specific values.">
+##INFO=<ID=ALERT,Number=0,Type=Flag,Description="Variant is adjacent to other variants, but case was too complex for joinAdjacentSNPs to handle. Please review.">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=PF,Number=1,Type=Integer,Description="The number of samples carry the variant">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=NTLEN,Number=.,Type=Integer,Description="Number of bases inserted in place of deleted code">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
+##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
+##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
+##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
+##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)">
+##INFO=<ID=ADERROR,Number=0,Type=Flag,Description="The AD field from the original variant caller VCF has an error at this locus. Please use caution when interpreting AD, GMIMAF, and GMICOV.">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+##FORMAT=<ID=BQ,Number=A,Type=Float,Description="Average base quality for reads supporting alleles">
+##FORMAT=<ID=FA,Number=A,Type=Float,Description="Allele fraction of the alternate allele with regard to reference">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal,0=wildtype,1=germline,2=somatic,3=LOH,4=post-transcriptional modification,5=unknown">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Reference depth, how many reads support the reference">
+##FORMAT=<ID=GMIMUT,Number=A,Type=Integer,Description="GMI-derived mutant read count: the number of reads observed at the variant locus that support each ALT allele.">
+##FORMAT=<ID=GMIMAF,Number=A,Type=Integer,Description="GMI-derived MAF: the proportion of reads observed at the variant locus that support each ALT allele.">
+##FORMAT=<ID=GMICOV,Number=1,Type=Integer,Description="GMI-derived coverage: total read depth at the variant locus.">
+##FORMAT=<ID=AD,Number=2,Type=Integer,Description="# of reads supporting consensus reference/indel at the site">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total coverage at the site">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MM,Number=2,Type=Float,Description="Average # of mismatches per ref-/consensus indel-supporting read">
+##FORMAT=<ID=MQS,Number=2,Type=Float,Description="Average mapping qualities of ref-/consensus indel-supporting reads">
+##FORMAT=<ID=NQSBQ,Number=2,Type=Float,Description="Within NQS window: average quality of bases in ref-/consensus indel-supporting reads">
+##FORMAT=<ID=NQSMM,Number=2,Type=Float,Description="Within NQS window: fraction of mismatching bases in ref/consensus indel-supporting reads">
+##FORMAT=<ID=REnd,Number=2,Type=Integer,Description="Median/mad of indel offsets from the ends of the reads">
+##FORMAT=<ID=RStart,Number=2,Type=Integer,Description="Median/mad of indel offsets from the starts of the reads">
+##FORMAT=<ID=SC,Number=4,Type=Integer,Description="Strandness: counts of forward-/reverse-aligned reference and indel-supporting reads (FwdRef,RevRef,FwdIndel,RevIndel)">
+##FORMAT=<ID=CallHC,Number=1,Type=Integer,Description="Variant was called by HaplotypeCaller">
+##FORMAT=<ID=CallUG,Number=1,Type=Integer,Description="Variant was called by UnifiedGenotyper">
+##FORMAT=<ID=CallFB,Number=1,Type=Integer,Description="Variant was called by freeBayes">
+##FORMAT=<ID=CallPI,Number=1,Type=Integer,Description="Variant was called by pindel">
+##FORMAT=<ID=CallSID,Number=1,Type=Integer,Description="Variant was called by SomaticIndelDetector">
+##FORMAT=<ID=CallMU,Number=1,Type=Integer,Description="Variant was called by MuTect">
+##FORMAT=<ID=LR,Number=1,Type=Float,Description="CNV log2 ratio">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=REJECT,Description="Not somatic due to normal call frequency or phred likelihoods: tumor: 35, normal 35.">
+##contig=<ID=chrM,length=16571>
+##contig=<ID=chr1,length=249250621>
+##contig=<ID=chr2,length=243199373>
+##contig=<ID=chr3,length=198022430>
+##contig=<ID=chr4,length=191154276>
+##contig=<ID=chr5,length=180915260>
+##contig=<ID=chr6,length=171115067>
+##contig=<ID=chr7,length=159138663>
+##contig=<ID=chr8,length=146364022>
+##contig=<ID=chr9,length=141213431>
+##contig=<ID=chr10,length=135534747>
+##contig=<ID=chr11,length=135006516>
+##contig=<ID=chr12,length=133851895>
+##contig=<ID=chr13,length=115169878>
+##contig=<ID=chr14,length=107349540>
+##contig=<ID=chr15,length=102531392>
+##contig=<ID=chr16,length=90354753>
+##contig=<ID=chr17,length=81195210>
+##contig=<ID=chr18,length=78077248>
+##contig=<ID=chr19,length=59128983>
+##contig=<ID=chr20,length=63025520>
+##contig=<ID=chr21,length=48129895>
+##contig=<ID=chr22,length=51304566>
+##contig=<ID=chrX,length=155270560>
+##contig=<ID=chrY,length=59373566>
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Blank
diff --git a/test/formats/chrM-Y-trunc.hg19.fa b/test/formats/chrM-Y-trunc.hg19.fa
new file mode 100644
index 0000000..15b8e4a
--- /dev/null
+++ b/test/formats/chrM-Y-trunc.hg19.fa
@@ -0,0 +1,821 @@
+>chrM
+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT
+TTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTG
+GAGCCGGAGCACCCTATGTCGNAGTATCTGTCTTTGATTCCTGCCTCATT
+CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACCTACTA
+AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT
+GTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA
+AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGC
+CAAACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAAT
+TTTATCTTTAGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACA
+TTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCC
+GCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAAC
+CAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA
+AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAA
+ATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGC
+AAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAG
+GGACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCC
+ACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGT
+TTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACC
+GCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTT
+TAGATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAA
+CTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAAC
+ACACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGC
+CCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGA
+GCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA
+GGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGC
+TCAGCCTATATACCGCCATCTNNNGCAAACCCTGATGANGGCTACAAAGT
+AAGCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGG
+TGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTT
+ATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTGAGAGTAGAGT
+GCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCC
+TCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATNNN
+NNNGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACG
+AACCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTT
+CAACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCAC
+CTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGG
+CGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGA
+TGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTT
+CTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAA
+GACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCC
+GTCTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCT
+ACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTT
+TAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAG
+TCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGA
+GTAAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGA
+AAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACT
+GAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAA
+TGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCA
+GATCAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCA
+ACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAG
+GAAAGGTTAAAAAAAGTAAAAGGAACTCGGCAAACCTTACCCCGCCTGTT
+TACCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCC
+CAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAaaggtagca
+taatcacttgttccttaaatagggacctgtatgaatggctccacgagggt
+tcagctgtctcttacttttaaccagtgaaattgacctgcccgtgaagagg
+cgggcatgacacagcaagacgagaagaccctatggagctttaatttaTTA
+ATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCA
+TTAAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCA
+GTACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGAT
+CCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATC
+CTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGAT
+CAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGA
+TTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTT
+CTATCTACTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCC
+TACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTAT
+TATACCCACACCCACCCAAGAACAGGGTTTgttaagatggcagagcccgg
+taatcgcataaaacttaaaactttacagtcagaggttcaattcctcttct
+taacaacaTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAA
+TCGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATA
+CAACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACC
+CTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCA
+CATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATC
+GCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCT
+CAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACT
+CAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGC
+GCACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCAT
+CATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCC
+TTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTG
+GCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTT
+CGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAAT
+ACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATT
+ATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGA
+CGCACTCTCCCCTGAACTCTACACAACATATTTTGTCACCAAGACCCTAC
+TTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCCCCGATTCCGC
+TACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCT
+AGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTC
+CCCCTCAAACCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGT
+AAATAATAGGAGCTTAAACCCCCTTATTTctaggactatgagaatcgaac
+ccatccctgagaatccaaaattctccgtgccacctatnncaccccatcct
+aAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTG
+GTTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTAC
+TCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATT
+TTTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTC
+TAACCAAAAAAATAAACCCTCGTTCCACAGAAGCTGCCATCAAGTATTTC
+CTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTATCCTCTTCAA
+CAATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACT
+CATCATTAATAATCATAATGGCTATAGCAATAAAACTAGGAATAGCCCCC
+TTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGG
+CCTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACC
+AAATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTA
+TCCATCATAGCAGGCAGTTGAGGTGGATTAAACCAAACCCAGCTACGCAA
+AATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAATAGCAGTTC
+TACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATC
+CTAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGAC
+CCTACTACTATCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAA
+TTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTT
+TTGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCAT
+CATCCCCACCATCATAGCCACCATCACCCTCCTTAACCTCTACTTCTACC
+TACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAAC
+GTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCC
+CACACTCATCGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATAC
+TAATAATCTTATAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAG
+CCCTCAGTAAGTTGCAATACTTAATTTCTGCAACAGCTAAGGACTGCAAA
+ACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAA
+GCCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGC
+TAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAA
+AAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCA
+ATTCAATATGAAAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTG
+TCTTTAGATTTACAGTCCAATGCTTCACTCAGCCATTTTACCTCACCCCC
+ACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTG
+GAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCT
+CTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGG
+TAACGACCACATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAA
+TCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTA
+GTTCCCCTAATAATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAA
+CATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTGCTCGCATCTG
+CTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTA
+GCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTC
+CTTACACCTAGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCA
+CAACAATTATCAATATAAAACCCCCTGCCATAACCCAATACCAAACGCCC
+CTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCT
+CCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGACCGCAACCTCA
+ACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCAA
+CACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACC
+AGGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAG
+AACCATTTGGATACATAGGTATGGTCTGAGCTATGATATCAATTGGCTTC
+CTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGAATAGACGT
+AGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCA
+CCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATG
+AAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCAC
+CGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCG
+TACTACACGACACGTACTACGTTGTAGCTCACTTCCACTATGTCCTATCA
+ATAGGAGCTGTATTTGCCATCATAGGAGGCTTCATTCACTGATTTCCCCT
+ATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCCATTTCACTA
+TCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGC
+CTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCAC
+ATGAAACATCCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAA
+TATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTC
+CTAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCC
+CCCACCCTACCACACATTCGAAGAACCCGTATACATAAAATCTAGACAaa
+aaaggaaggaatcgaaccccccaaagctggtttcaagccaaccccatggc
+ctccatgactttttcAAAAAGGTATTAGAAAAACCATTTCATAACTTTGT
+CAAAGTTAAATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGC
+GCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCA
+CCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTC
+CTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACAT
+CTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCA
+TCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGAC
+GAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTA
+CTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACA
+TACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTT
+GACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTAC
+ATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAA
+CAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGA
+CCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAG
+TTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAG
+GGCCCGTATTTACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTG
+TAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAAC
+ACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCA
+TAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATA
+TTAAACACAAACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAA
+AAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTTC
+ATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTC
+TATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGA
+CTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGAT
+AGCCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCT
+TAATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCA
+TTTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCTT
+ATGAGCGGGCGCAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCC
+TAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTA
+GTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGT
+ACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTG
+GAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATC
+ATCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTT
+AATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACA
+ACACATAATGACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCC
+CATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTA
+GCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACT
+AACCAACACACTAACCATATACCAATGGTGGCGCGATGTAACACGAGAAA
+GCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATAC
+GGGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTT
+CTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAACTAGGAGGGC
+ACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTC
+CTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCA
+CCATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTA
+TTACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTAC
+TTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTT
+TGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCC
+TCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACAT
+CACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGT
+TTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTA
+GTATAAATAGTACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAA
+AAAAGAGTAATAAACTTCGCCTTAATTTTAATAATCAACACCCTCCTAGC
+CTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACA
+TAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCC
+CGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATT
+ATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAA
+CAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATC
+CTAGCCCTAAGTCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAGC
+CGAATTGGTATATAGTTTAAACAAAACGAATGATTTCGACTCATTAAATT
+ATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTA
+GCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCAT
+ATCCTCCCTACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAG
+CTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAATATTGTGCCT
+ATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCT
+ACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTACATAACCTAA
+ACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCAC
+TGACATGACTTTCCAAAAAGCACATAATTTGAATCAACACAACCACCCAC
+AGCCTAATTATTAGCATCATCCCCCTACTATTTTTTAACCAAATCAACAA
+CAACCTATTTAGCTGTTCCCCAACCTTTTCCTCCGACCCCCTAACAACCC
+CCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATCATGGCAAGC
+CAACGCCACTTATCCAGCGAACCACTATCACGAAAAAAACTCTACCTCTC
+TATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAG
+AACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTG
+GCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCAC
+ATACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCAC
+TAATTTACACTCACAACACCCTAGGCTCACTAAACATTCTACTACTCACT
+CTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTTAATATGACT
+AGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACT
+TATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTA
+CTTGCCGCAGTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCAC
+ACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTAC
+TATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACA
+GACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACATAGCCCTCGT
+AGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCA
+TTCTCATAATCGCCCACGGACTCACATCCTCATTACTATTCTGCCTAGCA
+AACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGG
+ACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCC
+TCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCT
+GTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGG
+ACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAA
+CACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTC
+ACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCT
+ATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTT
+TAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTACGACCCCTT
+ATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAA
+CAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTA
+GGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACA
+CTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACC
+ACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATC
+CATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCA
+TGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACC
+CAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAAT
+ATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCAC
+TGTGATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTA
+CTCATTTTCCTAATTACCATACTAATCTTAGTTACCGCTAACAACCTATT
+CCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCA
+TCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCA
+GTCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATG
+ATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAA
+ACGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCA
+GGCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGA
+AGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAG
+CAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCA
+CTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGC
+AGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCT
+CCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAA
+CCACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCAT
+ACTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAG
+ATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACC
+TCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGG
+TTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAA
+ACGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCC
+TATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCC
+CACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTA
+AACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAAC
+ATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACT
+CACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCA
+ACTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTAT
+TTCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCC
+CTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACC
+TAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATC
+TCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTT
+CCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAAC
+CTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGT
+TCAACCAGTAACCACTACTAATCAACGCCCATAATCATACAAAGCCCCCG
+CACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATT
+ATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATA
+CTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAA
+CACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCA
+ATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATA
+AATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAA
+TAACACACCCGACCACACCGCTAACAATCAGTACTAAACCCCCATAAATA
+GGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACT
+CAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGA
+CCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATG
+ACCCCAATACGCAAAATTAACCCCCTAATAAAATTAATTAACCACTCATT
+CATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCT
+CACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTA
+GCCATACACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCA
+CATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCA
+ATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGC
+CTATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTAT
+CCTCCTGCTTGCAACTATAGCAACAGCCTTCATAGGCTATGTCCTCCCGT
+GAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCC
+GCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTA
+CTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCT
+TACCCTTCATTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTTGCAC
+GAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAAT
+CACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCT
+TCCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGC
+GACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACAT
+CAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCC
+CTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTA
+GCAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCG
+CCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTC
+TAACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGA
+CAAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAAC
+TATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTA
+TAAACTAATACACCAGTCTTGTAAACCGGAGACGAAAACCTTTTTCCAAG
+GACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAA
+GATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGG
+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC
+ATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCA
+CCTGTAGTACATAAAAACCCAACCCACATCAAACCCCCCCCCCCCATGCT
+TACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAAC
+TCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTT
+AACAGTACATAGTACATAAAGTCATTTACCGTACATAGCACATTACAGTC
+AAATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTG
+ACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCT
+CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGAC
+ATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCC
+CTTAAATAAGACATCACGATG
+>chrY
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+ctaaccctaaccctaaccctaaccctaaccctaaccctCTGaaagtggac
+ctatcagcaggatgtgggtgggagcagattagagaataaaagcagactgc
+ctgagccagcagtggcaacccaatggggtccctttccatactgtggaagc
+ttcgttctttcactctttgcaataaatcttgctattgctcactctttggg
+tccacactgcctttatgagctgtgacactcaccgcaaaggtctgcagctt
+cactcctgagccagtgagaccacaaccccaccagaaagaagaaactcaga
+acacatctgaacatcagaagaaacaaactccggacgcgccacctttaaga
+actgtaacactcaccgcgaggttccgcgtcttcattcttgaagtcagtga
+gaccaagaacccaccaattccagacacactaggaccctgagacaacCCCT
+AGAAGAGCACCTGGTTGATAACCCAGTTCCCATCTGGGATTTAGGGGACC
+TGGACAGCCCGGAAAATGAGCTCCTCATCTCTAACCCAGTTCCCCTGTGG
+GGATTTAGGGGACCAGGGACAGCCCGTTGCATGAGCCCCTGGACTCTAAC
+CCAGTTCCCTTCTGGAATTTAGGGGCCCTGGGACAGCCCTGTACATGAGC
+TCCTGGTCTGTAACACAGTTCCCCTGTGGGGATTTAGGGACTTGGGCCTT
+CTGTCTTTGGGATCTACTCTCTATGGGCCACACAGATATGTCTTCCAACT
+TCCCTACACAGGGGGGACTTCAAAGAGTGCCTTGAGCTGATCTGGTGATT
+GCTTTTTTGTACTGTTATTTATCTTATTCTTTTCATTGTGAGGTACTGAT
+GCAAACACTTTGTACGAAAAGGTCTTTCTCATCTCGGGAGTCCCCGTCTA
+TTTGTCCCGGTCCCTGTTAACCCAGTCCCCGACAGGAGCCCCTTCTGCAC
+CTTGAGCTCTCACCACTCACCGTCCATCCAGCCCCAGCTCTGCCTGCAAC
+CCACCCATCCCTGGGACTCGGGCCTCCCCTCTCTAGTGGTCTGGTCATCA
+GGCCAGGGGCACGTGGAAGAAGCTATCGTGGCAAAGGGAGCAGTCATATC
+CCCAAAATCTGTGGTTGGTTTACCACCACCATGGAAACCCCAGGGTGGGA
+CTCTAGTTTCAGGTTGGAGCTGAGCCCTGTCGGGAATGAGCTTTCCCCAG
+CTATGGCTTCTTGGGGCCCCTGTGCCCTGAGCTGTGTCTCCCAGCATCGG
+GTCCCCACCATGCATATGGCCCACTCAGGCACAGTGCCGCGATGGCTGCA
+TGCGTGAGGGGGGCCTGGGCCCAGGGCTGGGAGTCCTTTGTGTCTCATGG
+CCATGATTGTCCTTCCGAGTATGATATGGTGGCCAATTTCTTTTATTCTG
+TCGTTCAGAGTGAGTAAATGATGTAGAGTTCATGCAGAAAAAAATACAAC
+AAAAACCAAGGGAACATAGAATTGGAAAACGCGTCACAGCAATGAGTTAA
+ATAGGTAACAAATTTCATCATTTGAAGAAAGACTTAGAGTGCCAAAAGTG
+CCTCTTAAGTCTCCTTTAAAAAGTAGCAAAATTCATCCCTGAAGAAGCAT
+CTTGGCCTTTTTCATGTACTCAGAGTGCTGGTGAAGAACAAAGATTGCTG
+AAACATTATGTACCTAACAGCGTTACAGGGTGTAGATAACACACTGGAAA
+ACCTGGTCGTTACAGTGGACATATTCCAGGAAGTCCTTGCCTGAGGTTTT
+CCAAGTTATGGAATTGCTTGAGATTGGAAGAGGCGATGGAGGGTACAACt
+gtaatgcccaacctcatttttgctaaccctgtttttagactctccctttc
+cttcaatcacctagccttctttccacctgaaaggactctcccttaactga
+gagaaccggacagactccatcttggctctttcactggcagccccttcctc
+aaagacttaactcgtgcaagctgactcccaggacatccgagaatgcaatt
+aactgacaacctactgtggcgagctacatccgcagtccccaggaattcgt
+ccgattgataacgcccaattacccgcgtctatcaccttgtaatagtctta
+aagcacctgcacctggaactgtttactttcctgtaaccatttatcctttt
+aacattttgcctgatttacttatgtaaaattcttttaactagaccgccac
+tcccctttctaaacaaaagtataaaagaaaatctagccccttctttggga
+ctgagacaattttgaggttaacGCAGGGTGCCTGTAATCCtaagggagga
+gaccgccacttctgctgcccttcccttccccacacccccttctctagttt
+atgaaacagggaaaaagggagaaagcaaaaagataaaaaaaacagaagta
+agataaatagctagacgaccttggcagcaccacccggcactggtggttaa
+aataataataataataatattaacccctgacctaaactacttgtgttatc
+tgtaaattccagacactgtatgaggaagccctgcaaaactttctgttctg
+ttatctgatgcgtgtagcccccagtcacgttccgatgcttgctcgatcta
+tcacgaccctttcaagtgaaccccttagagtcgtaaacccttaaaagggc
+caggaatttcgttttcggggagctcggctcttcaggcccaagtaaacctg
+ccgTATCTCACCTGAGACCAACCCCCAACTACAAAACTCAACCTGGAATT
+TTCCCAGGACCAAACCCATCTATATTCTGTAACCCGAAACCTCAAAGcct
+aaccctaaccctaacccCTACAGTTGAGGTCCCCCCGCCCCTGTGGTTCC
+AGCTCAAGACAACCTGCCCCTCCGTGGGTTTGCAGGCCCTCTGGTGGGGG
+TGGGAGCTGGGGGCCACATACAGCTCTCTGAGCTTAAGCCATTTTcttcc
+ttcattccttccttcctccctcccttcccttccttcctccctccctccct
+ccttccctccctcccttttttttttcagggtcttgctctgtcacccaggc
+tggagtgcagtggcatgatcacagctgactgcagcctcggactcccaggc
+tcaagttatcttccctcctcagcctccagagtaggtgggactacaggagt
+gtgccatcgcacccagcgaatttcttaatttttattttgtagagatgagg
+cctctcgatattgtccaggctTGGAAGTAGTTCTTGAAATTCAAGAGGAT
+CTTGAAGTTCTGACCTCCTGTCAATATCCCTTCCCCTCACCTTGACCCTC
+CCATTCTGCCCCACCTGTCAGGATCACAAGGACCCCCAGATCAGCAGATG
+GGAACCGGACCAAAAAGAGAAATAGTGCTGTCCCGCCCATAAGTACCACC
+CCCAGACTCCCTGCTCCACCCTCTGGACCACAGGGAGGCCCCATGCTCCA
+TCCCTGAAAACCACCCCCAGACCCCCTGCTCCTCCCCACGGGACCGCCCC
+CAGATCCACTGTTCCTGTCCTCCGGACCACACCGGACAGCTCCTTCCCTC
+GGCGCCATCCCCAGAccccagctcctcccctcaggatcatccccagaccc
+ccgctcctcccatcaggaccgcccccagaaccccctgctcctccccacag
+gaccacccccagacccccgctcctcccctaaggaccacccacagaccccc
+acgcttcccctcgggaccacccccagacccccgctcctcccctcaggacc
+acccccaGATCCACTGTTCCTGTCCTCCGGACCACACCAGACAGCTCCTT
+CCCTCGGCGCCATCCCCAGACCCCCACGCTTCCCCTCGGGACCACCCCCA
+GACCCCCGCTCCTGCCCTCGGGACCACGCCCAGACCCCCTGCTCCTCCCC
+ACGAAACCACGCCCAGTAACCCCCCTCTTCTCCCCTCAGGACCACCCCCA
+GACCCCCGCTCCTCCCCTGGGAACCACCCCCAGACCCCCTGCTCCTCCCC
+ACGAAACCACCCCCAGACTCCCTGCTCCTGTCCTCCGGACCACGCGACTG
+CTCCTTCCCTCAGCGCCACCCCCAGACTGCCGCTCCTCCTGTCGGGACCC
+CCTGAGGCTTTCTCCACCCGGAGTGCGGGGTAGGGAGCAgacggagagtg
+acggagggtgacggagagtgacgAAAGTAGACGATGTCTGACGGAGAAGA
+GCCGAGCGGAGCTGAAGGGCGGCGGAGAGTGACGGAAAGTGGCGAGAATT
+GACGGAAAGTGACGGGGACTGACGGACAGTGACGAAGAGTCACGAAATTT
+ATCAGAGGGCGACAAAGAGGAAAGCGAAATGGTGAGATGCAGCCGGCCGA
+GCCTAATCGGAGATGACGGAAAGTGACGGAGAGGAACGAGGAGTAAAGAG
+GGGTGACGAAAAGAGCCGAAGCTGGTGGAGGCGAAGAACTGAGTGAGGGA
+AGATAGCCGAGATTAGCGGGTGGGCTGCAGCCGGGGCAGTCGCCCGAATG
+GGCGGGACCCCACGGAGTTAGCGAGAGGATGCGAACAGCGGCCAGCCGGG
+CAGCACGCGAGCGAGGGAGGGCGTGGAGGGCCGTGGGTCCGCCTGCACTG
+AGGCAGGCATGCGTGGCACCGAGGTGACCCGGGTGGGAGGTGCACCGCCG
+CCCCCTGGCAGTCTCTCCGCGGAGCCCAAGCCCGTCTTCTCCGCCCCTTT
+GCAGACCTCGGCGCCCAGCCTGGCCCCTGACGCCCACCCGCGGCCCCACC
+CAGCGCCCGGGCCCACGAGGCCGAGGAGCGGCGGAGACTAACGGCCCCTG
+GACCCCAGGCAGCACATGGCCCAGAGCATCCCAGCCCAGTGGAGGGCGGC
+ACATGGCGGGAGGGCGGGAGTCCGTGTCCACTCATGGCCGGGGAGGGGAG
+GGCAAGTTCTGGTGGCTGGGGAGGCCTAGAGCATCACAGCCCAGTGGAGG
+GCTGCACATGGCAGGGGAGGGGAGAGCAAGAGTGTGCGGGCGAGGGAGGA
+GAGGGCAAGACTgcgtgtccgctccagtctctcttcctcatcttataaag
+ccacgagtcccatgactggggacccaacctaataacattatctaatccta
+attgcctcccaaaggccatatctccaatcaggacatgaattcggggatta
+aattgccaacacatggctgggcgcgatggcttgtgctttttttttttttt
+tttttgagacggagtctcgctctgtcgcccaggctggagtgcagtggcgc
+tatctcggctcactgcaagctctgcctcccgggttcacgccattctcctg
+cctcagcctcctgagtagctgggactacaggcgcccgccaccacgcccag
+gtaatttttttttttttttttttgtatttctttgtagagacggggtttca
+ccatgttagccaggatggtctcgatctcctgacctcgtgatccacccatc
+tcggtctcccaaagtgctaggattgcaggcctgagccaccgcacccagct
+gccttgtgcttttaatcccagcactttcagaggccaaggcaggcgatcac
+ctgaggtcaggagttcaagaccagcctggccaacatggtgaaaccccatc
+tctaatacaaatacaaaaaaaaAacaaaaaacgttagccaggaatgaggc
+ccggtgcttgtaatcctaaggaaggagaccaccactcctcctgctgccct
+tcccttccccacaccgcttccttagtttataaaacagggaaaaagggaga
+aagcaaaaagcttaaaaaaaaaaaaaaaaaaacagaagtaagataaatag
+ctagatgatcttggcagcaccacccgaccctggtggttaaaataataata
+ataataatattaacccctgacctaaactacttgtgttatctgtaaattcc
+agacactgtatgaggaagccctgcaaaactttctgttctgttatctgatg
+cgtgtagcccccagtcacgttccccatgcttcctcgatctatcacaaccc
+tttcacgtaaaccccttagagttgtaaacccttaaaagggccaggaattt
+cgttttcggggagcttggctcttcaggcgcaagtgtgccgatgctcctgg
+cagagtaaagcccttccttctttaacccagtgtctgaggaattttgtctg
+cggcttgtcctgccacaatgccagctaccaggaggctgaggtgtgagaat
+cgctcgaacctgggaggcagaggttgcagcgagccgagatcccacgattg
+cactccagcctgggtgatagatgacagagcaagacaccatgtcaaaaaga
+aaagaaaaaaaattgccaacacatgaaatctggagaacacattcaagcaa
+tagcaCCATATAAATCTGTACATACCTTGCAAACACTGTAAACCTGCCGC
+ATCTCACCTGAGACCAACCCCCAACCGCAAAACCCAGACCTGGAATTTTC
+CCAGGACCAAACCCATCTATATTCTGTAACCCGAAATCTCAAAGcctaac
+cctaaccctaacccCGACAGTTCAGGTCCCCCCGTCCCCGTAGCTCCAGC
+TCAAGACAACCTGCCCCTCCGTGGGTTTGCAGGCCCTTTGGTGGGGGTGG
+GAGCTGGGGGCCACACACAGCTCTCTGAGCTTAAGCCATttccttccttc
+cttcattccttccttcctccctccctccctccttccctccctcccttttt
+tttttcagggtcttgctctgtcacccaggctggagtgcagtggcatgatc
+acagctgactgcagcctcggactcccaagctcaagcgatcttcccgcctc
+agcctccagagtaggtgggactacaggagtgtgccatcgcacgtggcgaa
+tttcttaatttttattttgtagagatgaggcctcccgatattgtccaggc
+tTGGAAGTAGTTCTTGAAATTCAAGAGGATCTGGAAGTTCTGGTCTCCTG
+TCAATATCCCTTTCTAAGATGAAATGTAGAATCCTCTAATCACCCCAGGA
+TACCTTTTCCAGCTATATTACCCTTTCCTTTCAGCCGACTAGAGTGGAAG
+CTCAGCAAAGAACGGATCTATGCCTGCACACAGGCAGCTTTGAACTCACT
+GAGATCTATAGAAGAATTTTTTAAAATTTGCCAGAATGAAAAAGAAGTAT
+CCTCCAGTGAGCCTCAAGGACAGCCAGGGAAGGCAGCTACTGGGACCTGC
+CACTGGCCAGGATTGAGAGAGTCTGAGGTGTCCATTCTCCTATGGATGGG
+TCACACATCAGAACTGAACCACAAACCCTTTCCTGCTCCCTTGGGACCAG
+GCTGCCACTCCTTCCTTCCCCTCACCTTGACCCTCCCATTCGGCCCCACC
+TGTCAGGATCACAAGGACCCCCAGATCAGCAGATGGGAACCGGACCAAAA
+AGAGAAATAGCGCTGTCCCGCCCAAAAGTACCAACCCCAGACCCCCTGCT
+CCACCCTCCGAACCACAGGGAGACCCCATGCTCCACCCCTGAAAACCACA
+TGCAGACCCCCGCTCCTCCTCTTAGGGCCATCCCCAGACCCCCCCTCCTA
+CCCACGGGACCACACCCAGAACccccagctcctcccctcgggaccacccc
+agacccccgctcctcccctcgggaccacccccagacccccgctcctcccc
+tcgggaccaccccagacccccgctcctcccctcgggaccaccccagaccc
+cctgctcctcctcttaggaccatccccagaccccccctcctacccacggg
+accacacccagaacccccagctcctcccctcgggaccaccccagaccccc
+gctcctcccctcgggaccaccccagacccccgctcctcccctcgggacca
+ccccagacccccgctcctcccctcgggaccacccccagaccccctgctcc
+tcctcttaggaccatccccagaccccccctcctacccacgggaccacacc
+cagaacccccagctcctcccctcgggaccacccccagaccccctgctcct
+cctcttaggaccaccccagacccccgctcctcccctcgggaccaccccag
+acccccgctcctcccctcgggaccaccccagacccccgctcctcccctcg
+ggaccacccccgaccccctgctcctcctcttaggaccatccccagacccc
+ccctcctacccacgggaccacacccagaacccccagctcctcccctcggg
+accaccccagacccccgctcctcccctcgggaccaccccagacccccgct
+cctcccctcgggaccaccccagacccccgctcctcccctcgggaccaccc
+ccagaccccctgctcctcctcttaggaccatccccagaccccccctccta
+cccacgggaccacacccagaacccccagctcctccccTCGGGACCACCCC
+AGAcccccgctcctcccctcgggaccaccccagacccccgctcctcccct
+cgggaccaccccagacccccgctcctcccctcgggaccacccccagaacc
+cccgctcctcccctcgggaccaccccagacccccgctcctcccctcggga
+ccaccccagacccccgctcctcccctcgggaccacccccAGACCCCCTGC
+TCCTCCTCTTAGGACCATCCCCAGAccccccctcctacccacgggaccac
+ccccagaccccccgctcctcccctcgggaccacctcagacccccgctcct
+cccctcgggaccaccccagacccccgctcctcccctcgggaccaccccag
+accccctgctcccATTTTCCAGACCACACCAGACGGCTTCTTCCCTCGGC
+ACCACCCCCAGACTGCCGCTCCTCCTATCGGGACCTCCTCGGGGCCATCT
+CCAGACCCTCCCCCCGCTCCACCCCTCGGGTCCCTCTCGGGACCACCCTC
+AGACCCCCGCTCCTTCCCTCGGGATCACCTCGAGACCTCCCGCTCACCAC
+CATCATTCAGGCCGGGTAGTGGGGAGAGGCCTCTCAGGAGGGACCAGGCC
+ACCCTCCCAGGAGTGAAGGGAGGAGGACAGAGTCACGAGCAGACCAGAAA
+TAACCAGGGACTGACAGACAGCAGGATCGGAGAGGGACGGAAAAGGGCTA
+AGGGCAGGAAAAGTCCCTGAGGCTTTCTCCACCCGGAGTGCGGGGTAGGG
+AGCAGACGGAGAGTGACGAAGGGTGACGGAGAGTGACGAAAGTAGACGAT
+GTCTGACGGAGAAGAGCCGAGCGGAGCTGAAGGGCGGCGGAGAGCGACGG
+AAAGTGGCGAGAATTGACGGAAAGTGACGGGGACTGACGGACAGTGACGA
+AGAGTCACGAAATTTATCAGAGGGCGACAAAGAGGAAAGCGAAATGGTGA
+GATGCAGCCGGCCGAGCCTATTCGGAGATGACGGAAAGTGACGGAGAGGA
+ACGGGGAGTAAAGAGGGGTGACGAAAAGAGCCGAAGCTGGTGGAGGCGAA
+GAACTGAGTGAGGGAAGATAGCCGAGATTAGCGGGTGGGCTGCAGCCGGG
+GCAGTCGCCCGAATGGGCGGGACCCCACGGAGTTAGCGAGAGGATGCGAA
+CAGCGGCCAGCCGGGCAGCACGCGAGCGAGGGAGGGCGTGGAGGGCCGTG
+GGTCCGCCTGCACTGAGGCAGGCATGGGTGGCACCGAGGTGACCCGGGTG
+GGAGGTGCACCGCCGCCCACTCGCAGGTTCTGCGCGGAGCCCAAGCCCGT
+CTTCTCCGCCCCTTTGCAGACCTCGGCGCCCAGCCTGGCCCCTGACGCCC
+ACCCGCGGCCCCACCCAGCGCCCGGGCCCACGAGGCCGAGGAGCGGCGGA
+GGCTCGCGGCCCCTGGACCGCAGACCGCGTTCCCGGAGCCCGGCCGAGCC
+CCGAGTGGGGCCCTCGCGCGGACTGAGAGGGCGGCGGAGGGGCCACGGGG
+TCCTGCCCAGCCCGCATCGCGCATGCTGCTCGGGACCGGCGGCTGCCTTG
+GGCCAACCCTGTTCCCGCAGCGGCCCAGCCCCGGGCGGGAGCCGACCTGG
+GGGACGCGGGACCCCGCGCGAGCTGCTCGGCCTGTAGGGGGCTgcgcggc
+ggggcggggcggggccggccgcggcgccctcgctcctcgccctccctctc
+tccctccctctctccctAAGACACTTTTTCTTCTTTGTGGCACAATATAC
+AAAACACGGAGTTTGCCATACTGGCCGTTTTCAGGGCGCAGGTCGGTGGG
+ACTGAGCACATCGCGTGGTGCGCTCGGCGCCACCGTCTGTCTGCAGAACG
+TTTGCACCTTTCCAAGCTGaacagctctcctttccgcctcccccagcccg
+tgacaacctcccctctacgtttcgtctctcagtttgacctactaggtacT
+GAGGTCCCCTGGGTACTGAGATCTCCTCGGTACTGAAGTCTCCTCGGTGC
+TGAGGTCGCCTCGGTGCTGAGACCTCCTAGGTATTGAGGTCGCCTCGGTA
+CTGAGGTTGCCTCGGTGCTGAGGTCGCCACGGTGCTGAGACCTCCTAGAT
+ACTGAGGTCTCCTAGGCACGGAGATCTCCTATGTACAGAGACCTCGTCGG
+TACTGAGGTCGCCTAGGTACTGAGACCTTCTAGGTCCTGAGGTCTAGGTA
+CTGAGGCCTTCTCCTGTCGGAGGTGGGAAACTACTCAGTGGTAAAGCAGA
+ACCAAGACCTTCCTCTGAGGGTGGTGGGCTGAGCTGTCTCTTCCTTTCTA
+GGGGCCTTGTATTCACGCCATGAGAGACCCCCCTACTCTTCTGACACGTT
+CCCATTTTGCTGAAGACACTTGGAGCCAGTGTCATCTTTGTGACTGTACC
+GTTGCGTGTTCGGGGTGCACTCTGCCGTATTCTCTTTGCAGAGCACCTAA
+GGAAGCAGgcgtcgtgcctaagaacgtgagtgctgcaaaaagggtggttt
+gttccaatccaaccttgaccgctcctggccctcccacatgggtcaagttc
+actaaacgtctctgtgcctccatttcctcggcagaagaacagggacagta
+aatgtaccCGTCtgtatgagtgttcagggccgccataaggtaccaagact
+ggagggcttcactgaaaattatcttcccacagacctggaggctgaggtcc
+gagagcaaggtgttgtcagcagggctggtttctcctctcctcggcttgcg
+gacgccgtctggtgtacgctcatagggtcttttcactgtgcacaagtatc
+cctatcgtctcttctgtgtgtgtccacacttcctctcatgagaacagcag
+gttgctttagggcccaccctgacagcctcgttctaatactatgaggccaa
+atacactcacgttctgaggcagtgggggttagggcttcaacatCGACAtc
+cgagactgggagatgataaattcctgttgacgaacccacccggtttctgg
+tcactggttatggcagcccccaggaaaccaGCCCACAGAAACAGCAGTCC
+CTCCACTTGGTTCTGATCCAGgatgaagctgttgtagaccgccagcgttt
+ggggaatgtgaatgcctgatacgaaggaattctttgcgccatattgttgc
+cttaatgtaactgtgaagttgcgtcaaaataaaCATTAATggccgggcgc
+ggtggctcacgcctgtaatcccagcactttgggaggccaaggcaggtgga
+tcacgaggtcaggagatcaagaccatcctggccaacacagtgaaacccca
+tctctactaaaaatacaaaaaattctccgggcgcggtggcgggcgcctgt
+agtcccagctactcaggaggctgaggcaggagaacagcgtgagcccggga
+ggtggagcttgcagtgagctgagattgcgccactgcactccggcctgggc
+gacagagcgagactccatctcaaaaaataaaaatagaaaataaaCATTAA
+TGaaaattctcagcaaaagtcatatatattctcgccaaggcgacacacca
+gctaattactgtgtcgactcctttgttttgggctcgattttatgaacttg
+gtgcagtaacacctgccgtttacctctggcctatccaaagcccagataag
+cacaggcaacaaaagcacaaatagacaaatggtccaacttcgaggttaaa
+catttctgcacaggaaacaacagtgaaaaggcaagacatggaataagagg
+aaataactgcagattatatgtctggtacgtcggatattcgtccagcacat
+ataaagagctcctgcaactgaacaattgaaaaacaagttaactgattgaa
+aaatgagcaaacgacctgaatagatatttctccagaaaagatatacaagt
+agcaaacaaacatggaaggatcctcaacatcagtaatcattagagaaata
+cacatcaaaaccacagtgatagcacctcacatccatgaaatgctacagtg
+aaacaaaaatagtgttaacaaggatgtgtggaaattggagccctcgtgga
+ttgcctgtaggactagaaaatggtgtggccaccgtggaaaacactatgga
+gcctcctcaaaaaAGCACTAAATATCAggctgggcacagtggctcacacc
+tgtcatcccagcactttgggagcccgaggcaggtggatcacaaagtcagg
+agttcgagaccagcctggccaacatggtgaaactccgtctctactaaaaa
+taaaaaattagccgggcgtggttgtgggtgccaggaatcccagctacccg
+ggaggctgaggcaggagaattgcttgaaccccggaggcagaggttgcatt
+gagccgagatcgcgccactgcactccagcctgggtgacaaaggaagactc
+catctcGGGGGGGCGGGGTGGGGGGAAGCaaacacaaaataattagctaa
+gtgtggtgacagatgcctatagtcccagctactcgggaggctaaggcagg
+agaagcgcctgaaccaggaggtggaggctgcagtgagccgattatgccac
+cgcactccaccctgggcggcacagtgaaactccatctccgcaaaaacaaa
+accagaaaaataacaaCTAAAAATCACTTgggtgtggtgatgtgcagctg
+cactaccggctacttgggaggctgagggaaggggatcactgaagcccagg
+agttcaaggccagcctgggcaacatataaaactctgtctcttaaaaaata
+aataaataaccagaaaTGGaaccacctatgaaccagcaatcacattactt
+ctccgactaaatccaaaaagattgaaagcagagtctggaagggattattg
+cacaaccgtggtcgttacagcagtattcacaatagccaaaagatggaagc
+agcccggtgcccatGATCGCATTATGTTatgacaccaccacttctcctgt
+tgtccttcccactttctccccaacctccccttttccctagtttataagac
+aagagaaaagagagaaagcaaaaagttggaaagaaacaaaagtaagataa
+atagctagacgaccttggtgccaccacctggccctggtgattaaaataat
+aatagtattaaccgctgaccaaaactactggtgctatctgtaaattccag
+acattgtatgagaaagcactgtaaaactttttgttctggccgggcgcggt
+ggctcacgcctgtaatcccaggactttgggaggccgaggtgggaggatca
+tgaggtcaggagattgagaccatcctggctaacacggtgaaaccccatct
+ctactaaaaatacaaaaaattagctgggtgCAggccgggcacggtggctc
+cagcctctaatcccagcactttgggaggccgaggcgggtggatcacaagg
+tcaggagatcgagaccatcctggttaacatgatgaaaccccgtgtctact
+aaaaatacaaaaaattagccgggcgcggtggcgggcgcctgtagtcccag
+ctactggggaggctgaggcaggagaatggtgtgaacccgggaggcggagc
+ttgcagtgagctgagatcacgccactgcactccagcctgggccacagagc
+gagattccgtctcaaaaaaaataaaaaaataaaaactttttgttctctta
+gctgatgtatgtagcccccactcacgttcctcacacttacttgatctatt
+atgactctttcacatagaccccttagagttcttagcccttaaaagggcta
+ggaatttctttttcggggagctcggctcttaagacacgagtctgccgaat
+ctcccggccaaataaaaaaacctcttccttctttaatctggtgtctgagg
+agttttgactgtgactcatcctgttacaGCatgactggaaaaagaaaatg
+tggttcatccatataatgaaatatgaatcagccctaaaaaggaaggaatg
+atgagacaggctaccacatggactcacctgttgttaacaagataagccag
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
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+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+TTTGTTAAGTGGTCAGAAATTCTCAATTTTTTGAATAGTTTCCATTTCAA
+ATATCTTGTTCTACTTGGTCCATAAAATAGTGGCTTTCAAACTGTAGAGC
+TCTGGACTTCTCACTTCTAGGGCAGAGGGAACCTGAACAAGTGAGGCTCT
+GGGTTCCCCATTCCTAATTAAACCAATGGAAAGAAGGGGTCTAATAACAA
+ACTACAGCAACACATTTTTCATTTCAGCTTCACTGCTGTATCTCCCAGTG
+TAACCCTAGCATCCAGAAGTGGCACAAAACCCCTCTGCTGGCTCATGTGT
+GCAACTGAGACTGTCAGAGCATGGCTAGCTCAGGGGTCCAGCTCTGCAGG
+GTGGGGGCTAGAGAGGAAGCAGGGAGTATCTGCACACAGGATGCCCGCGC
+TCAGGTGGTTGCAGAAGTCAGTGCCCAGGCCCCCCCACACAGTCTCCAAA
+GGTCCGGCCTCCCCAGCGCGGGGCTCCTCGTTTGAGGGGAGGTGACTTCC
+CTCCCAGCAGGCTCTTGGACACAGTAAGCTTCCCCAGCCCTGCCTGAGCA
+GCCTTTCCTCCTTGCCCTGTTCCCCACCTCCCGGCTCCAGTCCAGGGAGC
+TCCCAGGGAAGTGGTCGACCCCTCCGGTGGCTGGGCCACTCTGCTAGAGT
+CCATCCGCCAAGCTGGGGGCATCGGCAAGGCCAAGCTGCGCAGCATgaag
+gagcgaaagctggagaagaagaagcagaaggagcaggagcaaggtgaGCG
+GGCCCTGGAGCCTGCGGTCGGAGGGCCTTGGGCAAGATCGCCTCCTCCCC
+TCCAGCCCTGAGTCCACTGGGTGCTTTCTGCCCACCCCCTGCTCTTGCCA
+GCTGGCCCCTGCTTCCCCTAGGGCACATGCTGGAAGCCCTGGGCCGCCAC
+CAGAAGTCCTCAGCCCTCCTGCCTGGGCTATGGCTCCTTCCTGGTTTGGG
+AGCCATAGTGAAGCTTTCCTCTCTAAGCTCACCCAGCCCAAACTGTGACA
+GGAGAATCTTCTTCGACTGCCAAGAGCGGTCCAAGGCAATGGTCAGCCAC
+TGCAGCCCCCTGAGATATTTTTAGAGACTGGACCTGAGGCCTCTGGAGGC
+TACTGATGATGCCTGCTGTGAACGCAGACACTGGTGTGATGCGATGCCTG
+CGCCTGCAGCGGCAGTGCCCTGGGCACTATGGTTTtgagcttgtacccag
+cgctgcttttgccttgctctgtgaccccaggcaagctgcctcacctctct
+gggccagtttccccatcgtacagtggTGCTGCACACCCTGGCCCTGGCCC
+CGAGGTGGCTGGGAGGTGGCTCCTCAAACAGCCGCTTTCTCATCAGTGCC
+CGGTGCTGGGTCAGGGATCGACTGAGGCTCTGAGCTAACTAGGAAACACA
+GTGGCCTTGGAGGGCTGGGGAGTGTCATGGGGGTGGGGACAGGGAGCCAC
+CGGTCGCATGTGACTGAACTCTTCACCCCAGTCTGTGGCTTTCCCGTTGC
+AGTGAGAGCCACGAGCCAAGGTGGGCACTTGATGTCGGATCTCTTCAACA
+AGCTGGTCATGAGGCGCAAGGGTAGGAGGCAGGGCCGCTGCCCGCCCTGG
+GTCGGCACCTTGTAATTCTGTCCTGCCTTTTTCTTCCTGTATTTAAGTCT
+CCGGGGGCTGGGGGAATCAGGGTTTCCCACCAACCACCCTCACTCAGCCT
+TTTCCCTCCAGGCATCTCTGGGAAAGGACCTGGGGCTGGTGAGGGGCCCG
+GAGGAGCCTTTGCCCGCGTGTCAGACTCCATCCCTCCTGTGCCCCCACCG
+CAACAGCCACAGGCAGAGGAGGACGAGGACGACTGGGAATCCTAGGGGGC
+TCCATGACACCTTCCCCCCCAGACCCAGACTTGGGCTGTTGCTCTGACAT
+GGACACAGCCAGGACAAGCTGCTCAGACCTGCTTCCCTGGGAGGGGGTGA
+CGGAACCAGCACTGTGTGGAGACCAGCTTCAAGGAGCGGAAGGCTGGCTT
+GAGGCCACACAGCTGGGGCGGGGACTTCTGTCTGCCTGTGCTCCATGGGG
+GGACGGCTCCACCCAGCCTGCGCCACTGTGTTCTTAAGAGGCTTCCAGAG
+AAAACGGCACACCAATCAATAAAGAACTGAGCAGAAACCAACAGTGTGCT
+TTTAATAAAGGACCTCTAGCTGTGCAGGATGCAAACGTCTCGGGGTCAGT
+GACTGCCTCCTGCCCCTGTTGGTCCCTAGGCAGTGGGGGCAGAAGCTCCC
+AGCTGACCTGTTTCTCTGGGAGAGAAGGGCAGTCAGCAGGGGCAGCTGTT
+GCAGATGGGAGGAATAGTCTCCCACAAAAAAGGTTTCAGTGACAGACACG
+GGGTCTCTAAAAATAGTCATGCTGAGAGCCCAATGGCCCTTGGCACAATT
+GCTGGTGTTGGGGTAGAAGATGTCTTGGAGTTTGCTCAAGTGGTTGAGAG
+GGAGGGAGGTGCCATCAACTTGGAGGAACTGGCACCAAGCCAGGGAGATA
+GAAATCCAGGCAAGGCTGTGGGGCAGGTTAGGGAGCAAGGCTGCAGGGGT
+GACTCAGGAAGAAGGTGGGGGAGGTGACAAGCCCCCAGGCAGGGGCCCTG
+TGGCCATGGGGATCTTTTTAAATTGAGACTAGGGGGTGAATAGTCCAGGG
+CAGCTAACTTTAGTTATTATAGAAAGGGCAGTAGCAGATGGGTCTGCTCC
+GTCTCGCTTCTAAGAAGGTGGGCAGGACAAATGGCAGCCTCCTGCAGAGG
+CCCAGTGAGAAGCCTGGCCCTCGGCCACACAGGATGGAAGACAGATTGGA
+TTCCACAGAGGGGAGCTGCCCTGGGAAGATCTCACGGATGGCCAGGACCC
+ACCATTTCTTCGGGGTTCCCCTGTTTTCTCCAACGGGCACTAATGCCTGT
+GCCTGGGTCCTGGCAACACTCTGGACTCCACACTCTTCTGGGTTTCACCT
+TTGTAGCAGGATCCCTGCAGATCAGGCCCATGACAAACACCGTCTCCAGC
+GGGCAGAGCAAAGGAAGGGCGCAGCGCCAGGCAGTGGTGCAGCTGCCTGT
+CAGGAAGAGGCCTACTTCTGGTGAAACTGGGCAGACAAAAGGCAGTGAGA
+AATGTGATCTCGGGGTGGTGGAGGCTCTAGGGAAAGGAAAAGGCAGGAGT
+GAACTTCCACACAGCAGCAATGGCAGAACCAAAGGTGGCTTTGACCTCCA
+CGAGGGCTCAGATCCAGGCCAACAGCTTGTCCAGGACAGGGTGCCGGGTG
+TATCACTAATCCAGGAGCACTATGCTGGCAGAATCCCTTTGGTGCCTGAT
+GGCCCTGCCTTCGTGGGAACAGAGGCTAAGGCTTTGAGTTACAGCTGCCT
+CCCCAACAGTGCATCCCCTTCTCCTTCCTCAGCCTCAGGTAGGAGACAGG
+GCAGGCAACCCCCCTTTCCTCTTCTCCCCTTCTCCAGCCCCTGTCTGTCC
+ACCCAGCTGGAGGCAGCCAGGCTTGCCTATGGACTGGTTGACAGCCTTCA
+TGCACAGGTTCTCCACCAGAGCCTTTCTTGGGGGCCCCTGGCTGGGCTCT
+GAGCTGGGAGTGAAGGGGATGACCCATGCGGACTGTTTGCTGCTTGTAGC
+TTTCCCTGGGAAAGACTCTGCCAGGCCTTGGAGCCAGACCAGGAGGCTTT
+ATAGGCCACTGCAAGCAGCAGGGCTCCAGATGACATCACAGGGAATATCA
+AGAGGGTGTGGAGGGGCATCGAAGCCTCTCCAGGAGACAGGAGACGCCGG
+CCCAGTAGAGCCCTAGGGGCGACGCCACTCCCACTCACTGTCTACTCTCC
+TCTCACCTCTGCAACACTGGGGACACTCACAAGATTGTGATCCAAGTCGG
+CCGTCGTCTTCTGCAGCTCTGGAGACCTGATGCTGGGGAAGGGCATGCCT
+GGCATCACCACACACCTGGGAGGAGACAGGAGCCTGGGGCCGGTGGGCCC
+ACACATCACCAGCTGCTCCGTTCTACCATTTCTTCAGCCCTCTTGGCTGT
+GCCTGCGGCTCTGCCCCTCCCCTCTCTGCACCTACCACCCAGAGAGGGCT
+TGTTGAGCTCAGAGATCCCACCTAGGCCAATCCACTGGGTTCTGTGGCAG
+CGATGGCCTGCCTGATCTTCCACCTGCTCTCCCAGGGCCAAAGCCAGACC
+TGCTGAGCCCCTCCCTCCAGCCGGCTGGTCTGAGCAGTCACAGCCCGGCT
+TTGGGCTCCGATGGCAGCAGATGGCAGGTAGGGGTCCAGCTGCTGGAGCG
+AGGGCCGGCCACGTATCACAGCCAAGGAGATGAGCACAAGCACTACTTAC
+TGGCCTAGGTTGTCAGAGAAGTTGATGCTCTCACTCATCTTTCCTCCAAT
+CTTTCCCCTATGCCTGGTTGTGGTATTAAGTTACATGCAGACAACAGGGG
+CCAGAAGATGAACAATGGCCCATCCCACTCTAGGCATGGCTCCTCTCCAC
+AGGAAAACTCCACTCCAGTGCTCAGCTTGCACCCTGGCACAGGCCAGCAG
+TTGCTGGAAGTCAGACACCTGCAGATCAAGACCACAGCATCAAGACCCTG
+TGACCTCTCAAAGGCCTGGTGGAAAGGACACGGGAAGTCTGGGCTAAGAG
+ACAGCAAATACACATGAACAGAAAGAAGAGGTCAAAGAAAAGGCTGACGG
+CAAGTTAACAAAAAGAAAAATGGTGAATGATACCCGGTGCTGGCAATCTC
+GTTTAAACTACATGCAGGAACAGCAAAGGAAATCCGGCAAATTTGCGcag
+tcattctcaacaccggccatgcagcaaaatcatcagtggaaatttaaaaa
+aatacacgtggccaggccccagcccaaatcactaataagaatctccaggg
+CTtcacctgttagactggcaaaaaatccaaaagtaaacactttgtggaga
+aacaggcactcctagacattgctggtgggatacagaacagtacaattctg
+atggtaatcagttaacaaattaaacatatttattttatacttttaaaccc
+aggaatcccatatttaggagtctactgagaccaaacagcatatgCTCCTG
+GTGTTTCCCTATAATCCgccactactgttggagcaagagggcccagcagt
+gtccccagctgccagcaggcgggcgtgctgccagtacaccttgagcaaga
+ggaccctgcaatgtccgtagctgccagcaggcggcgtgccaccactatac
+agtaagcaagaggaccctgcagtgccccggcgccacgagggggcggtggc
+caccactctaagcaagagagccctgcagttgccctagtcgccagcagggg
+gcgccctggcacagcaccgtgagcaagcgggtcctgtagtgcccggctgc
+aagcaaggggcggtcgatcccggcttttcggattactgaagttccacccg
+tctctgcgccgcgccgccgtgacgtgagtttctgcgcgtgcacggcgccc
+ccgcacccccccgcccccagcccggcgccgtgcgactttgctcctgcaac
+acacgcacccccaacccccgcccgtaggcgtgcgtctctgcgcctgcgcc
+acgcctccacccctggacgcgctagcatgtgtctctgcgcctgcgccggc
+gcggcgcgcctctctgcgcctgcgccggcgcggcgcgcctctctgcgcct
+gcgccggcgcggcgcgcctctctgcgcctgcgccggcgcggcgcgcctct
+ctgcgcctgcgccggcgcggcgcgcctctctgcgcctgcgccggcgcggc
+gcgcctctctgcgcctgcgccggcgcggcgcgcctctctgcgcctgcgcc
+ggcgcggcgcgcctctctgcgcctgcgccggcgcggcgcgcctttgcgac
+ggccgagttgcgttctcgtcagcacagagcggcagagcaccgcgagggcg
+gagctgcgttgtcctctgcacagatttcggtggtactgcgaaggcggagc
+agagttctcctcaggtcagacccgggcgggcgggctgagggtaccgcgag
+ggcggagctgcgttctgctcagtacagacctgggggtcaccgtaaaggtg
+gagcagcattcccctaagcacagacgttggggccactgactggctttggg
+acaactcggggcgcatcaacggtgaataaaaatgtttcccggttgcagcc
+atgaataatcaaggtgagagaccagttagagcggttcagtgcggaaaacg
+ggaaagcaaaagcccctctgaatgctgcgcaccgagattctcccaaggca
+aggggaggggctgcattgcagggtccacttgcagcgtcggaacgcaaatg
+cagcattcctaatgcacacatgatacccaaaatataacacccacattcct
+catgtgcttagggtgagggtgagggttggggttggggttgcggttggggt
+tggggttggggttggggttggggttagggtttgggtttagggttggggta
+ggggtaggggtggggttggggttggggttggggttggggttaggggttgg
+ggttggggttggggttggggttggggttagggttaagggttagggttagg
+ggttaggggttagggttggggttggggttagggttagggtagggttaggg
+ttagggttaggggttaggggttagggtagggttagggtgagggtgagggt
+gagggtgagggtgagggtgagggttagggttagggttagggttagggtta
+ggggttaggggttagggttagggttaggggttaggggttagggttagggt
+taggggttagggttagggttaggggttaggggttaggggttaggggttag
+ggtagggtagggtagggtagggagggttagggttagggttagggttaggg
+ttagggttagggttagggttagggttagggttagggttagggttagggtt
+agggttagggttagggttagggttagggttagggttagggttagggttag
+ggttagggttagggttagggttagggttagggttagggttagggttaggg
+ttagggttagggttagggttagggttagggttagggttagggttagggtt
+agggttagggttagggttagggttagggttagggtgagggttagggttag
+ggttagggttagggttagggttagggttagggttagggttagggttaggg
+ttagggttagggttagggttagggttagggttagggttagggttagggtt
+agggttaggggttaggggttaggggttaggggttaggggttaggggttag
+ggttagggttagggttagggtgtggtgtgtgggtgtgtgtgggtgtggtg
+tgtgtgggtgtggtgtgtgggtgtgggtgtgggtgtgggtgtgtgggtgt
+ggtgtgtgggtgtggTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNN
diff --git a/test/formats/dac-my.bed b/test/formats/dac-my.bed
new file mode 100644
index 0000000..78daff6
--- /dev/null
+++ b/test/formats/dac-my.bed
@@ -0,0 +1,3 @@
+chrM 1 3 chrM 1000 .
+chrY 70 113 ALR/Alpha 1000 .
+chrY 207 310 Low_mappability_island 1000 .
diff --git a/test/formats/example.gff b/test/formats/example.gff
new file mode 100644
index 0000000..25641ad
--- /dev/null
+++ b/test/formats/example.gff
@@ -0,0 +1,8 @@
+##gff-version 3
+# Source: http://gmod.org/wiki/GFF3
+ctg123 . mRNA 1300 9000 . + . ID=mrna0001;Name=sonichedgehog
+ctg123 . exon 1300 1500 . + . ID=exon00001;Parent=mrna0001
+ctg123 . exon 1050 1500 . + . ID=exon00002;Parent=mrna0001
+ctg123 . exon 3000 3902 . + . ID=exon00003;Parent=mrna0001
+ctg123 . exon 5000 5500 . + . ID=exon00004;Parent=mrna0001
+ctg123 . exon 7000 9000 . + . ID=exon00005;Parent=mrna0001
diff --git a/test/formats/my-refflat.bed b/test/formats/my-refflat.bed
new file mode 100644
index 0000000..8c3a1fd
--- /dev/null
+++ b/test/formats/my-refflat.bed
@@ -0,0 +1,276 @@
+chrY 142989 170022 PLCXD1
+chrY 148059 170022 PLCXD1
+chrY 171415 180887 GTPBP6
+chrY 231383 232054 LINC00685
+chrY 244666 297690 PPP2R3B
+chrY 535077 557558 SHOX
+chrY 535077 570146 SHOX
+chrY 1264892 1281616 CRLF2
+chrY 1337691 1374711 CSF2RA
+chrY 1337691 1378828 CSF2RA
+chrY 1351569 1378828 CSF2RA
+chrY 1362809 1362885 MIR3690
+chrY 1405507 1451582 IL3RA
+chrY 1455043 1461039 SLC25A6
+chrY 1465916 1468291 LINC00106
+chrY 1469422 1482479 ASMTL-AS1
+chrY 1469422 1484314 ASMTL-AS1
+chrY 1472030 1521870 ASMTL
+chrY 1472030 1522655 ASMTL
+chrY 1531464 1606037 P2RY8
+chrY 1660484 1671407 AKAP17A
+chrY 1660484 1671411 AKAP17A
+chrY 1664346 1711974 ASMT
+chrY 1683939 1711974 ASMT
+chrY 1684024 1711974 ASMT
+chrY 2087553 2369015 DHRSX
+chrY 2354453 2368580 ZBED1
+chrY 2354453 2369008 ZBED1
+chrY 2477230 2477295 MIR6089
+chrY 2477304 2506370 CD99P1
+chrY 2477304 2525270 CD99P1
+chrY 2559172 2604479 CD99
+chrY 2559172 2609350 CD99
+chrY 2620335 2643037 XGY2
+chrY 2654894 2655782 SRY
+chrY 2709621 2734997 RPS4Y1
+chrY 2803110 2850547 ZFY
+chrY 2803516 2850547 ZFY
+chrY 2871035 2970313 LINC00278
+chrY 3447124 3448082 TGIF2LY
+chrY 4868265 4973639 PCDH11Y
+chrY 4924129 4973639 PCDH11Y
+chrY 4924129 5610269 PCDH11Y
+chrY 6110485 6111651 TTTY23
+chrY 6110485 6111651 TTTY23B
+chrY 6114262 6117053 TSPY2
+chrY 6225258 6229454 LINC00280
+chrY 6258440 6279605 TTTY1
+chrY 6258440 6279605 TTTY1B
+chrY 6274283 6296485 TTTY2
+chrY 6274283 6296485 TTTY2B
+chrY 6311473 6315118 TTTY21
+chrY 6311473 6315118 TTTY21B
+chrY 6317507 6325947 TTTY7
+chrY 6317507 6325947 TTTY7B
+chrY 6339070 6341671 TTTY8
+chrY 6339070 6341671 TTTY8B
+chrY 6733957 6742068 AMELY
+chrY 6778725 6959724 TBL1Y
+chrY 7142011 7249588 PRKY
+chrY 7567396 7569288 TTTY16
+chrY 7672963 7678723 TTTY12
+chrY 8506333 8513170 LINC00279
+chrY 8551409 8551919 TTTY18
+chrY 8572511 8573324 TTTY19
+chrY 8651357 8685423 TTTY11
+chrY 9154668 9160483 RBMY1A3P
+chrY 9167487 9172441 TTTY20
+chrY 9175071 9177887 TSPY10
+chrY 9175071 9177887 TSPY1
+chrY 9187187 9192791 FAM197Y2P
+chrY 9187187 9192791 FAM197Y5P
+chrY 9195450 9198202 TSPY8
+chrY 9195450 9218480 TSPY4
+chrY 9207464 9213071 FAM197Y2P
+chrY 9207464 9213071 FAM197Y5P
+chrY 9215729 9238826 TSPY4
+chrY 9236028 9238826 TSPY10
+chrY 9236028 9238826 TSPY3
+chrY 9236028 9238826 TSPY10
+chrY 9236074 9368285 TSPY4
+chrY 9296350 9301954 FAM197Y2P
+chrY 9296350 9301954 FAM197Y5P
+chrY 9304562 9307358 TSPY1
+chrY 9316660 9322263 FAM197Y5P
+chrY 9316660 9322263 FAM197Y2P
+chrY 9324874 9327690 TSPY10
+chrY 9357273 9362877 FAM197Y5P
+chrY 9357273 9362877 FAM197Y2P
+chrY 9365487 9368285 TSPY10
+chrY 9365487 9368285 TSPY3
+chrY 9365487 9368285 TSPY10
+chrY 9448328 9452762 RBMY3AP
+chrY 9528707 9531308 TTTY8
+chrY 9528707 9531308 TTTY8B
+chrY 9544431 9552871 TTTY7
+chrY 9544431 9552871 TTTY7B
+chrY 9555260 9558905 TTTY21
+chrY 9555260 9558905 TTTY21B
+chrY 9573893 9596085 TTTY2
+chrY 9573893 9596085 TTTY2B
+chrY 9590763 9611928 TTTY1
+chrY 9590763 9611928 TTTY1B
+chrY 9638760 9650854 TTTY22
+chrY 9748405 9749571 TTTY23
+chrY 9748405 9749571 TTTY23B
+chrY 14517913 14533389 GYG2P1
+chrY 14774296 14804153 TTTY15
+chrY 14813158 14972768 USP9Y
+chrY 15015908 15032390 DDX3Y
+chrY 15016695 15032390 DDX3Y
+chrY 15016767 15032390 DDX3Y
+chrY 15017614 15032390 DDX3Y
+chrY 15360257 15592550 UTY
+chrY 15409387 15592550 UTY
+chrY 15434912 15592550 UTY
+chrY 15815445 15817902 TMSB4Y
+chrY 16097650 16098388 VCY1B
+chrY 16097650 16098392 VCY
+chrY 16168096 16168838 VCY
+chrY 16168100 16168838 VCY1B
+chrY 16634486 16955848 NLGN4Y
+chrY 16635383 16955848 NLGN4Y
+chrY 16635624 16955848 NLGN4Y
+chrY 16636452 16955848 NLGN4Y
+chrY 16733899 16845429 NLGN4Y
+chrY 16905520 16915913 NLGN4Y-AS1
+chrY 19612836 19628622 FAM41AY2
+chrY 19612836 19628622 FAM41AY1
+chrY 19687039 19691332 FAM224B
+chrY 19687062 19691353 FAM224A
+chrY 19880858 19882440 XKRY2
+chrY 19880858 19882440 XKRY
+chrY 19990138 19992099 CDY2B
+chrY 19990139 19992100 CDY2A
+chrY 20137665 20139626 CDY2A
+chrY 20137666 20139627 CDY2B
+chrY 20297333 20298915 XKRY2
+chrY 20297333 20298915 XKRY
+chrY 20488417 20492712 FAM224A
+chrY 20488438 20492736 FAM224B
+chrY 20551154 20566932 FAM41AY2
+chrY 20551154 20566932 FAM41AY1
+chrY 20708555 20710477 HSFY2
+chrY 20708555 20750849 HSFY2
+chrY 20708572 20710478 HSFY1
+chrY 20708575 20750849 HSFY2
+chrY 20708575 20750849 HSFY1
+chrY 20743090 20752407 TTTY9A
+chrY 20743090 20752407 TTTY9B
+chrY 20891766 20901083 TTTY9A
+chrY 20891766 20901083 TTTY9B
+chrY 20893324 20935601 HSFY2
+chrY 20893324 20935601 HSFY1
+chrY 20893324 20935621 HSFY2
+chrY 20933698 20935604 HSFY1
+chrY 20933699 20935621 HSFY2
+chrY 21034385 21237889 TTTY14
+chrY 21034385 21239433 TTTY14
+chrY 21094583 21237889 TTTY14
+chrY 21094583 21239433 TTTY14
+chrY 21152524 21154528 CD24
+chrY 21152524 21154800 CD24
+chrY 21152524 21154962 CD24
+chrY 21152524 21438350 CD24
+chrY 21617315 21665039 BCORP1
+chrY 21729242 21752309 TXLNGY
+chrY 21729242 21769056 TXLNGY
+chrY 21867299 21906825 KDM5D
+chrY 22627552 22681114 TTTY10
+chrY 22737595 22755040 EIF1AY
+chrY 22917952 22942918 RPS4Y2
+chrY 23544858 23548246 PRORY
+chrY 23557032 23563448 RBMY2EP
+chrY 23673222 23687440 RBMY1B
+chrY 23673222 23687672 RBMY1D
+chrY 23673222 23687672 RBMY1A1
+chrY 23673222 23687672 RBMY1D
+chrY 23673222 23687672 RBMY1A1
+chrY 23673262 23687672 RBMY1E
+chrY 23696763 23710980 RBMY1B
+chrY 23696763 23711212 RBMY1D
+chrY 23696763 23711212 RBMY1A1
+chrY 23696763 23711212 RBMY1D
+chrY 23696763 23711212 RBMY1A1
+chrY 23745484 23756552 TTTY13
+chrY 24026221 24040633 RBMY1E
+chrY 24026221 24040673 RBMY1D
+chrY 24026221 24040673 RBMY1A1
+chrY 24026221 24040673 RBMY1D
+chrY 24026221 24040673 RBMY1A1
+chrY 24026453 24040673 RBMY1B
+chrY 24049763 24064174 RBMY1E
+chrY 24049763 24064214 RBMY1D
+chrY 24049763 24064214 RBMY1A1
+chrY 24049763 24064214 RBMY1D
+chrY 24049995 24064214 RBMY1B
+chrY 24217901 24242154 PRY2
+chrY 24217901 24242154 PRY
+chrY 24247837 24293631 LOC101929148
+chrY 24291110 24292978 TTTY6
+chrY 24291132 24292981 TTTY6B
+chrY 24314687 24329089 RBMY1F
+chrY 24314919 24329155 RBMY1J
+chrY 24442943 24445023 TTTY5
+chrY 24455004 24462352 RBMY2FP
+chrY 24455008 24564028 RBMY1F
+chrY 24462823 24466531 LOC100652931
+chrY 24549555 24563796 RBMY1J
+chrY 24585085 24630861 LOC101929148
+chrY 24585735 24587584 TTTY6B
+chrY 24585738 24587606 TTTY6
+chrY 24636542 24660784 PRY2
+chrY 24636542 24660784 PRY
+chrY 24997729 24998862 TTTY17A
+chrY 24997729 24998862 TTTY17C
+chrY 24997729 24998862 TTTY17B
+chrY 25082600 25119431 TTTY4
+chrY 25082600 25119431 TTTY4C
+chrY 25082600 25119431 TTTY4B
+chrY 25130408 25151610 BPY2
+chrY 25130408 25151610 BPY2B
+chrY 25130408 25151610 BPY2C
+chrY 25275500 25345239 DAZ1
+chrY 25275500 25345254 DAZ4
+chrY 25365579 25437503 DAZ3
+chrY 25365579 25437503 DAZ4
+chrY 25365602 25437503 DAZ2
+chrY 26082872 26087769 TTTY3
+chrY 26082872 26087769 TTTY3B
+chrY 26191375 26194161 CDY1
+chrY 26191375 26194161 CDY1B
+chrY 26191938 26194161 CDY1
+chrY 26191938 26194161 CDY1B
+chrY 26329579 26333378 CSPG4P1Y
+chrY 26356112 26360978 GOLGA2P2Y
+chrY 26356112 26360978 GOLGA2P3Y
+chrY 26631477 26632610 TTTY17A
+chrY 26631477 26632610 TTTY17C
+chrY 26631477 26632610 TTTY17B
+chrY 26716347 26753172 TTTY4
+chrY 26716347 26753172 TTTY4C
+chrY 26716347 26753172 TTTY4B
+chrY 26764149 26785352 BPY2
+chrY 26764149 26785352 BPY2B
+chrY 26764149 26785352 BPY2C
+chrY 26909214 26959639 DAZ4
+chrY 26909214 26959639 DAZ3
+chrY 26979965 27053187 DAZ3
+chrY 26979965 27053187 DAZ4
+chrY 26979988 27053187 DAZ2
+chrY 27177048 27198251 BPY2
+chrY 27177048 27198251 BPY2B
+chrY 27177048 27198251 BPY2C
+chrY 27209228 27246039 TTTY4
+chrY 27209228 27246039 TTTY4C
+chrY 27209228 27246039 TTTY4B
+chrY 27329788 27330920 TTTY17A
+chrY 27329788 27330920 TTTY17C
+chrY 27329788 27330920 TTTY17B
+chrY 27601456 27606322 GOLGA2P2Y
+chrY 27601456 27606322 GOLGA2P3Y
+chrY 27629053 27632852 CSPG4P1Y
+chrY 27768262 27770485 CDY1
+chrY 27768262 27770485 CDY1B
+chrY 27768262 27771048 CDY1
+chrY 27768262 27771048 CDY1B
+chrY 27874635 27879535 TTTY3
+chrY 27874635 27879535 TTTY3B
+chrY 59100401 59115125 SPRY3
+chrY 59213947 59276439 VAMP7
+chrY 59330250 59343488 IL9R
+chrY 59347233 59349501 WASIR1
+chrY 59358327 59360854 DDX11L16
+chrM 648 1603 RNR1
+chrM 1671 3230 RNR2
diff --git a/test/formats/my-targets.bed b/test/formats/my-targets.bed
new file mode 100644
index 0000000..6449c7f
--- /dev/null
+++ b/test/formats/my-targets.bed
@@ -0,0 +1,4 @@
+chrM 251 277 LSU-rRNA_Hsa 1000 .
+chrY 11170 11213 ALR/Alpha 1000 .
+chrY 14339 14355 LSU-rRNA_Hsa 1000 .
+chrY 14360 14378 BSR/Beta 1000 .
diff --git a/test/formats/na12878-chrM-Y-trunc.bam b/test/formats/na12878-chrM-Y-trunc.bam
new file mode 100644
index 0000000..320df7b
Binary files /dev/null and b/test/formats/na12878-chrM-Y-trunc.bam differ
diff --git a/test/formats/na12878_na12882_mix.vcf b/test/formats/na12878_na12882_mix.vcf
new file mode 100644
index 0000000..d8c7a54
--- /dev/null
+++ b/test/formats/na12878_na12882_mix.vcf
@@ -0,0 +1,4703 @@
+##fileformat=VCFv4.2
+##fileDate=20150729
+##source=SNV-Unifier
+##reference=file:///home/dnanexus/genome.fa
+##phasing=none
+##PEDIGREE=<Derived=NA12882,Original=NA12878>
+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic event">
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
+##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
+##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
+##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
+##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
+##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
+##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
+##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
+##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
+##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
+##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
+##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without.">
+##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
+##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
+##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
+##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
+##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
+##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
+##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
+##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
+##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
+##INFO=<ID=technology.ILLUMINA,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from ILLUMINA">
+##INFO=<ID=SPLITMULTIALLELIC,Number=0,Type=Flag,Description="Variant represents one alternate allele from a multiallelic variant call.">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=VT,Number=1,Type=String,Description="Variant type, can be SNP, MNP, INS or DEL">
+##INFO=<ID=JOINED,Number=0,Type=Flag,Description="Variant is the result of joining adjacent SNPs/MNPs. Please use caution when interpreting sample-specific values.">
+##INFO=<ID=ALERT,Number=0,Type=Flag,Description="Variant is adjacent to other variants, but case was too complex for joinAdjacentSNPs to handle. Please review.">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=PF,Number=1,Type=Integer,Description="The number of samples carry the variant">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=NTLEN,Number=.,Type=Integer,Description="Number of bases inserted in place of deleted code">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
+##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
+##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
+##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
+##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)">
+##INFO=<ID=ADERROR,Number=0,Type=Flag,Description="The AD field from the original variant caller VCF has an error at this locus. Please use caution when interpreting AD, GMIMAF, and GMICOV.">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+##FORMAT=<ID=BQ,Number=A,Type=Float,Description="Average base quality for reads supporting alleles">
+##FORMAT=<ID=FA,Number=A,Type=Float,Description="Allele fraction of the alternate allele with regard to reference">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal,0=wildtype,1=germline,2=somatic,3=LOH,4=post-transcriptional modification,5=unknown">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Reference depth, how many reads support the reference">
+##FORMAT=<ID=GMIMUT,Number=A,Type=Integer,Description="GMI-derived mutant read count: the number of reads observed at the variant locus that support each ALT allele.">
+##FORMAT=<ID=GMIMAF,Number=A,Type=Integer,Description="GMI-derived MAF: the proportion of reads observed at the variant locus that support each ALT allele.">
+##FORMAT=<ID=GMICOV,Number=1,Type=Integer,Description="GMI-derived coverage: total read depth at the variant locus.">
+##FORMAT=<ID=AD,Number=2,Type=Integer,Description="# of reads supporting consensus reference/indel at the site">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total coverage at the site">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MM,Number=2,Type=Float,Description="Average # of mismatches per ref-/consensus indel-supporting read">
+##FORMAT=<ID=MQS,Number=2,Type=Float,Description="Average mapping qualities of ref-/consensus indel-supporting reads">
+##FORMAT=<ID=NQSBQ,Number=2,Type=Float,Description="Within NQS window: average quality of bases in ref-/consensus indel-supporting reads">
+##FORMAT=<ID=NQSMM,Number=2,Type=Float,Description="Within NQS window: fraction of mismatching bases in ref/consensus indel-supporting reads">
+##FORMAT=<ID=REnd,Number=2,Type=Integer,Description="Median/mad of indel offsets from the ends of the reads">
+##FORMAT=<ID=RStart,Number=2,Type=Integer,Description="Median/mad of indel offsets from the starts of the reads">
+##FORMAT=<ID=SC,Number=4,Type=Integer,Description="Strandness: counts of forward-/reverse-aligned reference and indel-supporting reads (FwdRef,RevRef,FwdIndel,RevIndel)">
+##FORMAT=<ID=CallHC,Number=1,Type=Integer,Description="Variant was called by HaplotypeCaller">
+##FORMAT=<ID=CallUG,Number=1,Type=Integer,Description="Variant was called by UnifiedGenotyper">
+##FORMAT=<ID=CallFB,Number=1,Type=Integer,Description="Variant was called by freeBayes">
+##FORMAT=<ID=CallPI,Number=1,Type=Integer,Description="Variant was called by pindel">
+##FORMAT=<ID=CallSID,Number=1,Type=Integer,Description="Variant was called by SomaticIndelDetector">
+##FORMAT=<ID=CallMU,Number=1,Type=Integer,Description="Variant was called by MuTect">
+##FORMAT=<ID=LR,Number=1,Type=Float,Description="CNV log2 ratio">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=REJECT,Description="Not somatic due to normal call frequency or phred likelihoods: tumor: 35, normal 35.">
+##contig=<ID=chrM,length=16571>
+##contig=<ID=chr1,length=249250621>
+##contig=<ID=chr2,length=243199373>
+##contig=<ID=chr3,length=198022430>
+##contig=<ID=chr4,length=191154276>
+##contig=<ID=chr5,length=180915260>
+##contig=<ID=chr6,length=171115067>
+##contig=<ID=chr7,length=159138663>
+##contig=<ID=chr8,length=146364022>
+##contig=<ID=chr9,length=141213431>
+##contig=<ID=chr10,length=135534747>
+##contig=<ID=chr11,length=135006516>
+##contig=<ID=chr12,length=133851895>
+##contig=<ID=chr13,length=115169878>
+##contig=<ID=chr14,length=107349540>
+##contig=<ID=chr15,length=102531392>
+##contig=<ID=chr16,length=90354753>
+##contig=<ID=chr17,length=81195210>
+##contig=<ID=chr18,length=78077248>
+##contig=<ID=chr19,length=59128983>
+##contig=<ID=chr20,length=63025520>
+##contig=<ID=chr21,length=48129895>
+##contig=<ID=chr22,length=51304566>
+##contig=<ID=chrX,length=155270560>
+##contig=<ID=chrY,length=59373566>
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA12882
+chr1 1509034 . T C 6099.105 REJECT NS=2;DP=359;DPB=409.0;AC=2;AN=4;AF=0.5;RO=195;AO=213;PRO=0.0;PAO=0.0;QR=7425;QA=8141;PQR=0.0;PQA=0.0;SRF=103;SRR=92;SAF=102;SAR=111;SRP=4.35773;SAP=3.83607;AB=0.520782;ABP=4.54467;RUN=1;RPP=5.95657;RPPR=18.2551;RPL=98.0;RPR=115.0;EPP=3.02049;EPPR=3.02144;DPRA=0.0;ODDS=311.107;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.974359;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.194;Dels=0.0;FS=3.564;HaplotypeScore [...]
+chr1 2488153 . A G 1206.87 REJECT NS=1;DP=109;DPB=109.0;AC=1;AN=4;AF=0.5;RO=64;AO=45;PRO=0.0;PAO=0.0;QR=2394;QA=1733;PQR=0.0;PQA=0.0;SRF=33;SRR=31;SAF=19;SAR=26;SRP=3.14602;SAP=5.37479;AB=0.412844;ABP=10.2021;RUN=1;RPP=6.91895;RPPR=4.23175;RPL=27.0;RPR=18.0;EPP=6.91895;EPPR=7.89611;DPRA=0.0;ODDS=277.893;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=0.779;FS=3.623;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.567; [...]
+chr1 2490898 . C A 12580.15 REJECT NS=2;DP=490;DPB=576.0;AC=2;AN=4;AF=0.5;RO=144;AO=431;PRO=0.0;PAO=0.0;QR=5479;QA=15823;PQR=0.0;PQA=0.0;SRF=73;SRR=71;SAF=222;SAR=209;SRP=3.07062;SAP=3.86176;AB=0.748264;ABP=311.374;RUN=1;RPP=3.13626;RPPR=3.55317;RPL=218.0;RPR=213.0;EPP=3.86176;EPPR=3.0103;DPRA=0.0;ODDS=274.749;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993039;PAIREDR=0.993056;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.5685;Dels=0.0;FS=0.0;HaplotypeS [...]
+chr1 2490942 . C A 13104.5 REJECT NS=2;DP=486;DPB=568.0;AC=2;AN=4;AF=0.5;RO=135;AO=432;PRO=0.0;PAO=0.0;QR=5178;QA=16351;PQR=0.0;PQA=0.0;SRF=64;SRR=71;SAF=231;SAR=201;SRP=3.79846;SAP=7.5342;AB=0.760563;ABP=337.968;RUN=1;RPP=3.73412;RPPR=3.15506;RPL=210.0;RPR=222.0;EPP=3.03041;EPPR=13.0634;DPRA=0.0;ODDS=224.368;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997685;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.8075;Dels=0.0;FS=3.166;HaplotypeScore [...]
+chr1 2491205 . C T 10791.4 REJECT NS=2;DP=389;DPB=444.0;AC=2;AN=4;AF=0.5;RO=92;AO=351;PRO=0.0;PAO=0.0;QR=3544;QA=13430;PQR=0.0;PQA=0.0;SRF=37;SRR=55;SAF=144;SAR=207;SRP=10.6577;SAP=27.5646;AB=0.790541;ABP=328.555;RUN=1;RPP=3.01649;RPPR=9.05266;RPL=175.0;RPR=176.0;EPP=3.31344;EPPR=3.86001;DPRA=0.0;ODDS=140.684;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5655;Dels=0.0;FS=3.197;HaplotypeScore=5.898 [...]
+chr1 2494330 . G A 6263.125 REJECT NS=2;DP=369;DPB=432.0;AC=2;AN=4;AF=0.5;RO=202;AO=230;PRO=0.0;PAO=0.0;QR=7533;QA=8661;PQR=0.0;PQA=0.0;SRF=95;SRR=107;SAF=125;SAR=105;SRP=4.55828;SAP=6.78677;AB=0.532407;ABP=6.95112;RUN=1;RPP=3.61454;RPPR=4.55828;RPL=119.0;RPR=111.0;EPP=4.86077;EPPR=6.49326;DPRA=0.0;ODDS=349.62;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995652;PAIREDR=0.99505;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3445;Dels=0.0;FS=4.588;HaplotypeS [...]
+chr1 3003532 . G A 1226.88 REJECT NS=2;DP=257;DPB=295.0;AC=2;AN=4;AF=0.5;RO=230;AO=64;PRO=0.0;PAO=0.0;QR=8646;QA=2452;PQR=0.0;PQA=0.0;SRF=60;SRR=170;SAF=17;SAR=47;SRP=117.249;SAP=33.5466;AB=0.216949;ABP=208.299;RUN=1;RPP=37.7539;RPPR=97.4221;RPL=48.0;RPR=16.0;EPP=3.14602;EPPR=3.61454;DPRA=0.0;ODDS=90.5404;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991304;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.637;Dels=0.0;FS=4.497;HaplotypeScore=2.890 [...]
+chr1 6184092 . A G 8794.785 REJECT NS=2;DP=369;DPB=428.0;AC=3;AN=4;AF=0.75;RO=106;AO=321;PRO=0.0;PAO=0.0;QR=4013;QA=12209;PQR=0.0;PQA=0.0;SRF=54;SRR=52;SAF=190;SAR=131;SRP=3.09224;SAP=26.5583;AB=0.655949;ABP=68.7061;RUN=1;RPP=8.69942;RPPR=19.071;RPL=146.0;RPR=175.0;EPP=51.8853;EPPR=3.33807;DPRA=0.0;ODDS=74.0173;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993769;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.424;Dels=0.0;FS=4.661;HaplotypeScore [...]
+chr1 6188546 . G A 7068.445 REJECT NS=2;DP=295;DPB=333.0;AC=3;AN=4;AF=0.75;RO=86;AO=247;PRO=0.0;PAO=0.0;QR=3281;QA=9413;PQR=0.0;PQA=0.0;SRF=49;SRR=37;SAF=129;SAR=118;SRP=6.64625;SAP=4.07406;AB=0.667954;ABP=66.4693;RUN=1;RPP=31.5735;RPPR=17.5541;RPL=95.0;RPR=152.0;EPP=3.23008;EPPR=7.95924;DPRA=0.0;ODDS=46.2835;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.996;MQMR=60.0;PAIRED=0.979757;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.342;Dels=0.0;FS=1.47;HaplotypeScore [...]
+chr1 6196869 . A G 7434.14 REJECT NS=2;DP=351;DPB=396.0;AC=3;AN=4;AF=0.75;RO=129;AO=267;PRO=0.0;PAO=0.0;QR=4946;QA=10255;PQR=0.0;PQA=0.0;SRF=52;SRR=77;SAF=82;SAR=185;SRP=13.531;SAP=89.2918;AB=0.578431;ABP=19.3602;RUN=1;RPP=3.99438;RPPR=3.02713;RPL=139.0;RPR=128.0;EPP=3.0835;EPPR=3.83512;DPRA=0.0;ODDS=57.161;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.748;Dels=0.0;FS=3.6515;HaplotypeScore=5.8877; [...]
+chr1 6204222 . C G 4741.3 REJECT NS=2;DP=303;DPB=351.0;AC=2;AN=4;AF=0.5;RO=176;AO=175;PRO=0.0;PAO=0.0;QR=6612;QA=6717;PQR=0.0;PQA=0.0;SRF=68;SRR=108;SAF=47;SAR=128;SRP=22.751;SAP=84.4219;AB=0.498575;ABP=3.01649;RUN=1;RPP=25.9535;RPPR=31.4368;RPL=109.0;RPR=66.0;EPP=7.48974;EPPR=3.0103;DPRA=0.0;ODDS=258.439;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994318;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.815;Dels=0.0;FS=8.911;HaplotypeScore=3.899 [...]
+chr1 6209363 . T C 9234.93 REJECT NS=2;DP=377;DPB=419.0;AC=3;AN=4;AF=0.75;RO=109;AO=310;PRO=0.0;PAO=0.0;QR=4119;QA=11931;PQR=0.0;PQA=0.0;SRF=58;SRR=51;SAF=184;SAR=126;SRP=3.98647;SAP=26.5743;AB=0.674627;ABP=91.7425;RUN=1;RPP=6.4006;RPPR=3.1896;RPL=144.0;RPR=166.0;EPP=4.38323;EPPR=3.1896;DPRA=0.0;ODDS=53.3886;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993548;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.984;Dels=0.0;FS=2.2945;HaplotypeScore=8 [...]
+chr1 6211183 . G A 3775.1 REJECT NS=1;DP=110;DPB=110.0;AC=2;AN=4;AF=1.0;RO=0;AO=110;PRO=0.0;PAO=0.0;QR=0;QA=4241;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=63;SAR=47;SRP=0.0;SAP=8.06391;AB=0.0;ABP=0.0;RUN=1;RPP=4.98437;RPPR=0.0;RPL=60.0;RPR=50.0;EPP=4.2737;EPPR=0.0;DPRA=0.0;ODDS=73.2308;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.71;SOR=0.981 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:AD [...]
+chr1 6215736 . C G 5292.530000000001 REJECT NS=2;DP=361;DPB=420.0;AC=2;AN=4;AF=0.5;RO=223;AO=197;PRO=0.0;PAO=0.0;QR=8644;QA=7494;PQR=0.0;PQA=0.0;SRF=99;SRR=124;SAF=86;SAR=111;SRP=9.09627;SAP=9.89949;AB=0.469048;ABP=6.50534;RUN=1;RPP=16.5131;RPPR=17.8211;RPL=116.0;RPR=81.0;EPP=7.87131;EPPR=10.109;DPRA=0.0;ODDS=362.219;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994924;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.6875;Dels=0.0;FS=0.0;Haplotyp [...]
+chr1 10517944 . CTG C 11053.3 REJECT NS=2;DP=322;DPB=291.444;AC=4;AN=4;AF=1.0;RO=0;AO=341;PRO=27.0;PAO=27.0;QR=0;QA=12498;PQR=928.0;PQA=928.0;SRF=0;SRR=0;SAF=117;SAR=224;SRP=0.0;SAP=75.917;AB=0.0;ABP=0.0;RUN=1;RPP=40.7659;RPPR=0.0;RPL=209.0;RPR=132.0;EPP=40.7659;EPPR=0.0;DPRA=0.0;ODDS=51.0483;GTI=0;TYPE=del;CIGAR=1M2D6M;NUMALT=1;MEANALT=2.5;LEN=2;MQM=60.4399;MQMR=0.0;PAIRED=0.991202;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=10517946;HOMLEN=5;HOMSEQ=TGTGT;SVLEN=-2;SVTYPE=DEL;FS=0.0;ML [...]
+chr1 11187893 . T C 6178.69 REJECT NS=2;DP=167;DPB=188.0;AC=4;AN=4;AF=1.0;RO=0;AO=188;PRO=0.0;PAO=0.0;QR=0;QA=7132;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=53;SAR=135;SRP=0.0;SAP=80.6751;AB=0.0;ABP=0.0;RUN=1;RPP=105.07;RPPR=0.0;RPL=141.0;RPR=47.0;EPP=21.4909;EPPR=0.0;DPRA=0.0;ODDS=30.5445;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994681;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.845;SOR=2.2785 GT [...]
+chr1 11205058 . C T 13009.65 REJECT NS=2;DP=343;DPB=392.0;AC=4;AN=4;AF=1.0;RO=0;AO=392;PRO=0.0;PAO=0.0;QR=0;QA=14960;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=170;SAR=222;SRP=0.0;SAP=17.989;AB=0.0;ABP=0.0;RUN=1;RPP=9.41393;RPPR=0.0;RPL=213.0;RPR=179.0;EPP=4.80509;EPPR=0.0;DPRA=0.0;ODDS=64.1696;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997449;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.9301;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.73;SOR=1.0 [...]
+chr1 11288758 . G A 14033.75 REJECT NS=2;DP=371;DPB=421.0;AC=4;AN=4;AF=1.0;RO=0;AO=421;PRO=0.0;PAO=0.0;QR=0;QA=16129;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=245;SAR=176;SRP=0.0;SAP=27.567;AB=0.0;ABP=0.0;RUN=1;RPP=7.96703;RPPR=0.0;RPL=226.0;RPR=195.0;EPP=7.96703;EPPR=0.0;DPRA=0.0;ODDS=67.3574;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9242;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.08;SOR=0.972 GT [...]
+chr1 11301714 . A G 3852.53 REJECT NS=1;DP=117;DPB=117.0;AC=2;AN=4;AF=1.0;RO=0;AO=117;PRO=0.0;PAO=0.0;QR=0;QA=4348;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=51;SAR=66;SRP=0.0;SAP=7.18621;AB=0.0;ABP=0.0;RUN=1;RPP=11.1951;RPPR=0.0;RPL=48.0;RPR=69.0;EPP=16.5402;EPPR=0.0;DPRA=0.0;ODDS=77.4166;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.974359;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.3;SOR=0.965 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr1 15011554 . T A 4435.860000000001 REJECT NS=2;DP=352;DPB=402.0;AC=2;AN=4;AF=0.5;RO=234;AO=168;PRO=0.0;PAO=0.0;QR=8926;QA=6364;PQR=0.0;PQA=0.0;SRF=90;SRR=144;SAF=57;SAR=111;SRP=30.0702;SAP=40.7009;AB=0.41791;ABP=26.54;RUN=1;RPP=17.9521;RPPR=9.28344;RPL=101.0;RPR=67.0;EPP=3.0103;EPPR=13.7377;DPRA=0.0;ODDS=272.212;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9573;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5315;Dels=0.0;FS=3.3715;HaplotypeS [...]
+chr1 15011576 . T C 3910.3050000000003 REJECT NS=2;DP=306;DPB=352.0;AC=2;AN=4;AF=0.5;RO=204;AO=148;PRO=0.0;PAO=0.0;QR=7818;QA=5591;PQR=0.0;PQA=0.0;SRF=62;SRR=142;SAF=38;SAR=110;SRP=71.1349;SAP=79.0705;AB=0.420455;ABP=22.3561;RUN=1;RPP=12.9286;RPPR=49.3776;RPL=87.0;RPR=61.0;EPP=5.88603;EPPR=5.09662;DPRA=0.0;ODDS=235.289;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.679;Dels=0.0;FS=3.0685;Haplotype [...]
+chr1 16256007 . T C 8609.73 REJECT NS=2;DP=360;DPB=413.0;AC=3;AN=4;AF=0.75;RO=109;AO=304;PRO=0.0;PAO=0.0;QR=4182;QA=11651;PQR=0.0;PQA=0.0;SRF=61;SRR=48;SAF=148;SAR=156;SRP=6.37708;SAP=3.46745;AB=0.648387;ABP=62.2985;RUN=1;RPP=5.32463;RPPR=3.03022;RPL=161.0;RPR=143.0;EPP=3.03887;EPPR=6.37708;DPRA=0.0;ODDS=64.3457;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990132;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.826;Dels=0.0;FS=4.579;HaplotypeScor [...]
+chr1 16259813 . A G 8696.535 REJECT NS=2;DP=374;DPB=427.0;AC=3;AN=4;AF=0.75;RO=114;AO=313;PRO=0.0;PAO=0.0;QR=4320;QA=11769;PQR=0.0;PQA=0.0;SRF=66;SRR=48;SAF=173;SAR=140;SRP=9.18185;SAP=10.5654;AB=0.648148;ABP=64.7766;RUN=1;RPP=3.18374;RPPR=7.88659;RPL=154.0;RPR=159.0;EPP=42.0344;EPPR=5.75321;DPRA=0.0;ODDS=65.1196;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.98722;PAIREDR=0.991228;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.043;Dels=0.0;FS=3.087;Haploty [...]
+chr1 16265403 . A G 1581.665 REJECT NS=2;DP=256;DPB=291.0;AC=2;AN=4;AF=0.5;RO=215;AO=76;PRO=0.0;PAO=0.0;QR=7978;QA=2875;PQR=0.0;PQA=0.0;SRF=93;SRR=122;SAF=32;SAR=44;SRP=11.5043;SAP=7.12467;AB=0.261168;ABP=147.186;RUN=1;RPP=40.0396;RPPR=165.911;RPL=56.0;RPR=20.0;EPP=7.12467;EPPR=3.82839;DPRA=0.0;ODDS=134.912;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995349;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.487;Dels=0.0;FS=3.1615;HaplotypeScore=7. [...]
+chr1 16265904 . T A 4871.72 REJECT NS=2;DP=333;DPB=381.0;AC=2;AN=4;AF=0.5;RO=202;AO=178;PRO=0.0;PAO=0.0;QR=7682;QA=6906;PQR=0.0;PQA=0.0;SRF=85;SRR=117;SAF=62;SAR=116;SRP=14.0182;SAP=38.5834;AB=0.467192;ABP=6.57243;RUN=1;RPP=3.20549;RPPR=23.822;RPL=91.0;RPR=87.0;EPP=12.5745;EPPR=3.3973;DPRA=0.0;ODDS=299.303;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990099;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.455;Dels=0.0;FS=5.113;HaplotypeScore=5.80 [...]
+chr1 16464673 . G A 1752.85 REJECT NS=2;DP=309;DPB=357.0;AC=2;AN=4;AF=0.5;RO=273;AO=84;PRO=0.0;PAO=0.0;QR=10179;QA=3237;PQR=0.0;PQA=0.0;SRF=123;SRR=150;SAF=39;SAR=45;SRP=8.80885;SAP=3.94093;AB=0.235294;ABP=220.285;RUN=1;RPP=5.59539;RPPR=10.6542;RPL=47.0;RPR=37.0;EPP=4.66476;EPPR=5.30904;DPRA=0.0;ODDS=135.082;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996337;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.01;Dels=0.0;FS=4.672;HaplotypeScore=8.8 [...]
+chr1 16475123 . C T 1198.77 PASS DP=184;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.386;Dels=0.0;FS=6.7905;HaplotypeScore=6.8559;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.2205;QD=10.975;ReadPosRankSum=-1.4175;SOR=0.98;ClippingRankSum=1.18 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:46,47:93:99.0:1888,0,2734:47:51:93:1:.:.:.:.:.:-9.82249e-05 0/1:244,32:276:99.0:566,0,9520:32:12:276:.:1:.:.:.:.:-0.0436845
+chr1 16475123 . CAGC TAGT 1801.06 REJECT NS=2;DP=361;DPB=375.25;AC=2;AN=4;AF=0.5;RO=285;AO=74;PRO=15.0;PAO=9.0;QR=10789;QA=2731;PQR=452.0;PQA=330.0;SRF=153;SRR=132;SAF=43;SAR=31;SRP=6.37037;SAP=7.23587;AB=0.204986;ABP=275.912;RUN=1;RPP=3.12768;RPPR=7.04086;RPL=38.0;RPR=36.0;EPP=4.88833;EPPR=3.07887;DPRA=0.0;ODDS=118.384;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=1;MEANALT=2.0;LEN=4;MQM=59.7297;MQMR=60.0;PAIRED=0.986486;PAIREDR=0.992982;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr1 16475126 . C T 1149.77 PASS DP=186;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=1.459;Dels=0.0;FS=5.4905;HaplotypeScore=7.7891;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.0435;QD=10.89;ReadPosRankSum=-1.063;SOR=0.836;ClippingRankSum=0.395 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:44,48:92:99.0:1888,0,2734:48:52:92:1:.:.:.:.:.:-9.82249e-05 0/1:250,30:281:99.0:468,0,9792:30:11:280:.:1:.:.:.:.:-0.0436845
+chr1 17380497 . G T 3018.26 REJECT NS=1;DP=89;DPB=89.0;AC=2;AN=4;AF=1.0;RO=0;AO=89;PRO=0.0;PAO=0.0;QR=0;QA=3424;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=36;SAR=53;SRP=0.0;SAP=10.0615;AB=0.0;ABP=0.0;RUN=1;RPP=20.7969;RPPR=0.0;RPL=58.0;RPR=31.0;EPP=10.0615;EPPR=0.0;DPRA=0.0;ODDS=60.1447;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.31;SOR=1.116 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:AD [...]
+chr1 19027239 . A G 1900.915 REJECT NS=2;DP=391;DPB=449.0;AC=2;AN=4;AF=0.5;RO=347;AO=100;PRO=0.0;PAO=0.0;QR=13115;QA=3770;PQR=0.0;PQA=0.0;SRF=229;SRR=118;SAF=66;SAR=34;SRP=80.1132;SAP=25.2462;AB=0.222717;ABP=302.862;RUN=1;RPP=3.09716;RPPR=5.26938;RPL=51.0;RPR=49.0;EPP=13.5202;EPPR=10.6762;DPRA=0.0;ODDS=158.932;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.98;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.0445;Dels=0.0;FS=3.8185;HaplotypeScore=5 [...]
+chr1 22405378 . AC A 623.333 REJECT NS=2;DP=76;DPB=121.548;AC=2;AN=2;AF=0.0;RO=5;AO=5;PRO=41.4167;PAO=2.25;QR=179;QA=70;PQR=1471.33;PQA=77.0;SRF=2;SRR=3;SAF=0;SAR=5;SRP=3.44459;SAP=13.8677;AB=0.0657895;ABP=127.47;RUN=1;RPP=6.91895;RPPR=3.44459;RPL=4.0;RPR=1.0;EPP=6.91895;EPPR=6.91895;DPRA=0.0;ODDS=20.7783;GTI=0;TYPE=del;CIGAR=1M1D29M;NUMALT=5;MEANALT=17.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.8;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV [...]
+chr1 22405378 . AC TT 623.333 REJECT NS=2;DP=76;DPB=121.548;AC=2;AN=2;AF=0.0;RO=5;AO=3;PRO=41.4167;PAO=0.0;QR=179;QA=30;PQR=1471.33;PQA=0.0;SRF=2;SRR=3;SAF=0;SAR=3;SRP=3.44459;SAP=9.52472;AB=0.0394737;ABP=143.013;RUN=1;RPP=3.73412;RPPR=3.44459;RPL=1.0;RPR=2.0;EPP=3.73412;EPPR=6.91895;DPRA=0.0;ODDS=20.7783;GTI=0;TYPE=mnp;CIGAR=2X29M;NUMALT=5;MEANALT=17.0;LEN=2;MQM=59.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.8;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:C [...]
+chr1 22405378 . ACTTTTTTTTTTTTTTTTTTG TTTTTTTTTTTTTTTTTTTTA 623.333 REJECT NS=2;DP=76;DPB=121.548;AC=2;AN=2;AF=0.0;RO=5;AO=4;PRO=41.4167;PAO=0.0;QR=179;QA=44;PQR=1471.33;PQA=0.0;SRF=2;SRR=3;SAF=0;SAR=4;SRP=3.44459;SAP=11.6962;AB=0.0754717;ABP=85.9769;RUN=1;RPP=5.18177;RPPR=3.44459;RPL=3.0;RPR=1.0;EPP=5.18177;EPPR=6.91895;DPRA=0.0;ODDS=20.7783;GTI=0;TYPE=complex;CIGAR=2X18M1X10M;NUMALT=5;MEANALT=22.0;LEN=31;MQM=56.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.8;technology.ILLUMINA=1.0;SPLITMULTIALLELI [...]
+chr1 22405379 . CT C 623.333 REJECT NS=2;DP=76;DPB=121.548;AC=2;AN=4;AF=0.5;RO=5;AO=22;PRO=41.4167;PAO=38.4167;QR=179;QA=609;PQR=1471.33;PQA=1306.33;SRF=2;SRR=3;SAF=10;SAR=12;SRP=3.44459;SAP=3.40511;AB=0.289474;ABP=32.268;RUN=1;RPP=6.56362;RPPR=3.44459;RPL=14.0;RPR=8.0;EPP=12.8806;EPPR=6.91895;DPRA=0.0;ODDS=20.7783;GTI=0;TYPE=del;CIGAR=2M1D28M;NUMALT=5;MEANALT=17.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.8;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.054;FS=0.0;MLEAC=1 [...]
+chr1 22405379 . CTT C 623.333 REJECT NS=2;DP=76;DPB=121.548;AC=2;AN=2;AF=0.0;RO=5;AO=10;PRO=41.4167;PAO=31.9167;QR=179;QA=276;PQR=1471.33;PQA=1015.33;SRF=2;SRR=3;SAF=3;SAR=7;SRP=3.44459;SAP=6.48466;AB=0.131579;ABP=92.6121;RUN=1;RPP=24.725;RPPR=3.44459;RPL=10.0;RPR=0.0;EPP=6.48466;EPPR=6.91895;DPRA=0.0;ODDS=20.7783;GTI=0;TYPE=del;CIGAR=2M2D27M;NUMALT=5;MEANALT=17.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.8;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr1 23885498 . T C 8540.865 REJECT NS=2;DP=378;DPB=430.0;AC=3;AN=4;AF=0.75;RO=125;AO=305;PRO=0.0;PAO=0.0;QR=4756;QA=11655;PQR=0.0;PQA=0.0;SRF=65;SRR=60;SAF=167;SAR=138;SRP=3.44459;SAP=8.99787;AB=0.616564;ABP=41.484;RUN=1;RPP=4.21351;RPPR=6.91895;RPL=159.0;RPR=146.0;EPP=17.4275;EPPR=3.16665;DPRA=0.0;ODDS=65.8758;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.84;PAIRED=0.993443;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.802;Dels=0.0;FS=0.0;HaplotypeScore [...]
+chr1 23885599 . T C 8628.475 REJECT NS=2;DP=379;DPB=440.0;AC=3;AN=4;AF=0.75;RO=119;AO=320;PRO=0.0;PAO=0.0;QR=4514;QA=12052;PQR=0.0;PQA=0.0;SRF=66;SRR=53;SAF=164;SAR=156;SRP=6.09416;SAP=3.44459;AB=0.626959;ABP=47.6718;RUN=1;RPP=3.03744;RPPR=3.17453;RPL=159.0;RPR=161.0;EPP=3.25459;EPPR=8.28388;DPRA=0.0;ODDS=74.9897;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.303;Dels=0.0;FS=1.583;HaplotypeScore=6. [...]
+chr1 25508191 . C T 3234.05 PASS SOMATIC;NS=2;DP=399;DPB=399.0;AC=1;AN=3;AF=0.25;RO=278;AO=121;PRO=0.0;PAO=0.0;QR=10729;QA=4623;PQR=0.0;PQA=0.0;SRF=115;SRR=163;SAF=55;SAR=66;SRP=21.007;SAP=5.18177;AB=0.408784;ABP=24.4022;RUN=1;RPP=33.1776;RPPR=35.0044;RPL=81.0;RPR=40.0;EPP=39.3511;EPPR=33.036;DPRA=2.87379;ODDS=65.2446;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992806;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.123;Dels=0.0;FS=0.911 [...]
+chr1 31502118 . G A 6556.93 REJECT NS=2;DP=388;DPB=438.0;AC=2;AN=4;AF=0.5;RO=211;AO=226;PRO=0.0;PAO=0.0;QR=8098;QA=8751;PQR=0.0;PQA=0.0;SRF=78;SRR=133;SAF=84;SAR=142;SRP=34.1416;SAP=35.3326;AB=0.515982;ABP=3.98201;RUN=1;RPP=10.5432;RPPR=15.6172;RPL=127.0;RPR=99.0;EPP=33.1419;EPPR=17.0991;DPRA=0.0;ODDS=297.697;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.982301;PAIREDR=0.995261;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2615;Dels=0.0;FS=2.09;HaplotypeSc [...]
+chr1 39325063 . T C 2175.58 REJECT NS=1;DP=65;DPB=65.0;AC=2;AN=4;AF=1.0;RO=0;AO=65;PRO=0.0;PAO=0.0;QR=0;QA=2507;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=44;SAR=21;SRP=0.0;SAP=20.6827;AB=0.0;ABP=0.0;RUN=1;RPP=35.1147;RPPR=0.0;RPL=17.0;RPR=48.0;EPP=4.64726;EPPR=0.0;DPRA=0.0;ODDS=45.2132;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=20.09;SOR=1.721 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:AD [...]
+chr1 40261412 . T C 5768.27 REJECT NS=2;DP=335;DPB=382.0;AC=2;AN=4;AF=0.5;RO=179;AO=203;PRO=0.0;PAO=0.0;QR=6861;QA=7739;PQR=0.0;PQA=0.0;SRF=103;SRR=76;SAF=129;SAR=74;SRP=11.8539;SAP=35.3684;AB=0.531414;ABP=6.28456;RUN=1;RPP=16.114;RPPR=23.4027;RPL=84.0;RPR=119.0;EPP=7.72764;EPPR=7.38964;DPRA=0.0;ODDS=293.368;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994413;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1065;Dels=0.0;FS=3.274;HaplotypeScore=3 [...]
+chr1 40261421 . A T 5906.950000000001 REJECT NS=2;DP=346;DPB=393.0;AC=2;AN=4;AF=0.5;RO=183;AO=210;PRO=0.0;PAO=0.0;QR=6898;QA=7897;PQR=0.0;PQA=0.0;SRF=105;SRR=78;SAF=127;SAR=83;SRP=11.6606;SAP=23.0292;AB=0.534351;ABP=7.0383;RUN=1;RPP=17.9418;RPPR=21.0584;RPL=86.0;RPR=124.0;EPP=4.49931;EPPR=3.30695;DPRA=0.0;ODDS=285.525;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.315;Dels=0.0;FS=1.11;HaplotypeScor [...]
+chr1 40261449 . T C 6370.26 REJECT NS=2;DP=381;DPB=432.0;AC=2;AN=4;AF=0.5;RO=210;AO=222;PRO=0.0;PAO=0.0;QR=8065;QA=8462;PQR=0.0;PQA=0.0;SRF=117;SRR=93;SAF=124;SAR=98;SRP=8.96634;SAP=9.62253;AB=0.513889;ABP=3.73412;RUN=1;RPP=3.1668;RPPR=5.03701;RPL=113.0;RPR=109.0;EPP=6.92286;EPPR=3.67208;DPRA=0.0;ODDS=316.533;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1715;Dels=0.0;FS=0.3795;HaplotypeScore=6.77 [...]
+chr1 40261687 . G T 4939.795 REJECT NS=2;DP=303;DPB=352.0;AC=2;AN=4;AF=0.5;RO=169;AO=182;PRO=0.0;PAO=0.0;QR=6472;QA=6888;PQR=0.0;PQA=0.0;SRF=51;SRR=118;SAF=49;SAR=133;SRP=60.6892;SAP=87.1966;AB=0.517045;ABP=3.89863;RUN=1;RPP=68.3454;RPPR=9.80739;RPL=128.0;RPR=54.0;EPP=15.2278;EPPR=5.18177;DPRA=0.0;ODDS=301.513;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994505;PAIREDR=0.994083;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.4255;Dels=0.0;FS=3.28;Haplotype [...]
+chr1 40262143 . G T 6000.075000000001 REJECT NS=2;DP=400;DPB=455.0;AC=2;AN=4;AF=0.5;RO=235;AO=220;PRO=0.0;PAO=0.0;QR=8946;QA=8339;PQR=0.0;PQA=0.0;SRF=140;SRR=95;SAF=111;SAR=109;SRP=21.7219;SAP=3.04978;AB=0.483516;ABP=4.0841;RUN=1;RPP=17.2631;RPPR=3.75876;RPL=129.0;RPR=91.0;EPP=15.8022;EPPR=42.0506;DPRA=0.0;ODDS=336.777;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.1818;MQMR=60.0;PAIRED=0.995455;PAIREDR=0.987234;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7755;Dels=0.0;FS=6.3 [...]
+chr1 40262161 . T TA 4179.175 REJECT NS=2;DP=362;DPB=459.556;AC=2;AN=4;AF=0.5;RO=214;AO=178;PRO=38.5;PAO=39.5;QR=8098;QA=6631;PQR=1360.0;PQA=1380.0;SRF=104;SRR=110;SAF=72;SAR=106;SRP=3.37559;SAP=17.1127;AB=0.451777;ABP=10.9687;RUN=1;RPP=31.1174;RPPR=19.2456;RPL=113.0;RPR=65.0;EPP=15.5024;EPPR=34.8315;DPRA=0.0;ODDS=316.269;GTI=0;TYPE=ins;CIGAR=1M1I8M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.1124;MQMR=60.0;PAIRED=0.994382;PAIREDR=0.990654;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6895;FS=6.21; [...]
+chr1 40262178 . A G 4516.82 REJECT NS=2;DP=358;DPB=415.0;AC=2;AN=4;AF=0.5;RO=235;AO=179;PRO=0.0;PAO=0.0;QR=8979;QA=6745;PQR=0.0;PQA=0.0;SRF=99;SRR=136;SAF=59;SAR=120;SRP=15.6603;SAP=48.1502;AB=0.431325;ABP=20.0106;RUN=1;RPP=37.0866;RPPR=25.1963;RPL=116.0;RPR=63.0;EPP=13.2126;EPPR=42.0506;DPRA=0.0;ODDS=360.097;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.2235;MQMR=60.0;PAIRED=0.994413;PAIREDR=0.991489;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.552;Dels=0.0;FS=7.0;HaplotypeS [...]
+chr1 40363054 . G C 11540.7 REJECT NS=2;DP=308;DPB=354.0;AC=4;AN=4;AF=1.0;RO=1;AO=352;PRO=0.0;PAO=0.0;QR=15;QA=13524;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=247;SAR=105;SRP=5.18177;SAP=127.401;AB=0.0;ABP=0.0;RUN=1;RPP=3.0103;RPPR=5.18177;RPL=176.0;RPR=176.0;EPP=33.2382;EPPR=5.18177;DPRA=0.0;ODDS=59.8729;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991477;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.706;Dels=0.0;FS=0.0;HaplotypeScore=7.8225;MLEAC=2;ML [...]
+chr1 45291908 . G A 1585.675 REJECT NS=2;DP=286;DPB=331.0;AC=2;AN=4;AF=0.5;RO=250;AO=80;PRO=0.0;PAO=0.0;QR=9474;QA=3111;PQR=0.0;PQA=0.0;SRF=185;SRR=65;SAF=59;SAR=21;SRP=128.087;SAP=42.2054;AB=0.241692;ABP=194.841;RUN=1;RPP=16.1477;RPPR=32.2296;RPL=29.0;RPR=51.0;EPP=3.44459;EPPR=3.5662;DPRA=0.0;ODDS=165.725;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.217;Dels=0.0;FS=1.2455;HaplotypeScore=4.8906 [...]
+chr1 45292866 . G A 5287.895 REJECT NS=2;DP=338;DPB=385.0;AC=2;AN=4;AF=0.5;RO=194;AO=191;PRO=0.0;PAO=0.0;QR=7353;QA=7291;PQR=0.0;PQA=0.0;SRF=111;SRR=83;SAF=99;SAR=92;SRP=11.7857;SAP=3.56738;AB=0.496104;ABP=3.06106;RUN=1;RPP=4.93166;RPPR=4.62211;RPL=89.0;RPR=102.0;EPP=3.56738;EPPR=3.05507;DPRA=0.0;ODDS=273.237;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989691;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0915;Dels=0.0;FS=3.0725;HaplotypeScor [...]
+chr1 45293518 . A G 7197.06 REJECT NS=2;DP=332;DPB=375.0;AC=3;AN=4;AF=0.75;RO=115;AO=258;PRO=0.0;PAO=0.0;QR=4420;QA=9840;PQR=0.0;PQA=0.0;SRF=66;SRR=49;SAF=133;SAR=125;SRP=8.4673;SAP=3.54896;AB=0.595156;ABP=25.7394;RUN=1;RPP=41.9285;RPPR=8.4673;RPL=95.0;RPR=163.0;EPP=7.08391;EPPR=3.48236;DPRA=0.0;ODDS=53.7674;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996124;PAIREDR=0.991304;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.383;Dels=0.0;FS=0.7305;HaplotypeS [...]
+chr1 45293752 . T C 1648.73 REJECT NS=2;DP=349;DPB=398.0;AC=2;AN=4;AF=0.5;RO=318;AO=80;PRO=0.0;PAO=0.0;QR=12197;QA=3099;PQR=0.0;PQA=0.0;SRF=142;SRR=176;SAF=36;SAR=44;SRP=10.9041;SAP=4.74748;AB=0.201005;ABP=312.058;RUN=1;RPP=5.72464;RPPR=3.11956;RPL=45.0;RPR=35.0;EPP=5.72464;EPPR=8.36387;DPRA=0.0;ODDS=46.2078;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996855;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.034;Dels=0.0;FS=4.267;HaplotypeScore=4. [...]
+chr1 45294156 . T C 7563.120000000001 REJECT NS=2;DP=316;DPB=356.0;AC=3;AN=4;AF=0.75;RO=93;AO=263;PRO=0.0;PAO=0.0;QR=3457;QA=9940;PQR=0.0;PQA=0.0;SRF=45;SRR=48;SAF=108;SAR=155;SRP=3.22044;SAP=21.249;AB=0.66426;ABP=67.9271;RUN=1;RPP=5.39644;RPPR=3.22044;RPL=123.0;RPR=140.0;EPP=8.17064;EPPR=4.15441;DPRA=0.0;ODDS=50.187;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996198;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.055;Dels=0.0;FS=2.181;Haplotyp [...]
+chr1 45297753 . A G 2318.285 REJECT NS=2;DP=394;DPB=456.0;AC=2;AN=4;AF=0.5;RO=345;AO=110;PRO=0.0;PAO=0.0;QR=13279;QA=4217;PQR=0.0;PQA=0.0;SRF=187;SRR=158;SAF=66;SAR=44;SRP=8.30366;SAP=12.5648;AB=0.241228;ABP=268.235;RUN=1;RPP=3.32615;RPPR=4.42648;RPL=53.0;RPR=57.0;EPP=4.2737;EPPR=6.94413;DPRA=0.0;ODDS=177.02;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990909;PAIREDR=0.991304;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6465;Dels=0.0;FS=4.022;HaplotypeSc [...]
+chr1 45307506 . G A 5966.49 REJECT NS=2;DP=268;DPB=305.0;AC=3;AN=4;AF=0.75;RO=93;AO=212;PRO=0.0;PAO=0.0;QR=3554;QA=8215;PQR=0.0;PQA=0.0;SRF=55;SRR=38;SAF=126;SAR=86;SRP=9.75821;SAP=19.3988;AB=0.597403;ABP=22.0459;RUN=1;RPP=62.1727;RPPR=31.613;RPL=68.0;RPR=144.0;EPP=7.10742;EPPR=3.59403;DPRA=0.0;ODDS=47.1984;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990566;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.253;Dels=0.0;FS=0.2475;HaplotypeScore=1. [...]
+chr1 45796269 . G C 9504.895 REJECT NS=2;DP=256;DPB=302.0;AC=4;AN=4;AF=1.0;RO=0;AO=301;PRO=0.0;PAO=0.0;QR=0;QA=11434;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=74;SAR=227;SRP=0.0;SAP=171.887;AB=0.0;ABP=0.0;RUN=1;RPP=88.7221;RPPR=0.0;RPL=205.0;RPR=96.0;EPP=3.07523;EPPR=0.0;DPRA=0.0;ODDS=60.3863;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996678;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9243;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.4;SOR=2.308 [...]
+chr1 45797505 . C G 2393.79 REJECT NS=2;DP=398;DPB=451.0;AC=2;AN=4;AF=0.5;RO=334;AO=117;PRO=0.0;PAO=0.0;QR=12770;QA=4495;PQR=0.0;PQA=0.0;SRF=149;SRR=185;SAF=54;SAR=63;SRP=11.4361;SAP=4.51363;AB=0.259424;ABP=229.734;RUN=1;RPP=3.91972;RPPR=3.9465;RPL=62.0;RPR=55.0;EPP=3.02886;EPPR=10.5259;DPRA=0.0;ODDS=221.207;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991018;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.181;Dels=0.0;FS=3.85;HaplotypeScore=10. [...]
+chr1 45798555 . T C 16300.25 REJECT NS=2;DP=429;DPB=497.0;AC=4;AN=4;AF=1.0;RO=0;AO=497;PRO=0.0;PAO=0.0;QR=0;QA=19052;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=221;SAR=276;SRP=0.0;SAP=16.227;AB=0.0;ABP=0.0;RUN=1;RPP=3.22439;RPPR=0.0;RPL=252.0;RPR=245.0;EPP=3.04962;EPPR=0.0;DPRA=0.0;ODDS=88.5289;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8438;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.89;SOR=1.0125 G [...]
+chr1 46505309 . A G 2901.77 PASS SOMATIC;NS=2;DP=418;DPB=418.0;AC=1;AN=3;AF=0.25;RO=304;AO=113;PRO=0.0;PAO=0.0;QR=11667;QA=4264;PQR=0.0;PQA=0.0;SRF=168;SRR=136;SAF=65;SAR=48;SRP=10.3247;SAP=8.56389;AB=0.350932;ABP=65.1603;RUN=1;RPP=8.56389;RPPR=6.46751;RPL=48.0;RPR=65.0;EPP=3.49071;EPPR=13.3248;DPRA=3.35417;ODDS=60.0023;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99115;PAIREDR=0.993421;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.395;Dels=0.0;FS= [...]
+chr1 51340430 . C CTT 87.8 PASS DP=58;AC=2;AN=4;AF=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.79;QD=1.51;SOR=2.584 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:0,7:7:18.0:125,18,0:7:100:7:1:.:.:.:.:.:-9.82249e-05 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0182792
+chr1 51341695 . A G 1472.7849999999999 REJECT NS=2;DP=376;DPB=424.0;AC=2;AN=4;AF=0.5;RO=339;AO=85;PRO=0.0;PAO=0.0;QR=12976;QA=3221;PQR=0.0;PQA=0.0;SRF=152;SRR=187;SAF=31;SAR=54;SRP=10.8571;SAP=16.5245;AB=0.200472;ABP=333.422;RUN=1;RPP=3.64897;RPPR=8.39735;RPL=45.0;RPR=40.0;EPP=5.07959;EPPR=22.387;DPRA=0.0;ODDS=149.708;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.976471;PAIREDR=0.99705;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.157;Dels=0.0;FS=3.8025;Ha [...]
+chr1 51439777 . C T 3143.81 PASS SOMATIC;NS=2;DP=392;DPB=392.0;AC=1;AN=3;AF=0.25;RO=278;AO=114;PRO=0.0;PAO=0.0;QR=10532;QA=4413;PQR=0.0;PQA=0.0;SRF=136;SRR=142;SAF=59;SAR=55;SRP=3.2915;SAP=3.31507;AB=0.402827;ABP=26.2213;RUN=1;RPP=9.18185;RPPR=4.13509;RPL=48.0;RPR=66.0;EPP=3.31507;EPPR=5.00993;DPRA=2.59633;ODDS=69.0042;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.672;Dels=0.0;FS=2.039;Hapl [...]
+chr1 51528697 . C T 2361.3 PASS SOMATIC;NS=2;DP=407;DPB=407.0;AC=1;AN=3;AF=0.25;RO=311;AO=96;PRO=0.0;PAO=0.0;QR=11576;QA=3617;PQR=0.0;PQA=0.0;SRF=127;SRR=184;SAF=35;SAR=61;SRP=25.6956;SAP=18.3011;AB=0.315789;ABP=92.6121;RUN=1;RPP=3.8246;RPPR=3.01728;RPL=45.0;RPR=51.0;EPP=8.80089;EPPR=6.7039;DPRA=2.95146;ODDS=65.1974;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.979167;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.416;Dels=0.01;FS=4.215;H [...]
+chr1 51528752 . T C 2352.14 PASS SOMATIC;NS=2;DP=335;DPB=335.0;AC=1;AN=3;AF=0.25;RO=244;AO=91;PRO=0.0;PAO=0.0;QR=9461;QA=3464;PQR=0.0;PQA=0.0;SRF=74;SRR=170;SAF=26;SAR=65;SRP=85.0279;SAP=39.3049;AB=0.372951;ABP=37.2199;RUN=1;RPP=17.9243;RPPR=30.9191;RPL=58.0;RPR=33.0;EPP=3.03416;EPPR=3.57987;DPRA=2.68132;ODDS=57.7853;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.978022;PAIREDR=0.995902;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.913;Dels=0.0;FS=1 [...]
+chr1 51530486 . C T 2839.06 PASS SOMATIC;NS=2;DP=402;DPB=402.0;AC=1;AN=3;AF=0.25;RO=292;AO=109;PRO=0.0;PAO=0.0;QR=11234;QA=4136;PQR=0.0;PQA=0.0;SRF=122;SRR=170;SAF=44;SAR=65;SRP=20.1441;SAP=11.7958;AB=0.362126;ABP=52.7089;RUN=1;RPP=7.4927;RPPR=18.746;RPL=62.0;RPR=47.0;EPP=6.37708;EPPR=28.0269;DPRA=2.9802;ODDS=63.9894;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.686;Dels=0.0;FS=0.0;Haploty [...]
+chr1 51539890 . T C 2707.52 PASS SOMATIC;NS=2;DP=367;DPB=367.0;AC=1;AN=3;AF=0.25;RO=260;AO=107;PRO=0.0;PAO=0.0;QR=9642;QA=3951;PQR=0.0;PQA=0.0;SRF=94;SRR=166;SAF=41;SAR=66;SRP=46.3061;SAP=15.6941;AB=0.387681;ABP=33.2536;RUN=1;RPP=15.6941;RPPR=31.1058;RPL=66.0;RPR=41.0;EPP=25.1106;EPPR=31.1058;DPRA=3.03297;ODDS=57.7092;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990654;PAIREDR=0.992308;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.683;Dels=0.0;FS= [...]
+chr1 65311214 . G C 5139.555 REJECT NS=2;DP=369;DPB=422.0;AC=2;AN=4;AF=0.5;RO=236;AO=186;PRO=0.0;PAO=0.0;QR=8896;QA=7118;PQR=0.0;PQA=0.0;SRF=141;SRR=95;SAF=104;SAR=82;SRP=22.4799;SAP=8.6608;AB=0.440758;ABP=15.8745;RUN=1;RPP=7.68013;RPPR=4.81373;RPL=83.0;RPR=103.0;EPP=5.99899;EPPR=5.3658;DPRA=0.0;ODDS=287.023;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9915;PAIRED=0.989247;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.344;Dels=0.0;FS=2.08;HaplotypeScore= [...]
+chr1 65321250 . G A 5010.125 REJECT NS=2;DP=332;DPB=388.0;AC=2;AN=4;AF=0.5;RO=209;AO=179;PRO=0.0;PAO=0.0;QR=7952;QA=6844;PQR=0.0;PQA=0.0;SRF=136;SRR=73;SAF=108;SAR=71;SRP=44.2475;SAP=19.6178;AB=0.46134;ABP=8.04722;RUN=1;RPP=3.99292;RPPR=8.50651;RPL=85.0;RPR=94.0;EPP=3.02243;EPPR=3.27005;DPRA=0.0;ODDS=260.135;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994413;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7145;Dels=0.0;FS=2.675;HaplotypeScore=2 [...]
+chr1 65321388 . G A 4932.57 REJECT NS=2;DP=292;DPB=335.0;AC=2;AN=4;AF=0.5;RO=160;AO=175;PRO=0.0;PAO=0.0;QR=6087;QA=6637;PQR=0.0;PQA=0.0;SRF=59;SRR=101;SAF=63;SAR=112;SRP=26.9508;SAP=32.8029;AB=0.522388;ABP=4.46875;RUN=1;RPP=43.3252;RPPR=20.5992;RPL=116.0;RPR=59.0;EPP=4.01538;EPPR=7.40753;DPRA=0.0;ODDS=230.882;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994286;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.527;Dels=0.0;FS=0.241;HaplotypeScore=4 [...]
+chr1 65335095 . T C 5818.215 REJECT NS=2;DP=386;DPB=442.0;AC=2;AN=4;AF=0.5;RO=233;AO=209;PRO=0.0;PAO=0.0;QR=8899;QA=8004;PQR=0.0;PQA=0.0;SRF=94;SRR=139;SAF=95;SAR=114;SRP=21.8825;SAP=6.76103;AB=0.472851;ABP=5.84009;RUN=1;RPP=5.34801;RPPR=5.70367;RPL=112.0;RPR=97.0;EPP=8.50651;EPPR=7.12025;DPRA=0.0;ODDS=342.213;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995215;PAIREDR=0.995708;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.884;Dels=0.0;FS=2.8015;Haplotype [...]
+chr1 75001474 . A T 13065.0 REJECT NS=2;DP=342;DPB=390.0;AC=4;AN=4;AF=1.0;RO=0;AO=390;PRO=0.0;PAO=0.0;QR=0;QA=15049;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=243;SAR=147;SRP=0.0;SAP=54.3239;AB=0.0;ABP=0.0;RUN=1;RPP=12.832;RPPR=0.0;RPL=174.0;RPR=216.0;EPP=11.9189;EPPR=0.0;DPRA=0.0;ODDS=63.6127;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.987179;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9327;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=34.04;SOR=1.30 [...]
+chr1 78013771 . T C 5119.555 REJECT NS=2;DP=334;DPB=381.0;AC=2;AN=4;AF=0.5;RO=192;AO=189;PRO=0.0;PAO=0.0;QR=7387;QA=7108;PQR=0.0;PQA=0.0;SRF=108;SRR=84;SAF=119;SAR=70;SRP=9.52472;SAP=30.596;AB=0.496063;ABP=3.06159;RUN=1;RPP=43.0045;RPPR=3.19126;RPL=65.0;RPR=124.0;EPP=10.1911;EPPR=3.73412;DPRA=0.0;ODDS=301.446;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994709;PAIREDR=0.989583;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1135;Dels=0.0;FS=2.5245;Haplotype [...]
+chr1 78435701 . T TA 317.153 REJECT NS=2;DP=186;DPB=219.96;AC=2;AN=2;AF=0.0;RO=133;AO=14;PRO=44.0;PAO=21.0;QR=4962;QA=440;PQR=1574.83;PQA=708.833;SRF=8;SRR=125;SAF=1;SAR=13;SRP=226.509;SAP=25.3454;AB=0.0752688;ABP=294.455;RUN=1;RPP=3.63072;RPPR=13.2146;RPL=8.0;RPR=6.0;EPP=5.49198;EPPR=5.76954;DPRA=0.0;ODDS=38.0537;GTI=0;TYPE=ins;CIGAR=1M1I24M;NUMALT=2;MEANALT=6.5;LEN=1;MQM=60.0;MQMR=59.985;PAIRED=1.0;PAIREDR=0.984962;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr1 78435701 . TA T 317.153 REJECT NS=2;DP=186;DPB=219.96;AC=2;AN=4;AF=0.5;RO=133;AO=28;PRO=44.0;PAO=23.0;QR=4962;QA=934;PQR=1574.83;PQA=797.333;SRF=8;SRR=125;SAF=2;SAR=26;SRP=226.509;SAP=47.6806;AB=0.150538;ABP=200.311;RUN=1;RPP=14.1779;RPPR=13.2146;RPL=20.0;RPR=8.0;EPP=7.97367;EPPR=5.76954;DPRA=0.0;ODDS=38.0537;GTI=0;TYPE=del;CIGAR=1M1D23M;NUMALT=2;MEANALT=6.5;LEN=1;MQM=60.3571;MQMR=59.985;PAIRED=1.0;PAIREDR=0.984962;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=2.102;FS=0.0; [...]
+chr1 82510916 . G A 5739.66 REJECT NS=2;DP=339;DPB=391.0;AC=2;AN=4;AF=0.5;RO=187;AO=203;PRO=0.0;PAO=0.0;QR=7105;QA=7782;PQR=0.0;PQA=0.0;SRF=128;SRR=59;SAF=132;SAR=71;SRP=58.2958;SAP=42.8135;AB=0.519182;ABP=4.25987;RUN=1;RPP=12.0064;RPPR=22.5303;RPL=87.0;RPR=116.0;EPP=12.0064;EPPR=3.3006;DPRA=0.0;ODDS=330.236;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989305;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.2065;Dels=0.0;FS=7.3685;HaplotypeScore= [...]
+chr1 96018531 . C T 14267.45 REJECT NS=2;DP=372;DPB=418.0;AC=4;AN=4;AF=1.0;RO=0;AO=418;PRO=0.0;PAO=0.0;QR=0;QA=16173;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=172;SAR=246;SRP=0.0;SAP=31.4576;AB=0.0;ABP=0.0;RUN=1;RPP=9.01562;RPPR=0.0;RPL=226.0;RPR=192.0;EPP=15.9976;EPPR=0.0;DPRA=0.0;ODDS=61.1439;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995215;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.7482;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.68;SOR=1. [...]
+chr1 105029388 . G A 10236.0 REJECT NS=2;DP=403;DPB=459.0;AC=2;AN=4;AF=0.5;RO=128;AO=331;PRO=0.0;PAO=0.0;QR=4903;QA=12852;PQR=0.0;PQA=0.0;SRF=64;SRR=64;SAF=163;SAR=168;SRP=3.0103;SAP=3.17431;AB=0.721133;ABP=197.965;RUN=1;RPP=3.8041;RPPR=6.33537;RPL=160.0;RPR=171.0;EPP=18.7617;EPPR=8.50684;DPRA=0.0;ODDS=286.926;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9396;MQMR=60.0;PAIRED=0.996979;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2845;Dels=0.0;FS=2.8825;HaplotypeS [...]
+chr1 108002360 . T A 8547.57 REJECT NS=2;DP=318;DPB=363.0;AC=2;AN=4;AF=0.5;RO=90;AO=273;PRO=0.0;PAO=0.0;QR=3479;QA=10685;PQR=0.0;PQA=0.0;SRF=48;SRR=42;SAF=148;SAR=125;SRP=3.87889;SAP=7.21802;AB=0.752066;ABP=203.342;RUN=1;RPP=15.1085;RPPR=5.42305;RPL=117.0;RPR=156.0;EPP=4.79998;EPPR=10.8276;DPRA=0.0;ODDS=131.453;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.989;MQMR=60.0;PAIRED=0.992674;PAIREDR=0.988889;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.2735;Dels=0.0;FS=3.54;Haploty [...]
+chr1 111034818 . T C 4192.07 REJECT NS=2;DP=258;DPB=299.0;AC=2;AN=4;AF=0.5;RO=146;AO=152;PRO=0.0;PAO=0.0;QR=5578;QA=5750;PQR=0.0;PQA=0.0;SRF=82;SRR=64;SAF=101;SAR=51;SRP=7.82918;SAP=38.7253;AB=0.508361;ABP=3.19186;RUN=1;RPP=77.0689;RPPR=98.1981;RPL=40.0;RPR=112.0;EPP=5.81036;EPPR=3.96218;DPRA=0.0;ODDS=195.365;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.991;Dels=0.0;FS=7.845;HaplotypeScore=3.9128 [...]
+chr1 118165691 . C T 8898.61 REJECT NS=2;DP=343;DPB=398.0;AC=2;AN=4;AF=0.5;RO=108;AO=290;PRO=0.0;PAO=0.0;QR=4101;QA=11173;PQR=0.0;PQA=0.0;SRF=51;SRR=57;SAF=160;SAR=130;SRP=3.73412;SAP=9.74935;AB=0.728643;ABP=183.734;RUN=1;RPP=3.0103;RPPR=3.0103;RPL=145.0;RPR=145.0;EPP=7.32329;EPPR=3.73412;DPRA=0.0;ODDS=150.126;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0525;Dels=0.0;FS=3.0985;HaplotypeScore=4.8 [...]
+chr1 120075675 . T C 7779.745 REJECT NS=2;DP=369;DPB=416.0;AC=3;AN=4;AF=0.75;RO=139;AO=277;PRO=0.0;PAO=0.0;QR=5347;QA=10657;PQR=0.0;PQA=0.0;SRF=72;SRR=67;SAF=131;SAR=146;SRP=3.40085;SAP=4.77413;AB=0.569659;ABP=16.624;RUN=1;RPP=3.39442;RPPR=12.7741;RPL=135.0;RPR=142.0;EPP=18.8848;EPPR=14.3988;DPRA=0.0;ODDS=59.0282;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99278;PAIREDR=0.992806;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.5;Dels=0.0;FS=1.2015;Haplotype [...]
+chr1 120355513 . C T 6125.015 REJECT NS=2;DP=371;DPB=436.0;AC=2;AN=4;AF=0.5;RO=215;AO=221;PRO=0.0;PAO=0.0;QR=8173;QA=8508;PQR=0.0;PQA=0.0;SRF=102;SRR=113;SAF=98;SAR=123;SRP=4.23238;SAP=9.15134;AB=0.506881;ABP=3.1896;RUN=1;RPP=17.9551;RPPR=3.82839;RPL=130.0;RPR=91.0;EPP=13.7105;EPPR=21.685;DPRA=0.0;ODDS=417.64;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.972093;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.245;Dels=0.0;FS=2.22;HaplotypeScore=6. [...]
+chr1 120458004 . A T 1452.82 REJECT NS=2;DP=295;DPB=339.0;AC=2;AN=4;AF=0.5;RO=259;AO=79;PRO=0.0;PAO=0.0;QR=9885;QA=3003;PQR=0.0;PQA=0.0;SRF=137;SRR=122;SAF=43;SAR=36;SRP=4.89671;SAP=4.35716;AB=0.233038;ABP=212.862;RUN=1;RPP=12.9331;RPPR=5.43329;RPL=30.0;RPR=49.0;EPP=3.03779;EPPR=9.12228;DPRA=0.0;ODDS=169.124;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=59.9266;PAIRED=1.0;PAIREDR=0.996139;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.2;Dels=0.0;FS=0.413;HaplotypeScore= [...]
+chr1 120512104 . T C 6929.41 REJECT NS=2;DP=186;DPB=211.0;AC=4;AN=4;AF=1.0;RO=1;AO=210;PRO=0.0;PAO=0.0;QR=16;QA=8024;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=165;SAR=45;SRP=5.18177;SAP=151.911;AB=0.0;ABP=0.0;RUN=1;RPP=83.0859;RPPR=5.18177;RPL=61.0;RPR=149.0;EPP=12.3166;EPPR=5.18177;DPRA=0.0;ODDS=34.2066;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985714;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.965;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33 [...]
+chr1 120539331 . C T 3452.6549999999997 REJECT NS=2;DP=369;DPB=412.0;AC=2;AN=4;AF=0.5;RO=257;AO=155;PRO=0.0;PAO=0.0;QR=9661;QA=5771;PQR=0.0;PQA=0.0;SRF=115;SRR=142;SAF=74;SAR=81;SRP=9.16985;SAP=3.69677;AB=0.376214;ABP=57.8452;RUN=1;RPP=20.1719;RPPR=3.42432;RPL=60.0;RPR=95.0;EPP=3.69677;EPPR=4.91139;DPRA=0.0;ODDS=265.795;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=50.7935;MQMR=59.0272;PAIRED=0.980645;PAIREDR=0.992218;technology.ILLUMINA=1.0;MQ0=7;BaseQRankSum=-0.2855;Dels=0.0;F [...]
+chr1 120572547 . T C 931.103 REJECT NS=1;DP=106;DPB=106.0;AC=1;AN=4;AF=0.5;RO=55;AO=50;PRO=0.0;PAO=0.0;QR=2081;QA=1903;PQR=0.0;PQA=0.0;SRF=47;SRR=8;SAF=43;SAR=7;SRP=63.0614;SAP=59.2949;AB=0.471698;ABP=3.74778;RUN=1;RPP=7.35324;RPPR=17.2631;RPL=20.0;RPR=30.0;EPP=9.26414;EPPR=11.8936;DPRA=0.0;ODDS=214.394;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=32.3;MQMR=31.7636;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=0.467;FS=2.457;MLEAC=1;MLEAF=0.5;MQ=34.07;MQRankSum=0. [...]
+chr1 120572572 . C T 883.959 REJECT NS=1;DP=104;DPB=104.0;AC=1;AN=4;AF=0.5;RO=56;AO=48;PRO=0.0;PAO=0.0;QR=2134;QA=1886;PQR=0.0;PQA=0.0;SRF=48;SRR=8;SAF=43;SAR=5;SRP=65.0524;SAP=68.3354;AB=0.461538;ABP=4.34659;RUN=1;RPP=4.6389;RPPR=5.49198;RPL=27.0;RPR=21.0;EPP=3.73412;EPPR=3.63072;DPRA=0.0;ODDS=203.539;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=31.5833;MQMR=32.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=1.849;FS=2.697;MLEAC=1;MLEAF=0.5;MQ=33.67;MQRankSum=0.6 [...]
+chr1 145436887 . G GT 295.922 REJECT NS=2;DP=114;DPB=159.889;AC=2;AN=3;AF=0.25;RO=46;AO=19;PRO=24.3;PAO=18.3;QR=1641;QA=521;PQR=860.967;PQA=641.467;SRF=8;SRR=38;SAF=3;SAR=16;SRP=45.4956;SAP=22.325;AB=0.166667;ABP=113.032;RUN=1;RPP=22.325;RPPR=30.2009;RPL=16.0;RPR=3.0;EPP=8.61041;EPPR=9.80795;DPRA=0.0;ODDS=1.9398;GTI=0;TYPE=ins;CIGAR=1M1I26M;NUMALT=5;MEANALT=12.0;LEN=1;MQM=60.0;MQMR=59.7174;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-1.833;FS=0.0;M [...]
+chr1 145436887 . G GTT 295.922 REJECT NS=2;DP=114;DPB=159.889;AC=2;AN=3;AF=0.25;RO=46;AO=4;PRO=24.3;PAO=18.3;QR=1641;QA=72;PQR=860.967;PQA=649.467;SRF=8;SRR=38;SAF=0;SAR=4;SRP=45.4956;SAP=11.6962;AB=0.0350877;ABP=217.034;RUN=1;RPP=11.6962;RPPR=30.2009;RPL=4.0;RPR=0.0;EPP=11.6962;EPPR=9.80795;DPRA=0.0;ODDS=1.9398;GTI=0;TYPE=ins;CIGAR=1M2I26M;NUMALT=5;MEANALT=12.0;LEN=2;MQM=58.25;MQMR=59.7174;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr1 145436887 . GT G 295.922 REJECT NS=2;DP=114;DPB=159.889;AC=2;AN=2;AF=0.0;RO=46;AO=16;PRO=24.3;PAO=15.8;QR=1641;QA=446;PQR=860.967;PQA=550.967;SRF=8;SRR=38;SAF=0;SAR=16;SRP=45.4956;SAP=37.7539;AB=0.140351;ABP=131.089;RUN=1;RPP=3.55317;RPPR=30.2009;RPL=9.0;RPR=7.0;EPP=3.55317;EPPR=9.80795;DPRA=0.0;ODDS=1.9398;GTI=0;TYPE=del;CIGAR=1M1D25M;NUMALT=5;MEANALT=12.0;LEN=1;MQM=60.0;MQMR=59.7174;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr1 145436887 . GTT G 295.922 REJECT NS=2;DP=114;DPB=159.889;AC=2;AN=2;AF=0.0;RO=46;AO=9;PRO=24.3;PAO=12.0;QR=1641;QA=265;PQR=860.967;PQA=422.167;SRF=8;SRR=38;SAF=2;SAR=7;SRP=45.4956;SAP=9.04217;AB=0.0789474;ABP=178.557;RUN=1;RPP=5.18177;RPPR=30.2009;RPL=6.0;RPR=3.0;EPP=3.25157;EPPR=9.80795;DPRA=0.0;ODDS=1.9398;GTI=0;TYPE=del;CIGAR=1M2D24M;NUMALT=5;MEANALT=12.0;LEN=2;MQM=60.0;MQMR=59.7174;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr1 145436906 . C T 295.922 REJECT NS=2;DP=114;DPB=159.889;AC=2;AN=2;AF=0.0;RO=46;AO=2;PRO=24.3;PAO=16.3;QR=1641;QA=32;PQR=860.967;PQA=579.967;SRF=8;SRR=38;SAF=2;SAR=0;SRP=45.4956;SAP=7.35324;AB=0.0833333;ABP=39.2015;RUN=1;RPP=7.35324;RPPR=30.2009;RPL=2.0;RPR=0.0;EPP=7.35324;EPPR=9.80795;DPRA=0.0;ODDS=1.9398;GTI=0;TYPE=snp;CIGAR=19M1X7M;NUMALT=5;MEANALT=10.0;LEN=1;MQM=60.0;MQMR=59.7174;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr1 152487979 . C T 2645.42 REJECT NS=1;DP=79;DPB=79.0;AC=2;AN=4;AF=1.0;RO=0;AO=79;PRO=0.0;PAO=0.0;QR=0;QA=2986;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=31;SAR=48;SRP=0.0;SAP=10.954;AB=0.0;ABP=0.0;RUN=1;RPP=4.35716;RPPR=0.0;RPL=36.0;RPR=43.0;EPP=5.23675;EPPR=0.0;DPRA=0.0;ODDS=53.8705;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9747;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=34.11;SOR=1.179 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV [...]
+chr1 152488063 . C T 2641.45 REJECT NS=1;DP=79;DPB=79.0;AC=2;AN=4;AF=1.0;RO=0;AO=79;PRO=0.0;PAO=0.0;QR=0;QA=3005;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=23;SAR=56;SRP=0.0;SAP=32.9436;AB=0.0;ABP=0.0;RUN=1;RPP=3.25768;RPPR=0.0;RPL=41.0;RPR=38.0;EPP=5.23675;EPPR=0.0;DPRA=0.0;ODDS=53.9209;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.987342;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.87;SOR=1.936 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr1 155870416 . G A 4568.12 REJECT NS=2;DP=220;DPB=258.0;AC=3;AN=4;AF=0.75;RO=79;AO=179;PRO=0.0;PAO=0.0;QR=2968;QA=6764;PQR=0.0;PQA=0.0;SRF=30;SRR=49;SAF=57;SAR=122;SRP=12.9331;SAP=54.2643;AB=0.565934;ABP=9.88265;RUN=1;RPP=94.8308;RPPR=5.23675;RPL=133.0;RPR=46.0;EPP=3.31358;EPPR=6.33623;DPRA=0.0;ODDS=48.4016;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8481;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.476;Dels=0.0;FS=2.88;HaplotypeScore=2.93 [...]
+chr1 155880573 . C G 8036.885 REJECT NS=2;DP=337;DPB=382.0;AC=3;AN=4;AF=0.75;RO=101;AO=281;PRO=0.0;PAO=0.0;QR=3862;QA=10716;PQR=0.0;PQA=0.0;SRF=46;SRR=55;SAF=133;SAR=148;SRP=4.75178;SAP=4.74902;AB=0.65529;ABP=64.3822;RUN=1;RPP=7.84009;RPPR=3.0318;RPL=128.0;RPR=153.0;EPP=3.01803;EPPR=3.0318;DPRA=0.0;ODDS=56.4825;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996441;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.907;Dels=0.0;FS=0.744;HaplotypeScor [...]
+chr1 156785617 . G A 8090.74 REJECT NS=2;DP=376;DPB=428.0;AC=3;AN=4;AF=0.75;RO=136;AO=292;PRO=0.0;PAO=0.0;QR=5125;QA=11055;PQR=0.0;PQA=0.0;SRF=52;SRR=84;SAF=125;SAR=167;SRP=19.3602;SAP=16.1284;AB=0.581538;ABP=21.7785;RUN=1;RPP=3.27802;RPPR=3.5851;RPL=143.0;RPR=149.0;EPP=8.84055;EPPR=3.07417;DPRA=0.0;ODDS=64.2069;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.237;Dels=0.0;FS=0.689;HaplotypeScore=6.8 [...]
+chr1 156830779 . G A 1002.82 REJECT NS=1;DP=78;DPB=78.0;AC=1;AN=4;AF=0.5;RO=39;AO=39;PRO=0.0;PAO=0.0;QR=1436;QA=1418;PQR=0.0;PQA=0.0;SRF=27;SRR=12;SAF=26;SAR=13;SRP=15.538;SAP=12.42;AB=0.5;ABP=3.0103;RUN=1;RPP=9.74743;RPPR=15.538;RPL=25.0;RPR=14.0;EPP=3.06598;EPPR=3.06598;DPRA=0.0;ODDS=230.908;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.974359;technology.ILLUMINA=1.0;BaseQRankSum=-0.369;FS=0.92;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=1.231;QD=15 [...]
+chr1 156842336 . C T 8197.17 REJECT NS=2;DP=316;DPB=366.0;AC=2;AN=4;AF=0.5;RO=93;AO=273;PRO=0.0;PAO=0.0;QR=3357;QA=10292;PQR=0.0;PQA=0.0;SRF=37;SRR=56;SAF=124;SAR=149;SRP=11.4393;SAP=7.98162;AB=0.745902;ABP=195.239;RUN=1;RPP=5.88173;RPPR=3.22044;RPL=146.0;RPR=127.0;EPP=3.97275;EPPR=3.59403;DPRA=0.0;ODDS=127.603;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992674;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1855;Dels=0.0;FS=0.6965;HaplotypeSco [...]
+chr1 156842471 . C T 152.124 REJECT NS=2;DP=133;DPB=175.19;AC=2;AN=2;AF=0.0;RO=68;AO=10;PRO=27.2167;PAO=5.05;QR=2411;QA=136;PQR=914.467;PQA=133.8;SRF=22;SRR=46;SAF=1;SAR=9;SRP=21.4039;SAP=16.9077;AB=0.075188;ABP=211.488;RUN=1;RPP=6.48466;RPPR=28.0461;RPL=3.0;RPR=7.0;EPP=10.8276;EPPR=7.60871;DPRA=0.0;ODDS=0.836863;GTI=1;TYPE=snp;CIGAR=1X20M;NUMALT=4;MEANALT=14.0;LEN=1;MQM=51.2;MQMR=58.8676;PAIRED=1.0;PAIREDR=0.970588;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr1 156842471 . C CT 152.124 REJECT NS=2;DP=133;DPB=175.19;AC=2;AN=2;AF=0.0;RO=68;AO=12;PRO=27.2167;PAO=17.2167;QR=2411;QA=267;PQR=914.467;PQA=569.467;SRF=22;SRR=46;SAF=4;SAR=8;SRP=21.4039;SAP=5.9056;AB=0.0902256;ABP=196.99;RUN=1;RPP=5.9056;RPPR=28.0461;RPL=8.0;RPR=4.0;EPP=5.9056;EPPR=7.60871;DPRA=0.0;ODDS=0.836863;GTI=1;TYPE=ins;CIGAR=1M1I20M;NUMALT=4;MEANALT=14.0;LEN=1;MQM=54.8333;MQMR=58.8676;PAIRED=1.0;PAIREDR=0.970588;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr1 156842471 . CT C 152.124 REJECT NS=2;DP=133;DPB=175.19;AC=2;AN=3;AF=0.25;RO=68;AO=14;PRO=27.2167;PAO=20.2167;QR=2411;QA=387;PQR=914.467;PQA=656.467;SRF=22;SRR=46;SAF=6;SAR=8;SRP=21.4039;SAP=3.63072;AB=0.105263;ABP=183.014;RUN=1;RPP=8.59409;RPPR=28.0461;RPL=10.0;RPR=4.0;EPP=8.59409;EPPR=7.60871;DPRA=0.0;ODDS=0.836863;GTI=1;TYPE=del;CIGAR=1M1D19M;NUMALT=4;MEANALT=14.0;LEN=1;MQM=60.0;MQMR=58.8676;PAIRED=1.0;PAIREDR=0.970588;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr1 156842471 . CTT C 152.124 REJECT NS=2;DP=133;DPB=175.19;AC=2;AN=3;AF=0.25;RO=68;AO=6;PRO=27.2167;PAO=15.3;QR=2411;QA=201;PQR=914.467;PQA=479.8;SRF=22;SRR=46;SAF=3;SAR=3;SRP=21.4039;SAP=3.0103;AB=0.0451128;ABP=242.052;RUN=1;RPP=4.45795;RPPR=28.0461;RPL=4.0;RPR=2.0;EPP=3.0103;EPPR=7.60871;DPRA=0.0;ODDS=0.836863;GTI=1;TYPE=del;CIGAR=1M2D18M;NUMALT=4;MEANALT=14.0;LEN=2;MQM=60.0;MQMR=58.8676;PAIRED=1.0;PAIREDR=0.970588;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr1 156842810 . A AGT 273.813 REJECT NS=2;DP=29;DPB=59.7143;AC=2;AN=3;AF=0.5;RO=1;AO=7;PRO=16.6667;PAO=17.1667;QR=36;QA=235;PQR=556.583;PQA=570.083;SRF=1;SRR=0;SAF=7;SAR=0;SRP=5.18177;SAP=18.2106;AB=0.269231;ABP=15.0369;RUN=1;RPP=3.32051;RPPR=5.18177;RPL=4.0;RPR=3.0;EPP=3.32051;EPPR=5.18177;DPRA=0.0;ODDS=0.0;GTI=0;TYPE=ins;CIGAR=1M2I48M;NUMALT=3;MEANALT=11.0;LEN=2;MQM=61.4286;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.67;FS=0.0;MLEAC [...]
+chr1 156842810 . A AGTGT 273.813 REJECT NS=2;DP=29;DPB=59.7143;AC=2;AN=2;AF=0.25;RO=1;AO=6;PRO=16.6667;PAO=17.1667;QR=36;QA=157;PQR=556.583;PQA=570.083;SRF=1;SRR=0;SAF=6;SAR=0;SRP=5.18177;SAP=16.0391;AB=0.230769;ABP=19.3799;RUN=1;RPP=3.0103;RPPR=5.18177;RPL=3.0;RPR=3.0;EPP=3.0103;EPPR=5.18177;DPRA=0.0;ODDS=0.0;GTI=0;TYPE=ins;CIGAR=1M4I48M;NUMALT=3;MEANALT=11.0;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.67;FS=0.0;MLEAC=1 [...]
+chr1 156842810 . A AGTGTGTGT 208.73 PASS DP=9;AC=2;AN=4;AF=1.0;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.88;QD=23.19;SOR=3.258 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:0,5:5:15.0:193,15,0:5:100:5:1:.:.:.:.:.:-2.19428 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0139302
+chr1 156842810 . AGTGT A 273.813 REJECT NS=2;DP=29;DPB=59.7143;AC=1;AN=3;AF=0.0;RO=1;AO=3;PRO=16.6667;PAO=13.0;QR=36;QA=102;PQR=556.583;PQA=438.25;SRF=1;SRR=0;SAF=3;SAR=0;SRP=5.18177;SAP=9.52472;AB=0.115385;ABP=36.4176;RUN=1;RPP=9.52472;RPPR=5.18177;RPL=0.0;RPR=3.0;EPP=9.52472;EPPR=5.18177;DPRA=0.0;ODDS=0.0;GTI=0;TYPE=del;CIGAR=1M4D44M;NUMALT=3;MEANALT=11.0;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMIC [...]
+chr1 156845492 . A AGT 1870.6 REJECT NS=2;DP=169;DPB=297.105;AC=2;AN=2;AF=0.5;RO=17;AO=42;PRO=41.1167;PAO=41.45;QR=627;QA=1271;PQR=1481.88;PQA=1493.55;SRF=8;SRR=9;SAF=22;SAR=20;SRP=3.13803;SAP=3.21711;AB=0.248521;ABP=95.844;RUN=1;RPP=3.0103;RPPR=3.13803;RPL=21.0;RPR=21.0;EPP=3.83753;EPPR=4.1599;DPRA=0.0;ODDS=2.0948;GTI=0;TYPE=ins;CIGAR=1M2I37M;NUMALT=5;MEANALT=11.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.06;FS=1.029; [...]
+chr1 156845492 . A AGTGT 1870.6 REJECT SOMATIC;NS=2;DP=169;DPB=297.105;AC=1;AN=3;AF=0.25;RO=17;AO=54;PRO=41.1167;PAO=41.45;QR=627;QA=1605;PQR=1481.88;PQA=1493.55;SRF=8;SRR=9;SAF=25;SAR=29;SRP=3.13803;SAP=3.6537;AB=0.319527;ABP=50.8212;RUN=1;RPP=8.80089;RPPR=3.13803;RPL=21.0;RPR=33.0;EPP=3.17115;EPPR=4.1599;DPRA=0.0;ODDS=2.0948;GTI=0;TYPE=ins;CIGAR=1M4I37M;NUMALT=5;MEANALT=11.5;LEN=4;MQM=59.6296;MQMR=60.0;PAIRED=0.981481;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR [...]
+chr1 156845492 . A AGTGTGT 1870.6 REJECT NS=2;DP=169;DPB=297.105;AC=0;AN=4;AF=0.0;RO=17;AO=3;PRO=41.1167;PAO=41.45;QR=627;QA=47;PQR=1481.88;PQA=1493.55;SRF=8;SRR=9;SAF=1;SAR=2;SRP=3.13803;SAP=3.73412;AB=0.0177515;ABP=344.394;RUN=1;RPP=3.73412;RPPR=3.13803;RPL=2.0;RPR=1.0;EPP=9.52472;EPPR=4.1599;DPRA=0.0;ODDS=2.0948;GTI=0;TYPE=ins;CIGAR=1M6I37M;NUMALT=5;MEANALT=11.5;LEN=6;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr1 156845492 . AGT A 1870.6 REJECT NS=2;DP=169;DPB=297.105;AC=2;AN=2;AF=0.375;RO=17;AO=27;PRO=41.1167;PAO=36.3667;QR=627;QA=842;PQR=1481.88;PQA=1309.63;SRF=8;SRR=9;SAF=11;SAR=16;SRP=3.13803;SAP=5.02092;AB=0.159763;ABP=172.938;RUN=1;RPP=3.73412;RPPR=3.13803;RPL=15.0;RPR=12.0;EPP=3.73412;EPPR=4.1599;DPRA=0.0;ODDS=2.0948;GTI=0;TYPE=del;CIGAR=1M2D35M;NUMALT=5;MEANALT=11.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.003;FS=0 [...]
+chr1 156845492 . AGTGT A 1870.6 REJECT NS=2;DP=169;DPB=297.105;AC=0;AN=4;AF=0.0;RO=17;AO=12;PRO=41.1167;PAO=32.1667;QR=627;QA=352;PQR=1481.88;PQA=1158.83;SRF=8;SRR=9;SAF=6;SAR=6;SRP=3.13803;SAP=3.0103;AB=0.0710059;ABP=273.159;RUN=1;RPP=5.9056;RPPR=3.13803;RPL=8.0;RPR=4.0;EPP=5.9056;EPPR=4.1599;DPRA=0.0;ODDS=2.0948;GTI=0;TYPE=del;CIGAR=1M4D33M;NUMALT=5;MEANALT=11.5;LEN=4;MQM=58.3333;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr1 156845774 . C T 5236.57 REJECT NS=2;DP=334;DPB=382.0;AC=2;AN=4;AF=0.5;RO=197;AO=185;PRO=0.0;PAO=0.0;QR=7587;QA=7050;PQR=0.0;PQA=0.0;SRF=107;SRR=90;SAF=107;SAR=78;SRP=6.19586;SAP=12.8817;AB=0.484293;ABP=3.82887;RUN=1;RPP=3.96105;RPPR=3.55041;RPL=88.0;RPR=97.0;EPP=3.30374;EPPR=3.02132;DPRA=0.0;ODDS=258.835;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994924;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.5725;Dels=0.0;FS=1.583;HaplotypeScore [...]
+chr1 156846233 . G A 919.727 REJECT NS=1;DP=95;DPB=95.0;AC=1;AN=4;AF=0.5;RO=58;AO=37;PRO=0.0;PAO=0.0;QR=2236;QA=1373;PQR=0.0;PQA=0.0;SRF=37;SRR=21;SAF=17;SAR=20;SRP=12.5947;SAP=3.5385;AB=0.389474;ABP=13.0905;RUN=1;RPP=7.76406;RPPR=3.60933;RPL=14.0;RPR=23.0;EPP=10.1116;EPPR=4.35811;DPRA=0.0;ODDS=211.775;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-1.319;FS=8.842;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.097; [...]
+chr1 156848995 . C T 8687.99 REJECT NS=2;DP=332;DPB=379.0;AC=2;AN=4;AF=0.5;RO=95;AO=284;PRO=0.0;PAO=0.0;QR=3622;QA=10908;PQR=0.0;PQA=0.0;SRF=50;SRR=45;SAF=152;SAR=132;SRP=3.58174;SAP=6.06871;AB=0.74934;ABP=207.673;RUN=1;RPP=5.48761;RPPR=3.21602;RPL=151.0;RPR=133.0;EPP=36.3164;EPPR=4.86177;DPRA=0.0;ODDS=141.406;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989437;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.697;Dels=0.0;FS=3.7425;HaplotypeScore [...]
+chr1 158582646 . T C 2631.67 PASS SOMATIC;NS=2;DP=420;DPB=420.0;AC=1;AN=3;AF=0.25;RO=316;AO=104;PRO=0.0;PAO=0.0;QR=12186;QA=3928;PQR=0.0;PQA=0.0;SRF=156;SRR=160;SAF=47;SAR=57;SRP=3.12025;SAP=5.09825;AB=0.333333;ABP=78.288;RUN=1;RPP=5.09825;RPPR=38.6334;RPL=57.0;RPR=47.0;EPP=3.34437;EPPR=3.45009;DPRA=2.88889;ODDS=68.4063;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990385;PAIREDR=0.990506;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.554;Dels=0.0;F [...]
+chr1 158584091 . A G 2014.84 PASS SOMATIC;NS=2;DP=399;DPB=399.0;AC=1;AN=3;AF=0.25;RO=302;AO=96;PRO=0.0;PAO=0.0;QR=10238;QA=3226;PQR=0.0;PQA=0.0;SRF=94;SRR=208;SAF=33;SAR=63;SRP=96.4555;SAP=23.3679;AB=0.33218;ABP=73.7071;RUN=1;RPP=12.0581;RPPR=66.5438;RPL=58.0;RPR=38.0;EPP=29.1584;EPPR=4.4196;DPRA=2.62727;ODDS=67.7887;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.3125;MQMR=60.0993;PAIRED=0.979167;PAIREDR=0.990066;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.707;Dels=0. [...]
+chr1 158584103 . G A 953.838 REJECT NS=2;DP=241;DPB=291.2;AC=2;AN=2;AF=0.0;RO=124;AO=6;PRO=40.25;PAO=5.75;QR=4641;QA=84;PQR=1438.58;PQA=217.417;SRF=22;SRR=102;SAF=0;SAR=6;SRP=115.086;SAP=16.0391;AB=0.0248963;ABP=475.517;RUN=1;RPP=4.45795;RPPR=10.015;RPL=2.0;RPR=4.0;EPP=4.45795;EPPR=7.49334;DPRA=0.0;ODDS=1.85295;GTI=0;TYPE=snp;CIGAR=1X19M;NUMALT=3;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991935;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr1 158584103 . G GA 953.838 REJECT NS=2;DP=241;DPB=291.2;AC=2;AN=4;AF=0.5;RO=124;AO=59;PRO=40.25;PAO=36.75;QR=4641;QA=1615;PQR=1438.58;PQA=1268.58;SRF=22;SRR=102;SAF=8;SAR=51;SRP=115.086;SAP=71.062;AB=0.244813;ABP=139.327;RUN=1;RPP=3.93042;RPPR=10.015;RPL=32.0;RPR=27.0;EPP=7.46366;EPPR=7.49334;DPRA=0.0;ODDS=1.85295;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=3;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.966102;PAIREDR=0.991935;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0. [...]
+chr1 158584103 . GA G 953.838 REJECT NS=2;DP=241;DPB=291.2;AC=2;AN=2;AF=0.0;RO=124;AO=21;PRO=40.25;PAO=28.25;QR=4641;QA=730;PQR=1438.58;PQA=990.417;SRF=22;SRR=102;SAF=6;SAR=15;SRP=115.086;SAP=11.386;AB=0.0871369;ABP=359.826;RUN=1;RPP=3.94093;RPPR=10.015;RPL=12.0;RPR=9.0;EPP=3.94093;EPPR=7.49334;DPRA=0.0;ODDS=1.85295;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=3;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.952381;PAIREDR=0.991935;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr1 158587390 . C T 2440.06 PASS SOMATIC;NS=2;DP=399;DPB=399.0;AC=1;AN=3;AF=0.25;RO=303;AO=96;PRO=0.0;PAO=0.0;QR=11720;QA=3685;PQR=0.0;PQA=0.0;SRF=137;SRR=166;SAF=39;SAR=57;SRP=9.03739;SAP=10.339;AB=0.335664;ABP=70.0982;RUN=1;RPP=39.2015;RPPR=18.8413;RPL=68.0;RPR=28.0;EPP=7.44372;EPPR=24.6892;DPRA=2.53097;ODDS=71.4966;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990099;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.954;Dels=0.0;FS=3.50 [...]
+chr1 158587784 . T G 10679.65 REJECT NS=2;DP=283;DPB=328.0;AC=4;AN=4;AF=1.0;RO=0;AO=327;PRO=0.0;PAO=0.0;QR=0;QA=12507;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=219;SAR=108;SRP=0.0;SAP=84.829;AB=0.0;ABP=0.0;RUN=1;RPP=40.3636;RPPR=0.0;RPL=126.0;RPR=201.0;EPP=12.1013;EPPR=0.0;DPRA=0.0;ODDS=58.5937;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.990826;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9638;MLEAC=2;MLEAF=1.0;MQ=60.025;QD=31.595;SOR [...]
+chr1 158587858 . G A 2959.25 PASS SOMATIC;NS=2;DP=421;DPB=421.0;AC=1;AN=3;AF=0.25;RO=309;AO=112;PRO=0.0;PAO=0.0;QR=11711;QA=4319;PQR=0.0;PQA=0.0;SRF=139;SRR=170;SAF=46;SAR=66;SRP=9.76365;SAP=10.7656;AB=0.365132;ABP=51.0398;RUN=1;RPP=3.0103;RPPR=3.86062;RPL=56.0;RPR=56.0;EPP=34.0313;EPPR=18.5339;DPRA=0.0;ODDS=71.487;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987055;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.363;Dels=0.0;FS=3.245;Hap [...]
+chr1 158592935 . G A 3132.66 PASS SOMATIC;NS=2;DP=404;DPB=404.0;AC=1;AN=3;AF=0.25;RO=287;AO=117;PRO=0.0;PAO=0.0;QR=11156;QA=4484;PQR=0.0;PQA=0.0;SRF=121;SRR=166;SAF=54;SAR=63;SRP=18.3317;SAP=4.51363;AB=0.386139;ABP=37.1304;RUN=1;RPP=18.6189;RPPR=10.2813;RPL=73.0;RPR=44.0;EPP=12.8283;EPPR=14.5183;DPRA=3.0;ODDS=64.0392;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986063;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.062;Dels=0.0;FS=0.901; [...]
+chr1 158597507 . G C 2065.9 PASS SOMATIC;NS=2;DP=313;DPB=313.0;AC=1;AN=3;AF=0.25;RO=230;AO=83;PRO=0.0;PAO=0.0;QR=8830;QA=3096;PQR=0.0;PQA=0.0;SRF=73;SRR=157;SAF=21;SAR=62;SRP=69.6273;SAP=46.9892;AB=0.367257;ABP=37.6001;RUN=1;RPP=12.4549;RPPR=18.1162;RPL=51.0;RPR=32.0;EPP=5.12945;EPPR=11.5074;DPRA=2.5977;ODDS=55.3119;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987952;PAIREDR=0.991304;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.801;Dels=0.0;FS=4. [...]
+chr1 158606449 . G T 2842.96 PASS SOMATIC;NS=2;DP=399;DPB=399.0;AC=1;AN=3;AF=0.25;RO=290;AO=109;PRO=0.0;PAO=0.0;QR=10845;QA=4187;PQR=0.0;PQA=0.0;SRF=185;SRR=105;SAF=78;SAR=31;SRP=50.9324;SAP=47.0175;AB=0.360927;ABP=53.7451;RUN=1;RPP=3.98647;RPPR=9.74935;RPL=51.0;RPR=58.0;EPP=10.2021;EPPR=20.2623;DPRA=3.1134;ODDS=60.549;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8724;PAIRED=0.981651;PAIREDR=0.989655;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.086;Dels=0.0; [...]
+chr1 158607788 . T G 6188.08 REJECT NS=2;DP=175;DPB=198.0;AC=4;AN=4;AF=1.0;RO=0;AO=198;PRO=0.0;PAO=0.0;QR=0;QA=7243;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=148;SAR=50;SRP=0.0;SAP=108.338;AB=0.0;ABP=0.0;RUN=1;RPP=145.538;RPPR=0.0;RPL=42.0;RPR=156.0;EPP=30.4279;EPPR=0.0;DPRA=0.0;ODDS=32.3067;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.989899;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.585;SOR=2.213 G [...]
+chr1 158612236 . A G 2721.41 PASS SOMATIC;NS=2;DP=376;DPB=376.0;AC=1;AN=3;AF=0.25;RO=273;AO=103;PRO=0.0;PAO=0.0;QR=10586;QA=3908;PQR=0.0;PQA=0.0;SRF=165;SRR=108;SAF=66;SAR=37;SRP=28.8532;SAP=20.7405;AB=0.387218;ABP=32.3986;RUN=1;RPP=5.56125;RPPR=3.08189;RPL=46.0;RPR=57.0;EPP=4.04333;EPPR=34.5802;DPRA=2.41818;ODDS=69.6557;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989011;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.566;Dels=0.0;FS=3.5 [...]
+chr1 158612756 . G A 2247.86 PASS SOMATIC;NS=2;DP=344;DPB=344.0;AC=1;AN=3;AF=0.25;RO=257;AO=87;PRO=0.0;PAO=0.0;QR=9611;QA=3351;PQR=0.0;PQA=0.0;SRF=89;SRR=168;SAF=28;SAR=59;SRP=55.7424;SAP=26.9963;AB=0.349398;ABP=52.0646;RUN=1;RPP=24.0012;RPPR=4.03267;RPL=58.0;RPR=29.0;EPP=3.23494;EPPR=40.9392;DPRA=2.62105;ODDS=60.2484;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992218;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.513;Dels=0.0;FS=0.0;Ha [...]
+chr1 158614198 . C T 1781.75 PASS SOMATIC;NS=2;DP=315;DPB=315.0;AC=1;AN=3;AF=0.25;RO=244;AO=71;PRO=0.0;PAO=0.0;QR=9129;QA=2752;PQR=0.0;PQA=0.0;SRF=78;SRR=166;SAF=29;SAR=42;SRP=71.9279;SAP=8.17902;AB=0.306034;ABP=78.8246;RUN=1;RPP=11.8491;RPPR=12.1234;RPL=44.0;RPR=27.0;EPP=5.48761;EPPR=3.57987;DPRA=2.79518;ODDS=52.7212;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.295;Dels=0.0;FS=7.574;Haplo [...]
+chr1 158618480 . A T 1503.76 PASS SOMATIC;NS=2;DP=241;DPB=241.0;AC=1;AN=3;AF=0.25;RO=178;AO=63;PRO=0.0;PAO=0.0;QR=6601;QA=2450;PQR=0.0;PQA=0.0;SRF=59;SRR=119;SAF=13;SAR=50;SRP=46.9277;SAP=50.1967;AB=0.355932;ABP=34.9199;RUN=1;RPP=92.6611;RPPR=196.686;RPL=57.0;RPR=6.0;EPP=24.5527;EPPR=22.5292;DPRA=2.76562;ODDS=40.9144;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984127;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.711;Dels=0.0;FS=17.531; [...]
+chr1 158619728 . A C 3482.57 REJECT NS=1;DP=102;DPB=102.0;AC=2;AN=4;AF=1.0;RO=0;AO=102;PRO=0.0;PAO=0.0;QR=0;QA=3921;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=42;SAR=60;SRP=0.0;SAP=9.90792;AB=0.0;ABP=0.0;RUN=1;RPP=4.37279;RPPR=0.0;RPL=55.0;RPR=47.0;EPP=8.46027;EPPR=0.0;DPRA=0.0;ODDS=68.2658;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.990196;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=35.25;SOR=1.037 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr1 158637865 . G A 892.998 REJECT NS=2;DP=129;DPB=182.04;AC=2;AN=2;AF=0.0;RO=41;AO=5;PRO=36.8333;PAO=3.0;QR=1510;QA=70;PQR=1314.67;PQA=42.0;SRF=10;SRR=31;SAF=0;SAR=5;SRP=26.3669;SAP=13.8677;AB=0.0510204;ABP=174.601;RUN=1;RPP=6.91895;RPPR=4.33437;RPL=4.0;RPR=1.0;EPP=6.91895;EPPR=9.41879;DPRA=0.0;ODDS=14.6363;GTI=0;TYPE=snp;CIGAR=1X24M;NUMALT=5;MEANALT=11.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMIC [...]
+chr1 158637865 . G T 892.998 REJECT NS=2;DP=129;DPB=182.04;AC=2;AN=2;AF=0.0;RO=41;AO=4;PRO=36.8333;PAO=0.0;QR=1510;QA=64;PQR=1314.67;PQA=0.0;SRF=10;SRR=31;SAF=0;SAR=4;SRP=26.3669;SAP=11.6962;AB=0.0310078;ABP=249.464;RUN=1;RPP=3.0103;RPPR=4.33437;RPL=2.0;RPR=2.0;EPP=3.0103;EPPR=9.41879;DPRA=0.0;ODDS=14.6363;GTI=0;TYPE=snp;CIGAR=1X24M;NUMALT=5;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:C [...]
+chr1 158637865 . G GA 892.998 REJECT NS=2;DP=129;DPB=182.04;AC=2;AN=3;AF=0.25;RO=41;AO=14;PRO=36.8333;PAO=28.8333;QR=1510;QA=328;PQR=1314.67;PQA=951.667;SRF=10;SRR=31;SAF=3;SAR=11;SRP=26.3669;SAP=12.937;AB=0.108527;ABP=174.725;RUN=1;RPP=3.0103;RPPR=4.33437;RPL=7.0;RPR=7.0;EPP=3.63072;EPPR=9.41879;DPRA=0.0;ODDS=14.6363;GTI=0;TYPE=ins;CIGAR=1M1I24M;NUMALT=5;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr1 158637865 . GA G 892.998 REJECT NS=2;DP=129;DPB=182.04;AC=2;AN=3;AF=0.25;RO=41;AO=41;PRO=36.8333;PAO=27.3333;QR=1510;QA=1154;PQR=1314.67;PQA=903.167;SRF=10;SRR=31;SAF=8;SAR=33;SRP=26.3669;SAP=36.112;AB=0.317829;ABP=40.1947;RUN=1;RPP=14.9269;RPPR=4.33437;RPL=28.0;RPR=13.0;EPP=3.06326;EPPR=9.41879;DPRA=0.0;ODDS=14.6363;GTI=0;TYPE=del;CIGAR=1M1D23M;NUMALT=5;MEANALT=9.5;LEN=1;MQM=59.8049;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.33; [...]
+chr1 158637865 . GAA G 892.998 REJECT NS=2;DP=129;DPB=182.04;AC=2;AN=2;AF=0.0;RO=41;AO=14;PRO=36.8333;PAO=15.0;QR=1510;QA=319;PQR=1314.67;PQA=532.5;SRF=10;SRR=31;SAF=1;SAR=13;SRP=26.3669;SAP=25.3454;AB=0.108527;ABP=174.725;RUN=1;RPP=3.63072;RPPR=4.33437;RPL=8.0;RPR=6.0;EPP=3.0103;EPPR=9.41879;DPRA=0.0;ODDS=14.6363;GTI=0;TYPE=del;CIGAR=1M2D22M;NUMALT=5;MEANALT=9.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr1 158644105 . T A 6228.51 REJECT NS=2;DP=277;DPB=318.0;AC=3;AN=4;AF=0.75;RO=93;AO=225;PRO=0.0;PAO=0.0;QR=3586;QA=8604;PQR=0.0;PQA=0.0;SRF=54;SRR=39;SAF=148;SAR=77;SRP=8.26386;SAP=51.6609;AB=0.609244;ABP=27.6811;RUN=1;RPP=66.3304;RPPR=59.0716;RPL=72.0;RPR=153.0;EPP=7.26639;EPPR=3.03365;DPRA=0.0;ODDS=50.8755;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989247;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.081;Dels=0.0;FS=0.827;HaplotypeScore=1 [...]
+chr1 158647495 . A T 11338.15 REJECT NS=2;DP=298;DPB=354.0;AC=4;AN=4;AF=1.0;RO=0;AO=354;PRO=0.0;PAO=0.0;QR=0;QA=13718;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=229;SAR=125;SRP=0.0;SAP=69.3568;AB=0.0;ABP=0.0;RUN=1;RPP=29.7305;RPPR=0.0;RPL=144.0;RPR=210.0;EPP=14.8859;EPPR=0.0;DPRA=0.0;ODDS=73.5655;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.988701;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9328;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.485;SOR= [...]
+chr1 158647522 . A G 2909.07 PASS SOMATIC;NS=2;DP=401;DPB=401.0;AC=1;AN=3;AF=0.25;RO=293;AO=108;PRO=0.0;PAO=0.0;QR=11043;QA=4147;PQR=0.0;PQA=0.0;SRF=168;SRR=125;SAF=60;SAR=48;SRP=16.7136;SAP=5.9056;AB=0.382979;ABP=36.5526;RUN=1;RPP=5.02092;RPPR=6.27863;RPL=49.0;RPR=59.0;EPP=3.09072;EPPR=15.4685;DPRA=2.36975;ODDS=75.1497;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.981481;PAIREDR=0.993174;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.845;Dels=0.0;FS [...]
+chr1 158647631 . T A 10190.385 REJECT NS=2;DP=268;DPB=308.0;AC=4;AN=4;AF=1.0;RO=0;AO=308;PRO=0.0;PAO=0.0;QR=0;QA=11814;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=116;SAR=192;SRP=0.0;SAP=43.7325;AB=0.0;ABP=0.0;RUN=1;RPP=31.8881;RPPR=0.0;RPL=186.0;RPR=122.0;EPP=10.2297;EPPR=0.0;DPRA=0.0;ODDS=53.5785;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99026;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.105;SOR=1 [...]
+chr1 158647669 . T C 1037.35 PASS SOMATIC;NS=2;DP=151;DPB=151.0;AC=1;AN=3;AF=0.25;RO=107;AO=44;PRO=0.0;PAO=0.0;QR=4124;QA=1665;PQR=0.0;PQA=0.0;SRF=32;SRR=75;SAF=10;SAR=34;SRP=40.5342;SAP=31.4368;AB=0.427184;ABP=7.75381;RUN=1;RPP=74.2741;RPPR=149.635;RPL=41.0;RPR=3.0;EPP=26.8965;EPPR=15.6941;DPRA=2.14583;ODDS=30.9632;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990654;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.143;Dels=0.0;FS=7.015;Ha [...]
+chr1 158655036 . G A 14908.599999999999 REJECT NS=2;DP=399;DPB=450.0;AC=4;AN=4;AF=1.0;RO=0;AO=450;PRO=0.0;PAO=0.0;QR=0;QA=16944;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=235;SAR=215;SRP=0.0;SAP=4.9405;AB=0.0;ABP=0.0;RUN=1;RPP=3.18402;RPPR=0.0;RPL=228.0;RPR=222.0;EPP=5.78978;EPPR=0.0;DPRA=0.0;ODDS=65.9733;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.988889;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9469;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33 [...]
+chr1 158656281 . T C 14299.2 REJECT NS=2;DP=381;DPB=433.0;AC=4;AN=4;AF=1.0;RO=0;AO=433;PRO=0.0;PAO=0.0;QR=0;QA=16387;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=238;SAR=195;SRP=0.0;SAP=12.2829;AB=0.0;ABP=0.0;RUN=1;RPP=3.41651;RPPR=0.0;RPL=221.0;RPR=212.0;EPP=37.5583;EPPR=0.0;DPRA=0.0;ODDS=68.5293;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.1894;MQMR=0.0;PAIRED=0.995381;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.175;QD=28.125;S [...]
+chr1 158656347 . C CAG 5375.04 REJECT SOMATIC;NS=2;DP=202;DPB=304.174;AC=1;AN=3;AF=0.25;RO=2;AO=23;PRO=39.0;PAO=42.5;QR=78;QA=644;PQR=1418.0;PQA=1549.5;SRF=0;SRR=2;SAF=4;SAR=19;SRP=7.35324;SAP=24.253;AB=0.13245;ABP=180.194;RUN=1;RPP=3.10471;RPPR=3.0103;RPL=12.0;RPR=11.0;EPP=3.10471;EPPR=3.0103;DPRA=0.0;ODDS=7.20129;GTI=0;TYPE=ins;CIGAR=1M2I22M;NUMALT=2;MEANALT=5.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-1.066;FS=0.0;ML [...]
+chr1 158656347 . C CAGAG 5375.04 REJECT NS=2;DP=202;DPB=304.174;AC=3;AN=3;AF=0.75;RO=2;AO=166;PRO=39.0;PAO=42.5;QR=78;QA=5735;PQR=1418.0;PQA=1549.5;SRF=0;SRR=2;SAF=26;SAR=140;SRP=7.35324;SAP=173.013;AB=0.794702;ABP=116.919;RUN=1;RPP=8.24276;RPPR=3.0103;RPL=93.0;RPR=73.0;EPP=8.24276;EPPR=3.0103;DPRA=0.0;ODDS=7.20129;GTI=0;TYPE=ins;CIGAR=1M4I22M;NUMALT=2;MEANALT=5.5;LEN=4;MQM=59.8795;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-1.366;FS=0.0 [...]
+chr1 159003218 . T C 9052.015 REJECT NS=2;DP=238;DPB=267.0;AC=4;AN=4;AF=1.0;RO=0;AO=267;PRO=0.0;PAO=0.0;QR=0;QA=10318;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=161;SAR=106;SRP=0.0;SAP=27.6122;AB=0.0;ABP=0.0;RUN=1;RPP=155.656;RPPR=0.0;RPL=65.0;RPR=202.0;EPP=8.93915;EPPR=0.0;DPRA=0.0;ODDS=40.5371;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.9635;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.635;SOR=1.1785 [...]
+chr1 162740327 . T C 14515.45 REJECT NS=2;DP=385;DPB=443.0;AC=4;AN=4;AF=1.0;RO=1;AO=442;PRO=0.0;PAO=0.0;QR=39;QA=16903;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=189;SAR=253;SRP=5.18177;SAP=23.1333;AB=0.0;ABP=0.0;RUN=1;RPP=5.38811;RPPR=5.18177;RPL=232.0;RPR=210.0;EPP=4.97543;EPPR=5.18177;DPRA=0.0;ODDS=75.1232;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986425;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.461;Dels=0.0;FS=1.766;HaplotypeScore=4.9461;MLEAC [...]
+chr1 162743418 . G T 8024.18 REJECT NS=2;DP=214;DPB=248.0;AC=4;AN=4;AF=1.0;RO=0;AO=248;PRO=0.0;PAO=0.0;QR=0;QA=9582;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=83;SAR=165;SRP=0.0;SAP=61.8852;AB=0.0;ABP=0.0;RUN=1;RPP=216.095;RPPR=0.0;RPL=202.0;RPR=46.0;EPP=10.8906;EPPR=0.0;DPRA=0.0;ODDS=46.7542;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.899;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.165;SOR=1.91 GT:GQ [...]
+chr1 167906239 . A C 12899.5 REJECT NS=2;DP=340;DPB=383.0;AC=4;AN=4;AF=1.0;RO=0;AO=383;PRO=0.0;PAO=0.0;QR=0;QA=14681;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=161;SAR=222;SRP=0.0;SAP=24.107;AB=0.0;ABP=0.0;RUN=1;RPP=70.3713;RPPR=0.0;RPL=246.0;RPR=137.0;EPP=70.3713;EPPR=0.0;DPRA=0.0;ODDS=57.3748;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0261;MQMR=0.0;PAIRED=0.994778;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=7.7839;MLEAC=2;MLEAF=1.0;MQ=60.02;QD=31.555;SO [...]
+chr1 179087934 . T C 8065.56 REJECT NS=2;DP=218;DPB=244.0;AC=4;AN=4;AF=1.0;RO=0;AO=244;PRO=0.0;PAO=0.0;QR=0;QA=9287;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=97;SAR=147;SRP=0.0;SAP=25.259;AB=0.0;ABP=0.0;RUN=1;RPP=214.07;RPPR=0.0;RPL=199.0;RPR=45.0;EPP=6.57009;EPPR=0.0;DPRA=0.0;ODDS=36.1281;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.32;SOR=1.1825 GT:GQ [...]
+chr1 189045393 . G A 7087.18 REJECT NS=2;DP=278;DPB=315.0;AC=2;AN=4;AF=0.5;RO=76;AO=237;PRO=0.0;PAO=0.0;QR=2850;QA=9064;PQR=0.0;PQA=0.0;SRF=62;SRR=14;SAF=173;SAR=64;SRP=68.8402;SAP=111.868;AB=0.752381;ABP=177.286;RUN=1;RPP=44.14;RPPR=3.46745;RPL=85.0;RPR=152.0;EPP=7.05089;EPPR=3.0103;DPRA=0.0;ODDS=133.577;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.1688;MQMR=60.0;PAIRED=0.991561;PAIREDR=0.973684;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6355;Dels=0.0;FS=5.196;HaplotypeSc [...]
+chr1 189045458 . A ATAGTT 8046.21 REJECT NS=2;DP=352;DPB=886.0;AC=2;AN=4;AF=0.5;RO=115;AO=278;PRO=4.0;PAO=17.0;QR=4369;QA=9831;PQR=97.0;PQA=534.0;SRF=57;SRR=58;SAF=156;SAR=122;SRP=3.02918;SAP=12.0399;AB=0.703797;ABP=145.508;RUN=1;RPP=4.54127;RPPR=16.7755;RPL=132.0;RPR=146.0;EPP=22.5379;EPPR=44.7215;DPRA=0.0;ODDS=227.951;GTI=0;TYPE=ins;CIGAR=1M5I2M;NUMALT=1;MEANALT=2.0;LEN=5;MQM=60.0;MQMR=60.0;PAIRED=0.985612;PAIREDR=0.991304;technology.ILLUMINA=1.0;MQ0=0;END=189045458;HOMLEN=2;HOMSEQ=TA; [...]
+chr1 193111228 . TGA T 203.722 REJECT NS=2;DP=141;DPB=168.381;AC=2;AN=4;AF=0.5;RO=112;AO=22;PRO=38.5;PAO=33.5;QR=4141;QA=761;PQR=1354.0;PQA=1172.0;SRF=23;SRR=89;SAF=11;SAR=11;SRP=87.4651;SAP=3.0103;AB=0.156028;ABP=147.914;RUN=1;RPP=50.7827;RPPR=114.996;RPL=22.0;RPR=0.0;EPP=3.0103;EPPR=31.0068;DPRA=0.0;ODDS=23.6341;GTI=0;TYPE=del;CIGAR=1M2D18M;NUMALT=1;MEANALT=4.0;LEN=2;MQM=60.9091;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991071;technology.ILLUMINA=1.0;BaseQRankSum=0.085;FS=16.955;MLEAC=1;MLEAF=0.5 [...]
+chr1 193502759 . G A 1623.585 REJECT NS=2;DP=329;DPB=374.0;AC=2;AN=4;AF=0.5;RO=292;AO=82;PRO=0.0;PAO=0.0;QR=11204;QA=3096;PQR=0.0;PQA=0.0;SRF=122;SRR=170;SAF=30;SAR=52;SRP=20.1441;SAP=15.8273;AB=0.219251;ABP=259.058;RUN=1;RPP=4.70511;RPPR=9.70319;RPL=45.0;RPR=37.0;EPP=4.70511;EPPR=16.1284;DPRA=0.0;ODDS=93.9564;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.982877;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0565;Dels=0.0;FS=2.2735;HaplotypeScor [...]
+chr1 201981218 . C G 5983.765 REJECT NS=2;DP=361;DPB=411.0;AC=2;AN=4;AF=0.5;RO=201;AO=210;PRO=0.0;PAO=0.0;QR=7635;QA=8012;PQR=0.0;PQA=0.0;SRF=94;SRR=107;SAF=102;SAR=108;SRP=4.83607;SAP=3.38255;AB=0.510949;ABP=3.43825;RUN=1;RPP=3.67208;RPPR=3.53966;RPL=109.0;RPR=101.0;EPP=7.14644;EPPR=9.76239;DPRA=0.0;ODDS=315.996;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995238;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.505;Dels=0.0;FS=2.862;HaplotypeSco [...]
+chr1 201981862 . T C 1316.61 REJECT NS=1;DP=101;DPB=101.0;AC=1;AN=4;AF=0.5;RO=52;AO=49;PRO=0.0;PAO=0.0;QR=1909;QA=1827;PQR=0.0;PQA=0.0;SRF=27;SRR=25;SAF=23;SAR=26;SRP=3.17734;SAP=3.40914;AB=0.485149;ABP=3.2038;RUN=1;RPP=10.4997;RPPR=3.0103;RPL=18.0;RPR=31.0;EPP=5.18177;EPPR=3.17734;DPRA=0.0;ODDS=303.16;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.959184;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.59;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=1.06 [...]
+chr1 204386265 . A G 1297.99 REJECT NS=1;DP=91;DPB=91.0;AC=1;AN=4;AF=0.5;RO=42;AO=49;PRO=0.0;PAO=0.0;QR=1604;QA=1845;PQR=0.0;PQA=0.0;SRF=35;SRR=7;SAF=41;SAR=8;SRP=43.5445;SAP=51.2702;AB=0.538462;ABP=4.17955;RUN=1;RPP=19.0083;RPPR=6.31921;RPL=15.0;RPR=34.0;EPP=3.40914;EPPR=4.87156;DPRA=0.0;ODDS=253.732;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.959184;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=0.394;FS=1.169;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=1.6 [...]
+chr1 204386685 . T G 3071.8 PASS SOMATIC;NS=2;DP=441;DPB=441.0;AC=1;AN=3;AF=0.25;RO=324;AO=117;PRO=0.0;PAO=0.0;QR=12492;QA=4463;PQR=0.0;PQA=0.0;SRF=154;SRR=170;SAF=51;SAR=66;SRP=4.72603;SAP=7.18621;AB=0.363354;ABP=55.2335;RUN=1;RPP=9.71031;RPPR=3.11753;RPL=68.0;RPR=49.0;EPP=9.71031;EPPR=18.4519;DPRA=2.70588;ODDS=75.2661;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990741;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.072;Dels=0.0;FS=6.18 [...]
+chr1 204388877 . G GT 277.858 REJECT NS=2;DP=123;DPB=243.31;AC=2;AN=2;AF=0.0;RO=53;AO=13;PRO=82.0833;PAO=63.0833;QR=1875;QA=266;PQR=2838.67;PQA=2149.67;SRF=5;SRR=48;SAF=4;SAR=9;SRP=78.766;SAP=7.18621;AB=0.105691;ABP=169.119;RUN=1;RPP=11.1951;RPPR=3.05127;RPL=10.0;RPR=3.0;EPP=3.17734;EPPR=5.01789;DPRA=0.0;ODDS=16.8127;GTI=0;TYPE=ins;CIGAR=1M1I28M;NUMALT=3;MEANALT=11.5;LEN=1;MQM=55.0769;MQMR=59.8302;PAIRED=1.0;PAIREDR=0.981132;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr1 204388877 . GT G 277.858 REJECT NS=2;DP=123;DPB=243.31;AC=2;AN=4;AF=0.5;RO=53;AO=20;PRO=82.0833;PAO=59.5833;QR=1875;QA=496;PQR=2838.67;PQA=1976.67;SRF=5;SRR=48;SAF=5;SAR=15;SRP=78.766;SAP=13.8677;AB=0.162602;ABP=124.63;RUN=1;RPP=4.74748;RPPR=3.05127;RPL=12.0;RPR=8.0;EPP=3.44459;EPPR=5.01789;DPRA=0.0;ODDS=16.8127;GTI=0;TYPE=del;CIGAR=1M1D27M;NUMALT=3;MEANALT=11.5;LEN=1;MQM=59.7;MQMR=59.8302;PAIRED=1.0;PAIREDR=0.981132;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-1.449;FS=1 [...]
+chr1 204388877 . GTT G 277.858 REJECT NS=2;DP=123;DPB=243.31;AC=2;AN=2;AF=0.0;RO=53;AO=13;PRO=82.0833;PAO=46.25;QR=1875;QA=294;PQR=2838.67;PQA=1536.0;SRF=5;SRR=48;SAF=4;SAR=9;SRP=78.766;SAP=7.18621;AB=0.105691;ABP=169.119;RUN=1;RPP=11.1951;RPPR=3.05127;RPL=10.0;RPR=3.0;EPP=3.17734;EPPR=5.01789;DPRA=0.0;ODDS=16.8127;GTI=0;TYPE=del;CIGAR=1M2D26M;NUMALT=3;MEANALT=11.5;LEN=2;MQM=59.1538;MQMR=59.8302;PAIRED=1.0;PAIREDR=0.981132;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr1 204501383 . C T 8139.52 REJECT NS=2;DP=306;DPB=346.0;AC=2;AN=4;AF=0.5;RO=78;AO=268;PRO=0.0;PAO=0.0;QR=3044;QA=10226;PQR=0.0;PQA=0.0;SRF=32;SRR=46;SAF=100;SAR=168;SRP=8.46682;SAP=40.4763;AB=0.774566;ABP=229.571;RUN=1;RPP=8.4876;RPPR=4.79202;RPL=147.0;RPR=121.0;EPP=20.1552;EPPR=3.45573;DPRA=0.0;ODDS=142.31;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992537;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.028;Dels=0.0;FS=6.4415;HaplotypeScore [...]
+chr1 204505976 . GA G 1060.57 REJECT NS=2;DP=246;DPB=295.81;AC=2;AN=4;AF=0.5;RO=190;AO=52;PRO=57.0;PAO=49.0;QR=7279;QA=1984;PQR=1983.5;PQA=1676.5;SRF=133;SRR=57;SAF=35;SAR=17;SRP=69.0231;SAP=16.5402;AB=0.211382;ABP=181.0;RUN=1;RPP=7.18621;RPPR=31.5823;RPL=21.0;RPR=31.0;EPP=3.67845;EPPR=11.9705;DPRA=0.0;ODDS=79.9169;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=1;MEANALT=3.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.678;FS=1.137;MLEAC=1;MLEAF=0.5;MQ=60. [...]
+chr1 204506107 . C T 8910.3 REJECT NS=2;DP=233;DPB=264.0;AC=4;AN=4;AF=1.0;RO=0;AO=264;PRO=0.0;PAO=0.0;QR=0;QA=10243;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=80;SAR=184;SRP=0.0;SAP=91.9749;AB=0.0;ABP=0.0;RUN=1;RPP=48.0519;RPPR=0.0;RPL=169.0;RPR=95.0;EPP=38.8396;EPPR=0.0;DPRA=0.0;ODDS=42.431;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.1136;MQMR=0.0;PAIRED=0.996212;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.08;QD=29.69;SOR=1. [...]
+chr1 204516025 . A G 8293.915 REJECT NS=2;DP=224;DPB=268.0;AC=4;AN=4;AF=1.0;RO=0;AO=267;PRO=0.0;PAO=0.0;QR=0;QA=10165;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=76;SAR=191;SRP=0.0;SAP=110.567;AB=0.0;ABP=0.0;RUN=1;RPP=64.5679;RPPR=0.0;RPL=177.0;RPR=90.0;EPP=16.6816;EPPR=0.0;DPRA=0.0;ODDS=58.5575;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996255;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.25;SOR=2.01 [...]
+chr1 204624998 . C T 1217.73 REJECT NS=2;DP=298;DPB=340.0;AC=2;AN=4;AF=0.5;RO=274;AO=66;PRO=0.0;PAO=0.0;QR=10309;QA=2489;PQR=0.0;PQA=0.0;SRF=70;SRR=204;SAF=20;SAR=46;SRP=145.313;SAP=25.2514;AB=0.194118;ABP=279.324;RUN=1;RPP=28.8048;RPPR=37.532;RPL=47.0;RPR=19.0;EPP=3.0103;EPPR=3.042;DPRA=0.0;ODDS=47.9098;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.969697;PAIREDR=0.981752;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.156;Dels=0.0;FS=1.394;HaplotypeScore=4 [...]
+chr1 204625007 . T C 3930.51 REJECT NS=2;DP=264;DPB=303.0;AC=2;AN=4;AF=0.5;RO=156;AO=147;PRO=0.0;PAO=0.0;QR=5936;QA=5620;PQR=0.0;PQA=0.0;SRF=41;SRR=115;SAF=35;SAR=112;SRP=79.2345;SAP=90.593;AB=0.485149;ABP=3.59079;RUN=1;RPP=125.337;RPPR=126.005;RPL=119.0;RPR=28.0;EPP=27.8419;EPPR=21.0502;DPRA=0.0;ODDS=214.779;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.979592;PAIREDR=0.974359;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.136;Dels=0.0;FS=0.296;HaplotypeS [...]
+chr1 204625455 . A G 1898.39 REJECT NS=2;DP=378;DPB=434.0;AC=2;AN=4;AF=0.5;RO=337;AO=97;PRO=0.0;PAO=0.0;QR=13089;QA=3713;PQR=0.0;PQA=0.0;SRF=176;SRR=161;SAF=51;SAR=46;SRP=4.4601;SAP=3.56996;AB=0.223502;ABP=291.206;RUN=1;RPP=3.21178;RPPR=3.06829;RPL=47.0;RPR=50.0;EPP=3.56996;EPPR=13.8419;DPRA=0.0;ODDS=146.194;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988131;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4705;Dels=0.0;FS=1.009;HaplotypeScore= [...]
+chr1 204626549 . C T 1144.405 REJECT NS=2;DP=381;DPB=432.0;AC=2;AN=4;AF=0.5;RO=354;AO=77;PRO=0.0;PAO=0.0;QR=13186;QA=2823;PQR=0.0;PQA=0.0;SRF=207;SRR=147;SAF=45;SAR=32;SRP=25.0931;SAP=7.77626;AB=0.178241;ABP=391.483;RUN=1;RPP=11.1604;RPPR=18.3456;RPL=30.0;RPR=47.0;EPP=6.42261;EPPR=7.81944;DPRA=0.0;ODDS=126.254;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=59.9915;PAIRED=0.987013;PAIREDR=0.991525;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0755;Dels=0.0;FS=5.551;Haplot [...]
+chr1 204627052 . C T 5717.865 REJECT NS=2;DP=369;DPB=440.0;AC=2;AN=4;AF=0.5;RO=225;AO=215;PRO=0.0;PAO=0.0;QR=8445;QA=7986;PQR=0.0;PQA=0.0;SRF=99;SRR=126;SAF=90;SAR=125;SRP=10.0459;SAP=15.3826;AB=0.488636;ABP=3.50382;RUN=1;RPP=59.8221;RPPR=19.2336;RPL=145.0;RPR=70.0;EPP=21.685;EPPR=41.3151;DPRA=0.0;ODDS=297.682;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.930233;PAIREDR=0.92;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1475;Dels=0.0;FS=4.486;HaplotypeScor [...]
+chr1 206647742 . A G 13659.099999999999 REJECT NS=2;DP=360;DPB=410.0;AC=4;AN=4;AF=1.0;RO=0;AO=409;PRO=0.0;PAO=0.0;QR=0;QA=15655;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=229;SAR=180;SRP=0.0;SAP=15.7577;AB=0.0;ABP=0.0;RUN=1;RPP=21.4917;RPPR=0.0;RPL=175.0;RPR=234.0;EPP=5.35167;EPPR=0.0;DPRA=0.0;ODDS=66.0601;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997555;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.7896;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=3 [...]
+chr1 206647787 . T C 14351.65 REJECT NS=2;DP=380;DPB=435.0;AC=4;AN=4;AF=1.0;RO=0;AO=435;PRO=0.0;PAO=0.0;QR=0;QA=16616;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=191;SAR=244;SRP=0.0;SAP=17.0325;AB=0.0;ABP=0.0;RUN=1;RPP=6.13023;RPPR=0.0;RPL=230.0;RPR=205.0;EPP=42.5511;EPPR=0.0;DPRA=0.0;ODDS=72.9043;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8239;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.395;SOR=0.928 [...]
+chr1 206650065 . A G 6064.165000000001 REJECT NS=2;DP=393;DPB=452.0;AC=2;AN=4;AF=0.5;RO=232;AO=220;PRO=0.0;PAO=0.0;QR=8982;QA=8433;PQR=0.0;PQA=0.0;SRF=113;SRR=119;SAF=117;SAR=103;SRP=3.34725;SAP=4.94488;AB=0.486726;ABP=3.7021;RUN=1;RPP=3.642;RPPR=6.75422;RPL=106.0;RPR=114.0;EPP=6.20829;EPPR=4.84482;DPRA=0.0;ODDS=392.553;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995455;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.65;Dels=0.0;FS=3.45;Haploty [...]
+chr1 206651107 . G A 1342.55 REJECT NS=1;DP=95;DPB=95.0;AC=1;AN=4;AF=0.5;RO=46;AO=49;PRO=0.0;PAO=0.0;QR=1783;QA=1854;PQR=0.0;PQA=0.0;SRF=29;SRR=17;SAF=30;SAR=19;SRP=9.80795;SAP=8.37251;AB=0.515789;ABP=3.21602;RUN=1;RPP=12.9813;RPPR=3.19912;RPL=17.0;RPR=32.0;EPP=8.37251;EPPR=9.80795;DPRA=0.0;ODDS=296.987;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=0.418;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.254;QD [...]
+chr1 206665896 . C G 16090.6 REJECT NS=2;DP=427;DPB=486.0;AC=4;AN=4;AF=1.0;RO=0;AO=485;PRO=0.0;PAO=0.0;QR=0;QA=18556;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=201;SAR=284;SRP=0.0;SAP=33.8542;AB=0.0;ABP=0.0;RUN=1;RPP=4.30423;RPPR=0.0;RPL=234.0;RPR=251.0;EPP=33.8542;EPPR=0.0;DPRA=0.0;ODDS=76.7351;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995876;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=7.7458;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.355;SOR=1 [...]
+chr1 207014776 . C T 13723.5 REJECT NS=2;DP=366;DPB=417.0;AC=4;AN=4;AF=1.0;RO=0;AO=417;PRO=0.0;PAO=0.0;QR=0;QA=15814;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=182;SAR=235;SRP=0.0;SAP=17.6378;AB=0.0;ABP=0.0;RUN=1;RPP=18.7626;RPPR=0.0;RPL=236.0;RPR=181.0;EPP=5.30675;EPPR=0.0;DPRA=0.0;ODDS=67.2749;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992806;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.957;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.685;SOR=0. [...]
+chr1 210001048 . A C 2868.7 PASS SOMATIC;NS=2;DP=414;DPB=414.0;AC=1;AN=3;AF=0.25;RO=304;AO=110;PRO=0.0;PAO=0.0;QR=11735;QA=4169;PQR=0.0;PQA=0.0;SRF=172;SRR=132;SAF=62;SAR=48;SRP=14.4391;SAP=6.87947;AB=0.361842;ABP=53.4113;RUN=1;RPP=3.72096;RPPR=3.7246;RPL=52.0;RPR=58.0;EPP=3.72096;EPPR=3.03887;DPRA=2.76364;ODDS=69.587;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0909;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996711;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.06;Dels=0.0;FS=1.4 [...]
+chr1 210001125 . GC G 1950.68 PASS SOMATIC;NS=2;DP=279;DPB=284.0;AC=1;AN=4;AF=0.25;RO=198;AO=78;PRO=17.5;PAO=9.5;QR=7504;QA=2883;PQR=617.0;PQA=334.0;SRF=68;SRR=130;SAF=29;SAR=49;SRP=45.1676;SAP=14.1461;AB=0.371429;ABP=33.1627;RUN=1;RPP=16.4846;RPPR=12.8806;RPL=50.0;RPR=28.0;EPP=31.5178;EPPR=30.4279;DPRA=3.04348;ODDS=47.1865;GTI=0;TYPE=del;CIGAR=1M1D6M;NUMALT=1;MEANALT=4.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987179;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.535;FS=0.534;MLEAC= [...]
+chr1 211520433 . G GT 233.672 REJECT NS=2;DP=198;DPB=240.312;AC=2;AN=4;AF=0.5;RO=162;AO=23;PRO=48.0;PAO=26.0;QR=6048;QA=797;PQR=1732.5;PQA=942.5;SRF=46;SRR=116;SAF=5;SAR=18;SRP=68.6906;SAP=18.9659;AB=0.116162;ABP=256.393;RUN=1;RPP=5.3706;RPPR=31.3735;RPL=9.0;RPR=14.0;EPP=7.63648;EPPR=15.074;DPRA=0.0;ODDS=21.4271;GTI=0;TYPE=ins;CIGAR=1M1I15M;NUMALT=1;MEANALT=4.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:Call [...]
+chr1 214503489 . T G 6263.3150000000005 REJECT NS=2;DP=287;DPB=334.0;AC=3;AN=4;AF=0.75;RO=97;AO=237;PRO=0.0;PAO=0.0;QR=3708;QA=8937;PQR=0.0;PQA=0.0;SRF=52;SRR=45;SAF=137;SAR=100;SRP=4.10723;SAP=15.5535;AB=0.599174;ABP=23.6842;RUN=1;RPP=82.2553;RPPR=19.3299;RPL=72.0;RPR=165.0;EPP=3.23936;EPPR=11.0918;DPRA=0.0;ODDS=58.3368;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995781;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.317;Dels=0.0;FS=1.467;Hapl [...]
+chr1 225060249 . A C 2802.07 PASS SOMATIC;NS=2;DP=392;DPB=392.0;AC=1;AN=3;AF=0.25;RO=286;AO=106;PRO=0.0;PAO=0.0;QR=10965;QA=4091;PQR=0.0;PQA=0.0;SRF=130;SRR=156;SAF=43;SAR=63;SRP=8.14287;SAP=11.2045;AB=0.358108;ABP=54.7735;RUN=1;RPP=14.81;RPPR=17.7095;RPL=65.0;RPR=41.0;EPP=7.02548;EPPR=8.96287;DPRA=3.08333;ODDS=60.8539;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990566;PAIREDR=0.986014;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.56;Dels=0.0;FS=2 [...]
+chr1 238504498 . G A 1067.125 REJECT NS=2;DP=264;DPB=302.0;AC=2;AN=4;AF=0.5;RO=241;AO=60;PRO=0.0;PAO=0.0;QR=9145;QA=2282;PQR=0.0;PQA=0.0;SRF=162;SRR=79;SAF=38;SAR=22;SRP=65.082;SAP=12.2752;AB=0.198675;ABP=241.182;RUN=1;RPP=17.4868;RPPR=62.1266;RPL=20.0;RPR=40.0;EPP=3.0103;EPPR=3.01931;DPRA=0.0;ODDS=78.3795;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987552;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.207;Dels=0.0;FS=0.862;HaplotypeScore=16.4 [...]
+chr1 238504548 . T C 8880.575 REJECT NS=2;DP=386;DPB=438.0;AC=3;AN=4;AF=0.75;RO=116;AO=319;PRO=0.0;PAO=0.0;QR=4444;QA=11890;PQR=0.0;PQA=0.0;SRF=65;SRR=51;SAF=173;SAR=146;SRP=6.67934;SAP=7.97269;AB=0.645833;ABP=65.0782;RUN=1;RPP=6.61127;RPPR=6.67934;RPL=148.0;RPR=171.0;EPP=16.7947;EPPR=7.80251;DPRA=0.0;ODDS=64.5447;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996865;PAIREDR=0.982759;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.042;Dels=0.0;FS=0.6935;Hapl [...]
+chr1 241511550 . A G 2320.21 REJECT NS=2;DP=202;DPB=236.0;AC=2;AN=4;AF=0.5;RO=141;AO=95;PRO=0.0;PAO=0.0;QR=5337;QA=3537;PQR=0.0;PQA=0.0;SRF=113;SRR=28;SAF=75;SAR=20;SRP=114.279;SAP=72.1546;AB=0.402542;ABP=22.4799;RUN=1;RPP=49.2969;RPPR=43.067;RPL=25.0;RPR=70.0;EPP=17.2963;EPPR=3.1489;DPRA=0.0;ODDS=152.126;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.978947;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.6035;Dels=0.0;FS=3.984;HaplotypeScore=2.9 [...]
+chr1 243558785 . A G 1605.025 REJECT NS=2;DP=358;DPB=421.0;AC=2;AN=4;AF=0.5;RO=333;AO=88;PRO=0.0;PAO=0.0;QR=12624;QA=3209;PQR=0.0;PQA=0.0;SRF=178;SRR=155;SAF=44;SAR=44;SRP=6.45988;SAP=3.0103;AB=0.209026;ABP=312.613;RUN=1;RPP=3.40511;RPPR=13.972;RPL=46.0;RPR=42.0;EPP=6.56362;EPPR=13.972;DPRA=0.0;ODDS=74.1667;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996997;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.156;Dels=0.0;FS=1.07;HaplotypeScore=1.9 [...]
+chr1 244500057 . C G 5224.545 REJECT NS=2;DP=345;DPB=392.0;AC=2;AN=4;AF=0.5;RO=201;AO=191;PRO=0.0;PAO=0.0;QR=7635;QA=7322;PQR=0.0;PQA=0.0;SRF=109;SRR=92;SAF=104;SAR=87;SRP=6.13247;SAP=6.29593;AB=0.487245;ABP=3.56425;RUN=1;RPP=4.93166;RPPR=6.91031;RPL=89.0;RPR=102.0;EPP=4.93166;EPPR=3.0211;DPRA=0.0;ODDS=274.817;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6025;Dels=0.0;FS=1.2825;HaplotypeScore=3.9 [...]
+chr1 249066372 . T C 1635.365 REJECT NS=2;DP=293;DPB=339.0;AC=2;AN=4;AF=0.5;RO=256;AO=83;PRO=0.0;PAO=0.0;QR=9768;QA=3139;PQR=0.0;PQA=0.0;SRF=98;SRR=158;SAF=30;SAR=53;SRP=33.5466;SAP=16.8502;AB=0.244838;ABP=194.721;RUN=1;RPP=10.5712;RPPR=62.8615;RPL=50.0;RPR=33.0;EPP=12.4549;EPPR=29.6108;DPRA=0.0;ODDS=142.628;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996094;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.6075;Dels=0.0;FS=1.128;HaplotypeScore= [...]
+chr2 3003010 . G A 2792.7 PASS SOMATIC;NS=2;DP=449;DPB=449.0;AC=1;AN=3;AF=0.25;RO=336;AO=113;PRO=0.0;PAO=0.0;QR=12772;QA=4173;PQR=0.0;PQA=0.0;SRF=158;SRR=178;SAF=54;SAR=59;SRP=5.59539;SAP=3.49071;AB=0.338323;ABP=78.8428;RUN=1;RPP=3.02952;RPPR=3.94093;RPL=56.0;RPR=57.0;EPP=6.2579;EPPR=44.3717;DPRA=2.90435;ODDS=71.6891;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99115;PAIREDR=0.991071;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-2.615;Dels=0.0;FS=0. [...]
+chr2 3003071 . G A 2643.95 PASS SOMATIC;NS=2;DP=350;DPB=350.0;AC=1;AN=3;AF=0.25;RO=251;AO=99;PRO=0.0;PAO=0.0;QR=9516;QA=3836;PQR=0.0;PQA=0.0;SRF=82;SRR=169;SAF=27;SAR=72;SRP=68.4919;SAP=47.4268;AB=0.380769;ABP=35.1147;RUN=1;RPP=5.66432;RPPR=29.1804;RPL=55.0;RPR=44.0;EPP=5.66432;EPPR=3.01895;DPRA=2.88889;ODDS=57.1035;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989899;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.575;Dels=0.0;FS=3.18;Hap [...]
+chr2 6004017 . T A 3038.33 PASS SOMATIC;NS=2;DP=401;DPB=401.0;AC=1;AN=3;AF=0.25;RO=287;AO=114;PRO=0.0;PAO=0.0;QR=10880;QA=4375;PQR=0.0;PQA=0.0;SRF=125;SRR=162;SAF=44;SAR=70;SRP=13.3683;SAP=15.8868;AB=0.378738;ABP=41.4547;RUN=1;RPP=17.9439;RPPR=24.2635;RPL=71.0;RPR=43.0;EPP=4.22937;EPPR=3.62315;DPRA=3.01;ODDS=63.3268;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9338;PAIRED=0.982456;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.911;Dels=0.0;FS=3.296 [...]
+chr2 8178735 . A G 2867.29 PASS SOMATIC;NS=2;DP=417;DPB=417.0;AC=1;AN=3;AF=0.25;RO=306;AO=111;PRO=0.0;PAO=0.0;QR=11837;QA=4244;PQR=0.0;PQA=0.0;SRF=156;SRR=150;SAF=58;SAR=53;SRP=3.26577;SAP=3.49937;AB=0.341538;ABP=73.8938;RUN=1;RPP=7.41193;RPPR=11.2136;RPL=63.0;RPR=48.0;EPP=15.2371;EPPR=4.40118;DPRA=3.53261;ODDS=58.4033;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990991;PAIREDR=0.996732;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.86;Dels=0.0;FS=1 [...]
+chr2 8178798 . C T 2122.23 PASS SOMATIC;NS=2;DP=303;DPB=303.0;AC=1;AN=3;AF=0.25;RO=220;AO=83;PRO=0.0;PAO=0.0;QR=8479;QA=3184;PQR=0.0;PQA=0.0;SRF=74;SRR=146;SAF=25;SAR=58;SRP=54.1781;SAP=31.5011;AB=0.344398;ABP=53.693;RUN=1;RPP=12.4549;RPPR=48.6507;RPL=51.0;RPR=32.0;EPP=3.24576;EPPR=10.7486;DPRA=3.8871;ODDS=39.6739;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987952;PAIREDR=0.995455;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.107;Dels=0.0;FS=1.12 [...]
+chr2 12002854 . C A 6476.735000000001 REJECT NS=2;DP=393;DPB=448.0;AC=2;AN=4;AF=0.5;RO=219;AO=229;PRO=0.0;PAO=0.0;QR=8313;QA=8888;PQR=0.0;PQA=0.0;SRF=92;SRR=127;SAF=96;SAR=133;SRP=15.1567;SAP=15.9917;AB=0.511161;ABP=3.495;RUN=1;RPP=7.19204;RPPR=3.02022;RPL=125.0;RPR=104.0;EPP=20.5433;EPPR=33.0044;DPRA=0.0;ODDS=314.376;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991266;PAIREDR=0.995434;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.845;Dels=0.0;FS=0.368;Ha [...]
+chr2 13620587 . A G 5041.545 REJECT NS=2;DP=308;DPB=357.0;AC=2;AN=4;AF=0.5;RO=179;AO=178;PRO=0.0;PAO=0.0;QR=6929;QA=6838;PQR=0.0;PQA=0.0;SRF=58;SRR=121;SAF=67;SAR=111;SRP=51.1588;SAP=26.6281;AB=0.498599;ABP=3.01638;RUN=1;RPP=3.79105;RPPR=7.38964;RPL=93.0;RPR=85.0;EPP=28.824;EPPR=10.5923;DPRA=0.0;ODDS=267.782;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994382;PAIREDR=0.988827;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6405;Dels=0.0;FS=2.5465;HaplotypeS [...]
+chr2 15983164 . C T 5612.79 REJECT NS=2;DP=371;DPB=418.0;AC=2;AN=4;AF=0.5;RO=219;AO=199;PRO=0.0;PAO=0.0;QR=8471;QA=7570;PQR=0.0;PQA=0.0;SRF=116;SRR=103;SAF=109;SAR=90;SRP=4.686;SAP=6.9495;AB=0.476077;ABP=5.08826;RUN=1;RPP=3.02121;RPPR=3.49615;RPL=99.0;RPR=100.0;EPP=3.54498;EPPR=8.25555;DPRA=0.0;ODDS=233.227;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.98995;PAIREDR=0.995434;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.415;Dels=0.0;FS=1.3095;HaplotypeSco [...]
+chr2 15983501 . T C 13729.05 REJECT NS=2;DP=364;DPB=413.0;AC=4;AN=4;AF=1.0;RO=0;AO=413;PRO=0.0;PAO=0.0;QR=0;QA=15692;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=206;SAR=207;SRP=0.0;SAP=3.01556;AB=0.0;ABP=0.0;RUN=1;RPP=5.32899;RPPR=0.0;RPL=217.0;RPR=196.0;EPP=3.64649;EPPR=0.0;DPRA=0.0;ODDS=62.952;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.983051;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.6975;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.83;SOR=0.7 [...]
+chr2 15983519 . A G 3143.3 PASS SOMATIC;NS=2;DP=408;DPB=408.0;AC=1;AN=3;AF=0.25;RO=290;AO=118;PRO=0.0;PAO=0.0;QR=10983;QA=4490;PQR=0.0;PQA=0.0;SRF=149;SRR=141;SAF=55;SAR=63;SRP=3.48952;SAP=4.18805;AB=0.383117;ABP=39.5587;RUN=1;RPP=3.08391;RPPR=4.08855;RPL=60.0;RPR=58.0;EPP=10.3712;EPPR=4.47792;DPRA=3.08;ODDS=63.344;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991525;PAIREDR=0.982759;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.36;Dels=0.0;FS=3.23; [...]
+chr2 18013072 . A G 7584.41 REJECT NS=2;DP=299;DPB=337.0;AC=2;AN=4;AF=0.5;RO=89;AO=248;PRO=0.0;PAO=0.0;QR=3471;QA=9625;PQR=0.0;PQA=0.0;SRF=62;SRR=27;SAF=164;SAR=84;SRP=32.8985;SAP=59.0483;AB=0.735905;ABP=165.909;RUN=1;RPP=32.4653;RPPR=18.2594;RPL=95.0;RPR=153.0;EPP=15.6539;EPPR=3.62026;DPRA=0.0;ODDS=211.56;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991935;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.2175;Dels=0.0;FS=0.314;HaplotypeScore=6.9 [...]
+chr2 19514304 . T G 8245.630000000001 REJECT NS=2;DP=366;DPB=417.0;AC=3;AN=4;AF=0.75;RO=119;AO=298;PRO=0.0;PAO=0.0;QR=4552;QA=11268;PQR=0.0;PQA=0.0;SRF=70;SRR=49;SAF=146;SAR=152;SRP=11.0575;SAP=3.27263;AB=0.623418;ABP=44.818;RUN=1;RPP=4.87573;RPPR=3.02855;RPL=141.0;RPR=157.0;EPP=59.4394;EPPR=11.0575;DPRA=0.0;ODDS=63.949;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.386;Dels=0.0;FS=3.4745;Haplotype [...]
+chr2 19514400 . C T 2301.04 PASS SOMATIC;NS=2;DP=228;DPB=228.0;AC=1;AN=3;AF=0.25;RO=146;AO=82;PRO=0.0;PAO=0.0;QR=5537;QA=3194;PQR=0.0;PQA=0.0;SRF=32;SRR=114;SAF=27;SAR=55;SRP=103.017;SAP=23.7717;AB=0.476744;ABP=3.81829;RUN=1;RPP=37.3302;RPPR=53.0434;RPL=59.0;RPR=23.0;EPP=3.11623;EPPR=3.06979;DPRA=3.07143;ODDS=35.9001;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.403;Dels=0.0;FS=7.698;Haplot [...]
+chr2 25462327 . C G 2016.29 REJECT NS=2;DP=345;DPB=391.0;AC=2;AN=4;AF=0.5;RO=291;AO=100;PRO=0.0;PAO=0.0;QR=11187;QA=3881;PQR=0.0;PQA=0.0;SRF=186;SRR=105;SAF=57;SAR=43;SRP=51.9692;SAP=7.26639;AB=0.255754;ABP=205.613;RUN=1;RPP=3.79203;RPPR=30.7768;RPL=47.0;RPR=53.0;EPP=8.56927;EPPR=3.19685;DPRA=0.0;ODDS=227.822;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4735;Dels=0.0;FS=3.4215;HaplotypeScore=1.9 [...]
+chr2 25463483 . G A 6493.165000000001 REJECT NS=2;DP=286;DPB=326.0;AC=3;AN=4;AF=0.75;RO=96;AO=230;PRO=0.0;PAO=0.0;QR=3702;QA=8892;PQR=0.0;PQA=0.0;SRF=62;SRR=34;SAF=129;SAR=101;SRP=20.744;SAP=10.4122;AB=0.611336;ABP=29.6042;RUN=1;RPP=79.4839;RPPR=35.6729;RPL=70.0;RPR=160.0;EPP=3.0103;EPPR=5.27225;DPRA=0.0;ODDS=50.2989;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.351;Dels=0.0;FS=4.7415;HaplotypeSco [...]
+chr2 25469502 . C T 2240.13 REJECT NS=2;DP=376;DPB=427.0;AC=2;AN=4;AF=0.5;RO=317;AO=110;PRO=0.0;PAO=0.0;QR=12215;QA=4247;PQR=0.0;PQA=0.0;SRF=175;SRR=142;SAF=65;SAR=45;SRP=10.47;SAP=10.9066;AB=0.257611;ABP=220.915;RUN=1;RPP=5.85295;RPPR=3.01715;RPL=49.0;RPR=61.0;EPP=4.98437;EPPR=3.01715;DPRA=0.0;ODDS=232.486;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.981818;PAIREDR=0.987382;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.016;Dels=0.0;FS=1.2955;HaplotypeSc [...]
+chr2 25469913 . C T 7127.115 REJECT NS=2;DP=314;DPB=369.0;AC=3;AN=4;AF=0.75;RO=100;AO=269;PRO=0.0;PAO=0.0;QR=3804;QA=10156;PQR=0.0;PQA=0.0;SRF=57;SRR=43;SAF=167;SAR=102;SRP=7.26639;SAP=37.1161;AB=0.616858;ABP=33.9683;RUN=1;RPP=66.9517;RPPR=41.3151;RPL=90.0;RPR=179.0;EPP=10.7679;EPPR=8.56927;DPRA=0.0;ODDS=68.2834;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992565;PAIREDR=0.98;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.23;Dels=0.0;FS=5.344;HaplotypeScor [...]
+chr2 29318077 . A G 6215.895 REJECT NS=2;DP=382;DPB=442.0;AC=2;AN=4;AF=0.5;RO=221;AO=221;PRO=0.0;PAO=0.0;QR=8542;QA=8558;PQR=0.0;PQA=0.0;SRF=97;SRR=124;SAF=115;SAR=106;SRP=10.1732;SAP=3.80618;AB=0.5;ABP=3.0103;RUN=1;RPP=3.49176;RPPR=3.25594;RPL=107.0;RPR=114.0;EPP=4.67084;EPPR=3.25594;DPRA=0.0;ODDS=387.632;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995475;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6975;Dels=0.0;FS=8.6565;HaplotypeScore=5. [...]
+chr2 29318100 . T A 6131.375 REJECT NS=2;DP=395;DPB=460.0;AC=2;AN=4;AF=0.5;RO=232;AO=228;PRO=0.0;PAO=0.0;QR=8810;QA=8634;PQR=0.0;PQA=0.0;SRF=95;SRR=137;SAF=109;SAR=119;SRP=19.521;SAP=3.9627;AB=0.495652;ABP=3.08583;RUN=1;RPP=4.877;RPPR=10.3484;RPL=121.0;RPR=107.0;EPP=3.16268;EPPR=6.04287;DPRA=0.0;ODDS=399.886;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995614;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.2895;Dels=0.0;FS=4.14;HaplotypeScore=8. [...]
+chr2 29416366 . G C 6006.88 REJECT NS=2;DP=379;DPB=428.0;AC=2;AN=4;AF=0.5;RO=212;AO=216;PRO=0.0;PAO=0.0;QR=8109;QA=8239;PQR=0.0;PQA=0.0;SRF=101;SRR=111;SAF=100;SAR=116;SRP=4.03458;SAP=5.5839;AB=0.504673;ABP=3.09148;RUN=1;RPP=3.05051;RPPR=11.0407;RPL=109.0;RPR=107.0;EPP=3.37221;EPPR=6.32897;DPRA=0.0;ODDS=275.996;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99537;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0985;Dels=0.0;FS=3.394;HaplotypeScore [...]
+chr2 29416481 . T C 1788.38 REJECT NS=2;DP=402;DPB=456.0;AC=2;AN=4;AF=0.5;RO=359;AO=97;PRO=0.0;PAO=0.0;QR=13698;QA=3674;PQR=0.0;PQA=0.0;SRF=171;SRR=188;SAF=41;SAR=56;SRP=4.75837;SAP=8.04722;AB=0.212719;ABP=329.893;RUN=1;RPP=9.47994;RPPR=20.001;RPL=57.0;RPR=40.0;EPP=4.82359;EPPR=5.67776;DPRA=0.0;ODDS=175.887;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989691;PAIREDR=0.997214;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9055;Dels=0.0;FS=4.4015;HaplotypeSc [...]
+chr2 29416572 . T C 12624.5 REJECT NS=2;DP=336;DPB=385.0;AC=4;AN=4;AF=1.0;RO=1;AO=384;PRO=0.0;PAO=0.0;QR=2;QA=14549;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=194;SAR=190;SRP=5.18177;SAP=3.10078;AB=0.0;ABP=0.0;RUN=1;RPP=3.37221;RPPR=5.18177;RPL=188.0;RPR=196.0;EPP=12.0581;EPPR=5.18177;DPRA=0.0;ODDS=66.4318;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9974;MQMR=60.0;PAIRED=0.994792;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD= [...]
+chr2 29416615 . G A 2706.91 PASS SOMATIC;NS=2;DP=346;DPB=346.0;AC=1;AN=3;AF=0.25;RO=244;AO=102;PRO=0.0;PAO=0.0;QR=9262;QA=3891;PQR=0.0;PQA=0.0;SRF=124;SRR=120;SAF=52;SAR=50;SRP=3.15269;SAP=3.09546;AB=0.373626;ABP=40.8798;RUN=1;RPP=4.37279;RPPR=3.33068;RPL=55.0;RPR=47.0;EPP=3.35092;EPPR=5.89373;DPRA=3.73973;ODDS=46.5487;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995902;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.519;Dels=0.0;FS=0.96; [...]
+chr2 29416794 . G A 1916.6 PASS SOMATIC;NS=2;DP=225;DPB=225.0;AC=1;AN=3;AF=0.25;RO=153;AO=72;PRO=0.0;PAO=0.0;QR=5909;QA=2764;PQR=0.0;PQA=0.0;SRF=39;SRR=114;SAF=20;SAR=52;SRP=82.8438;SAP=33.8935;AB=0.413793;ABP=14.2421;RUN=1;RPP=17.6074;RPPR=14.9463;RPL=47.0;RPR=25.0;EPP=6.02623;EPPR=14.9463;DPRA=3.41176;ODDS=32.8217;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986928;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.503;Dels=0.0;FS=1.36;Hap [...]
+chr2 29430942 . GTC G 1557.45 REJECT NS=2;DP=368;DPB=404.857;AC=2;AN=4;AF=0.5;RO=277;AO=83;PRO=56.0;PAO=35.0;QR=10487;QA=2912;PQR=2015.5;PQA=1249.5;SRF=102;SRR=175;SAF=24;SAR=59;SRP=44.7857;SAP=35.0591;AB=0.225543;ABP=243.784;RUN=1;RPP=6.17594;RPPR=28.48;RPL=47.0;RPR=36.0;EPP=3.66436;EPPR=10.5438;DPRA=0.0;ODDS=79.4939;GTI=0;TYPE=del;CIGAR=1M2D11M;NUMALT=1;MEANALT=5.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=0.987952;PAIREDR=0.99639;technology.ILLUMINA=1.0;BaseQRankSum=-1.912;FS=10.557;MLEAC=1;MLE [...]
+chr2 29444095 . C T 9550.095000000001 REJECT NS=2;DP=252;DPB=285.0;AC=4;AN=4;AF=1.0;RO=0;AO=285;PRO=0.0;PAO=0.0;QR=0;QA=10887;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=108;SAR=177;SRP=0.0;SAP=39.2853;AB=0.0;ABP=0.0;RUN=1;RPP=7.04086;RPPR=0.0;RPL=154.0;RPR=131.0;EPP=4.29794;EPPR=0.0;DPRA=0.0;ODDS=45.4787;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.465;S [...]
+chr2 29446202 . G A 4089.21 REJECT NS=2;DP=239;DPB=268.0;AC=2;AN=4;AF=0.5;RO=125;AO=142;PRO=0.0;PAO=0.0;QR=4708;QA=5501;PQR=0.0;PQA=0.0;SRF=82;SRR=43;SAF=95;SAR=47;SRP=29.4328;SAP=38.2432;AB=0.529851;ABP=5.08454;RUN=1;RPP=47.6019;RPPR=15.6743;RPL=44.0;RPR=98.0;EPP=5.21236;EPPR=8.03074;DPRA=0.0;ODDS=186.303;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985915;PAIREDR=0.992;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.4095;Dels=0.0;FS=0.2695;HaplotypeScore= [...]
+chr2 29446701 . T C 5795.0650000000005 REJECT NS=2;DP=358;DPB=423.0;AC=2;AN=4;AF=0.5;RO=212;AO=211;PRO=0.0;PAO=0.0;QR=8131;QA=8129;PQR=0.0;PQA=0.0;SRF=119;SRR=93;SAF=118;SAR=93;SRP=9.93443;SAP=9.44239;AB=0.498818;ABP=3.01543;RUN=1;RPP=3.8439;RPPR=9.93443;RPL=110.0;RPR=101.0;EPP=8.45442;EPPR=5.63246;DPRA=0.0;ODDS=418.483;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995261;PAIREDR=0.990566;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6385;Dels=0.0;FS=1.136 [...]
+chr2 29446721 . A G 13943.0 REJECT NS=2;DP=370;DPB=432.0;AC=4;AN=4;AF=1.0;RO=0;AO=432;PRO=0.0;PAO=0.0;QR=0;QA=16468;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=231;SAR=201;SRP=0.0;SAP=7.5342;AB=0.0;ABP=0.0;RUN=1;RPP=4.6389;RPPR=0.0;RPL=225.0;RPR=207.0;EPP=21.1059;EPPR=0.0;DPRA=0.0;ODDS=81.627;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997685;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8574;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.865;SOR=0.82 [...]
+chr2 29447108 . G A 10211.5 REJECT NS=2;DP=370;DPB=416.0;AC=2;AN=4;AF=0.5;RO=81;AO=335;PRO=0.0;PAO=0.0;QR=3112;QA=12678;PQR=0.0;PQA=0.0;SRF=43;SRR=38;SAF=160;SAR=175;SRP=3.68051;SAP=4.46875;AB=0.805288;ABP=339.776;RUN=1;RPP=4.46875;RPPR=12.6881;RPL=175.0;RPR=160.0;EPP=3.01678;EPPR=3.03711;DPRA=0.0;ODDS=109.563;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99403;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.668;Dels=0.0;FS=1.958;HaplotypeScore= [...]
+chr2 29447253 . A G 2120.75 REJECT NS=2;DP=382;DPB=438.0;AC=2;AN=4;AF=0.5;RO=338;AO=100;PRO=0.0;PAO=0.0;QR=12855;QA=3818;PQR=0.0;PQA=0.0;SRF=153;SRR=185;SAF=50;SAR=50;SRP=9.58896;SAP=3.0103;AB=0.228311;ABP=283.834;RUN=1;RPP=11.6962;RPPR=3.93542;RPL=40.0;RPR=60.0;EPP=3.35774;EPPR=3.036;DPRA=0.0;ODDS=124.493;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0275;Dels=0.0;FS=2.4095;HaplotypeScore=6.7793 [...]
+chr2 29448760 . C T 1884.145 REJECT NS=2;DP=409;DPB=472.0;AC=2;AN=4;AF=0.5;RO=372;AO=100;PRO=0.0;PAO=0.0;QR=14179;QA=3735;PQR=0.0;PQA=0.0;SRF=168;SRR=204;SAF=42;SAR=58;SRP=10.5754;SAP=8.56927;AB=0.211864;ABP=343.379;RUN=1;RPP=3.35774;RPPR=4.50465;RPL=48.0;RPR=52.0;EPP=3.0103;EPPR=7.58674;DPRA=0.0;ODDS=121.923;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997312;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.666;Dels=0.0;FS=0.3465;HaplotypeScore= [...]
+chr2 29448846 . C G 5681.790000000001 REJECT NS=2;DP=358;DPB=406.0;AC=2;AN=4;AF=0.5;RO=199;AO=207;PRO=0.0;PAO=0.0;QR=7520;QA=7706;PQR=0.0;PQA=0.0;SRF=107;SRR=92;SAF=97;SAR=110;SRP=5.46548;SAP=4.78314;AB=0.509852;ABP=3.3526;RUN=1;RPP=3.52432;RPPR=3.89417;RPL=100.0;RPR=107.0;EPP=9.56668;EPPR=5.46548;DPRA=0.0;ODDS=298.782;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995169;PAIREDR=0.98995;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7725;Dels=0.0;FS=3.7525; [...]
+chr2 29449005 . G T 2999.74 PASS SOMATIC;NS=2;DP=391;DPB=391.0;AC=1;AN=3;AF=0.25;RO=279;AO=112;PRO=0.0;PAO=0.0;QR=10668;QA=4277;PQR=0.0;PQA=0.0;SRF=120;SRR=159;SAF=54;SAR=58;SRP=14.8483;SAP=3.32051;AB=0.382253;ABP=38.2949;RUN=1;RPP=3.70827;RPPR=18.771;RPL=59.0;RPR=53.0;EPP=3.08785;EPPR=4.76149;DPRA=2.9898;ODDS=62.1241;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996416;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.435;Dels=0.0;FS=3.276; [...]
+chr2 29449344 . CAA C 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=31.4354;PAO=26.9354;QR=0;QA=2;PQR=1062.05;PQA=892.55;SRF=0;SRR=0;SAF=0;SAR=1;SRP=0.0;SAP=5.18177;AB=0.0555556;ABP=33.8935;RUN=1;RPP=5.18177;RPPR=0.0;RPL=1.0;RPR=0.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=del;CIGAR=1M2D40M;NUMALT=21;MEANALT=14.0;LEN=2;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC: [...]
+chr2 29449344 . CAAA C 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=31.4354;PAO=22.9354;QR=0;QA=27;PQR=1062.05;PQA=787.55;SRF=0;SRR=0;SAF=0;SAR=1;SRP=0.0;SAP=5.18177;AB=0.0555556;ABP=33.8935;RUN=1;RPP=5.18177;RPPR=0.0;RPL=0.0;RPR=1.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=del;CIGAR=1M3D39M;NUMALT=21;MEANALT=14.0;LEN=3;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallH [...]
+chr2 29449344 . CAAAA C 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=4;PRO=31.4354;PAO=22.3798;QR=0;QA=73;PQR=1062.05;PQA=757.327;SRF=0;SRR=0;SAF=1;SAR=3;SRP=0.0;SAP=5.18177;AB=0.222222;ABP=15.074;RUN=1;RPP=3.0103;RPPR=0.0;RPL=2.0;RPR=2.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=del;CIGAR=1M4D38M;NUMALT=21;MEANALT=14.0;LEN=4;MQM=62.5;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.493;FS=0.0;MLEAC=1;MLEAF=0.5;M [...]
+chr2 29449344 . CAAAAA C 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=2;PRO=31.4354;PAO=19.1441;QR=0;QA=29;PQR=1062.05;PQA=655.699;SRF=0;SRR=0;SAF=1;SAR=1;SRP=0.0;SAP=3.0103;AB=0.0740741;ABP=45.5551;RUN=1;RPP=7.35324;RPPR=0.0;RPL=0.0;RPR=2.0;EPP=3.0103;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=del;CIGAR=1M5D37M;NUMALT=21;MEANALT=11.5;LEN=5;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.0;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=56 [...]
+chr2 29449344 . CAAAAAAA C 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=31.4354;PAO=18.0495;QR=0;QA=2;PQR=1062.05;PQA=619.194;SRF=0;SRR=0;SAF=0;SAR=1;SRP=0.0;SAP=5.18177;AB=0.0555556;ABP=33.8935;RUN=1;RPP=5.18177;RPPR=0.0;RPL=0.0;RPR=1.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=del;CIGAR=1M7D35M;NUMALT=21;MEANALT=14.0;LEN=7;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:C [...]
+chr2 29449361 . AAAAAAAAGAGGAGGAG GGGGAGGAA 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=31.4354;PAO=2.26163;QR=0;QA=15;PQR=1062.05;PQA=68.1857;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.0555556;ABP=33.8935;RUN=1;RPP=5.18177;RPPR=0.0;RPL=0.0;RPR=1.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=complex;CIGAR=1M8D17M1X6M1X9M;NUMALT=21;MEANALT=14.0;LEN=35;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR: [...]
+chr2 29449362 . AAAAAAAGAGGAGGAG GAGGAGGAA 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=31.4354;PAO=3.07116;QR=0;QA=16;PQR=1062.05;PQA=83.7095;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.111111;ABP=14.8328;RUN=1;RPP=5.18177;RPPR=0.0;RPL=0.0;RPR=1.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=complex;CIGAR=1M7D25M1X9M;NUMALT=21;MEANALT=9.0;LEN=36;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr2 29449362 . AAAAAAAGAGGAGGAGAAT GAGGAGGAGAAA 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=31.4354;PAO=2.84199;QR=0;QA=16;PQR=1062.05;PQA=69.0429;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.0555556;ABP=33.8935;RUN=1;RPP=5.18177;RPPR=0.0;RPL=1.0;RPR=0.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=complex;CIGAR=1M7D28M1X6M;NUMALT=21;MEANALT=14.0;LEN=36;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR [...]
+chr2 29449362 . AAAAAAAGAGGAGGAGAAT GAGGAGGAGAAC 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=31.4354;PAO=1.84199;QR=0;QA=16;PQR=1062.05;PQA=53.0429;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.111111;ABP=14.8328;RUN=1;RPP=5.18177;RPPR=0.0;RPL=1.0;RPR=0.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=complex;CIGAR=1M7D28M1X6M;NUMALT=21;MEANALT=9.0;LEN=36;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:A [...]
+chr2 29449363 . AAAAAAGAGGA GGG 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=31.4354;PAO=4.21198;QR=0;QA=2;PQR=1062.05;PQA=135.39;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.111111;ABP=14.8328;RUN=1;RPP=5.18177;RPPR=0.0;RPL=1.0;RPR=0.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=complex;CIGAR=18M8D3M1X13M;NUMALT=21;MEANALT=9.0;LEN=35;MQM=58.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr2 29449364 . AAAAAGAGGAGGAG GGGGAGGAA 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=31.4354;PAO=3.2991;QR=0;QA=15;PQR=1062.05;PQA=102.947;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.0555556;ABP=33.8935;RUN=1;RPP=5.18177;RPPR=0.0;RPL=0.0;RPR=1.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=complex;CIGAR=1M5D20M1X6M1X9M;NUMALT=21;MEANALT=14.0;LEN=38;MQM=40.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:Q [...]
+chr2 29449365 . AAAAGA GG 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=31.4354;PAO=8.5965;QR=0;QA=15;PQR=1062.05;PQA=263.394;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.111111;ABP=14.8328;RUN=1;RPP=5.18177;RPPR=0.0;RPL=1.0;RPR=0.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=complex;CIGAR=1M4D21M1X16M;NUMALT=21;MEANALT=9.0;LEN=39;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr2 29449365 . AAAAGAGGA GGGGG 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=2;PRO=31.4354;PAO=5.53936;QR=0;QA=28;PQR=1062.05;PQA=178.194;SRF=0;SRR=0;SAF=2;SAR=0;SRP=0.0;SAP=7.35324;AB=0.0740741;ABP=45.5551;RUN=1;RPP=7.35324;RPPR=0.0;RPL=0.0;RPR=2.0;EPP=7.35324;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=complex;CIGAR=1M4D21M1X2M1X13M;NUMALT=21;MEANALT=11.5;LEN=39;MQM=62.5;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr2 29449365 . AAAAGAGGAGGAG GAGGAGGAA 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=2;PRO=31.4354;PAO=4.75148;QR=0;QA=32;PQR=1062.05;PQA=139.043;SRF=0;SRR=0;SAF=2;SAR=0;SRP=0.0;SAP=7.35324;AB=0.111111;ABP=26.6552;RUN=1;RPP=7.35324;RPPR=0.0;RPL=0.0;RPR=2.0;EPP=7.35324;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=complex;CIGAR=1M4D28M1X9M;NUMALT=21;MEANALT=14.0;LEN=39;MQM=65.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr2 29449365 . AAAAGAGGAGGAGAATGGGAGC GGGGGGGAAAAGGGGAGA 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=4;AF=0.5;RO=0;AO=1;PRO=31.4354;PAO=3.47469;QR=0;QA=15;PQR=1062.05;PQA=100.44;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.111111;ABP=14.8328;RUN=1;RPP=5.18177;RPPR=0.0;RPL=0.0;RPR=1.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=complex;CIGAR=1M4D21M1X2M1X3M1X2M1X5M1X;NUMALT=21;MEANALT=9.0;LEN=39;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIAL [...]
+chr2 29449366 . AAAGAGGA GAGGG 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=31.4354;PAO=8.09491;QR=0;QA=15;PQR=1062.05;PQA=247.416;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.0555556;ABP=33.8935;RUN=1;RPP=5.18177;RPPR=0.0;RPL=0.0;RPR=1.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=complex;CIGAR=1M3D25M1X13M;NUMALT=21;MEANALT=14.0;LEN=40;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr2 29449366 . AAAGAGGA GGGGG 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=31.4354;PAO=7.09491;QR=0;QA=25;PQR=1062.05;PQA=232.416;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.0555556;ABP=33.8935;RUN=1;RPP=5.18177;RPPR=0.0;RPL=0.0;RPR=1.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=complex;CIGAR=1M3D22M1X2M1X13M;NUMALT=21;MEANALT=14.0;LEN=40;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr2 29449366 . AAAGAGGAGGAG GAGGAGGAA 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=31.4354;PAO=6.30704;QR=0;QA=16;PQR=1062.05;PQA=193.265;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.0555556;ABP=33.8935;RUN=1;RPP=5.18177;RPPR=0.0;RPL=0.0;RPR=1.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=complex;CIGAR=1M3D29M1X9M;NUMALT=21;MEANALT=14.0;LEN=40;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr2 29449366 . AAAGAGGAGGAGAAT GAGGGGGAAAAA 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=31.4354;PAO=4.9112;QR=0;QA=15;PQR=1062.05;PQA=158.848;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.111111;ABP=14.8328;RUN=1;RPP=5.18177;RPPR=0.0;RPL=0.0;RPR=1.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=complex;CIGAR=1M3D25M1X3M1X2M1X6M;NUMALT=21;MEANALT=9.0;LEN=40;MQM=41.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:Q [...]
+chr2 29449366 . AAAGAGGAGGAGAATGGGA GGAGGAGAATGGGG 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=31.4354;PAO=4.4112;QR=0;QA=2;PQR=1062.05;PQA=141.948;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.111111;ABP=14.8328;RUN=1;RPP=5.18177;RPPR=0.0;RPL=1.0;RPR=0.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=complex;CIGAR=21M5D14M1X2M;NUMALT=21;MEANALT=9.0;LEN=38;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR: [...]
+chr2 29449368 . AGAGGAGGAGAAT GGAGGAAAAG 5210.39 REJECT NS=2;DP=27;DPB=118.953;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=31.4354;PAO=12.4112;QR=0;QA=14;PQR=1062.05;PQA=342.348;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.0555556;ABP=33.8935;RUN=1;RPP=5.18177;RPPR=0.0;RPL=0.0;RPR=1.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=18.2346;GTI=0;TYPE=complex;CIGAR=23M3D7M1X2M1X6M;NUMALT=21;MEANALT=14.0;LEN=40;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO: [...]
+chr2 29449423 . G A 6003.585 REJECT NS=2;DP=276;DPB=315.0;AC=3;AN=4;AF=0.75;RO=90;AO=225;PRO=0.0;PAO=0.0;QR=3201;QA=8210;PQR=0.0;PQA=0.0;SRF=69;SRR=21;SAF=158;SAR=67;SRP=58.6;SAP=82.9301;AB=0.623431;ABP=34.6375;RUN=1;RPP=9.04217;RPPR=5.42305;RPL=100.0;RPR=125.0;EPP=3.25157;EPPR=3.39634;DPRA=0.0;ODDS=48.2523;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0667;MQMR=60.1111;PAIRED=0.995556;PAIREDR=0.966667;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.038;Dels=0.0;FS=1.3605;Haplot [...]
+chr2 29449819 . C T 2720.43 PASS SOMATIC;NS=2;DP=418;DPB=418.0;AC=1;AN=3;AF=0.25;RO=315;AO=103;PRO=0.0;PAO=0.0;QR=12060;QA=4014;PQR=0.0;PQA=0.0;SRF=143;SRR=172;SAF=39;SAR=64;SRP=8.80779;SAP=16.1867;AB=0.338816;ABP=71.6117;RUN=1;RPP=3.03138;RPPR=25.4075;RPL=52.0;RPR=51.0;EPP=4.71796;EPPR=3.01719;DPRA=2.66667;ODDS=72.1109;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990291;PAIREDR=0.993651;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.245;Dels=0.0;FS [...]
+chr2 29451790 . T C 90.6937 REJECT NS=2;DP=422;DPB=435.0;AC=2;AN=2;AF=0.0;RO=359;AO=17;PRO=13.0;PAO=5.5;QR=11200;QA=238;PQR=334.0;PQA=136.5;SRF=189;SRR=170;SAF=17;SAR=0;SRP=5.19387;SAP=39.9253;AB=0.0625;ABP=189.214;RUN=1;RPP=18.4661;RPPR=3.06474;RPL=14.0;RPR=3.0;EPP=18.4661;EPPR=8.82307;DPRA=0.0;ODDS=16.9701;GTI=0;TYPE=snp;CIGAR=1X3M;NUMALT=3;MEANALT=5.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994429;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr2 29451790 . TCCA CCCC 90.6937 REJECT NS=2;DP=422;DPB=435.0;AC=2;AN=2;AF=0.0;RO=359;AO=9;PRO=13.0;PAO=0.0;QR=11200;QA=131;PQR=334.0;PQA=0.0;SRF=189;SRR=170;SAF=9;SAR=0;SRP=5.19387;SAP=22.5536;AB=0.0535714;ABP=196.892;RUN=1;RPP=22.5536;RPPR=3.06474;RPL=9.0;RPR=0.0;EPP=22.5536;EPPR=8.82307;DPRA=0.0;ODDS=16.9701;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=3;MEANALT=5.5;LEN=4;MQM=57.7778;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994429;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr2 29451793 . A C 90.6937 REJECT NS=2;DP=422;DPB=435.0;AC=2;AN=3;AF=0.25;RO=359;AO=31;PRO=13.0;PAO=7.5;QR=11200;QA=503;PQR=334.0;PQA=197.5;SRF=189;SRR=170;SAF=29;SAR=2;SRP=5.19387;SAP=54.0749;AB=0.0892857;ABP=167.112;RUN=1;RPP=8.68415;RPPR=3.06474;RPL=20.0;RPR=11.0;EPP=8.68415;EPPR=8.82307;DPRA=0.0;ODDS=16.9701;GTI=0;TYPE=snp;CIGAR=3M1X;NUMALT=3;MEANALT=5.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994429;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr2 29451799 . T C 145.587 REJECT NS=2;DP=417;DPB=429.25;AC=2;AN=2;AF=0.0;RO=313;AO=37;PRO=10.0;PAO=6.5;QR=9901;QA=529;PQR=222.0;PQA=108.0;SRF=132;SRR=181;SAF=37;SAR=0;SRP=19.6675;SAP=83.3548;AB=0.117117;ABP=144.352;RUN=1;RPP=10.1116;RPPR=5.51478;RPL=24.0;RPR=13.0;EPP=10.1116;EPPR=8.84483;DPRA=0.0;ODDS=9.9964;GTI=0;TYPE=snp;CIGAR=1X3M;NUMALT=3;MEANALT=8.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99361;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr2 29451799 . TCCG CCCC 145.587 REJECT NS=2;DP=417;DPB=429.25;AC=2;AN=2;AF=0.0;RO=313;AO=26;PRO=10.0;PAO=1.5;QR=9901;QA=383;PQR=222.0;PQA=9.0;SRF=132;SRR=181;SAF=26;SAR=0;SRP=19.6675;SAP=59.4686;AB=0.0990991;ABP=157.967;RUN=1;RPP=19.3799;RPPR=5.51478;RPL=20.0;RPR=6.0;EPP=19.3799;EPPR=8.84483;DPRA=0.0;ODDS=9.9964;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=3;MEANALT=8.5;LEN=4;MQM=59.2308;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99361;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr2 29451802 . G C 145.587 REJECT NS=2;DP=417;DPB=429.25;AC=2;AN=3;AF=0.25;RO=313;AO=24;PRO=10.0;PAO=5.0;QR=9901;QA=395;PQR=222.0;PQA=123.0;SRF=132;SRR=181;SAF=24;SAR=0;SRP=19.6675;SAP=55.1256;AB=0.0990991;ABP=157.967;RUN=1;RPP=12.0581;RPPR=5.51478;RPL=17.0;RPR=7.0;EPP=12.0581;EPPR=8.84483;DPRA=0.0;ODDS=9.9964;GTI=0;TYPE=snp;CIGAR=3M1X;NUMALT=3;MEANALT=8.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99361;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr2 29455199 . A T 1781.365 REJECT NS=2;DP=353;DPB=407.0;AC=2;AN=4;AF=0.5;RO=315;AO=92;PRO=0.0;PAO=0.0;QR=12093;QA=3513;PQR=0.0;PQA=0.0;SRF=169;SRR=146;SAF=49;SAR=43;SRP=6.65699;SAP=3.86001;AB=0.226044;ABP=268.33;RUN=1;RPP=12.4515;RPPR=12.4476;RPL=36.0;RPR=56.0;EPP=3.86001;EPPR=5.49888;DPRA=0.0;ODDS=143.907;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993651;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3685;Dels=0.0;FS=6.045;HaplotypeScore= [...]
+chr2 29455267 . A G 13067.7 REJECT NS=2;DP=345;DPB=389.0;AC=4;AN=4;AF=1.0;RO=1;AO=388;PRO=0.0;PAO=0.0;QR=40;QA=14908;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=166;SAR=222;SRP=5.18177;SAP=20.5612;AB=0.0;ABP=0.0;RUN=1;RPP=11.9648;RPPR=5.18177;RPL=214.0;RPR=174.0;EPP=54.5884;EPPR=5.18177;DPRA=0.0;ODDS=58.6171;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.769;Dels=0.0;FS=1.797;HaplotypeScore=1.9997;MLEAC=2;MLE [...]
+chr2 29497967 . G A 1635.385 REJECT NS=2;DP=301;DPB=354.0;AC=2;AN=4;AF=0.5;RO=273;AO=81;PRO=0.0;PAO=0.0;QR=10417;QA=3069;PQR=0.0;PQA=0.0;SRF=184;SRR=89;SAF=47;SAR=34;SRP=74.7962;SAP=7.5409;AB=0.228814;ABP=229.138;RUN=1;RPP=10.7579;RPPR=16.3812;RPL=32.0;RPR=49.0;EPP=17.1919;EPPR=22.1081;DPRA=0.0;ODDS=93.0801;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.985348;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.18;Dels=0.0;FS=2.3115;HaplotypeScore=4.8 [...]
+chr2 29543663 . T C 13336.15 REJECT NS=2;DP=356;DPB=408.0;AC=4;AN=4;AF=1.0;RO=0;AO=407;PRO=0.0;PAO=0.0;QR=0;QA=15457;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=202;SAR=205;SRP=0.0;SAP=3.05832;AB=0.0;ABP=0.0;RUN=1;RPP=3.27173;RPPR=0.0;RPL=207.0;RPR=200.0;EPP=11.979;EPPR=0.0;DPRA=0.0;ODDS=68.5337;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995086;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.8569;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.525;SOR=0. [...]
+chr2 29940529 . A T 8633.905 REJECT NS=2;DP=381;DPB=435.0;AC=3;AN=4;AF=0.75;RO=119;AO=316;PRO=0.0;PAO=0.0;QR=4424;QA=11763;PQR=0.0;PQA=0.0;SRF=61;SRR=58;SAF=170;SAR=146;SRP=3.17453;SAP=6.96843;AB=0.637195;ABP=56.6351;RUN=1;RPP=6.33623;RPPR=3.02855;RPL=147.0;RPR=169.0;EPP=17.5509;EPPR=6.09416;DPRA=0.0;ODDS=67.6716;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987342;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.175;Dels=0.0;FS=0.951;HaplotypeSco [...]
+chr2 30143499 . G C 1653.46 REJECT NS=1;DP=48;DPB=48.0;AC=2;AN=4;AF=1.0;RO=0;AO=48;PRO=0.0;PAO=0.0;QR=0;QA=1874;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=18;SAR=30;SRP=0.0;SAP=9.52472;AB=0.0;ABP=0.0;RUN=1;RPP=3.73412;RPPR=0.0;RPL=26.0;RPR=22.0;EPP=3.0103;EPPR=0.0;DPRA=0.0;ODDS=34.6113;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.34;SOR=1.298 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:AD: [...]
+chr2 30240720 . A G 14059.349999999999 REJECT NS=2;DP=377;DPB=431.0;AC=4;AN=4;AF=1.0;RO=3;AO=428;PRO=0.0;PAO=0.0;QR=117;QA=16376;PQR=0.0;PQA=0.0;SRF=0;SRR=3;SAF=237;SAR=191;SRP=9.52472;SAP=13.7459;AB=0.0;ABP=0.0;RUN=1;RPP=4.65412;RPPR=3.73412;RPL=205.0;RPR=223.0;EPP=11.128;EPPR=3.73412;DPRA=0.0;ODDS=71.7069;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.078;Dels=0.0;FS=5.2425;HaplotypeScore=3.9204 [...]
+chr2 30241053 . T C 14109.55 REJECT NS=2;DP=369;DPB=423.0;AC=4;AN=4;AF=1.0;RO=0;AO=423;PRO=0.0;PAO=0.0;QR=0;QA=16271;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=225;SAR=198;SRP=0.0;SAP=6.75262;AB=0.0;ABP=0.0;RUN=1;RPP=3.13864;RPPR=0.0;RPL=209.0;RPR=214.0;EPP=7.9436;EPPR=0.0;DPRA=0.0;ODDS=69.1822;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.98818;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.97;SOR=0.85 [...]
+chr2 30243877 . C G 4396.29 REJECT NS=1;DP=140;DPB=140.0;AC=2;AN=4;AF=1.0;RO=0;AO=137;PRO=0.0;PAO=0.0;QR=0;QA=4969;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=44;SAR=93;SRP=0.0;SAP=41.0665;AB=0.0;ABP=0.0;RUN=1;RPP=3.78696;RPPR=0.0;RPL=65.0;RPR=72.0;EPP=3.15295;EPPR=0.0;DPRA=0.0;ODDS=89.8618;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=59.927;MQMR=0.0;PAIRED=0.978102;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.43;SOR=1.743 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr2 30243931 . C CTT 8.42138 REJECT NS=1;DP=52;DPB=83.1429;AC=1;AN=3;AF=0.0;RO=20;AO=3;PRO=16.25;PAO=16.25;QR=704;QA=69;PQR=563.917;PQA=563.917;SRF=6;SRR=14;SAF=1;SAR=2;SRP=9.95901;SAP=3.73412;AB=0.0576923;ABP=91.3725;RUN=1;RPP=9.52472;RPPR=3.44459;RPL=3.0;RPR=0.0;EPP=3.73412;EPPR=6.91895;DPRA=0.0;ODDS=1.78378;GTI=0;TYPE=ins;CIGAR=1M2I20M;NUMALT=3;MEANALT=13.0;LEN=2;MQM=60.0;MQMR=55.55;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr2 30243931 . C CTTT 8.42138 REJECT NS=1;DP=52;DPB=83.1429;AC=1;AN=4;AF=0.5;RO=20;AO=9;PRO=16.25;PAO=16.25;QR=704;QA=153;PQR=563.917;PQA=563.917;SRF=6;SRR=14;SAF=1;SAR=8;SRP=9.95901;SAP=14.8328;AB=0.173077;ABP=51.2838;RUN=1;RPP=3.25157;RPPR=3.44459;RPL=5.0;RPR=4.0;EPP=3.25157;EPPR=6.91895;DPRA=0.0;ODDS=1.78378;GTI=0;TYPE=ins;CIGAR=1M3I20M;NUMALT=3;MEANALT=13.0;LEN=3;MQM=48.8889;MQMR=55.55;PAIRED=0.888889;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.831;FS=0.0;ML [...]
+chr2 30243931 . CT C 8.42138 REJECT NS=1;DP=52;DPB=83.1429;AC=1;AN=3;AF=0.0;RO=20;AO=5;PRO=16.25;PAO=14.25;QR=704;QA=87;PQR=563.917;PQA=482.25;SRF=6;SRR=14;SAF=0;SAR=5;SRP=9.95901;SAP=13.8677;AB=0.0961538;ABP=76.6733;RUN=1;RPP=6.91895;RPPR=3.44459;RPL=1.0;RPR=4.0;EPP=6.91895;EPPR=6.91895;DPRA=0.0;ODDS=1.78378;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=3;MEANALT=13.0;LEN=1;MQM=52.0;MQMR=55.55;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr2 31502382 . G A 5669.57 REJECT NS=2;DP=232;DPB=262.0;AC=3;AN=4;AF=0.75;RO=62;AO=199;PRO=0.0;PAO=0.0;QR=2393;QA=7597;PQR=0.0;PQA=0.0;SRF=32;SRR=30;SAF=131;SAR=68;SRP=3.15039;SAP=46.3197;AB=0.689655;ABP=66.4323;RUN=1;RPP=97.3875;RPPR=38.8746;RPL=53.0;RPR=146.0;EPP=6.16385;EPPR=5.25182;DPRA=0.0;ODDS=37.8483;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.979899;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.388;Dels=0.0;FS=6.202;HaplotypeScore=2 [...]
+chr2 34505480 . C T 14375.55 REJECT NS=2;DP=376;DPB=434.0;AC=4;AN=4;AF=1.0;RO=0;AO=434;PRO=0.0;PAO=0.0;QR=0;QA=16682;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=250;SAR=184;SRP=0.0;SAP=24.8051;AB=0.0;ABP=0.0;RUN=1;RPP=14.5381;RPPR=0.0;RPL=193.0;RPR=241.0;EPP=12.6969;EPPR=0.0;DPRA=0.0;ODDS=75.438;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995392;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8903;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.92;SOR=0.9 [...]
+chr2 36002916 . C A 550.44 REJECT NS=2;DP=195;DPB=232.957;AC=2;AN=2;AF=0.0;RO=125;AO=6;PRO=42.0;PAO=0.0;QR=4588;QA=109;PQR=1510.17;PQA=0.0;SRF=25;SRR=100;SAF=0;SAR=6;SRP=100.727;SAP=16.0391;AB=0.0307692;ABP=375.936;RUN=1;RPP=3.0103;RPPR=13.8677;RPL=3.0;RPR=3.0;EPP=3.0103;EPPR=3.16665;DPRA=0.0;ODDS=0.155808;GTI=1;TYPE=snp;CIGAR=1X22M;NUMALT=3;MEANALT=8.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV [...]
+chr2 36002916 . C CA 550.44 REJECT NS=2;DP=195;DPB=232.957;AC=2;AN=2;AF=0.0;RO=125;AO=14;PRO=42.0;PAO=22.0;QR=4588;QA=443;PQR=1510.17;PQA=747.167;SRF=25;SRR=100;SAF=1;SAR=13;SRP=100.727;SAP=25.3454;AB=0.0717949;ABP=313.575;RUN=1;RPP=3.63072;RPPR=13.8677;RPL=8.0;RPR=6.0;EPP=5.49198;EPPR=3.16665;DPRA=0.0;ODDS=0.155808;GTI=1;TYPE=ins;CIGAR=1M1I22M;NUMALT=3;MEANALT=8.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr2 36002916 . CA C 550.44 REJECT NS=2;DP=195;DPB=232.957;AC=2;AN=4;AF=0.5;RO=125;AO=35;PRO=42.0;PAO=21.0;QR=4588;QA=1108;PQR=1510.17;PQA=741.667;SRF=25;SRR=100;SAF=6;SAR=29;SRP=100.727;SAP=35.8306;AB=0.179487;ABP=177.006;RUN=1;RPP=16.9698;RPPR=13.8677;RPL=25.0;RPR=10.0;EPP=6.05036;EPPR=3.16665;DPRA=0.0;ODDS=0.155808;GTI=1;TYPE=del;CIGAR=1M1D21M;NUMALT=3;MEANALT=8.0;LEN=1;MQM=60.2857;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.7;FS=4 [...]
+chr2 39281730 . G C 7866.01 REJECT NS=2;DP=208;DPB=243.0;AC=4;AN=4;AF=1.0;RO=0;AO=242;PRO=0.0;PAO=0.0;QR=0;QA=9381;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=166;SAR=76;SRP=0.0;SAP=75.6918;AB=0.0;ABP=0.0;RUN=1;RPP=111.584;RPPR=0.0;RPL=66.0;RPR=176.0;EPP=9.07607;EPPR=0.0;DPRA=0.0;ODDS=47.9984;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995868;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8103;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.285;SOR=1.949 [...]
+chr2 42012217 . G A 1257.4099999999999 REJECT NS=2;DP=242;DPB=278.0;AC=2;AN=4;AF=0.5;RO=216;AO=61;PRO=0.0;PAO=0.0;QR=8211;QA=2351;PQR=0.0;PQA=0.0;SRF=69;SRR=147;SAF=21;SAR=40;SRP=64.1734;SAP=15.8611;AB=0.219424;ABP=193.1;RUN=1;RPP=32.9481;RPPR=46.8017;RPL=45.0;RPR=16.0;EPP=5.89373;EPPR=8.80089;DPRA=0.0;ODDS=61.6752;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983607;PAIREDR=0.990741;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.9155;Dels=0.0;FS=6.3735;Hap [...]
+chr2 47596853 . C CG 1476.32 REJECT NS=1;DP=101;DPB=113.5;AC=1;AN=4;AF=0.5;RO=46;AO=54;PRO=5.0;PAO=2.0;QR=1730;QA=2014;PQR=172.0;PQA=70.0;SRF=19;SRR=27;SAF=26;SAR=28;SRP=6.03148;SAP=3.17115;AB=0.534653;ABP=4.06379;RUN=1;RPP=5.5839;RPPR=6.03148;RPL=23.0;RPR=31.0;EPP=8.80089;EPPR=7.73089;DPRA=0.0;ODDS=302.009;GTI=0;TYPE=ins;CIGAR=1M1I5M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.978261;technology.ILLUMINA=1.0;END=47596853;HOMLEN=2;HOMSEQ=GG;SVLEN=1;SVTYPE=INS;BaseQR [...]
+chr2 47601106 . T C 1952.845 REJECT NS=2;DP=340;DPB=394.0;AC=2;AN=4;AF=0.5;RO=305;AO=89;PRO=0.0;PAO=0.0;QR=11697;QA=3424;PQR=0.0;PQA=0.0;SRF=145;SRR=160;SAF=41;SAR=48;SRP=4.61221;SAP=4.20583;AB=0.225888;ABP=260.148;RUN=1;RPP=3.22989;RPPR=9.85222;RPL=43.0;RPR=46.0;EPP=4.20583;EPPR=3.87177;DPRA=0.0;ODDS=73.1581;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988764;PAIREDR=0.993443;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.02;Dels=0.0;FS=1.295;HaplotypeSco [...]
+chr2 48010488 . G A 1279.74 REJECT NS=1;DP=101;DPB=101.0;AC=1;AN=4;AF=0.5;RO=51;AO=50;PRO=0.0;PAO=0.0;QR=1968;QA=1799;PQR=0.0;PQA=0.0;SRF=20;SRR=31;SAF=24;SAR=26;SRP=8.16222;SAP=3.18402;AB=0.49505;ABP=3.0318;RUN=1;RPP=9.26414;RPPR=6.45911;RPL=31.0;RPR=19.0;EPP=14.1282;EPPR=4.07475;DPRA=0.0;ODDS=294.672;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.249;FS=3.748;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-2.209 [...]
+chr2 48018293 . T TTG 118.352 REJECT NS=2;DP=143;DPB=171.75;AC=2;AN=2;AF=0.0;RO=117;AO=4;PRO=22.8333;PAO=22.8333;QR=4387;QA=146;PQR=822.0;PQA=822.0;SRF=31;SRR=86;SAF=0;SAR=4;SRP=59.1531;SAP=11.6962;AB=0.0789474;ABP=61.5258;RUN=1;RPP=11.6962;RPPR=143.488;RPL=4.0;RPR=0.0;EPP=11.6962;EPPR=28.4184;DPRA=0.0;ODDS=8.14022;GTI=0;TYPE=ins;CIGAR=1M2I23M;NUMALT=2;MEANALT=4.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991453;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr2 48018293 . TTG T 118.352 REJECT NS=2;DP=143;DPB=171.75;AC=2;AN=3;AF=0.25;RO=117;AO=17;PRO=22.8333;PAO=21.3333;QR=4387;QA=593;PQR=822.0;PQA=771.0;SRF=31;SRR=86;SAF=3;SAR=14;SRP=59.1531;SAP=18.4661;AB=0.210526;ABP=30.668;RUN=1;RPP=13.3567;RPPR=143.488;RPL=13.0;RPR=4.0;EPP=4.1599;EPPR=28.4184;DPRA=0.0;ODDS=8.14022;GTI=0;TYPE=del;CIGAR=1M2D21M;NUMALT=2;MEANALT=4.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991453;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.819;FS=0.0;MLE [...]
+chr2 48030692 . T A 5315.620000000001 REJECT NS=2;DP=316;DPB=369.0;AC=2;AN=4;AF=0.5;RO=177;AO=192;PRO=0.0;PAO=0.0;QR=6800;QA=7195;PQR=0.0;PQA=0.0;SRF=92;SRR=85;SAF=94;SAR=98;SRP=3.61144;SAP=3.19126;AB=0.520325;ABP=4.33437;RUN=1;RPP=7.5342;RPPR=3.61144;RPL=106.0;RPR=86.0;EPP=7.5342;EPPR=7.43912;DPRA=0.0;ODDS=301.785;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994792;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.44;Dels=0.0;FS=1.107;HaplotypeS [...]
+chr2 48030838 . A T 1077.36 REJECT NS=2;DP=206;DPB=232.0;AC=2;AN=4;AF=0.5;RO=181;AO=51;PRO=0.0;PAO=0.0;QR=7065;QA=2003;PQR=0.0;PQA=0.0;SRF=49;SRR=132;SAF=14;SAR=37;SRP=85.6582;SAP=25.534;AB=0.219828;ABP=161.191;RUN=1;RPP=25.534;RPPR=44.7722;RPL=37.0;RPR=14.0;EPP=3.05288;EPPR=4.46195;DPRA=0.0;ODDS=46.0707;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994475;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0055;Dels=0.0;FS=0.6015;HaplotypeScore=0.99 [...]
+chr2 48032874 . ACTAT A 4497.41 REJECT NS=2;DP=241;DPB=216.5;AC=2;AN=4;AF=0.5;RO=67;AO=178;PRO=59.5;PAO=20.5;QR=2542;QA=6137;PQR=2195.5;PQA=742.5;SRF=18;SRR=49;SAF=49;SAR=129;SRP=34.1563;SAP=81.0857;AB=0.723577;ABP=109.818;RUN=1;RPP=110.803;RPPR=30.2671;RPL=136.0;RPR=42.0;EPP=6.13332;EPPR=3.04271;DPRA=0.0;ODDS=179.503;GTI=0;TYPE=del;CIGAR=1M4D5M;NUMALT=1;MEANALT=1.5;LEN=4;MQM=60.2809;MQMR=60.0;PAIRED=0.994382;PAIREDR=0.985075;technology.ILLUMINA=1.0;MQ0=0;END=48032878;HOMLEN=6;HOMSEQ=CTA [...]
+chr2 51288460 . C G 1390.26 REJECT NS=1;DP=100;DPB=100.0;AC=1;AN=4;AF=0.5;RO=49;AO=51;PRO=0.0;PAO=0.0;QR=1877;QA=1921;PQR=0.0;PQA=0.0;SRF=32;SRR=17;SAF=34;SAR=17;SRP=12.9813;SAP=15.3153;AB=0.51;ABP=3.09716;RUN=1;RPP=8.16222;RPPR=3.40914;RPL=31.0;RPR=20.0;EPP=5.09662;EPPR=12.9813;DPRA=0.0;ODDS=310.834;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=61.1765;MQMR=60.0;PAIRED=0.980392;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.814;FS=0.802;MLEAC=1;MLEAF=0.5;MQ=60.65;MQRankSum [...]
+chr2 51288511 . TAC T 1007.84 REJECT NS=1;DP=28;DPB=99.7778;AC=1;AN=3;AF=0.0;RO=12;AO=6;PRO=26.9;PAO=22.9;QR=437;QA=185;PQR=965.1;PQA=819.1;SRF=8;SRR=4;SAF=3;SAR=3;SRP=5.9056;SAP=3.0103;AB=0.214286;ABP=22.8638;RUN=1;RPP=3.0103;RPPR=9.52472;RPL=3.0;RPR=3.0;EPP=4.45795;EPPR=3.73412;DPRA=0.0;ODDS=73.0469;GTI=0;TYPE=del;CIGAR=1M2D42M;NUMALT=4;MEANALT=8.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.581;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59 [...]
+chr2 51288523 . C CACACACACACACAT 1007.84 REJECT NS=1;DP=28;DPB=99.7778;AC=1;AN=3;AF=0.0;RO=12;AO=2;PRO=26.9;PAO=22.9;QR=437;QA=72;PQR=965.1;PQA=742.1;SRF=8;SRR=4;SAF=1;SAR=1;SRP=5.9056;SAP=3.0103;AB=0.0714286;ABP=47.6806;RUN=1;RPP=7.35324;RPPR=9.52472;RPL=2.0;RPR=0.0;EPP=3.0103;EPPR=3.73412;DPRA=0.0;ODDS=73.0469;GTI=0;TYPE=ins;CIGAR=13M14I32M;NUMALT=4;MEANALT=8.0;LEN=14;MQM=44.5;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr2 51288523 . C CACACACACACACACAT 1007.84 REJECT NS=1;DP=28;DPB=99.7778;AC=1;AN=4;AF=0.5;RO=12;AO=2;PRO=26.9;PAO=26.9;QR=437;QA=67;PQR=965.1;PQA=852.1;SRF=8;SRR=4;SAF=2;SAR=0;SRP=5.9056;SAP=7.35324;AB=0.0714286;ABP=47.6806;RUN=1;RPP=7.35324;RPPR=9.52472;RPL=2.0;RPR=0.0;EPP=7.35324;EPPR=3.73412;DPRA=0.0;ODDS=73.0469;GTI=0;TYPE=ins;CIGAR=13M16I32M;NUMALT=4;MEANALT=8.0;LEN=16;MQM=40.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.375;FS=0.0;MLE [...]
+chr2 51288525 . C CACACACACACACAT 1007.84 REJECT NS=1;DP=28;DPB=99.7778;AC=1;AN=3;AF=0.0;RO=12;AO=2;PRO=26.9;PAO=25.4;QR=437;QA=31;PQR=965.1;PQA=802.6;SRF=8;SRR=4;SAF=1;SAR=1;SRP=5.9056;SAP=3.0103;AB=0.0714286;ABP=47.6806;RUN=1;RPP=7.35324;RPPR=9.52472;RPL=2.0;RPR=0.0;EPP=3.0103;EPPR=3.73412;DPRA=0.0;ODDS=73.0469;GTI=0;TYPE=ins;CIGAR=15M14I30M;NUMALT=4;MEANALT=8.0;LEN=14;MQM=45.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr2 54048358 . G A 3149.58 PASS SOMATIC;NS=2;DP=441;DPB=441.0;AC=1;AN=3;AF=0.25;RO=320;AO=121;PRO=0.0;PAO=0.0;QR=12136;QA=4540;PQR=0.0;PQA=0.0;SRF=164;SRR=156;SAF=49;SAR=72;SRP=3.44459;SAP=12.5038;AB=0.38535;ABP=38.8603;RUN=1;RPP=18.1029;RPPR=22.7978;RPL=46.0;RPR=75.0;EPP=9.48883;EPPR=14.9805;DPRA=2.47244;ODDS=80.1322;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991736;PAIREDR=0.990625;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.926;Dels=0.0;FS [...]
+chr2 54048424 . C CT 323.465 REJECT NS=2;DP=258;DPB=307.188;AC=2;AN=2;AF=0.0;RO=193;AO=24;PRO=40.3333;PAO=26.3333;QR=7190;QA=807;PQR=1425.83;PQA=958.833;SRF=71;SRR=122;SAF=7;SAR=17;SRP=32.2745;SAP=12.0581;AB=0.0930233;ABP=374.181;RUN=1;RPP=16.0391;RPPR=73.2287;RPL=18.0;RPR=6.0;EPP=3.37221;EPPR=27.8641;DPRA=0.0;ODDS=17.4184;GTI=0;TYPE=ins;CIGAR=1M1I15M;NUMALT=2;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=59.9948;PAIRED=1.0;PAIREDR=0.989637;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:Q [...]
+chr2 54048424 . CT C 323.465 REJECT NS=2;DP=258;DPB=307.188;AC=2;AN=4;AF=0.5;RO=193;AO=30;PRO=40.3333;PAO=25.3333;QR=7190;QA=1110;PQR=1425.83;PQA=920.333;SRF=71;SRR=122;SAF=10;SAR=20;SRP=32.2745;SAP=10.2485;AB=0.116279;ABP=332.973;RUN=1;RPP=13.4334;RPPR=73.2287;RPL=21.0;RPR=9.0;EPP=7.64277;EPPR=27.8641;DPRA=0.0;ODDS=17.4184;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=2;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=59.9948;PAIRED=1.0;PAIREDR=0.989637;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO: [...]
+chr2 55516588 . G C 12740.05 REJECT NS=2;DP=329;DPB=373.0;AC=4;AN=4;AF=1.0;RO=0;AO=373;PRO=0.0;PAO=0.0;QR=0;QA=14550;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=143;SAR=230;SRP=0.0;SAP=47.0743;AB=0.0;ABP=0.0;RUN=1;RPP=34.0338;RPPR=0.0;RPL=223.0;RPR=150.0;EPP=45.0717;EPPR=0.0;DPRA=0.0;ODDS=58.5812;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991957;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9469;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.205;SOR=1 [...]
+chr2 57011171 . T C 9772.14 REJECT NS=2;DP=345;DPB=396.0;AC=2;AN=4;AF=0.5;RO=80;AO=316;PRO=0.0;PAO=0.0;QR=2977;QA=12184;PQR=0.0;PQA=0.0;SRF=45;SRR=35;SAF=140;SAR=176;SRP=5.72464;SAP=11.9161;AB=0.79798;ABP=308.42;RUN=1;RPP=27.7486;RPPR=3.98746;RPL=128.0;RPR=188.0;EPP=21.5915;EPPR=9.95901;DPRA=0.0;ODDS=62.0469;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990506;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0245;Dels=0.0;FS=7.312;HaplotypeScore=4 [...]
+chr2 58388696 . A G 9492.67 REJECT NS=2;DP=378;DPB=438.0;AC=2;AN=4;AF=0.5;RO=115;AO=323;PRO=0.0;PAO=0.0;QR=4359;QA=12027;PQR=0.0;PQA=0.0;SRF=71;SRR=44;SAF=192;SAR=131;SRP=16.7755;SAP=28.0259;AB=0.737443;ABP=217.5;RUN=1;RPP=42.8699;RPPR=3.93554;RPL=123.0;RPR=200.0;EPP=14.3114;EPPR=6.20142;DPRA=0.0;ODDS=207.8;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990712;PAIREDR=0.991304;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0705;Dels=0.0;FS=4.4765;HaplotypeS [...]
+chr2 58390218 . T TA 119.568 REJECT NS=2;DP=224;DPB=305.458;AC=2;AN=2;AF=0.0;RO=174;AO=16;PRO=85.6667;PAO=35.6667;QR=6553;QA=610;PQR=3151.0;PQA=1280.0;SRF=52;SRR=122;SAF=6;SAR=10;SRP=64.161;SAP=5.18177;AB=0.0714286;ABP=360.373;RUN=1;RPP=5.18177;RPPR=34.2096;RPL=10.0;RPR=6.0;EPP=11.6962;EPPR=21.031;DPRA=0.0;ODDS=12.6889;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=2;MEANALT=8.5;LEN=1;MQM=60.0;MQMR=59.8506;PAIRED=1.0;PAIREDR=0.982759;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr2 58390218 . TA T 119.568 REJECT NS=2;DP=224;DPB=305.458;AC=2;AN=4;AF=0.5;RO=174;AO=20;PRO=85.6667;PAO=37.6667;QR=6553;QA=743;PQR=3151.0;PQA=1367.0;SRF=52;SRR=122;SAF=1;SAR=19;SRP=64.161;SAP=38.1882;AB=0.0892857;ABP=331.213;RUN=1;RPP=3.44459;RPPR=34.2096;RPL=11.0;RPR=9.0;EPP=3.0103;EPPR=21.031;DPRA=0.0;ODDS=12.6889;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=2;MEANALT=8.5;LEN=1;MQM=61.5;MQMR=59.8506;PAIRED=1.0;PAIREDR=0.982759;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr2 58390538 . T C 1754.75 PASS SOMATIC;NS=2;DP=285;DPB=285.0;AC=1;AN=3;AF=0.25;RO=214;AO=70;PRO=0.0;PAO=0.0;QR=8218;QA=2716;PQR=0.0;PQA=0.0;SRF=158;SRR=56;SAF=55;SAR=15;SRP=108.58;SAP=52.644;AB=0.330189;ABP=56.1089;RUN=1;RPP=18.0245;RPPR=58.5756;RPL=24.0;RPR=46.0;EPP=3.50664;EPPR=4.02501;DPRA=2.90411;ODDS=46.5536;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985714;PAIREDR=0.990654;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.676;Dels=0.0;FS=1.36 [...]
+chr2 58390547 . G A 2119.38 PASS SOMATIC;NS=2;DP=345;DPB=345.0;AC=1;AN=3;AF=0.25;RO=261;AO=83;PRO=0.0;PAO=0.0;QR=9826;QA=3227;PQR=0.0;PQA=0.0;SRF=187;SRR=74;SAF=60;SAR=23;SRP=109.246;SAP=38.8265;AB=0.330677;ABP=65.5158;RUN=1;RPP=16.8502;RPPR=42.621;RPL=30.0;RPR=53.0;EPP=8.89682;EPPR=11.0056;DPRA=2.67021;ODDS=59.6312;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987952;PAIREDR=0.988506;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.713;Dels=0.0;FS=0.5 [...]
+chr2 58453843 . GA G 55.5239 REJECT NS=1;DP=82;DPB=91.8824;AC=1;AN=4;AF=0.5;RO=64;AO=9;PRO=11.5;PAO=9.5;QR=2430;QA=332;PQR=367.5;PQA=301.5;SRF=44;SRR=20;SAF=6;SAR=3;SRP=22.5536;SAP=5.18177;AB=0.109756;ABP=111.478;RUN=1;RPP=3.25157;RPPR=25.9465;RPL=4.0;RPR=5.0;EPP=3.25157;EPPR=3.14602;DPRA=0.0;ODDS=12.7848;GTI=0;TYPE=del;CIGAR=1M1D15M;NUMALT=1;MEANALT=6.0;LEN=1;MQM=61.1111;MQMR=60.0;PAIRED=1.0;PAIREDR=0.96875;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:Call [...]
+chr2 61108926 . C G 1021.4 REJECT NS=1;DP=71;DPB=71.0;AC=1;AN=4;AF=0.5;RO=34;AO=37;PRO=0.0;PAO=0.0;QR=1307;QA=1427;PQR=0.0;PQA=0.0;SRF=29;SRR=5;SAF=27;SAR=10;SRP=39.7976;SAP=19.9713;AB=0.521127;ABP=3.28556;RUN=1;RPP=5.88603;RPPR=19.3602;RPL=15.0;RPR=22.0;EPP=7.76406;EPPR=5.30951;DPRA=0.0;ODDS=202.732;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.357;FS=6.168;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.621;QD [...]
+chr2 61726050 . T TA 341.474 REJECT NS=2;DP=167;DPB=210.769;AC=2;AN=3;AF=0.25;RO=111;AO=17;PRO=41.1667;PAO=28.1667;QR=4138;QA=548;PQR=1489.67;PQA=1009.67;SRF=12;SRR=99;SAF=3;SAR=14;SRP=151.081;SAP=18.4661;AB=0.101796;ABP=233.017;RUN=1;RPP=4.1599;RPPR=11.6375;RPL=10.0;RPR=7.0;EPP=3.13803;EPPR=4.59489;DPRA=0.0;ODDS=24.5733;GTI=0;TYPE=ins;CIGAR=1M1I25M;NUMALT=2;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.981982;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr2 61726050 . TA T 341.474 REJECT NS=2;DP=167;DPB=210.769;AC=2;AN=3;AF=0.25;RO=111;AO=15;PRO=41.1667;PAO=18.6667;QR=4138;QA=527;PQR=1489.67;PQA=670.667;SRF=12;SRR=99;SAF=1;SAR=14;SRP=151.081;SAP=27.4756;AB=0.0898204;ABP=247.06;RUN=1;RPP=4.31318;RPPR=11.6375;RPL=9.0;RPR=6.0;EPP=3.15506;EPPR=4.59489;DPRA=0.0;ODDS=24.5733;GTI=0;TYPE=del;CIGAR=1M1D24M;NUMALT=2;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.981982;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-1.261;FS= [...]
+chr2 61749716 . C T 6018.95 REJECT NS=2;DP=236;DPB=272.0;AC=2;AN=4;AF=0.5;RO=70;AO=202;PRO=0.0;PAO=0.0;QR=2719;QA=7737;PQR=0.0;PQA=0.0;SRF=45;SRR=25;SAF=138;SAR=64;SRP=15.4187;SAP=61.8766;AB=0.742647;ABP=142.112;RUN=1;RPP=82.5163;RPPR=18.0245;RPL=58.0;RPR=144.0;EPP=6.49326;EPPR=7.47733;DPRA=0.0;ODDS=167.182;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990099;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.063;Dels=0.0;FS=2.4395;HaplotypeScore=8 [...]
+chr2 61760893 . G C 1628.0 REJECT NS=2;DP=332;DPB=382.0;AC=2;AN=4;AF=0.5;RO=299;AO=83;PRO=0.0;PAO=0.0;QR=11027;QA=3183;PQR=0.0;PQA=0.0;SRF=210;SRR=89;SAF=60;SAR=23;SRP=109.34;SAP=38.8265;AB=0.217277;ABP=268.226;RUN=1;RPP=14.5479;RPPR=31.835;RPL=31.0;RPR=52.0;EPP=5.12945;EPPR=5.63204;DPRA=0.0;ODDS=91.523;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987952;PAIREDR=0.996656;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.54;Dels=0.0;FS=2.9225;HaplotypeScore=7. [...]
+chr2 64518912 . C A 2191.74 PASS SOMATIC;NS=2;DP=292;DPB=292.0;AC=1;AN=3;AF=0.25;RO=210;AO=82;PRO=0.0;PAO=0.0;QR=7993;QA=3182;PQR=0.0;PQA=0.0;SRF=131;SRR=79;SAF=51;SAR=31;SRP=30.9706;SAP=13.6028;AB=0.381395;ABP=29.2801;RUN=1;RPP=30.1272;RPPR=137.393;RPL=25.0;RPR=57.0;EPP=3.11623;EPPR=7.14644;DPRA=2.79221;ODDS=49.0439;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.97619;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.13;Dels=0.0;FS=1.797;Hap [...]
+chr2 67241174 . G A 8023.7 REJECT NS=2;DP=334;DPB=382.0;AC=3;AN=4;AF=0.75;RO=104;AO=278;PRO=0.0;PAO=0.0;QR=4063;QA=10868;PQR=0.0;PQA=0.0;SRF=38;SRR=66;SAF=129;SAR=149;SRP=19.3799;SAP=6.13472;AB=0.637631;ABP=50.2304;RUN=1;RPP=3.79141;RPPR=8.35546;RPL=144.0;RPR=134.0;EPP=31.1301;EPPR=8.35546;DPRA=0.0;ODDS=60.28;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996403;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.457;Dels=0.0;FS=3.8275;HaplotypeScore= [...]
+chr2 70515067 . G GTT 5158.03 REJECT NS=2;DP=224;DPB=374.0;AC=3;AN=4;AF=0.75;RO=68;AO=178;PRO=9.0;PAO=9.0;QR=2585;QA=6518;PQR=337.5;PQA=337.5;SRF=15;SRR=53;SAF=42;SAR=136;SRP=49.1222;SAP=110.803;AB=0.632979;ABP=31.8863;RUN=1;RPP=35.9972;RPPR=11.1853;RPL=115.0;RPR=63.0;EPP=3.79105;EPPR=3.13803;DPRA=0.0;ODDS=37.8171;GTI=0;TYPE=ins;CIGAR=1M2I2M;NUMALT=1;MEANALT=2.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=70515067;HOMLEN=0;SVLEN=2;SVTYPE=INS;BaseQRan [...]
+chr2 76508288 . T C 11074.9 REJECT NS=2;DP=296;DPB=340.0;AC=4;AN=4;AF=1.0;RO=0;AO=340;PRO=0.0;PAO=0.0;QR=0;QA=13037;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=257;SAR=83;SRP=0.0;SAP=196.374;AB=0.0;ABP=0.0;RUN=1;RPP=15.3749;RPPR=0.0;RPL=148.0;RPR=192.0;EPP=10.3933;EPPR=0.0;DPRA=0.0;ODDS=58.6467;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9676;MQMR=0.0;PAIRED=0.994118;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9328;MLEAC=2;MLEAF=1.0;MQ=59.98;QD=25.955;SOR [...]
+chr2 78017912 . C A 3410.81 PASS SOMATIC;NS=2;DP=415;DPB=415.0;AC=1;AN=3;AF=0.25;RO=288;AO=127;PRO=0.0;PAO=0.0;QR=11057;QA=4867;PQR=0.0;PQA=0.0;SRF=164;SRR=124;SAF=77;SAR=50;SRP=15.074;SAP=15.4749;AB=0.39441;ABP=34.1932;RUN=1;RPP=29.0167;RPPR=58.7749;RPL=44.0;RPR=83.0;EPP=5.8999;EPPR=21.8599;DPRA=3.46237;ODDS=59.052;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993056;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.919;Dels=0.0;FS=1.941;Ha [...]
+chr2 79516586 . T A 12167.0 REJECT NS=2;DP=327;DPB=382.0;AC=4;AN=4;AF=1.0;RO=0;AO=382;PRO=0.0;PAO=0.0;QR=0;QA=14491;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=164;SAR=218;SRP=0.0;SAP=19.5863;AB=0.0;ABP=0.0;RUN=1;RPP=84.8669;RPPR=0.0;RPL=251.0;RPR=131.0;EPP=84.8669;EPPR=0.0;DPRA=0.0;ODDS=71.0621;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9476;MQMR=0.0;PAIRED=0.994764;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8464;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.155;SOR [...]
+chr2 100516102 . G A 2663.7799999999997 REJECT NS=2;DP=378;DPB=438.0;AC=2;AN=4;AF=0.5;RO=315;AO=123;PRO=0.0;PAO=0.0;QR=12088;QA=4771;PQR=0.0;PQA=0.0;SRF=144;SRR=171;SAF=50;SAR=73;SRP=8.03571;SAP=12.3494;AB=0.280822;ABP=185.771;RUN=1;RPP=19.976;RPPR=5.49888;RPL=77.0;RPR=46.0;EPP=10.7958;EPPR=25.4075;DPRA=0.0;ODDS=259.82;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996825;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.081;Dels=0.0;FS=1.7035;Haplo [...]
+chr2 100516134 . T C 7911.6 REJECT NS=2;DP=303;DPB=346.0;AC=2;AN=4;AF=0.5;RO=82;AO=264;PRO=0.0;PAO=0.0;QR=3119;QA=10042;PQR=0.0;PQA=0.0;SRF=21;SRR=61;SAF=93;SAR=171;SRP=45.3805;SAP=53.0529;AB=0.763006;ABP=210.894;RUN=1;RPP=69.635;RPPR=11.5903;RPL=177.0;RPR=87.0;EPP=7.74806;EPPR=3.434;DPRA=0.0;ODDS=154.324;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996212;PAIREDR=0.987805;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.266;Dels=0.0;FS=3.9975;HaplotypeScore [...]
+chr2 102010609 . A G 11337.95 REJECT NS=2;DP=302;DPB=354.0;AC=4;AN=4;AF=1.0;RO=0;AO=354;PRO=0.0;PAO=0.0;QR=0;QA=13500;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=197;SAR=157;SRP=0.0;SAP=12.8249;AB=0.0;ABP=0.0;RUN=1;RPP=15.9901;RPPR=0.0;RPL=154.0;RPR=200.0;EPP=3.40288;EPPR=0.0;DPRA=0.0;ODDS=69.1832;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99435;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.15;SOR=0. [...]
+chr2 112641666 . T C 2513.23 PASS SOMATIC;NS=2;DP=352;DPB=352.0;AC=1;AN=3;AF=0.25;RO=255;AO=96;PRO=0.0;PAO=0.0;QR=9449;QA=3703;PQR=0.0;PQA=0.0;SRF=164;SRR=91;SAF=67;SAR=29;SRP=48.3898;SAP=35.6729;AB=0.366795;ABP=42.9268;RUN=1;RPP=16.0391;RPPR=89.8777;RPL=36.0;RPR=60.0;EPP=10.339;EPPR=12.2838;DPRA=0.0;ODDS=54.7931;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992157;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.715;Dels=0.0;FS=4.643;Haplo [...]
+chr2 113977862 . T G 12940.5 REJECT NS=2;DP=344;DPB=395.0;AC=4;AN=4;AF=1.0;RO=1;AO=394;PRO=0.0;PAO=0.0;QR=40;QA=14929;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=186;SAR=208;SRP=5.18177;SAP=5.67779;AB=0.0;ABP=0.0;RUN=1;RPP=3.56144;RPPR=5.18177;RPL=202.0;RPR=192.0;EPP=10.9687;EPPR=5.18177;DPRA=0.0;ODDS=61.0496;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997462;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.414;Dels=0.0;FS=0.0;HaplotypeScore=5.8434;MLEAC=2 [...]
+chr2 113977936 . C T 10029.5 REJECT NS=2;DP=362;DPB=414.0;AC=2;AN=4;AF=0.5;RO=87;AO=327;PRO=0.0;PAO=0.0;QR=3334;QA=12480;PQR=0.0;PQA=0.0;SRF=51;SRR=36;SAF=143;SAR=184;SRP=8.62618;SAP=14.1731;AB=0.789855;ABP=305.128;RUN=1;RPP=4.13256;RPPR=18.61;RPL=157.0;RPR=170.0;EPP=3.01694;EPPR=3.23494;DPRA=0.0;ODDS=118.063;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.9995;Dels=0.0;FS=10.1085;HaplotypeScore=7. [...]
+chr2 113978650 . C T 1853.425 REJECT NS=2;DP=378;DPB=422.0;AC=2;AN=4;AF=0.5;RO=323;AO=99;PRO=0.0;PAO=0.0;QR=12397;QA=3703;PQR=0.0;PQA=0.0;SRF=178;SRR=145;SAF=58;SAR=41;SRP=10.3315;SAP=9.34924;AB=0.234597;ABP=261.199;RUN=1;RPP=3.20771;RPPR=6.56667;RPL=48.0;RPR=51.0;EPP=3.55865;EPPR=3.55485;DPRA=0.0;ODDS=192.484;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.979798;PAIREDR=0.996904;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.3015;Dels=0.0;FS=0.4095;Haplotyp [...]
+chr2 113978940 . C G 1677.205 REJECT NS=2;DP=370;DPB=417.0;AC=2;AN=4;AF=0.5;RO=324;AO=92;PRO=0.0;PAO=0.0;QR=12272;QA=3489;PQR=0.0;PQA=0.0;SRF=158;SRR=166;SAF=47;SAR=45;SRP=3.43923;SAP=3.10471;AB=0.220624;ABP=285.713;RUN=1;RPP=3.38795;RPPR=5.18177;RPL=44.0;RPR=48.0;EPP=5.3706;EPPR=6.2541;DPRA=0.0;ODDS=198.364;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=59.9846;PAIRED=1.0;PAIREDR=0.993827;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7515;Dels=0.0;FS=0.95;HaplotypeScore [...]
+chr2 113979355 . G C 2539.2 REJECT NS=2;DP=420;DPB=485.0;AC=2;AN=4;AF=0.5;RO=368;AO=117;PRO=0.0;PAO=0.0;QR=14154;QA=4454;PQR=0.0;PQA=0.0;SRF=193;SRR=175;SAF=65;SAR=52;SRP=4.92214;SAP=6.14687;AB=0.241237;ABP=285.082;RUN=1;RPP=3.02886;RPPR=5.86626;RPL=58.0;RPR=59.0;EPP=3.91972;EPPR=3.10471;DPRA=0.0;ODDS=161.688;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.98913;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3675;Dels=0.0;FS=3.341;HaplotypeScore= [...]
+chr2 113980645 . C G 2181.915 REJECT NS=2;DP=407;DPB=466.0;AC=2;AN=4;AF=0.5;RO=363;AO=103;PRO=0.0;PAO=0.0;QR=13883;QA=3938;PQR=0.0;PQA=0.0;SRF=179;SRR=184;SAF=47;SAR=56;SRP=3.15985;SAP=4.71796;AB=0.22103;ABP=318.014;RUN=1;RPP=3.20004;RPPR=4.02126;RPL=53.0;RPR=50.0;EPP=3.20004;EPPR=3.15985;DPRA=0.0;ODDS=114.495;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990291;PAIREDR=0.997245;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.946;Dels=0.0;FS=3.4105;Haplotype [...]
+chr2 113980968 . G A 7096.72 REJECT NS=2;DP=432;DPB=495.0;AC=2;AN=4;AF=0.5;RO=232;AO=262;PRO=0.0;PAO=0.0;QR=8776;QA=9506;PQR=0.0;PQA=0.0;SRF=124;SRR=108;SAF=135;SAR=127;SRP=5.40641;SAP=3.54074;AB=0.529293;ABP=6.69961;RUN=1;RPP=3.0103;RPPR=7.54044;RPL=131.0;RPR=131.0;EPP=3.30867;EPPR=13.8302;DPRA=0.0;ODDS=378.156;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992366;PAIREDR=0.982759;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.852;Dels=0.0;FS=3.8775;Haplot [...]
+chr2 113981022 . G A 2326.3599999999997 REJECT NS=2;DP=451;DPB=515.0;AC=2;AN=4;AF=0.5;RO=399;AO=115;PRO=0.0;PAO=0.0;QR=15171;QA=4427;PQR=0.0;PQA=0.0;SRF=194;SRR=205;SAF=51;SAR=64;SRP=3.66882;SAP=6.20142;AB=0.223301;ABP=345.492;RUN=1;RPP=3.02918;RPPR=4.23481;RPL=57.0;RPR=58.0;EPP=3.18024;EPPR=3.05928;DPRA=0.0;ODDS=194.077;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989975;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.4405;Dels=0.0;FS=2.0755;Ha [...]
+chr2 113981137 . T C 2409.745 REJECT NS=2;DP=430;DPB=499.0;AC=2;AN=4;AF=0.5;RO=381;AO=117;PRO=0.0;PAO=0.0;QR=14570;QA=4466;PQR=0.0;PQA=0.0;SRF=198;SRR=183;SAF=60;SAR=57;SRP=4.29267;SAP=3.17734;AB=0.234469;ABP=308.605;RUN=1;RPP=5.25601;RPPR=3.9735;RPL=64.0;RPR=53.0;EPP=6.14687;EPPR=4.65743;DPRA=0.0;ODDS=180.808;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991453;PAIREDR=0.989501;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.113;Dels=0.0;FS=2.0225;Haplotype [...]
+chr2 113981810 . A G 1949.8899999999999 REJECT NS=2;DP=351;DPB=394.0;AC=2;AN=4;AF=0.5;RO=301;AO=93;PRO=0.0;PAO=0.0;QR=11505;QA=3567;PQR=0.0;PQA=0.0;SRF=120;SRR=181;SAF=31;SAR=62;SRP=29.8543;SAP=25.4488;AB=0.236041;ABP=241.453;RUN=1;RPP=22.6469;RPPR=57.6145;RPL=61.0;RPR=32.0;EPP=3.03365;EPPR=5.0952;DPRA=0.0;ODDS=115.728;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.978495;PAIREDR=0.986711;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1915;Dels=0.0;FS=1.6955 [...]
+chr2 113982039 . A G 3447.03 REJECT NS=2;DP=111;DPB=128.0;AC=2;AN=2;AF=0.75;RO=0;AO=36;PRO=0.0;PAO=1.0;QR=0;QA=1200;PQR=0.0;PQA=35.0;SRF=0;SRR=0;SAF=21;SAR=15;SRP=0.0;SAP=5.18177;AB=0.283465;ABP=54.7324;RUN=1;RPP=9.04217;RPPR=0.0;RPL=23.0;RPR=13.0;EPP=3.9754;EPPR=0.0;DPRA=0.0;ODDS=34.6706;GTI=0;TYPE=snp;CIGAR=1X1M;NUMALT=2;MEANALT=2.0;LEN=1;MQM=59.5833;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;M [...]
+chr2 113982039 . AC GA 3447.03 REJECT NS=2;DP=127;DPB=128.0;AC=2;AN=2;AF=0.5;RO=0;AO=91;PRO=0.0;PAO=1.0;QR=0;QA=2975;PQR=0.0;PQA=35.0;SRF=0;SRR=0;SAF=52;SAR=39;SRP=0.0;SAP=7.04303;AB=0.716535;ABP=54.7324;RUN=1;RPP=4.17955;RPPR=0.0;RPL=49.0;RPR=42.0;EPP=3.22506;EPPR=0.0;DPRA=0.0;ODDS=34.6706;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=2;MEANALT=2.0;LEN=2;MQM=59.9341;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:Call [...]
+chr2 113982040 . C A 1515.77 PASS DP=63;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.05;Dels=0.0;FS=0.56;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.5;MQ=59.97;MQRankSum=0.079;QD=18.505;ReadPosRankSum=-0.158;SOR=0.7415;ClippingRankSum=0.436 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:21,11:32:99.0:259,0,608:11:34:32:1:.:.:.:.:.:-0.00174608 0/1:13,81:94:99.0:2829,0,208:81:86:94:.:1:.:.:.:.:-0.0116954
+chr2 113982143 . G A 273.095 REJECT NS=2;DP=90;DPB=184.375;AC=2;AN=3;AF=0.25;RO=19;AO=7;PRO=112.0;PAO=63.0;QR=680;QA=275;PQR=3887.5;PQA=2122.0;SRF=6;SRR=13;SAF=0;SAR=7;SRP=8.61041;SAP=18.2106;AB=0.142857;ABP=26.2761;RUN=1;RPP=18.2106;RPPR=36.0395;RPL=0.0;RPR=7.0;EPP=18.2106;EPPR=5.8675;DPRA=0.0;ODDS=11.5168;GTI=0;TYPE=snp;CIGAR=19M1X12M;NUMALT=2;MEANALT=25.5;LEN=1;MQM=60.0;MQMR=59.8947;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=1.428;FS=5.943;MLEAC=1;ML [...]
+chr2 113982150 . TGGAT GGGAG 273.095 REJECT NS=2;DP=90;DPB=184.375;AC=2;AN=2;AF=0.0;RO=19;AO=4;PRO=112.0;PAO=26.0;QR=680;QA=55;PQR=3887.5;PQA=836.5;SRF=6;SRR=13;SAF=4;SAR=0;SRP=8.61041;SAP=11.6962;AB=0.0952381;ABP=32.8939;RUN=1;RPP=3.0103;RPPR=36.0395;RPL=2.0;RPR=2.0;EPP=3.0103;EPPR=5.8675;DPRA=0.0;ODDS=11.5168;GTI=0;TYPE=complex;CIGAR=26M1X3M1X1M;NUMALT=2;MEANALT=25.5;LEN=32;MQM=55.0;MQMR=59.8947;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr2 113982416 . TATAAAATAAAATAAA T 6699.215 PASS DP=157;AC=2;AN=2;AF=0.5;SPLITMULTIALLELIC;MQ0=0;END=113982431;HOMLEN=33;HOMSEQ=ATAAAATAAAATAAAATAAAATAAAATAAAATA;SVLEN=-15;SVTYPE=DEL;BaseQRankSum=2.8795;FS=1.807;MLEAC=1;MLEAF=0.5;MQ=60.59;MQRankSum=1.483;QD=17.24;RPA=9;RU=ATAAA;ReadPosRankSum=-1.7685;SOR=1.0425;STR;ClippingRankSum=-1.199 GT:AD:GMIMUT:GMIMAF:GMICOV:DP:GQ:PL:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR ./1:12,40:40:57:70:65:99.0:2531,1357,1274:1:.:.:1:.:.:-0.00174608 ./1 [...]
+chr2 113982416 . TATAAAATAAAATAAAATAAAATAAA T 6699.215 PASS DP=157;AC=2;AN=2;AF=0.5;SPLITMULTIALLELIC;MQ0=0;END=113982441;HOMLEN=23;HOMSEQ=ATAAAATAAAATAAAATAAAATA;SVLEN=-25;SVTYPE=DEL;BaseQRankSum=2.8795;FS=1.807;MLEAC=1;MLEAF=0.5;MQ=60.59;MQRankSum=1.483;QD=17.24;RPA=9;RU=ATAAA;ReadPosRankSum=-1.7685;SOR=1.0425;STR;ClippingRankSum=-1.199 GT:AD:GMIMUT:GMIMAF:GMICOV:DP:GQ:PL:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR ./1:12,50:50:64:77:65:99.0:2531,1184,1490:1:.:.:1:.:.:-0.00174608 ./1 [...]
+chr2 113982428 . TAAA T 639.024 REJECT NS=2;DP=52;DPB=184.864;AC=2;AN=2;AF=0.0;RO=0;AO=12;PRO=130.5;PAO=60.5;QR=0;QA=458;PQR=4819.58;PQA=2173.25;SRF=0;SRR=0;SAF=8;SAR=4;SRP=0.0;SAP=5.9056;AB=0.230769;ABP=35.7494;RUN=1;RPP=29.068;RPPR=0.0;RPL=0.0;RPR=12.0;EPP=5.9056;EPPR=0.0;DPRA=0.0;ODDS=17.9669;GTI=0;TYPE=del;CIGAR=1M3D40M;NUMALT=3;MEANALT=5.0;LEN=3;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:Call [...]
+chr2 113982431 . A AAT 639.024 REJECT NS=2;DP=52;DPB=184.864;AC=2;AN=3;AF=0.25;RO=0;AO=15;PRO=130.5;PAO=67.5;QR=0;QA=539;PQR=4819.58;PQA=2432.58;SRF=0;SRR=0;SAF=9;SAR=6;SRP=0.0;SAP=4.31318;AB=0.288462;ABP=23.2217;RUN=1;RPP=35.5824;RPPR=0.0;RPL=0.0;RPR=15.0;EPP=4.31318;EPPR=0.0;DPRA=0.0;ODDS=17.9669;GTI=0;TYPE=ins;CIGAR=4M2I40M;NUMALT=3;MEANALT=5.0;LEN=2;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:C [...]
+chr2 113982438 . TAAA T 639.024 REJECT NS=2;DP=52;DPB=184.864;AC=2;AN=3;AF=0.25;RO=0;AO=21;PRO=130.5;PAO=84.5;QR=0;QA=687;PQR=4819.58;PQA=3097.58;SRF=0;SRR=0;SAF=13;SAR=8;SRP=0.0;SAP=5.59539;AB=0.403846;ABP=7.18621;RUN=1;RPP=15.5221;RPPR=0.0;RPL=5.0;RPR=16.0;EPP=3.1137;EPPR=0.0;DPRA=0.0;ODDS=17.9669;GTI=0;TYPE=del;CIGAR=11M3D30M;NUMALT=3;MEANALT=5.0;LEN=3;MQM=57.5714;MQMR=0.0;PAIRED=0.952381;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICO [...]
+chr2 113982584 . T C 2154.99 REJECT NS=2;DP=369;DPB=426.0;AC=2;AN=4;AF=0.5;RO=322;AO=103;PRO=0.0;PAO=0.0;QR=12299;QA=3862;PQR=0.0;PQA=0.0;SRF=150;SRR=172;SAF=36;SAR=67;SRP=6.27425;SAP=23.2703;AB=0.241784;ABP=249.722;RUN=1;RPP=5.56125;RPPR=3.25307;RPL=46.0;RPR=57.0;EPP=3.03138;EPPR=3.03727;DPRA=0.0;ODDS=168.143;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.980583;PAIREDR=0.984472;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.242;Dels=0.0;FS=5.407;Haplotype [...]
+chr2 113982608 . G A 2334.59 REJECT NS=2;DP=372;DPB=428.0;AC=2;AN=4;AF=0.5;RO=324;AO=102;PRO=0.0;PAO=0.0;QR=12499;QA=3949;PQR=0.0;PQA=0.0;SRF=158;SRR=166;SAF=44;SAR=58;SRP=3.43923;SAP=7.18293;AB=0.238318;ABP=257.58;RUN=1;RPP=6.07591;RPPR=37.7539;RPL=45.0;RPR=57.0;EPP=4.37279;EPPR=3.11753;DPRA=0.0;ODDS=129.983;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.970588;PAIREDR=0.987654;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.266;Dels=0.0;FS=3.49;HaplotypeSc [...]
+chr2 113984033 . G A 11204.6 REJECT NS=2;DP=403;DPB=464.0;AC=2;AN=4;AF=0.5;RO=99;AO=365;PRO=0.0;PAO=0.0;QR=3808;QA=13930;PQR=0.0;PQA=0.0;SRF=46;SRR=53;SAF=185;SAR=180;SRP=4.08507;SAP=3.15903;AB=0.786638;ABP=334.141;RUN=1;RPP=6.72857;RPPR=4.78696;RPL=195.0;RPR=170.0;EPP=3.49219;EPPR=9.34924;DPRA=0.0;ODDS=109.081;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986301;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2625;Dels=0.0;FS=5.5;HaplotypeScore= [...]
+chr2 113984246 . G GTCA 1621.47 REJECT NS=2;DP=317;DPB=407.923;AC=2;AN=4;AF=0.5;RO=233;AO=75;PRO=88.0;PAO=90.0;QR=8855;QA=2744;PQR=3137.0;PQA=3208.0;SRF=122;SRR=111;SAF=47;SAR=28;SRP=4.13797;SAP=13.4623;AB=0.236593;ABP=194.052;RUN=1;RPP=7.90335;RPPR=13.1594;RPL=31.0;RPR=44.0;EPP=5.35549;EPPR=3.09418;DPRA=0.0;ODDS=152.296;GTI=0;TYPE=ins;CIGAR=1M3I25M;NUMALT=1;MEANALT=4.5;LEN=3;MQM=60.8;MQMR=60.0;PAIRED=0.986667;PAIREDR=0.987124;technology.ILLUMINA=1.0;BaseQRankSum=-0.669;FS=7.501;MLEAC=1; [...]
+chr2 113984303 . T C 2072.4449999999997 REJECT NS=2;DP=388;DPB=447.0;AC=2;AN=4;AF=0.5;RO=341;AO=104;PRO=0.0;PAO=0.0;QR=12882;QA=3909;PQR=0.0;PQA=0.0;SRF=174;SRR=167;SAF=60;SAR=44;SRP=3.32233;SAP=8.35546;AB=0.232662;ABP=280.497;RUN=1;RPP=3.09382;RPPR=3.06761;RPL=53.0;RPR=51.0;EPP=13.116;EPPR=5.81857;DPRA=0.0;ODDS=169.577;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.6731;MQMR=60.0293;PAIRED=0.980769;PAIREDR=0.994135;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.28;Dels=0.0;FS=2 [...]
+chr2 113985170 . C T 1618.71 REJECT NS=2;DP=387;DPB=436.0;AC=2;AN=4;AF=0.5;RO=346;AO=89;PRO=0.0;PAO=0.0;QR=13377;QA=3471;PQR=0.0;PQA=0.0;SRF=164;SRR=182;SAF=53;SAR=36;SRP=5.0437;SAP=10.0615;AB=0.204128;ABP=334.528;RUN=1;RPP=3.0347;RPPR=5.52067;RPL=45.0;RPR=44.0;EPP=3.62026;EPPR=4.61694;DPRA=0.0;ODDS=181.645;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99422;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7275;Dels=0.0;FS=6.519;HaplotypeScore=2.9 [...]
+chr2 113985186 . C G 1454.69 REJECT NS=2;DP=380;DPB=430.0;AC=2;AN=4;AF=0.5;RO=345;AO=85;PRO=0.0;PAO=0.0;QR=13357;QA=3197;PQR=0.0;PQA=0.0;SRF=166;SRR=179;SAF=51;SAR=34;SRP=4.07401;SAP=10.3933;AB=0.197674;ABP=344.386;RUN=1;RPP=5.07959;RPPR=3.16765;RPL=47.0;RPR=38.0;EPP=8.75832;EPPR=4.8293;DPRA=0.0;ODDS=144.438;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988406;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.5255;Dels=0.0;FS=6.7565;HaplotypeScore [...]
+chr2 113986629 . C T 2124.94 REJECT NS=2;DP=373;DPB=427.0;AC=2;AN=4;AF=0.5;RO=322;AO=104;PRO=0.0;PAO=0.0;QR=12240;QA=3994;PQR=0.0;PQA=0.0;SRF=179;SRR=143;SAF=55;SAR=49;SRP=11.7501;SAP=3.76196;AB=0.24356;ABP=246.912;RUN=1;RPP=3.34437;RPPR=3.1182;RPL=54.0;RPR=50.0;EPP=3.76196;EPPR=6.27425;DPRA=0.0;ODDS=210.417;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990683;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.91;Dels=0.0;FS=4.647;HaplotypeScore=5.8 [...]
+chr2 113988492 . G A 2199.8900000000003 REJECT NS=2;DP=402;DPB=450.0;AC=2;AN=4;AF=0.5;RO=340;AO=110;PRO=0.0;PAO=0.0;QR=12867;QA=4148;PQR=0.0;PQA=0.0;SRF=162;SRR=178;SAF=62;SAR=48;SRP=4.64529;SAP=6.87947;AB=0.244444;ABP=258.279;RUN=1;RPP=3.08926;RPPR=8.75832;RPL=56.0;RPR=54.0;EPP=4.98437;EPPR=7.3277;DPRA=0.0;ODDS=190.21;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990909;PAIREDR=0.997059;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.556;Dels=0.0;FS=4.98;H [...]
+chr2 113989122 . A AG 1837.55 REJECT NS=2;DP=434;DPB=476.333;AC=2;AN=4;AF=0.5;RO=339;AO=92;PRO=11.5;PAO=11.5;QR=12870;QA=3405;PQR=321.5;PQA=321.5;SRF=176;SRR=163;SAF=43;SAR=49;SRP=4.09283;SAP=3.86001;AB=0.211982;ABP=315.722;RUN=1;RPP=4.52089;RPPR=9.16601;RPL=42.0;RPR=50.0;EPP=3.86001;EPPR=3.52915;DPRA=0.0;ODDS=95.5905;GTI=0;TYPE=ins;CIGAR=1M1I2M;NUMALT=1;MEANALT=2.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99705;technology.ILLUMINA=1.0;END=113989122;HOMLEN=1;HOMSEQ=G;SVLEN=1;SVTYPE= [...]
+chr2 113989236 . C T 2210.145 REJECT NS=2;DP=397;DPB=461.0;AC=2;AN=4;AF=0.5;RO=352;AO=109;PRO=0.0;PAO=0.0;QR=13046;QA=4081;PQR=0.0;PQA=0.0;SRF=166;SRR=186;SAF=46;SAR=63;SRP=5.47788;SAP=8.76769;AB=0.236443;ABP=281.152;RUN=1;RPP=19.7645;RPPR=26.7238;RPL=40.0;RPR=69.0;EPP=24.7051;EPPR=18.4327;DPRA=0.0;ODDS=137.127;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988636;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2905;Dels=0.0;FS=1.163;HaplotypeScor [...]
+chr2 113989267 . T C 1873.315 REJECT NS=2;DP=362;DPB=423.0;AC=2;AN=4;AF=0.5;RO=326;AO=96;PRO=0.0;PAO=0.0;QR=12444;QA=3672;PQR=0.0;PQA=0.0;SRF=145;SRR=181;SAF=32;SAR=64;SRP=11.6429;SAP=26.1727;AB=0.22695;ABP=276.939;RUN=1;RPP=20.744;RPPR=25.4178;RPL=62.0;RPR=34.0;EPP=6.26751;EPPR=3.11688;DPRA=0.0;ODDS=153.647;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984663;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0675;Dels=0.0;FS=6.5965;HaplotypeScore= [...]
+chr2 113989327 . T C 604.5995 REJECT NS=2;DP=201;DPB=229.0;AC=2;AN=4;AF=0.5;RO=188;AO=41;PRO=0.0;PAO=0.0;QR=7052;QA=1557;PQR=0.0;PQA=0.0;SRF=55;SRR=133;SAF=7;SAR=34;SRP=73.2828;SAP=41.6201;AB=0.179039;ABP=207.916;RUN=1;RPP=3.48696;RPPR=23.3852;RPL=22.0;RPR=19.0;EPP=3.48696;EPPR=5.9672;DPRA=0.0;ODDS=66.0471;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8564;PAIRED=1.0;PAIREDR=0.994681;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7815;Dels=0.0;FS=4.1475;HaplotypeScore [...]
+chr2 113990242 . T C 2168.84 REJECT NS=2;DP=399;DPB=452.0;AC=2;AN=4;AF=0.5;RO=341;AO=110;PRO=0.0;PAO=0.0;QR=13039;QA=4228;PQR=0.0;PQA=0.0;SRF=162;SRR=179;SAF=64;SAR=46;SRP=4.85064;SAP=9.40627;AB=0.243363;ABP=261.588;RUN=1;RPP=12.5648;RPPR=3.01667;RPL=44.0;RPR=66.0;EPP=3.08926;EPPR=3.1695;DPRA=0.0;ODDS=234.629;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990909;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.326;Dels=0.0;FS=7.8875;HaplotypeScore= [...]
+chr2 113990261 . G A 2345.825 REJECT NS=2;DP=408;DPB=464.0;AC=2;AN=4;AF=0.5;RO=349;AO=115;PRO=0.0;PAO=0.0;QR=13373;QA=4375;PQR=0.0;PQA=0.0;SRF=160;SRR=189;SAF=62;SAR=53;SRP=8.24299;SAP=4.53977;AB=0.247845;ABP=259.263;RUN=1;RPP=4.53977;RPPR=4.06182;RPL=53.0;RPR=62.0;EPP=6.20142;EPPR=3.01652;DPRA=0.0;ODDS=212.751;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991304;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.331;Dels=0.0;FS=4.0325;HaplotypeScor [...]
+chr2 113990393 . C A 1843.425 REJECT NS=2;DP=317;DPB=365.0;AC=2;AN=4;AF=0.5;RO=272;AO=92;PRO=0.0;PAO=0.0;QR=10330;QA=3456;PQR=0.0;PQA=0.0;SRF=131;SRR=141;SAF=33;SAR=59;SRP=3.80864;SAP=18.9659;AB=0.252055;ABP=197.913;RUN=1;RPP=3.38795;RPPR=15.7837;RPL=48.0;RPR=44.0;EPP=7.63648;EPPR=17.0929;DPRA=0.0;ODDS=158.288;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0205;Dels=0.0;FS=10.313;HaplotypeScore=1. [...]
+chr2 113990612 . T C 84.77 PASS SOMATIC;DP=154;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-5.272;Dels=0.0;FS=76.004;HaplotypeScore=60.2868;MLEAC=1;MLEAF=0.5;MQ=59.35;MQRankSum=-0.496;QD=0.55;ReadPosRankSum=-0.083;SOR=6.868 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00174608 0/1:118,36:154:99.0:113,0,3056:36:23:154:.:1:.:.:.:.:-0.0116954
+chr2 113990617 . T C 144.77 PASS SOMATIC;DP=148;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-3.513;Dels=0.0;FS=80.951;HaplotypeScore=60.2078;MLEAC=1;MLEAF=0.5;MQ=59.32;MQRankSum=-0.467;QD=0.98;ReadPosRankSum=-0.914;SOR=6.438 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00174608 0/1:115,30:148:99.0:173,0,2995:30:21:145:.:1:.:.:.:.:-0.0116954
+chr2 113990622 . T C 152.77 PASS SOMATIC;DP=148;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-4.363;Dels=0.0;FS=82.892;HaplotypeScore=42.1484;MLEAC=1;MLEAF=0.5;MQ=59.38;MQRankSum=-1.834;QD=1.03;ReadPosRankSum=0.118;SOR=4.161 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00174608 0/1:120,28:148:99.0:181,0,3317:28:19:148:.:1:.:.:.:.:-0.0116954
+chr2 113990907 . G A 1645.5 REJECT NS=2;DP=146;DPB=229.476;AC=2;AN=2;AF=0.0;RO=29;AO=6;PRO=42.1333;PAO=10.8;QR=1045;QA=72;PQR=1468.93;PQA=372.6;SRF=11;SRR=18;SAF=0;SAR=6;SRP=6.67934;SAP=16.0391;AB=0.0410959;ABP=270.072;RUN=1;RPP=4.45795;RPPR=3.68421;RPL=4.0;RPR=2.0;EPP=4.45795;EPPR=4.88226;DPRA=0.0;ODDS=60.759;GTI=0;TYPE=snp;CIGAR=1X20M;NUMALT=4;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMIC [...]
+chr2 113990907 . G GA 1423.115 REJECT NS=2;DP=146;DPB=229.476;AC=2;AN=4;AF=0.5;RO=29;AO=76;PRO=42.1333;PAO=45.1333;QR=1045;QA=2097;PQR=1468.93;PQA=1565.93;SRF=11;SRR=18;SAF=19;SAR=57;SRP=6.67934;SAP=44.2683;AB=0.520548;ABP=3.54573;RUN=1;RPP=3.46745;RPPR=3.68421;RPL=40.0;RPR=36.0;EPP=12.2676;EPPR=4.88226;DPRA=0.0;ODDS=60.759;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=4;MEANALT=9.5;LEN=1;MQM=59.8684;MQMR=60.0;PAIRED=0.986842;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum [...]
+chr2 113990907 . G AA 1645.5 REJECT NS=2;DP=146;DPB=229.476;AC=2;AN=2;AF=0.0;RO=29;AO=5;PRO=42.1333;PAO=10.8;QR=1045;QA=86;PQR=1468.93;PQA=372.6;SRF=11;SRR=18;SAF=0;SAR=5;SRP=6.67934;SAP=13.8677;AB=0.0342466;ABP=278.103;RUN=1;RPP=3.44459;RPPR=3.68421;RPL=3.0;RPR=2.0;EPP=3.44459;EPPR=4.88226;DPRA=0.0;ODDS=60.759;GTI=0;TYPE=complex;CIGAR=1X1I20M;NUMALT=4;MEANALT=9.5;LEN=22;MQM=70.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr2 113990907 . G GAA 1645.5 REJECT NS=2;DP=146;DPB=229.476;AC=2;AN=2;AF=0.0;RO=29;AO=11;PRO=42.1333;PAO=40.1333;QR=1045;QA=331;PQR=1468.93;PQA=1389.93;SRF=11;SRR=18;SAF=5;SAR=6;SRP=6.67934;SAP=3.20771;AB=0.0753425;ABP=231.699;RUN=1;RPP=4.78696;RPPR=3.68421;RPL=4.0;RPR=7.0;EPP=4.78696;EPPR=4.88226;DPRA=0.0;ODDS=60.759;GTI=0;TYPE=ins;CIGAR=1M2I20M;NUMALT=4;MEANALT=9.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr2 113991260 . AC A 7478.26 REJECT NS=2;DP=125;DPB=215.967;AC=2;AN=2;AF=0.5;RO=0;AO=15;PRO=22.8143;PAO=34.231;QR=0;QA=547;PQR=803.467;PQA=1216.13;SRF=0;SRR=0;SAF=9;SAR=6;SRP=0.0;SAP=4.31318;AB=0.12;ABP=159.791;RUN=1;RPP=14.7363;RPPR=0.0;RPL=3.0;RPR=12.0;EPP=6.62942;EPPR=0.0;DPRA=0.0;ODDS=1.71224;GTI=0;TYPE=del;CIGAR=7M1D22M;NUMALT=6;MEANALT=18.0;LEN=1;MQM=56.6667;MQMR=0.0;PAIRED=0.933333;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;END=113991261;HOMLEN=0;SVLEN=-1;SVTYPE=DEL GT [...]
+chr2 113991261 . C A 7478.26 REJECT NS=2;DP=125;DPB=215.967;AC=2;AN=2;AF=0.5;RO=0;AO=48;PRO=22.8143;PAO=34.731;QR=0;QA=1804;PQR=803.467;PQA=1240.13;SRF=0;SRR=0;SAF=36;SAR=12;SRP=0.0;SAP=29.068;AB=0.384;ABP=17.62;RUN=1;RPP=21.1059;RPPR=0.0;RPL=14.0;RPR=34.0;EPP=29.068;EPPR=0.0;DPRA=0.0;ODDS=1.71224;GTI=0;TYPE=snp;CIGAR=7M1X22M;NUMALT=6;MEANALT=18.0;LEN=1;MQM=59.375;MQMR=0.0;PAIRED=0.979167;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.783;FS=2.917;MLEAC=2;MLEAF=1.0 [...]
+chr2 113991261 . C AA 7478.26 REJECT NS=2;DP=125;DPB=215.967;AC=0;AN=4;AF=0.0;RO=0;AO=12;PRO=22.8143;PAO=34.3976;QR=0;QA=380;PQR=803.467;PQA=1192.13;SRF=0;SRR=0;SAF=9;SAR=3;SRP=0.0;SAP=9.52472;AB=0.096;ABP=180.22;RUN=1;RPP=3.73412;RPPR=0.0;RPL=5.0;RPR=7.0;EPP=3.0103;EPPR=0.0;DPRA=0.0;ODDS=1.71224;GTI=0;TYPE=complex;CIGAR=1M1I6M1X22M;NUMALT=6;MEANALT=18.0;LEN=31;MQM=56.4167;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMIC [...]
+chr2 113991261 . C AAA 7478.26 REJECT NS=2;DP=125;DPB=215.967;AC=0;AN=4;AF=0.0;RO=0;AO=3;PRO=22.8143;PAO=32.3976;QR=0;QA=86;PQR=803.467;PQA=1109.13;SRF=0;SRR=0;SAF=3;SAR=0;SRP=0.0;SAP=9.52472;AB=0.024;ABP=249.012;RUN=1;RPP=3.73412;RPPR=0.0;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=0.0;DPRA=0.0;ODDS=1.71224;GTI=0;TYPE=complex;CIGAR=1M2I6M1X22M;NUMALT=6;MEANALT=18.0;LEN=32;MQM=53.3333;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr2 113991261 . CAAAAAAAC AAAAAAAACA 7478.26 REJECT NS=2;DP=125;DPB=215.967;AC=0;AN=4;AF=0.0;RO=0;AO=6;PRO=22.8143;PAO=23.7143;QR=0;QA=159;PQR=803.467;PQA=788.833;SRF=0;SRR=0;SAF=6;SAR=0;SRP=0.0;SAP=16.0391;AB=0.048;ABP=224.831;RUN=1;RPP=8.80089;RPPR=0.0;RPL=1.0;RPR=5.0;EPP=8.80089;EPPR=0.0;DPRA=0.0;ODDS=1.71224;GTI=0;TYPE=complex;CIGAR=7M1X8M1I14M;NUMALT=6;MEANALT=18.0;LEN=31;MQM=57.8333;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr2 113991261 . CAAAAAAACAAAAAAAAAAGGGT AAAAAAAACAAAAAAAAAAGGGG 7478.26 REJECT NS=2;DP=125;DPB=215.967;AC=0;AN=4;AF=0.0;RO=0;AO=9;PRO=22.8143;PAO=6.71429;QR=0;QA=135;PQR=803.467;PQA=248.167;SRF=0;SRR=0;SAF=9;SAR=0;SRP=0.0;SAP=22.5536;AB=0.072;ABP=201.9;RUN=1;RPP=9.04217;RPPR=0.0;RPL=7.0;RPR=2.0;EPP=9.04217;EPPR=0.0;DPRA=0.0;ODDS=1.71224;GTI=0;TYPE=complex;CIGAR=7M1X21M1X;NUMALT=6;MEANALT=18.0;LEN=30;MQM=59.2222;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT [...]
+chr2 113991970 . A G 1120.48 REJECT NS=2;DP=240;DPB=271.0;AC=2;AN=4;AF=0.5;RO=214;AO=57;PRO=0.0;PAO=0.0;QR=8143;QA=2144;PQR=0.0;PQA=0.0;SRF=101;SRR=113;SAF=20;SAR=37;SRP=4.47148;SAP=14.02;AB=0.210332;ABP=200.518;RUN=1;RPP=3.35316;RPPR=3.0103;RPL=30.0;RPR=27.0;EPP=3.0484;EPPR=14.7403;DPRA=0.0;ODDS=60.2633;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.981308;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.3385;Dels=0.0;FS=2.06;HaplotypeScore=1.9654 [...]
+chr2 113992201 . G A 551.573 REJECT NS=2;DP=112;DPB=129.0;AC=2;AN=4;AF=0.5;RO=99;AO=30;PRO=0.0;PAO=0.0;QR=3702;QA=1153;PQR=0.0;PQA=0.0;SRF=49;SRR=50;SAF=13;SAR=17;SRP=3.03223;SAP=4.16842;AB=0.232558;ABP=83.1528;RUN=1;RPP=5.61607;RPPR=3.20771;RPL=18.0;RPR=12.0;EPP=4.16842;EPPR=21.4568;DPRA=0.0;ODDS=61.497;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.969697;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1815;Dels=0.0;FS=1.551;HaplotypeScore=0.957 [...]
+chr2 113992374 . G C 879.275 REJECT NS=2;DP=205;DPB=233.0;AC=2;AN=4;AF=0.5;RO=187;AO=46;PRO=0.0;PAO=0.0;QR=7082;QA=1775;PQR=0.0;PQA=0.0;SRF=141;SRR=46;SAF=35;SAR=11;SRP=107.81;SAP=30.2009;AB=0.197425;ABP=188.294;RUN=1;RPP=12.2627;RPPR=12.7761;RPL=16.0;RPR=30.0;EPP=3.0103;EPPR=28.6615;DPRA=0.0;ODDS=17.7319;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8824;PAIRED=1.0;PAIREDR=0.989305;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6515;Dels=0.0;FS=3.53;HaplotypeScore=4. [...]
+chr2 113992800 . TCC T 2164.38 REJECT NS=2;DP=391;DPB=384.429;AC=2;AN=4;AF=0.5;RO=289;AO=101;PRO=29.0;PAO=14.0;QR=10834;QA=3684;PQR=1016.5;PQA=503.5;SRF=120;SRR=169;SAF=35;SAR=66;SRP=21.0508;SAP=23.6715;AB=0.258312;ABP=201.392;RUN=1;RPP=4.75178;RPPR=4.70089;RPL=55.0;RPR=46.0;EPP=7.84774;EPPR=7.70639;DPRA=0.0;ODDS=137.713;GTI=0;TYPE=del;CIGAR=1M2D4M;NUMALT=1;MEANALT=1.5;LEN=2;MQM=60.198;MQMR=60.0;PAIRED=0.990099;PAIREDR=0.99654;technology.ILLUMINA=1.0;END=113992802;HOMLEN=2;HOMSEQ=CC;SVLE [...]
+chr2 113993344 . A C 1495.355 REJECT NS=2;DP=270;DPB=318.0;AC=2;AN=4;AF=0.5;RO=241;AO=76;PRO=0.0;PAO=0.0;QR=8874;QA=2724;PQR=0.0;PQA=0.0;SRF=110;SRR=131;SAF=35;SAR=41;SRP=6.98382;SAP=4.03889;AB=0.238994;ABP=191.177;RUN=1;RPP=4.03889;RPPR=3.4518;RPL=41.0;RPR=35.0;EPP=4.83891;EPPR=6.98382;DPRA=0.0;ODDS=79.8721;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986842;PAIREDR=0.995851;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4825;Dels=0.0;FS=2.7925;Haplotype [...]
+chr2 113993385 . C G 1307.09 REJECT NS=2;DP=261;DPB=305.0;AC=2;AN=4;AF=0.5;RO=241;AO=64;PRO=0.0;PAO=0.0;QR=8661;QA=2445;PQR=0.0;PQA=0.0;SRF=137;SRR=104;SAF=40;SAR=24;SRP=12.8225;SAP=11.6962;AB=0.209836;ABP=226.06;RUN=1;RPP=3.14602;RPPR=3.4518;RPL=33.0;RPR=31.0;EPP=14.0034;EPPR=32.2846;DPRA=0.0;ODDS=57.8006;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.96875;PAIREDR=0.995851;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4955;Dels=0.0;FS=1.813;HaplotypeScore [...]
+chr2 113993608 . G A 61.6046 REJECT NS=2;DP=313;DPB=313.0;AC=2;AN=3;AF=0.25;RO=267;AO=31;PRO=0.0;PAO=0.0;QR=8927;QA=981;PQR=0.0;PQA=0.0;SRF=125;SRR=142;SAF=21;SAR=10;SRP=5.3607;SAP=11.486;AB=0.161616;ABP=101.472;RUN=1;RPP=14.8483;RPPR=15.3804;RPL=9.0;RPR=22.0;EPP=6.44263;EPPR=5.3607;DPRA=0.0;ODDS=14.185;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=2;MEANALT=2.0;LEN=1;MQM=36.0;MQMR=47.1273;PAIRED=0.935484;PAIREDR=0.996255;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.658;FS=11.496;MLEAC=1;M [...]
+chr2 113993608 . G C 61.6046 REJECT NS=2;DP=313;DPB=313.0;AC=2;AN=2;AF=0.0;RO=267;AO=15;PRO=0.0;PAO=0.0;QR=8927;QA=226;PQR=0.0;PQA=0.0;SRF=125;SRR=142;SAF=4;SAR=11;SRP=5.3607;SAP=10.1038;AB=0.0505051;ABP=176.75;RUN=1;RPP=14.7363;RPPR=15.3804;RPL=3.0;RPR=12.0;EPP=27.4756;EPPR=5.3607;DPRA=0.0;ODDS=14.185;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=2;MEANALT=2.0;LEN=1;MQM=22.6;MQMR=47.1273;PAIRED=1.0;PAIREDR=0.996255;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV: [...]
+chr2 113993734 . G C 52.77 PASS DP=81;AC=1;AN=4;AF=0.5;BaseQRankSum=1.125;FS=7.591;MLEAC=1;MLEAF=0.5;MQ=45.32;MQRankSum=1.678;QD=0.65;ReadPosRankSum=-3.104;SOR=0.324;ClippingRankSum=-0.883 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:35,45:80:81.0:81,0,995:45:56:80:1:.:.:.:.:.:-0.00174608 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0116954
+chr2 113993789 . A G 18.5286 REJECT NS=2;DP=298;DPB=298.0;AC=1;AN=4;AF=0.25;RO=260;AO=34;PRO=0.0;PAO=0.0;QR=8973;QA=972;PQR=0.0;PQA=0.0;SRF=145;SRR=115;SAF=13;SAR=21;SRP=10.5269;SAP=7.09778;AB=0.164706;ABP=86.0116;RUN=1;RPP=3.26577;RPPR=5.71629;RPL=18.0;RPR=16.0;EPP=7.09778;EPPR=9.55812;DPRA=0.0;ODDS=4.25222;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.5;LEN=1;MQM=27.7059;MQMR=39.3308;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG: [...]
+chr2 114035923 . A G 918.816 REJECT NS=1;DP=84;DPB=84.0;AC=1;AN=4;AF=0.5;RO=48;AO=35;PRO=0.0;PAO=0.0;QR=1759;QA=1331;PQR=0.0;PQA=0.0;SRF=37;SRR=11;SAF=22;SAR=13;SRP=33.5919;SAP=8.03571;AB=0.416667;ABP=8.07707;RUN=1;RPP=10.5174;RPPR=3.0103;RPL=12.0;RPR=23.0;EPP=3.07234;EPPR=3.19126;DPRA=0.0;ODDS=211.565;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=1.697;FS=6.529;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.666;Q [...]
+chr2 120014609 . C T 7144.200000000001 REJECT NS=2;DP=317;DPB=358.0;AC=3;AN=4;AF=0.75;RO=103;AO=255;PRO=0.0;PAO=0.0;QR=4003;QA=9717;PQR=0.0;PQA=0.0;SRF=53;SRR=50;SAF=149;SAR=106;SRP=3.20004;SAP=18.7556;AB=0.626812;ABP=41.5618;RUN=1;RPP=76.6615;RPPR=10.621;RPL=81.0;RPR=174.0;EPP=6.08442;EPPR=3.20004;DPRA=0.0;ODDS=52.1473;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992157;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.594;Dels=0.0;FS=2.101;Haplo [...]
+chr2 121713022 . C G 1830.97 REJECT NS=1;DP=58;DPB=58.0;AC=2;AN=4;AF=1.0;RO=0;AO=58;PRO=0.0;PAO=0.0;QR=0;QA=2128;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=15;SAR=43;SRP=0.0;SAP=32.3626;AB=0.0;ABP=0.0;RUN=1;RPP=28.3192;RPPR=0.0;RPL=42.0;RPR=16.0;EPP=3.60933;EPPR=0.0;DPRA=0.0;ODDS=40.7543;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.41;SOR=2.147 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:A [...]
+chr2 121713030 . G A 1652.51 REJECT NS=1;DP=54;DPB=54.0;AC=2;AN=4;AF=1.0;RO=0;AO=54;PRO=0.0;PAO=0.0;QR=0;QA=1959;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=13;SAR=41;SRP=0.0;SAP=34.5369;AB=0.0;ABP=0.0;RUN=1;RPP=44.1879;RPPR=0.0;RPL=43.0;RPR=11.0;EPP=10.8919;EPPR=0.0;DPRA=0.0;ODDS=38.2591;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.31;SOR=2.303 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:A [...]
+chr2 121726447 . G A 12234.099999999999 REJECT NS=2;DP=322;DPB=366.0;AC=4;AN=4;AF=1.0;RO=0;AO=366;PRO=0.0;PAO=0.0;QR=0;QA=14059;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=139;SAR=227;SRP=0.0;SAP=48.9553;AB=0.0;ABP=0.0;RUN=1;RPP=19.0531;RPPR=0.0;RPL=209.0;RPR=157.0;EPP=13.4761;EPPR=0.0;DPRA=0.0;ODDS=58.0232;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991803;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8798;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=2 [...]
+chr2 121729490 . C T 2440.67 REJECT NS=1;DP=76;DPB=76.0;AC=2;AN=4;AF=1.0;RO=0;AO=75;PRO=0.0;PAO=0.0;QR=0;QA=2819;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=46;SAR=29;SRP=0.0;SAP=11.3777;AB=0.0;ABP=0.0;RUN=1;RPP=56.5443;RPPR=0.0;RPL=16.0;RPR=59.0;EPP=5.35549;EPPR=0.0;DPRA=0.0;ODDS=51.4034;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.986667;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=25.97;SOR=1.24 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMIC [...]
+chr2 121745879 . A T 20.5306 REJECT NS=2;DP=117;DPB=117.0;AC=1;AN=4;AF=0.25;RO=109;AO=8;PRO=0.0;PAO=0.0;QR=4210;QA=307;PQR=0.0;PQA=0.0;SRF=43;SRR=66;SAF=1;SAR=7;SRP=13.5489;SAP=12.7819;AB=0.166667;ABP=20.3821;RUN=1;RPP=4.09604;RPPR=13.5489;RPL=5.0;RPR=3.0;EPP=3.0103;EPPR=5.42083;DPRA=0.0;ODDS=4.71845;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-1.303;FS=2.823;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.711;Q [...]
+chr2 121746956 . G T 20076.75 REJECT NS=2;DP=544;DPB=623.0;AC=4;AN=4;AF=1.0;RO=1;AO=620;PRO=0.0;PAO=0.0;QR=15;QA=23319;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=284;SAR=336;SRP=5.18177;SAP=12.4807;AB=0.0;ABP=0.0;RUN=1;RPP=3.0103;RPPR=5.18177;RPL=310.0;RPR=310.0;EPP=11.0798;EPPR=5.18177;DPRA=0.0;ODDS=102.788;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995161;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.725;Dels=0.0;FS=0.0;HaplotypeScore=14.6132;MLEAC=2 [...]
+chr2 121747406 . G A 16046.6 REJECT NS=2;DP=420;DPB=482.0;AC=4;AN=4;AF=1.0;RO=0;AO=482;PRO=0.0;PAO=0.0;QR=0;QA=18558;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=208;SAR=274;SRP=0.0;SAP=22.6346;AB=0.0;ABP=0.0;RUN=1;RPP=3.89331;RPPR=0.0;RPL=248.0;RPR=234.0;EPP=4.46996;EPPR=0.0;DPRA=0.0;ODDS=80.4083;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.989627;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8239;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.94;SOR=0. [...]
+chr2 121747429 . A G 14618.599999999999 REJECT NS=2;DP=388;DPB=439.0;AC=4;AN=4;AF=1.0;RO=1;AO=438;PRO=0.0;PAO=0.0;QR=40;QA=16713;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=195;SAR=243;SRP=5.18177;SAP=14.4328;AB=0.0;ABP=0.0;RUN=1;RPP=9.43548;RPPR=5.18177;RPL=237.0;RPR=201.0;EPP=3.50607;EPPR=5.18177;DPRA=0.0;ODDS=66.1013;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990868;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.687;Dels=0.0;FS=0.0;HaplotypeScore=8.8 [...]
+chr2 127504051 . G A 1008.64 REJECT NS=2;DP=252;DPB=293.0;AC=2;AN=4;AF=0.5;RO=239;AO=54;PRO=0.0;PAO=0.0;QR=9114;QA=2118;PQR=0.0;PQA=0.0;SRF=188;SRR=51;SAF=40;SAR=14;SRP=173.539;SAP=30.1939;AB=0.1843;ABP=256.658;RUN=1;RPP=26.1727;RPPR=103.18;RPL=15.0;RPR=39.0;EPP=3.6537;EPPR=9.63375;DPRA=0.0;ODDS=9.59375;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995816;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.454;Dels=0.0;FS=4.2125;HaplotypeScore=1.933; [...]
+chr2 128079806 . A G 7556.12 REJECT NS=2;DP=301;DPB=347.0;AC=2;AN=4;AF=0.5;RO=84;AO=262;PRO=0.0;PAO=0.0;QR=3223;QA=9749;PQR=0.0;PQA=0.0;SRF=21;SRR=63;SAF=55;SAR=207;SRP=48.6112;SAP=194.498;AB=0.755043;ABP=199.062;RUN=1;RPP=13.7516;RPPR=8.07707;RPL=149.0;RPR=113.0;EPP=4.63476;EPPR=6.73282;DPRA=0.0;ODDS=149.366;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=59.7619;PAIRED=0.996183;PAIREDR=0.97619;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.1345;Dels=0.0;FS=5.332;Haploty [...]
+chr2 133489401 . A G 1423.135 REJECT NS=2;DP=378;DPB=426.0;AC=2;AN=4;AF=0.5;RO=345;AO=79;PRO=0.0;PAO=0.0;QR=13159;QA=2971;PQR=0.0;PQA=0.0;SRF=183;SRR=162;SAF=33;SAR=46;SRP=5.78601;SAP=7.6556;AB=0.185446;ABP=369.123;RUN=1;RPP=6.33623;RPPR=3.31871;RPL=34.0;RPR=45.0;EPP=4.35716;EPPR=3.31871;DPRA=0.0;ODDS=82.1113;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=59.8957;PAIRED=0.974684;PAIREDR=0.994203;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.086;Dels=0.0;FS=6.354;Haplotyp [...]
+chr2 133489601 . A G 4881.59 REJECT NS=2;DP=316;DPB=362.0;AC=2;AN=4;AF=0.5;RO=184;AO=178;PRO=0.0;PAO=0.0;QR=7027;QA=6857;PQR=0.0;PQA=0.0;SRF=76;SRR=108;SAF=57;SAR=121;SRP=15.095;SAP=52.9786;AB=0.491713;ABP=3.22625;RUN=1;RPP=6.13332;RPPR=4.19045;RPL=97.0;RPR=81.0;EPP=20.6261;EPPR=16.6528;DPRA=0.0;ODDS=273.647;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988764;PAIREDR=0.98913;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.826;Dels=0.0;FS=7.087;HaplotypeScor [...]
+chr2 133539566 . G A 5312.82 REJECT NS=2;DP=339;DPB=388.0;AC=2;AN=4;AF=0.5;RO=192;AO=196;PRO=0.0;PAO=0.0;QR=7322;QA=7424;PQR=0.0;PQA=0.0;SRF=113;SRR=79;SAF=108;SAR=88;SRP=16.0844;SAP=7.44188;AB=0.505155;ABP=3.09985;RUN=1;RPP=10.4997;RPPR=6.67466;RPL=85.0;RPR=111.0;EPP=5.18177;EPPR=3.19126;DPRA=0.0;ODDS=276.94;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994898;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1585;Dels=0.0;FS=5.5335;HaplotypeScore [...]
+chr2 133540605 . G T 3344.98 PASS SOMATIC;NS=2;DP=420;DPB=420.0;AC=1;AN=3;AF=0.25;RO=297;AO=123;PRO=0.0;PAO=0.0;QR=11316;QA=4724;PQR=0.0;PQA=0.0;SRF=134;SRR=163;SAF=48;SAR=75;SRP=9.15915;SAP=15.8802;AB=0.398058;ABP=30.9021;RUN=1;RPP=3.87536;RPPR=6.23461;RPL=65.0;RPR=58.0;EPP=3.45166;EPPR=4.24592;DPRA=2.78378;ODDS=70.1976;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993266;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.93;Dels=0.0;FS=4.65 [...]
+chr2 133541107 . T A 1930.355 REJECT NS=2;DP=396;DPB=452.0;AC=2;AN=4;AF=0.5;RO=354;AO=98;PRO=0.0;PAO=0.0;QR=13571;QA=3741;PQR=0.0;PQA=0.0;SRF=175;SRR=179;SAF=53;SAR=45;SRP=3.10845;SAP=4.4284;AB=0.216814;ABP=317.855;RUN=1;RPP=3.36483;RPPR=5.46394;RPL=47.0;RPR=51.0;EPP=22.9524;EPPR=11.8679;DPRA=0.0;ODDS=150.153;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997175;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.125;Dels=0.0;FS=1.745;HaplotypeScore=7 [...]
+chr2 133541444 . T C 4847.01 REJECT NS=2;DP=313;DPB=356.0;AC=2;AN=4;AF=0.5;RO=185;AO=171;PRO=0.0;PAO=0.0;QR=7211;QA=6555;PQR=0.0;PQA=0.0;SRF=104;SRR=81;SAF=83;SAR=88;SRP=9.21954;SAP=3.32777;AB=0.480337;ABP=4.20583;RUN=1;RPP=15.2137;RPPR=3.58545;RPL=101.0;RPR=70.0;EPP=16.8392;EPPR=3.30374;DPRA=0.0;ODDS=250.616;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994152;PAIREDR=0.994595;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.392;Dels=0.0;FS=4.595;HaplotypeS [...]
+chr2 133541454 . A G 5174.790000000001 REJECT NS=2;DP=334;DPB=379.0;AC=2;AN=4;AF=0.5;RO=196;AO=183;PRO=0.0;PAO=0.0;QR=7492;QA=7053;PQR=0.0;PQA=0.0;SRF=106;SRR=90;SAF=87;SAR=96;SRP=5.84651;SAP=3.97144;AB=0.48285;ABP=3.97858;RUN=1;RPP=6.43957;RPPR=8.37251;RPL=100.0;RPR=83.0;EPP=11.6606;EPPR=6.59988;DPRA=0.0;ODDS=294.089;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994536;PAIREDR=0.994898;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.71;Dels=0.0;FS=4.8855;Ha [...]
+chr2 133541575 . C T 2388.44 PASS SOMATIC;NS=2;DP=310;DPB=310.0;AC=1;AN=3;AF=0.25;RO=222;AO=88;PRO=0.0;PAO=0.0;QR=8550;QA=3399;PQR=0.0;PQA=0.0;SRF=110;SRR=112;SAF=38;SAR=50;SRP=3.04943;SAP=6.56362;AB=0.389381;ABP=27.031;RUN=1;RPP=5.47788;RPPR=8.64439;RPL=49.0;RPR=39.0;EPP=3.109;EPPR=6.92286;DPRA=2.69048;ODDS=53.415;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995495;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.329;Dels=0.0;FS=3.822;Hap [...]
+chr2 133542014 . T C 5525.16 REJECT NS=2;DP=355;DPB=408.0;AC=2;AN=4;AF=0.5;RO=206;AO=201;PRO=0.0;PAO=0.0;QR=7813;QA=7566;PQR=0.0;PQA=0.0;SRF=104;SRR=102;SAF=102;SAR=99;SRP=3.05246;SAP=3.10753;AB=0.492647;ABP=3.2019;RUN=1;RPP=3.0211;RPPR=3.17896;RPL=100.0;RPR=101.0;EPP=5.44105;EPPR=5.70883;DPRA=0.0;ODDS=317.252;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99005;PAIREDR=0.990291;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0905;Dels=0.0;FS=1.0495;Haplotype [...]
+chr2 133542545 . G A 3445.11 PASS SOMATIC;NS=2;DP=446;DPB=446.0;AC=1;AN=3;AF=0.25;RO=317;AO=129;PRO=0.0;PAO=0.0;QR=11981;QA=4965;PQR=0.0;PQA=0.0;SRF=153;SRR=164;SAF=66;SAR=63;SRP=3.83916;SAP=3.1618;AB=0.361345;ABP=62.6254;RUN=1;RPP=3.02713;RPPR=3.18155;RPL=65.0;RPR=64.0;EPP=3.83512;EPPR=7.29159;DPRA=4.01124;ODDS=56.4831;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9369;PAIRED=1.0;PAIREDR=0.987382;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.631;Dels=0.0;FS=0 [...]
+chr2 133542574 . C T 2168.4449999999997 REJECT NS=2;DP=385;DPB=434.0;AC=2;AN=4;AF=0.5;RO=330;AO=104;PRO=0.0;PAO=0.0;QR=12621;QA=3956;PQR=0.0;PQA=0.0;SRF=168;SRR=162;SAF=45;SAR=59;SRP=3.24719;SAP=7.10269;AB=0.239631;ABP=258.564;RUN=1;RPP=5.09825;RPPR=18.1711;RPL=57.0;RPR=47.0;EPP=6.01695;EPPR=3.11558;DPRA=0.0;ODDS=157.815;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8077;MQMR=60.0;PAIRED=0.990385;PAIREDR=0.987879;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.936;Dels=0.0;FS=4 [...]
+chr2 133542585 . C G 2741.22 PASS SOMATIC;NS=2;DP=400;DPB=400.0;AC=1;AN=3;AF=0.25;RO=295;AO=104;PRO=0.0;PAO=0.0;QR=11326;QA=4037;PQR=0.0;PQA=0.0;SRF=142;SRR=153;SAF=51;SAR=53;SRP=3.90097;SAP=3.09382;AB=0.33657;ABP=74.697;RUN=1;RPP=3.76196;RPPR=4.2543;RPL=55.0;RPR=49.0;EPP=6.01695;EPPR=3.07655;DPRA=3.3956;ODDS=57.783;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=59.9322;PAIRED=1.0;PAIREDR=0.983051;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.046;Dels=0.0;FS=2.623 [...]
+chr2 133554288 . A G 4750.790000000001 REJECT NS=2;DP=315;DPB=360.0;AC=2;AN=4;AF=0.5;RO=187;AO=173;PRO=0.0;PAO=0.0;QR=7126;QA=6610;PQR=0.0;PQA=0.0;SRF=63;SRR=124;SAF=50;SAR=123;SRP=46.2191;SAP=69.8992;AB=0.480556;ABP=4.19255;RUN=1;RPP=28.4278;RPPR=20.6724;RPL=109.0;RPR=64.0;EPP=3.3241;EPPR=7.20229;DPRA=0.0;ODDS=276.27;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99422;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.214;Dels=0.0;FS=1.567;Haplotyp [...]
+chr2 133618220 . A G 962.715 REJECT NS=2;DP=206;DPB=233.0;AC=2;AN=4;AF=0.5;RO=177;AO=56;PRO=0.0;PAO=0.0;QR=6691;QA=2125;PQR=0.0;PQA=0.0;SRF=42;SRR=135;SAF=14;SAR=42;SRP=109.118;SAP=33.4109;AB=0.240343;ABP=139.459;RUN=1;RPP=78.0812;RPPR=220.023;RPL=50.0;RPR=6.0;EPP=12.937;EPPR=32.4663;DPRA=0.0;ODDS=116.124;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0085;Dels=0.0;FS=0.422;HaplotypeScore=0.0;MLEAC [...]
+chr2 133683658 . G T 4482.92 REJECT NS=1;DP=132;DPB=132.0;AC=2;AN=4;AF=1.0;RO=0;AO=132;PRO=0.0;PAO=0.0;QR=0;QA=5071;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=60;SAR=72;SRP=0.0;SAP=5.37918;AB=0.0;ABP=0.0;RUN=1;RPP=37.8197;RPPR=0.0;RPL=89.0;RPR=43.0;EPP=10.9724;EPPR=0.0;DPRA=0.0;ODDS=86.9542;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.984848;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.18;SOR=0.859 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr2 134060719 . T C 1476.67 PASS SOMATIC;NS=2;DP=217;DPB=217.0;AC=1;AN=3;AF=0.25;RO=158;AO=59;PRO=0.0;PAO=0.0;QR=6005;QA=2260;PQR=0.0;PQA=0.0;SRF=31;SRR=127;SAF=13;SAR=46;SRP=129.67;SAP=43.0905;AB=0.355422;ABP=33.1493;RUN=1;RPP=19.2411;RPPR=59.3037;RPL=40.0;RPR=19.0;EPP=3.93042;EPPR=9.66215;DPRA=3.2549;ODDS=32.8548;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983051;PAIREDR=0.993671;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.94;Dels=0.0;FS=1.61 [...]
+chr2 139519524 . C T 8105.72 REJECT NS=2;DP=355;DPB=395.0;AC=3;AN=4;AF=0.75;RO=119;AO=276;PRO=0.0;PAO=0.0;QR=4498;QA=10620;PQR=0.0;PQA=0.0;SRF=57;SRR=62;SAF=130;SAR=146;SRP=3.46649;SAP=5.02442;AB=0.623418;ABP=44.818;RUN=1;RPP=3.04177;RPPR=4.48836;RPL=139.0;RPR=137.0;EPP=3.79707;EPPR=3.46649;DPRA=0.0;ODDS=50.2505;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992754;PAIREDR=0.991597;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.429;Dels=0.0;FS=0.2115;Haploty [...]
+chr2 140992337 . C A 2018.5 PASS SOMATIC;NS=2;DP=277;DPB=277.0;AC=1;AN=3;AF=0.25;RO=197;AO=80;PRO=0.0;PAO=0.0;QR=7601;QA=3010;PQR=0.0;PQA=0.0;SRF=136;SRR=61;SAF=58;SAR=22;SRP=65.013;SAP=38.1882;AB=0.377358;ABP=30.7068;RUN=1;RPP=30.8051;RPPR=15.014;RPL=24.0;RPR=56.0;EPP=3.44459;EPPR=29.4758;DPRA=3.26154;ODDS=41.5644;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994924;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.02;Dels=0.0;FS=2.677;Hap [...]
+chr2 140992340 . A T 3513.64 REJECT NS=2;DP=256;DPB=291.0;AC=2;AN=4;AF=0.5;RO=162;AO=129;PRO=0.0;PAO=0.0;QR=6168;QA=4917;PQR=0.0;PQA=0.0;SRF=111;SRR=51;SAF=91;SAR=38;SRP=51.2652;SAP=50.2945;AB=0.443299;ABP=11.1365;RUN=1;RPP=9.08706;RPPR=36.5207;RPL=55.0;RPR=74.0;EPP=13.531;EPPR=10.7311;DPRA=0.0;ODDS=167.639;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992248;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.851;Dels=0.0;FS=2.678;HaplotypeScore=35. [...]
+chr2 141032088 . C T 10866.4 REJECT NS=2;DP=407;DPB=466.0;AC=2;AN=4;AF=0.5;RO=109;AO=357;PRO=0.0;PAO=0.0;QR=4172;QA=13625;PQR=0.0;PQA=0.0;SRF=51;SRR=58;SAF=179;SAR=178;SRP=3.98647;SAP=3.01638;AB=0.766094;ABP=289.607;RUN=1;RPP=10.4614;RPPR=3.50834;RPL=196.0;RPR=161.0;EPP=57.9054;EPPR=17.5333;DPRA=0.0;ODDS=159.854;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.958;MQMR=60.0;PAIRED=0.994398;PAIREDR=0.981651;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.9065;Dels=0.0;FS=0.9695;Hapl [...]
+chr2 141110677 . C A 3901.2 REJECT NS=2;DP=236;DPB=270.0;AC=2;AN=4;AF=0.5;RO=129;AO=141;PRO=0.0;PAO=0.0;QR=4693;QA=5352;PQR=0.0;PQA=0.0;SRF=41;SRR=88;SAF=51;SAR=90;SRP=40.1947;SAP=26.4345;AB=0.522222;ABP=4.16842;RUN=1;RPP=99.1249;RPPR=124.63;RPL=110.0;RPR=31.0;EPP=4.25774;EPPR=3.83512;DPRA=0.0;ODDS=202.357;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992908;PAIREDR=0.992248;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.4995;Dels=0.0;FS=1.4305;HaplotypeSco [...]
+chr2 141116447 . G T 1722.455 REJECT NS=2;DP=367;DPB=420.0;AC=2;AN=4;AF=0.5;RO=324;AO=94;PRO=0.0;PAO=0.0;QR=12267;QA=3597;PQR=0.0;PQA=0.0;SRF=142;SRR=182;SAF=48;SAR=46;SRP=13.7336;SAP=3.1027;AB=0.22381;ABP=281.29;RUN=1;RPP=3.37991;RPPR=3.03711;RPL=49.0;RPR=45.0;EPP=16.3163;EPPR=12.6881;DPRA=0.0;ODDS=202.184;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996914;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.211;Dels=0.0;FS=3.8185;HaplotypeScore=3. [...]
+chr2 141130695 . C T 4190.79 REJECT NS=2;DP=320;DPB=365.0;AC=2;AN=4;AF=0.5;RO=209;AO=155;PRO=0.0;PAO=0.0;QR=7757;QA=5880;PQR=0.0;PQA=0.0;SRF=65;SRR=144;SAF=48;SAR=107;SRP=67.8532;SAP=51.7774;AB=0.424658;ABP=21.0067;RUN=1;RPP=8.06773;RPPR=8.50651;RPL=87.0;RPR=68.0;EPP=3.36054;EPPR=3.10381;DPRA=0.0;ODDS=207.847;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987097;PAIREDR=0.990431;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.166;Dels=0.0;FS=1.759;HaplotypeSc [...]
+chr2 141135863 . T TA 2586.77 REJECT NS=2;DP=229;DPB=275.417;AC=2;AN=4;AF=0.5;RO=140;AO=106;PRO=15.5;PAO=16.5;QR=5326;QA=4052;PQR=568.0;PQA=608.0;SRF=28;SRR=112;SAF=25;SAR=81;SRP=112.453;SAP=67.2531;AB=0.424;ABP=15.5527;RUN=1;RPP=16.8586;RPPR=23.1119;RPL=66.0;RPR=40.0;EPP=3.0103;EPPR=3.25847;DPRA=0.0;ODDS=144.543;GTI=0;TYPE=ins;CIGAR=1M1I11M;NUMALT=1;MEANALT=3.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992857;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.122;FS=3.686;MLEAC=1;MLEAF=0. [...]
+chr2 141260668 . A G 2542.32 PASS SOMATIC;NS=2;DP=387;DPB=387.0;AC=1;AN=3;AF=0.25;RO=287;AO=100;PRO=0.0;PAO=0.0;QR=11112;QA=3829;PQR=0.0;PQA=0.0;SRF=92;SRR=195;SAF=34;SAR=66;SRP=83.2791;SAP=25.2462;AB=0.330033;ABP=79.0405;RUN=1;RPP=4.40004;RPPR=19.7238;RPL=54.0;RPR=46.0;EPP=8.56927;EPPR=3.62315;DPRA=3.60714;ODDS=53.3961;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.98;PAIREDR=0.989547;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.084;Dels=0.0;FS=0.4 [...]
+chr2 141267573 . G A 1047.97 REJECT NS=1;DP=94;DPB=94.0;AC=1;AN=4;AF=0.5;RO=55;AO=39;PRO=0.0;PAO=0.0;QR=2101;QA=1534;PQR=0.0;PQA=0.0;SRF=26;SRR=29;SAF=13;SAR=26;SRP=3.36563;SAP=12.42;AB=0.414894;ABP=8.9241;RUN=1;RPP=12.42;RPPR=9.68264;RPL=13.0;RPR=26.0;EPP=15.538;EPPR=6.20829;DPRA=0.0;ODDS=241.305;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.974359;PAIREDR=0.981818;technology.ILLUMINA=1.0;BaseQRankSum=2.172;FS=6.851;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0. [...]
+chr2 141272360 . G GA 322.813 REJECT NS=2;DP=184;DPB=204.471;AC=2;AN=2;AF=0.0;RO=141;AO=10;PRO=25.0;PAO=14.0;QR=5351;QA=352;PQR=904.333;PQA=498.333;SRF=27;SRR=114;SAF=2;SAR=8;SRP=119.577;SAP=10.8276;AB=0.0543478;ABP=320.423;RUN=1;RPP=24.725;RPPR=119.577;RPL=10.0;RPR=0.0;EPP=10.8276;EPPR=28.8986;DPRA=0.0;ODDS=20.993;GTI=0;TYPE=ins;CIGAR=1M1I16M;NUMALT=2;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992908;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr2 141272360 . GA G 322.813 REJECT NS=2;DP=184;DPB=204.471;AC=2;AN=4;AF=0.5;RO=141;AO=25;PRO=25.0;PAO=15.0;QR=5351;QA=947;PQR=904.333;PQA=532.333;SRF=27;SRR=114;SAF=7;SAR=18;SRP=119.577;SAP=13.5202;AB=0.13587;ABP=214.918;RUN=1;RPP=22.5536;RPPR=119.577;RPL=20.0;RPR=5.0;EPP=3.09716;EPPR=28.8986;DPRA=0.0;ODDS=20.993;GTI=0;TYPE=del;CIGAR=1M1D15M;NUMALT=2;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992908;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr2 141274576 . T C 10996.2 REJECT NS=2;DP=292;DPB=330.0;AC=4;AN=4;AF=1.0;RO=1;AO=329;PRO=0.0;PAO=0.0;QR=39;QA=12667;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=91;SAR=238;SRP=5.18177;SAP=145.634;AB=0.0;ABP=0.0;RUN=1;RPP=22.976;RPPR=5.18177;RPL=192.0;RPR=137.0;EPP=11.0956;EPPR=5.18177;DPRA=0.0;ODDS=51.1409;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993921;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.232;Dels=0.0;FS=2.7985;HaplotypeScore=0.9665;MLEAC=2 [...]
+chr2 141294285 . G A 238.486 REJECT NS=2;DP=187;DPB=219.5;AC=2;AN=2;AF=0.0;RO=114;AO=10;PRO=33.5;PAO=1.0;QR=4197;QA=184;PQR=1148.17;PQA=14.0;SRF=14;SRR=100;SAF=0;SAR=10;SRP=143.889;SAP=24.725;AB=0.0534759;ABP=326.862;RUN=1;RPP=3.87889;RPPR=5.75321;RPL=4.0;RPR=6.0;EPP=3.87889;EPPR=5.75321;DPRA=0.0;ODDS=23.1129;GTI=0;TYPE=snp;CIGAR=1X19M;NUMALT=3;MEANALT=10.0;LEN=1;MQM=60.0;MQMR=59.8246;PAIRED=1.0;PAIREDR=0.991228;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr2 141294285 . G GA 238.486 REJECT NS=2;DP=187;DPB=219.5;AC=2;AN=2;AF=0.0;RO=114;AO=16;PRO=33.5;PAO=25.5;QR=4197;QA=343;PQR=1148.17;PQA=865.167;SRF=14;SRR=100;SAF=0;SAR=16;SRP=143.889;SAP=37.7539;AB=0.0855615;ABP=281.992;RUN=1;RPP=3.0103;RPPR=5.75321;RPL=8.0;RPR=8.0;EPP=3.0103;EPPR=5.75321;DPRA=0.0;ODDS=23.1129;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=3;MEANALT=10.0;LEN=1;MQM=60.0;MQMR=59.8246;PAIRED=1.0;PAIREDR=0.991228;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr2 141294285 . GA G 238.486 REJECT NS=2;DP=187;DPB=219.5;AC=2;AN=4;AF=0.5;RO=114;AO=28;PRO=33.5;PAO=23.0;QR=4197;QA=812;PQR=1148.17;PQA=760.667;SRF=14;SRR=100;SAF=4;SAR=24;SRP=143.889;SAP=34.0313;AB=0.149733;ABP=202.286;RUN=1;RPP=3.32051;RPPR=5.75321;RPL=13.0;RPR=15.0;EPP=10.7656;EPPR=5.75321;DPRA=0.0;ODDS=23.1129;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=3;MEANALT=10.0;LEN=1;MQM=60.0;MQMR=59.8246;PAIRED=1.0;PAIREDR=0.991228;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr2 141474402 . G GA 951.426 REJECT NS=2;DP=193;DPB=224.062;AC=2;AN=4;AF=0.5;RO=146;AO=46;PRO=33.5;PAO=20.5;QR=5568;QA=1702;PQR=1208.0;PQA=732.0;SRF=23;SRR=123;SAF=5;SAR=41;SRP=151.741;SAP=64.1892;AB=0.238342;ABP=117.783;RUN=1;RPP=30.2009;RPPR=75.8885;RPL=35.0;RPR=11.0;EPP=18.305;EPPR=14.6708;DPRA=0.0;ODDS=90.7923;GTI=0;TYPE=ins;CIGAR=1M1I15M;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993151;technology.ILLUMINA=1.0;BaseQRankSum=-0.631;FS=1.524;MLEAC=1;MLEAF=0.5;M [...]
+chr2 141528592 . T C 8050.91 REJECT NS=2;DP=226;DPB=264.0;AC=4;AN=4;AF=1.0;RO=2;AO=262;PRO=0.0;PAO=0.0;QR=56;QA=9814;PQR=0.0;PQA=0.0;SRF=0;SRR=2;SAF=47;SAR=215;SRP=7.35324;SAP=236.933;AB=0.0;ABP=0.0;RUN=1;RPP=118.413;RPPR=7.35324;RPL=190.0;RPR=72.0;EPP=13.7516;EPPR=7.35324;DPRA=0.0;ODDS=51.6679;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.803;Dels=0.0;FS=0.0;HaplotypeScore=7.8319;MLEAC=2;MLEAF=1. [...]
+chr2 141533646 . A T 1904.99 PASS SOMATIC;NS=2;DP=282;DPB=282.0;AC=1;AN=3;AF=0.25;RO=205;AO=76;PRO=0.0;PAO=0.0;QR=7844;QA=2907;PQR=0.0;PQA=0.0;SRF=148;SRR=57;SAF=59;SAR=17;SRP=90.7272;SAP=53.4113;AB=0.347032;ABP=47.5205;RUN=1;RPP=16.8392;RPPR=62.5934;RPL=27.0;RPR=49.0;EPP=3.46745;EPPR=3.02089;DPRA=3.47619;ODDS=39.6499;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986842;PAIREDR=0.985366;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.686;Dels=0.0;FS=2 [...]
+chr2 141533662 . T C 11279.7 REJECT NS=2;DP=299;DPB=341.0;AC=4;AN=4;AF=1.0;RO=0;AO=341;PRO=0.0;PAO=0.0;QR=0;QA=13045;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=239;SAR=102;SRP=0.0;SAP=122.53;AB=0.0;ABP=0.0;RUN=1;RPP=22.2734;RPPR=0.0;RPL=143.0;RPR=198.0;EPP=29.9149;EPPR=0.0;DPRA=0.0;ODDS=55.459;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.98827;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.315;SOR=1.844 [...]
+chr2 141571329 . T C 7861.1 REJECT NS=2;DP=355;DPB=409.0;AC=3;AN=4;AF=0.75;RO=120;AO=289;PRO=0.0;PAO=0.0;QR=4591;QA=10987;PQR=0.0;PQA=0.0;SRF=47;SRR=73;SAF=127;SAR=162;SRP=15.2429;SAP=12.2146;AB=0.602649;ABP=30.6498;RUN=1;RPP=9.32936;RPPR=4.16842;RPL=159.0;RPR=130.0;EPP=13.2966;EPPR=6.55704;DPRA=0.0;ODDS=67.7077;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99654;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.157;Dels=0.0;FS=0.4595;HaplotypeScor [...]
+chr2 141598473 . A AT 9208.63 REJECT NS=2;DP=243;DPB=346.0;AC=4;AN=4;AF=1.0;RO=0;AO=275;PRO=6.0;PAO=13.0;QR=0;QA=10300;PQR=161.0;PQA=394.0;SRF=0;SRR=0;SAF=196;SAR=79;SRP=0.0;SAP=111.102;AB=0.0;ABP=0.0;RUN=1;RPP=118.619;RPPR=0.0;RPL=77.0;RPR=198.0;EPP=3.0182;EPPR=0.0;DPRA=0.0;ODDS=46.1454;GTI=0;TYPE=ins;CIGAR=1M1I4M;NUMALT=1;MEANALT=1.5;LEN=1;MQM=61.2364;MQMR=0.0;PAIRED=0.989091;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=141598473;HOMLEN=0;SVLEN=1;SVTYPE=INS;FS=0.0;MLEAC=2;MLEAF=1.0;MQ [...]
+chr2 141625410 . A C 3207.7200000000003 REJECT NS=2;DP=228;DPB=270.0;AC=2;AN=4;AF=0.5;RO=147;AO=123;PRO=0.0;PAO=0.0;QR=5639;QA=4739;PQR=0.0;PQA=0.0;SRF=38;SRR=109;SAF=34;SAR=89;SRP=77.4756;SAP=56.4144;AB=0.455556;ABP=7.64277;RUN=1;RPP=17.8575;RPPR=7.27939;RPL=76.0;RPR=47.0;EPP=3.16919;EPPR=8.34296;DPRA=0.0;ODDS=257.725;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.98374;PAIREDR=0.965986;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.127;Dels=0.0;FS=3.895;Ha [...]
+chr2 141625828 . G A 8.39687 REJECT NS=2;DP=272;DPB=272.0;AC=2;AN=4;AF=0.5;RO=207;AO=65;PRO=0.0;PAO=0.0;QR=6352;QA=1113;PQR=0.0;PQA=0.0;SRF=44;SRR=163;SAF=0;SAR=65;SRP=151.562;SAP=144.156;AB=0.238971;ABP=163.987;RUN=1;RPP=17.7429;RPPR=177.578;RPL=22.0;RPR=43.0;EPP=17.7429;EPPR=47.3314;DPRA=0.0;ODDS=0.743295;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.8462;MQMR=59.942;PAIRED=1.0;PAIREDR=0.990338;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:Call [...]
+chr2 141625834 . TAA T 192.73 PASS SOMATIC;DP=180;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-0.521;FS=9.426;MLEAC=1;MLEAF=0.5;MQ=59.97;MQRankSum=0.521;QD=1.07;RPA=19,17;RU=A;ReadPosRankSum=-0.503;SOR=0.061;STR GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00174608 0/1:68,19:180:99.0:230,0,1418:19:22:87:.:1:.:.:.:.:-0.0116954
+chr2 141709419 . T G 1556.355 REJECT NS=2;DP=286;DPB=331.0;AC=2;AN=4;AF=0.5;RO=249;AO=82;PRO=0.0;PAO=0.0;QR=9710;QA=3187;PQR=0.0;PQA=0.0;SRF=148;SRR=101;SAF=51;SAR=31;SRP=22.2745;SAP=13.6028;AB=0.247734;ABP=185.972;RUN=1;RPP=15.8273;RPPR=46.9717;RPL=30.0;RPR=52.0;EPP=4.70511;EPPR=7.62359;DPRA=0.0;ODDS=218.547;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.97561;PAIREDR=0.983936;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.063;Dels=0.0;FS=1.9965;HaplotypeSc [...]
+chr2 141747249 . A T 5368.19 REJECT NS=2;DP=202;DPB=233.0;AC=2;AN=4;AF=0.5;RO=51;AO=182;PRO=0.0;PAO=0.0;QR=1940;QA=6926;PQR=0.0;PQA=0.0;SRF=9;SRR=42;SAF=45;SAR=137;SRP=49.3776;SAP=103.996;AB=0.781116;ABP=162.944;RUN=1;RPP=68.3454;RPPR=34.0496;RPL=128.0;RPR=54.0;EPP=4.72839;EPPR=10.206;DPRA=0.0;ODDS=114.138;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994505;PAIREDR=0.960784;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3245;Dels=0.0;FS=4.895;HaplotypeSco [...]
+chr2 141751592 . G A 9535.95 REJECT NS=2;DP=348;DPB=399.0;AC=2;AN=4;AF=0.5;RO=90;AO=307;PRO=0.0;PAO=0.0;QR=3446;QA=11905;PQR=0.0;PQA=0.0;SRF=57;SRR=33;SAF=183;SAR=124;SRP=16.9077;SAP=27.6321;AB=0.769424;ABP=254.58;RUN=1;RPP=6.12958;RPPR=3.10681;RPL=143.0;RPR=164.0;EPP=9.80765;EPPR=6.48466;DPRA=0.0;ODDS=121.512;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996743;PAIREDR=0.988889;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1925;Dels=0.0;FS=1.7215;Haploty [...]
+chr2 141816621 . A G 9469.545 REJECT NS=2;DP=252;DPB=289.0;AC=4;AN=4;AF=1.0;RO=0;AO=288;PRO=0.0;PAO=0.0;QR=0;QA=11079;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=77;SAR=211;SRP=0.0;SAP=138.396;AB=0.0;ABP=0.0;RUN=1;RPP=64.083;RPPR=0.0;RPL=189.0;RPR=99.0;EPP=7.35324;EPPR=0.0;DPRA=0.0;ODDS=50.4708;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996528;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.9315;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.175;SOR=2.0 [...]
+chr2 142567860 . A T 2475.14 PASS SOMATIC;NS=2;DP=363;DPB=363.0;AC=1;AN=3;AF=0.25;RO=268;AO=95;PRO=0.0;PAO=0.0;QR=10227;QA=3631;PQR=0.0;PQA=0.0;SRF=176;SRR=92;SAF=65;SAR=30;SRP=60.1816;SAP=31.0109;AB=0.363985;ABP=44.9505;RUN=1;RPP=11.2619;RPPR=28.4198;RPL=38.0;RPR=57.0;EPP=3.21602;EPPR=4.17706;DPRA=2.55882;ODDS=64.6338;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992537;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.452;Dels=0.0;FS=2.31 [...]
+chr2 142567910 . T C 9981.26 REJECT NS=2;DP=382;DPB=437.0;AC=2;AN=4;AF=0.5;RO=110;AO=327;PRO=0.0;PAO=0.0;QR=4201;QA=12569;PQR=0.0;PQA=0.0;SRF=50;SRR=60;SAF=153;SAR=174;SRP=4.98437;SAP=5.9388;AB=0.748284;ABP=236.998;RUN=1;RPP=3.17631;RPPR=3.32615;RPL=166.0;RPR=161.0;EPP=76.2228;EPPR=28.5942;DPRA=0.0;ODDS=169.153;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996942;PAIREDR=0.990909;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.146;Dels=0.0;FS=4.259;Haplotype [...]
+chr2 142888376 . G C 2104.84 PASS SOMATIC;NS=2;DP=310;DPB=310.0;AC=1;AN=3;AF=0.25;RO=224;AO=86;PRO=0.0;PAO=0.0;QR=8498;QA=3200;PQR=0.0;PQA=0.0;SRF=41;SRR=183;SAF=13;SAR=73;SRP=198.482;SAP=93.9091;AB=0.375546;ABP=33.8187;RUN=1;RPP=4.62628;RPPR=21.778;RPL=47.0;RPR=39.0;EPP=5.53527;EPPR=9.56349;DPRA=2.82716;ODDS=51.5236;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9535;MQMR=60.0;PAIRED=0.988372;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.299;Dels=0.0;FS=2.29 [...]
+chr2 148512364 . G A 11377.0 REJECT NS=2;DP=308;DPB=360.0;AC=4;AN=4;AF=1.0;RO=0;AO=360;PRO=0.0;PAO=0.0;QR=0;QA=13553;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=90;SAR=270;SRP=0.0;SAP=198.443;AB=0.0;ABP=0.0;RUN=1;RPP=9.98314;RPPR=0.0;RPL=197.0;RPR=163.0;EPP=60.9404;EPPR=0.0;DPRA=0.0;ODDS=68.459;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997222;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8994;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.97;SOR=2.12 [...]
+chr2 158626980 . C T 12775.599999999999 REJECT NS=2;DP=339;DPB=388.0;AC=4;AN=4;AF=1.0;RO=0;AO=388;PRO=0.0;PAO=0.0;QR=0;QA=14793;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=157;SAR=231;SRP=0.0;SAP=33.6572;AB=0.0;ABP=0.0;RUN=1;RPP=24.5235;RPPR=0.0;RPL=225.0;RPR=163.0;EPP=11.9648;EPPR=0.0;DPRA=0.0;ODDS=64.8544;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994845;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9108;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=3 [...]
+chr2 158636910 . G A 5155.950000000001 REJECT NS=2;DP=322;DPB=373.0;AC=2;AN=4;AF=0.5;RO=186;AO=186;PRO=0.0;PAO=0.0;QR=6955;QA=7056;PQR=0.0;PQA=0.0;SRF=98;SRR=88;SAF=100;SAR=86;SRP=4.17776;SAP=5.29852;AB=0.49866;ABP=3.01612;RUN=1;RPP=4.17776;RPPR=5.29852;RPL=98.0;RPR=88.0;EPP=3.43058;EPPR=5.29852;DPRA=0.0;ODDS=308.052;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994624;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.4175;Dels=0.0;FS=4.597;Haploty [...]
+chr2 158637136 . G GA 4361.46 REJECT NS=2;DP=114;DPB=156.08;AC=2;AN=2;AF=0.0;RO=28;AO=6;PRO=23.4762;PAO=15.4762;QR=1040;QA=153;PQR=826.762;PQA=480.762;SRF=4;SRR=24;SAF=0;SAR=6;SRP=34.0313;SAP=16.0391;AB=0.0526316;ABP=201.186;RUN=1;RPP=8.80089;RPPR=34.0313;RPL=5.0;RPR=1.0;EPP=8.80089;EPPR=14.1779;DPRA=0.0;ODDS=32.4483;GTI=0;TYPE=ins;CIGAR=1M1I24M;NUMALT=6;MEANALT=11.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr2 158637136 . G GGA 4361.46 REJECT NS=2;DP=114;DPB=156.08;AC=2;AN=2;AF=0.0;RO=28;AO=3;PRO=23.4762;PAO=11.9762;QR=1040;QA=92;PQR=826.762;PQA=360.012;SRF=4;SRR=24;SAF=1;SAR=2;SRP=34.0313;SAP=3.73412;AB=0.0263158;ABP=225.186;RUN=1;RPP=3.73412;RPPR=34.0313;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=14.1779;DPRA=0.0;ODDS=32.4483;GTI=0;TYPE=ins;CIGAR=1M2I24M;NUMALT=6;MEANALT=11.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr2 158637136 . GA G 4361.46 REJECT NS=2;DP=114;DPB=156.08;AC=2;AN=2;AF=0.0;RO=28;AO=12;PRO=23.4762;PAO=12.4762;QR=1040;QA=420;PQR=826.762;PQA=437.762;SRF=4;SRR=24;SAF=3;SAR=9;SRP=34.0313;SAP=9.52472;AB=0.105263;ABP=157.299;RUN=1;RPP=14.5915;RPPR=34.0313;RPL=10.0;RPR=2.0;EPP=3.73412;EPPR=14.1779;DPRA=0.0;ODDS=32.4483;GTI=0;TYPE=del;CIGAR=1M1D23M;NUMALT=6;MEANALT=11.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.903;FS=1.63;MLE [...]
+chr2 158637137 . A G 4361.46 REJECT NS=2;DP=114;DPB=156.08;AC=2;AN=4;AF=0.5;RO=28;AO=41;PRO=23.4762;PAO=19.9762;QR=1040;QA=1541;PQR=826.762;PQA=653.012;SRF=4;SRR=24;SAF=14;SAR=27;SRP=34.0313;SAP=11.961;AB=0.359649;ABP=22.5155;RUN=1;RPP=11.961;RPPR=34.0313;RPL=27.0;RPR=14.0;EPP=5.60547;EPPR=14.1779;DPRA=0.0;ODDS=32.4483;GTI=0;TYPE=snp;CIGAR=1M1X23M;NUMALT=6;MEANALT=11.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr2 158637137 . AA G 4361.46 REJECT NS=2;DP=114;DPB=156.08;AC=2;AN=2;AF=0.0;RO=28;AO=10;PRO=23.4762;PAO=9.47619;QR=1040;QA=313;PQR=826.762;PQA=309.512;SRF=4;SRR=24;SAF=3;SAR=7;SRP=34.0313;SAP=6.48466;AB=0.0877193;ABP=171.318;RUN=1;RPP=10.8276;RPPR=34.0313;RPL=8.0;RPR=2.0;EPP=3.0103;EPPR=14.1779;DPRA=0.0;ODDS=32.4483;GTI=0;TYPE=complex;CIGAR=1M1D1X22M;NUMALT=6;MEANALT=11.0;LEN=24;MQM=60.0;MQMR=60.0;PAIRED=0.9;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr2 158637137 . AAAA G 4361.46 REJECT NS=2;DP=114;DPB=156.08;AC=2;AN=2;AF=0.0;RO=28;AO=2;PRO=23.4762;PAO=9.14286;QR=1040;QA=77;PQR=826.762;PQA=301.179;SRF=4;SRR=24;SAF=1;SAR=1;SRP=34.0313;SAP=3.0103;AB=0.0555556;ABP=64.7766;RUN=1;RPP=3.0103;RPPR=34.0313;RPL=1.0;RPR=1.0;EPP=7.35324;EPPR=14.1779;DPRA=0.0;ODDS=32.4483;GTI=0;TYPE=complex;CIGAR=1M3D1X20M;NUMALT=6;MEANALT=9.0;LEN=22;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr2 173427053 . T G 1780.4 REJECT NS=2;DP=253;DPB=290.0;AC=2;AN=4;AF=0.5;RO=210;AO=80;PRO=0.0;PAO=0.0;QR=7972;QA=3112;PQR=0.0;PQA=0.0;SRF=74;SRR=136;SAF=34;SAR=46;SRP=42.7586;SAP=6.91895;AB=0.275862;ABP=129.555;RUN=1;RPP=11.8048;RPPR=90.531;RPL=49.0;RPR=31.0;EPP=21.3592;EPPR=3.67208;DPRA=0.0;ODDS=136.841;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.9875;PAIREDR=0.980952;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.3965;Dels=0.0;FS=8.7945;HaplotypeScore= [...]
+chr2 173460640 . T C 1959.055 REJECT NS=2;DP=394;DPB=446.0;AC=2;AN=4;AF=0.5;RO=347;AO=99;PRO=0.0;PAO=0.0;QR=13314;QA=3764;PQR=0.0;PQA=0.0;SRF=166;SRR=181;SAF=44;SAR=55;SRP=4.41832;SAP=5.66432;AB=0.221973;ABP=302.459;RUN=1;RPP=4.08507;RPPR=5.26938;RPL=53.0;RPR=46.0;EPP=6.71716;EPPR=18.0354;DPRA=0.0;ODDS=133.841;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994236;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.171;Dels=0.0;FS=2.558;HaplotypeScore= [...]
+chr2 177000391 . G A 7741.780000000001 REJECT NS=2;DP=206;DPB=232.0;AC=4;AN=4;AF=1.0;RO=1;AO=230;PRO=0.0;PAO=0.0;QR=16;QA=8858;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=160;SAR=70;SRP=5.18177;SAP=79.4839;AB=0.0;ABP=0.0;RUN=1;RPP=101.236;RPPR=5.18177;RPL=64.0;RPR=166.0;EPP=6.06924;EPPR=5.18177;DPRA=0.0;ODDS=34.2824;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986957;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.8995;MLEAC=2;MLEAF=1.0;MQ [...]
+chr2 178098087 . CA C 1370.57 REJECT NS=2;DP=237;DPB=245.636;AC=2;AN=4;AF=0.5;RO=173;AO=62;PRO=23.0;PAO=10.0;QR=6535;QA=2299;PQR=806.0;PQA=358.0;SRF=41;SRR=132;SAF=13;SAR=49;SRP=106.952;SAP=48.4011;AB=0.261603;ABP=120.004;RUN=1;RPP=34.5317;RPPR=52.8286;RPL=46.0;RPR=16.0;EPP=5.25182;EPPR=6.63779;DPRA=0.0;ODDS=126.951;GTI=0;TYPE=del;CIGAR=1M1D9M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983871;PAIREDR=0.99422;technology.ILLUMINA=1.0;END=178098088;HOMLEN=2;HOMSEQ=AA;SVLEN=-1;SV [...]
+chr2 186010721 . C T 13574.8 REJECT NS=2;DP=360;DPB=399.0;AC=4;AN=4;AF=1.0;RO=0;AO=399;PRO=0.0;PAO=0.0;QR=0;QA=15243;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=152;SAR=247;SRP=0.0;SAP=52.1269;AB=0.0;ABP=0.0;RUN=1;RPP=9.6771;RPPR=0.0;RPL=217.0;RPR=182.0;EPP=42.3308;EPPR=0.0;DPRA=0.0;ODDS=52.3434;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994987;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.9323;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.375;SOR=1. [...]
+chr2 187516446 . A G 4198.87 REJECT NS=2;DP=245;DPB=278.0;AC=2;AN=4;AF=0.5;RO=130;AO=148;PRO=0.0;PAO=0.0;QR=5049;QA=5656;PQR=0.0;PQA=0.0;SRF=45;SRR=85;SAF=45;SAR=103;SRP=29.7361;SAP=52.3673;AB=0.532374;ABP=5.54108;RUN=1;RPP=26.4857;RPPR=18.0436;RPL=94.0;RPR=54.0;EPP=7.76406;EPPR=4.07933;DPRA=0.0;ODDS=207.725;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.97973;PAIREDR=0.984615;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.006;Dels=0.0;FS=5.013;HaplotypeScor [...]
+chr2 189008267 . A C 14665.849999999999 REJECT NS=2;DP=386;DPB=444.0;AC=4;AN=4;AF=1.0;RO=0;AO=444;PRO=0.0;PAO=0.0;QR=0;QA=17072;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=213;SAR=231;SRP=0.0;SAP=4.59489;AB=0.0;ABP=0.0;RUN=1;RPP=11.6375;RPPR=0.0;RPL=201.0;RPR=243.0;EPP=51.9173;EPPR=0.0;DPRA=0.0;ODDS=74.8145;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.988739;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.7989;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=3 [...]
+chr2 190670539 . T TA 3497.0699999999997 REJECT NS=2;DP=332;DPB=428.294;AC=2;AN=4;AF=0.5;RO=148;AO=161;PRO=35.0;PAO=34.0;QR=5617;QA=5832;PQR=1241.0;PQA=1214.5;SRF=65;SRR=83;SAF=78;SAR=83;SRP=7.76406;SAP=3.34749;AB=0.449721;ABP=10.8713;RUN=1;RPP=3.13169;RPPR=5.88603;RPL=82.0;RPR=79.0;EPP=14.3532;EPPR=5.12308;DPRA=0.0;ODDS=185.623;GTI=0;TYPE=ins;CIGAR=1M1I16M;NUMALT=3;MEANALT=8.5;LEN=1;MQM=60.2484;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum [...]
+chr2 190670539 . T TAA 4650.41 REJECT NS=2;DP=358;DPB=428.294;AC=2;AN=2;AF=0.0;RO=148;AO=10;PRO=35.0;PAO=32.0;QR=5617;QA=356;PQR=1241.0;PQA=1137.5;SRF=65;SRR=83;SAF=4;SAR=6;SRP=7.76406;SAP=3.87889;AB=0.027933;ABP=695.965;RUN=1;RPP=10.8276;RPPR=5.88603;RPL=8.0;RPR=2.0;EPP=3.87889;EPPR=5.12308;DPRA=0.0;ODDS=185.623;GTI=0;TYPE=ins;CIGAR=1M2I16M;NUMALT=3;MEANALT=8.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr2 190670539 . TA T 4650.41 REJECT NS=2;DP=358;DPB=428.294;AC=2;AN=2;AF=0.0;RO=148;AO=23;PRO=35.0;PAO=26.0;QR=5617;QA=852;PQR=1241.0;PQA=916.0;SRF=65;SRR=83;SAF=12;SAR=11;SRP=7.76406;SAP=3.10471;AB=0.0642458;ABP=593.457;RUN=1;RPP=3.10471;RPPR=5.88603;RPL=12.0;RPR=11.0;EPP=5.3706;EPPR=5.12308;DPRA=0.0;ODDS=185.623;GTI=0;TYPE=del;CIGAR=1M1D15M;NUMALT=3;MEANALT=8.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr2 191922841 . G A 13083.25 REJECT NS=2;DP=348;DPB=402.0;AC=4;AN=4;AF=1.0;RO=0;AO=401;PRO=0.0;PAO=0.0;QR=0;QA=15289;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=201;SAR=200;SRP=0.0;SAP=3.01572;AB=0.0;ABP=0.0;RUN=1;RPP=3.92546;RPPR=0.0;RPL=194.0;RPR=207.0;EPP=3.01572;EPPR=0.0;DPRA=0.0;ODDS=71.0458;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=7.7899;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.095;SOR=0.872 [...]
+chr2 191996518 . T C 1298.325 REJECT NS=2;DP=258;DPB=302.0;AC=2;AN=4;AF=0.5;RO=235;AO=67;PRO=0.0;PAO=0.0;QR=9181;QA=2577;PQR=0.0;PQA=0.0;SRF=148;SRR=87;SAF=43;SAR=24;SRP=37.3935;SAP=14.7103;AB=0.221854;ABP=205.949;RUN=1;RPP=10.3026;RPPR=20.0956;RPL=26.0;RPR=41.0;EPP=5.63551;EPPR=7.89842;DPRA=0.0;ODDS=105.148;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985075;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.9605;Dels=0.0;FS=0.804;HaplotypeScore= [...]
+chr2 192011485 . T TA 407.05 REJECT NS=2;DP=239;DPB=266.118;AC=2;AN=3;AF=0.25;RO=166;AO=27;PRO=23.9167;PAO=15.9167;QR=6173;QA=781;PQR=876.0;PQA=580.0;SRF=39;SRR=127;SAF=6;SAR=21;SRP=104.311;SAP=21.1059;AB=0.112971;ABP=313.967;RUN=1;RPP=6.95112;RPPR=13.2659;RPL=17.0;RPR=10.0;EPP=3.09072;EPPR=14.7833;DPRA=0.0;ODDS=12.7365;GTI=0;TYPE=ins;CIGAR=1M1I16M;NUMALT=3;MEANALT=9.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993976;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.648;FS=19 [...]
+chr2 192011485 . TA T 407.05 REJECT NS=2;DP=239;DPB=266.118;AC=2;AN=3;AF=0.25;RO=166;AO=29;PRO=23.9167;PAO=12.9167;QR=6173;QA=1033;PQR=876.0;PQA=469.0;SRF=39;SRR=127;SAF=8;SAR=21;SRP=104.311;SAP=15.6647;AB=0.121339;ABP=300.666;RUN=1;RPP=12.0706;RPPR=13.2659;RPL=20.0;RPR=9.0;EPP=4.88226;EPPR=14.7833;DPRA=0.0;ODDS=12.7365;GTI=0;TYPE=del;CIGAR=1M1D15M;NUMALT=3;MEANALT=9.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993976;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr2 192011485 . TAA T 407.05 REJECT NS=2;DP=239;DPB=266.118;AC=2;AN=2;AF=0.0;RO=166;AO=5;PRO=23.9167;PAO=10.25;QR=6173;QA=140;PQR=876.0;PQA=370.0;SRF=39;SRR=127;SAF=0;SAR=5;SRP=104.311;SAP=13.8677;AB=0.0209205;ABP=479.471;RUN=1;RPP=6.91895;RPPR=13.2659;RPL=4.0;RPR=1.0;EPP=6.91895;EPPR=14.7833;DPRA=0.0;ODDS=12.7365;GTI=0;TYPE=del;CIGAR=1M2D14M;NUMALT=3;MEANALT=9.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993976;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr2 198257795 . T C 5987.765 REJECT NS=2;DP=376;DPB=436.0;AC=2;AN=4;AF=0.5;RO=219;AO=217;PRO=0.0;PAO=0.0;QR=8378;QA=8336;PQR=0.0;PQA=0.0;SRF=123;SRR=96;SAF=110;SAR=107;SRP=10.2386;SAP=3.10036;AB=0.497706;ABP=3.03022;RUN=1;RPP=6.62275;RPPR=3.02022;RPL=118.0;RPR=99.0;EPP=3.82085;EPPR=3.25818;DPRA=0.0;ODDS=386.459;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995392;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4575;Dels=0.0;FS=2.695;HaplotypeSco [...]
+chr2 198265526 . A G 6618.445 REJECT NS=2;DP=397;DPB=454.0;AC=2;AN=4;AF=0.5;RO=219;AO=235;PRO=0.0;PAO=0.0;QR=8328;QA=8982;PQR=0.0;PQA=0.0;SRF=113;SRR=106;SAF=113;SAR=122;SRP=3.49615;SAP=3.75876;AB=0.517621;ABP=4.23474;RUN=1;RPP=4.12838;RPPR=4.686;RPL=123.0;RPR=112.0;EPP=3.01954;EPPR=3.81345;DPRA=0.0;ODDS=352.55;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991489;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7845;Dels=0.0;FS=1.247;HaplotypeScor [...]
+chr2 198267770 . G GAA 3035.51 REJECT NS=2;DP=210;DPB=255.2;AC=2;AN=4;AF=0.5;RO=112;AO=102;PRO=26.5;PAO=23.5;QR=4299;QA=3795;PQR=948.0;PQA=841.0;SRF=26;SRR=86;SAF=25;SAR=77;SRP=72.8076;SAP=60.5756;AB=0.470046;ABP=4.70145;RUN=1;RPP=17.4016;RPPR=18.2106;RPL=64.0;RPR=38.0;EPP=8.46027;EPPR=5.80219;DPRA=0.0;ODDS=187.929;GTI=0;TYPE=ins;CIGAR=1M2I14M;NUMALT=1;MEANALT=2.5;LEN=2;MQM=60.098;MQMR=60.0;PAIRED=1.0;PAIREDR=0.982143;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.174;FS=0.5895;MLEAC=1;MLE [...]
+chr2 198283305 . T C 4841.67 REJECT NS=2;DP=329;DPB=376.0;AC=2;AN=4;AF=0.5;RO=195;AO=180;PRO=0.0;PAO=0.0;QR=7100;QA=6722;PQR=0.0;PQA=0.0;SRF=85;SRR=110;SAF=70;SAR=110;SRP=9.97015;SAP=22.3123;AB=0.478723;ABP=4.48875;RUN=1;RPP=18.6449;RPPR=16.6516;RPL=108.0;RPR=72.0;EPP=3.78238;EPPR=16.6516;DPRA=0.0;ODDS=275.619;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.977778;PAIREDR=0.984615;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.1765;Dels=0.0;FS=3.859;Haplotype [...]
+chr2 207008763 . C A 3268.81 REJECT NS=2;DP=240;DPB=282.0;AC=2;AN=4;AF=0.5;RO=158;AO=124;PRO=0.0;PAO=0.0;QR=5962;QA=4710;PQR=0.0;PQA=0.0;SRF=95;SRR=63;SAF=83;SAR=41;SRP=17.0836;SAP=33.9012;AB=0.439716;ABP=11.9118;RUN=1;RPP=57.9275;RPPR=32.0915;RPL=34.0;RPR=90.0;EPP=8.68415;EPPR=10.9266;DPRA=0.0;ODDS=200.061;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993671;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.016;Dels=0.0;FS=3.057;HaplotypeScore=5. [...]
+chr2 209101905 . GA G 6901.11 REJECT NS=2;DP=218;DPB=256.905;AC=4;AN=4;AF=1.0;RO=2;AO=211;PRO=31.0;PAO=68.0;QR=76;QA=7872;PQR=1131.5;PQA=2466.5;SRF=1;SRR=1;SAF=44;SAR=167;SRP=3.0103;SAP=158.708;AB=0.0;ABP=0.0;RUN=1;RPP=14.2176;RPPR=7.35324;RPL=122.0;RPR=89.0;EPP=15.6172;EPPR=3.0103;DPRA=0.0;ODDS=22.2627;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=1;MEANALT=3.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990521;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.008;FS=5.822;MLEAC=2;MLEAF=1.0;MQ=60.0 [...]
+chr2 212141680 . G A 5353.31 REJECT NS=2;DP=388;DPB=448.0;AC=2;AN=4;AF=0.5;RO=253;AO=195;PRO=0.0;PAO=0.0;QR=9724;QA=7453;PQR=0.0;PQA=0.0;SRF=126;SRR=127;SAF=117;SAR=78;SRP=3.01888;SAP=19.9478;AB=0.435268;ABP=19.3157;RUN=1;RPP=3.02144;RPPR=3.70551;RPL=97.0;RPR=98.0;EPP=19.9478;EPPR=27.1197;DPRA=0.0;ODDS=294.25;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994872;PAIREDR=0.988142;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6125;Dels=0.0;FS=8.2855;Haplotype [...]
+chr2 212146485 . T C 12664.849999999999 REJECT NS=2;DP=337;DPB=392.0;AC=2;AN=2;AF=0.75;RO=0;AO=199;PRO=2.0;PAO=7.0;QR=0;QA=7646;PQR=19.0;PQA=197.0;SRF=0;SRR=0;SAF=103;SAR=96;SRP=0.0;SAP=3.54498;AB=0.518229;ABP=4.11866;RUN=1;RPP=3.02121;RPPR=0.0;RPL=99.0;RPR=100.0;EPP=27.1147;EPPR=0.0;DPRA=0.0;ODDS=309.065;GTI=0;TYPE=snp;CIGAR=1X2M;NUMALT=2;MEANALT=3.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.98995;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=9.7981;M [...]
+chr2 212146485 . TTG CTC 12876.9 REJECT NS=2;DP=384;DPB=392.0;AC=2;AN=2;AF=0.5;RO=0;AO=181;PRO=2.0;PAO=6.0;QR=0;QA=6775;PQR=19.0;PQA=218.0;SRF=0;SRR=0;SAF=96;SAR=85;SRP=0.0;SAP=4.46195;AB=0.471354;ABP=5.74726;RUN=1;RPP=7.34125;RPPR=0.0;RPL=100.0;RPR=81.0;EPP=27.3044;EPPR=0.0;DPRA=0.0;ODDS=309.065;GTI=0;TYPE=complex;CIGAR=1X1M1X;NUMALT=2;MEANALT=3.5;LEN=3;MQM=60.0;MQMR=0.0;PAIRED=0.994475;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:Ca [...]
+chr2 212146487 . G C 3259.7700000000004 PASS DP=194;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.842;Dels=0.0;FS=1.8975;HaplotypeScore=8.8316;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.362;QD=16.115;ReadPosRankSum=1.762;SOR=0.908;ClippingRankSum=0.702 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:57,44:101:99.0:1511,0,1930:44:44:101:1:.:.:.:.:.:-0.00174608 0/1:147,139:287:99.0:5065,0,5433:139:49:286:.:1:.:.:.:.:-0.0116954
+chr2 212251864 . T C 2053.61 PASS SOMATIC;NS=2;DP=316;DPB=316.0;AC=1;AN=3;AF=0.25;RO=236;AO=80;PRO=0.0;PAO=0.0;QR=9092;QA=3020;PQR=0.0;PQA=0.0;SRF=71;SRR=165;SAF=34;SAR=46;SRP=84.3117;SAP=6.91895;AB=0.357143;ABP=42.7172;RUN=1;RPP=4.74748;RPPR=3.59917;RPL=36.0;RPR=44.0;EPP=3.44459;EPPR=3.93042;DPRA=2.43478;ODDS=58.4073;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995763;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.375;Dels=0.0;FS=6.22; [...]
+chr2 212495336 . G A 6.9082 REJECT NS=2;DP=152;DPB=199.654;AC=2;AN=2;AF=0.0;RO=121;AO=6;PRO=63.0;PAO=1.0;QR=4545;QA=84;PQR=2266.0;PQA=14.0;SRF=19;SRR=102;SAF=0;SAR=6;SRP=126.641;SAP=16.0391;AB=0.0967742;ABP=46.79;RUN=1;RPP=3.0103;RPPR=88.4515;RPL=3.0;RPR=3.0;EPP=3.0103;EPPR=36.1926;DPRA=0.0;ODDS=1.36278;GTI=0;TYPE=snp;CIGAR=1X25M;NUMALT=3;MEANALT=5.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.983471;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV [...]
+chr2 212495336 . G GA 6.9082 REJECT NS=2;DP=152;DPB=199.654;AC=2;AN=2;AF=0.0;RO=121;AO=10;PRO=63.0;PAO=20.0;QR=4545;QA=354;PQR=2266.0;PQA=704.0;SRF=19;SRR=102;SAF=1;SAR=9;SRP=126.641;SAP=16.9077;AB=0.0322581;ABP=61.9202;RUN=1;RPP=16.9077;RPPR=88.4515;RPL=9.0;RPR=1.0;EPP=10.8276;EPPR=36.1926;DPRA=0.0;ODDS=1.36278;GTI=0;TYPE=ins;CIGAR=1M1I25M;NUMALT=3;MEANALT=5.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.983471;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr2 212495336 . GA G 6.9082 REJECT NS=2;DP=152;DPB=199.654;AC=2;AN=3;AF=0.25;RO=121;AO=10;PRO=63.0;PAO=24.0;QR=4545;QA=359;PQR=2266.0;PQA=818.0;SRF=19;SRR=102;SAF=2;SAR=8;SRP=126.641;SAP=10.8276;AB=0.0967742;ABP=46.79;RUN=1;RPP=3.87889;RPPR=88.4515;RPL=6.0;RPR=4.0;EPP=3.87889;EPPR=36.1926;DPRA=0.0;ODDS=1.36278;GTI=0;TYPE=del;CIGAR=1M1D24M;NUMALT=3;MEANALT=5.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.9;PAIREDR=0.983471;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr2 212543924 . A G 2231.525 REJECT NS=2;DP=291;DPB=340.0;AC=2;AN=4;AF=0.5;RO=241;AO=99;PRO=0.0;PAO=0.0;QR=9157;QA=3822;PQR=0.0;PQA=0.0;SRF=59;SRR=182;SAF=21;SAR=78;SRP=139.327;SAP=74.2741;AB=0.291176;ABP=131.791;RUN=1;RPP=16.7191;RPPR=68.1094;RPL=62.0;RPR=37.0;EPP=3.55865;EPPR=3.01931;DPRA=0.0;ODDS=189.178;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.962656;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6765;Dels=0.0;FS=5.4265;HaplotypeScore= [...]
+chr2 212578379 . T TA 619.828 REJECT NS=2;DP=155;DPB=198.667;AC=2;AN=2;AF=0.0;RO=81;AO=17;PRO=35.5;PAO=18.5;QR=3038;QA=480;PQR=1252.92;PQA=641.917;SRF=8;SRR=73;SAF=0;SAR=17;SRP=116.275;SAP=39.9253;AB=0.109677;ABP=208.123;RUN=1;RPP=3.13803;RPPR=3.25157;RPL=8.0;RPR=9.0;EPP=3.13803;EPPR=3.68051;DPRA=0.0;ODDS=36.5376;GTI=0;TYPE=ins;CIGAR=1M1I26M;NUMALT=3;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.941176;PAIREDR=0.975309;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr2 212578379 . TA T 476.279 REJECT NS=2;DP=155;DPB=198.667;AC=2;AN=4;AF=0.5;RO=81;AO=23;PRO=35.5;PAO=27.5;QR=3038;QA=732;PQR=1252.92;PQA=991.917;SRF=8;SRR=73;SAF=1;SAR=22;SRP=116.275;SAP=44.6459;AB=0.148387;ABP=169.457;RUN=1;RPP=3.86001;RPPR=3.25157;RPL=10.0;RPR=13.0;EPP=5.3706;EPPR=3.68051;DPRA=0.0;ODDS=36.5376;GTI=0;TYPE=del;CIGAR=1M1D25M;NUMALT=3;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.975309;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=2.112;FS=2. [...]
+chr2 212578379 . TAA T 619.828 REJECT NS=2;DP=155;DPB=198.667;AC=2;AN=2;AF=0.0;RO=81;AO=12;PRO=35.5;PAO=17.5;QR=3038;QA=329;PQR=1252.92;PQA=584.25;SRF=8;SRR=73;SAF=1;SAR=11;SRP=116.275;SAP=21.1059;AB=0.0774194;ABP=243.427;RUN=1;RPP=5.9056;RPPR=3.25157;RPL=4.0;RPR=8.0;EPP=3.73412;EPPR=3.68051;DPRA=0.0;ODDS=36.5376;GTI=0;TYPE=del;CIGAR=1M2D24M;NUMALT=3;MEANALT=12.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.975309;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr2 213490883 . G A 1200.47 REJECT NS=1;DP=111;DPB=111.0;AC=1;AN=4;AF=0.5;RO=64;AO=47;PRO=0.0;PAO=0.0;QR=2413;QA=1763;PQR=0.0;PQA=0.0;SRF=26;SRR=38;SAF=13;SAR=34;SRP=7.89611;SAP=23.3852;AB=0.423423;ABP=8.66395;RUN=1;RPP=16.3625;RPPR=29.6108;RPL=32.0;RPR=15.0;EPP=6.75262;EPPR=22.5536;DPRA=0.0;ODDS=276.418;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.563;FS=5.213;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.2 [...]
+chr2 213491656 . T TCA 1511.02 REJECT NS=1;DP=59;DPB=81.2222;AC=1;AN=3;AF=0.5;RO=5;AO=23;PRO=14.6667;PAO=19.6667;QR=167;QA=777;PQR=500.333;PQA=686.333;SRF=2;SRR=3;SAF=13;SAR=10;SRP=3.44459;SAP=3.86001;AB=0.389831;ABP=9.23028;RUN=1;RPP=5.3706;RPPR=3.44459;RPL=9.0;RPR=14.0;EPP=7.63648;EPPR=13.8677;DPRA=0.0;ODDS=149.281;GTI=0;TYPE=ins;CIGAR=1M2I35M;NUMALT=2;MEANALT=6.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=1.461;FS=3.844;MLEAC [...]
+chr2 213491656 . TCACA T 1511.02 REJECT NS=1;DP=59;DPB=81.2222;AC=1;AN=3;AF=0.5;RO=5;AO=26;PRO=14.6667;PAO=17.6667;QR=167;QA=987;PQR=500.333;PQA=597.333;SRF=2;SRR=3;SAF=16;SAR=10;SRP=3.44459;SAP=6.01695;AB=0.440678;ABP=4.81373;RUN=1;RPP=4.34659;RPPR=3.44459;RPL=11.0;RPR=15.0;EPP=15.0369;EPPR=13.8677;DPRA=0.0;ODDS=149.281;GTI=0;TYPE=del;CIGAR=1M4D31M;NUMALT=2;MEANALT=6.0;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=1.461;FS=3.844;M [...]
+chr2 213492898 . G A 5017.25 REJECT NS=2;DP=198;DPB=221.0;AC=2;AN=4;AF=0.5;RO=52;AO=169;PRO=0.0;PAO=0.0;QR=1958;QA=6507;PQR=0.0;PQA=0.0;SRF=11;SRR=41;SAF=37;SAR=132;SRP=40.5935;SAP=118.972;AB=0.764706;ABP=137.514;RUN=1;RPP=57.2971;RPPR=16.5402;RPL=117.0;RPR=52.0;EPP=5.90131;EPPR=3.67845;DPRA=0.0;ODDS=123.459;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994083;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3005;Dels=0.0;FS=1.996;HaplotypeScore=3 [...]
+chr2 213499899 . T C 5416.370000000001 REJECT NS=2;DP=389;DPB=449.0;AC=2;AN=4;AF=0.5;RO=245;AO=203;PRO=0.0;PAO=0.0;QR=9140;QA=7647;PQR=0.0;PQA=0.0;SRF=145;SRR=100;SAF=114;SAR=89;SRP=20.9582;SAP=9.69587;AB=0.452116;ABP=11.9525;RUN=1;RPP=7.72764;RPPR=20.9582;RPL=112.0;RPR=91.0;EPP=26.6398;EPPR=24.2907;DPRA=0.0;ODDS=328.057;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0816;PAIRED=0.990148;PAIREDR=0.995918;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.385;Dels=0.0;FS=1. [...]
+chr2 213886454 . A T 5168.200000000001 REJECT NS=2;DP=355;DPB=414.0;AC=2;AN=4;AF=0.5;RO=221;AO=193;PRO=0.0;PAO=0.0;QR=8490;QA=7346;PQR=0.0;PQA=0.0;SRF=87;SRR=134;SAF=77;SAR=116;SRP=24.7152;SAP=20.1233;AB=0.466184;ABP=7.12246;RUN=1;RPP=8.96216;RPPR=3.49176;RPL=108.0;RPR=85.0;EPP=4.37169;EPPR=3.80618;DPRA=0.0;ODDS=352.386;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989637;PAIREDR=0.995475;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3965;Dels=0.0;FS=0.354 [...]
+chr2 214012403 . CAA C 13884.5 REJECT NS=2;DP=337;DPB=440.4;AC=1;AN=3;AF=0.25;RO=0;AO=16;PRO=34.6667;PAO=41.1667;QR=0;QA=612;PQR=1179.5;PQA=1398.5;SRF=0;SRR=0;SAF=12;SAR=4;SRP=0.0;SAP=11.6962;AB=0.105882;ABP=117.69;RUN=1;RPP=3.55317;RPPR=0.0;RPL=9.0;RPR=7.0;EPP=7.89611;EPPR=0.0;DPRA=0.0;ODDS=4.37764;GTI=0;TYPE=del;CIGAR=1M2D17M;NUMALT=2;MEANALT=5.5;LEN=2;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC: [...]
+chr2 214012405 . A C 13417.65 REJECT NS=2;DP=329;DPB=440.4;AC=3;AN=3;AF=0.75;RO=0;AO=314;PRO=34.6667;PAO=117.167;QR=0;QA=12072;PQR=1179.5;PQA=4289.0;SRF=0;SRR=0;SAF=162;SAR=152;SRP=0.0;SAP=3.70185;AB=0.870588;ABP=104.405;RUN=1;RPP=4.36574;RPPR=0.0;RPL=164.0;RPR=150.0;EPP=4.36574;EPPR=0.0;DPRA=0.0;ODDS=4.37764;GTI=0;TYPE=snp;CIGAR=2M1X17M;NUMALT=2;MEANALT=5.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996815;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.1845;Dels=0.03;F [...]
+chr2 214012508 . C T 2164.36 PASS SOMATIC;NS=2;DP=383;DPB=383.0;AC=1;AN=3;AF=0.25;RO=296;AO=87;PRO=0.0;PAO=0.0;QR=11229;QA=3350;PQR=0.0;PQA=0.0;SRF=109;SRR=187;SAF=36;SAR=51;SRP=47.6429;SAP=8.62618;AB=0.3;ABP=103.767;RUN=1;RPP=5.03202;RPPR=29.4201;RPL=48.0;RPR=39.0;EPP=8.62618;EPPR=13.6036;DPRA=3.11828;ODDS=59.0243;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988506;PAIREDR=0.993243;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.514;Dels=0.0;FS=2.22 [...]
+chr2 215595164 . G A 5824.15 REJECT NS=2;DP=382;DPB=427.0;AC=2;AN=4;AF=0.5;RO=224;AO=203;PRO=0.0;PAO=0.0;QR=8635;QA=7884;PQR=0.0;PQA=0.0;SRF=119;SRR=105;SAF=112;SAR=91;SRP=4.91034;SAP=7.72764;AB=0.47541;ABP=5.25297;RUN=1;RPP=3.10657;RPPR=4.40625;RPL=103.0;RPR=100.0;EPP=48.2047;EPPR=14.2166;DPRA=0.0;ODDS=267.77;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.9815;Dels=0.0;FS=1.432;HaplotypeScore=7.92 [...]
+chr2 215595645 . C T 1941.925 REJECT NS=2;DP=356;DPB=403.0;AC=2;AN=4;AF=0.5;RO=310;AO=93;PRO=0.0;PAO=0.0;QR=11904;QA=3515;PQR=0.0;PQA=0.0;SRF=145;SRR=165;SAF=46;SAR=47;SRP=5.8122;SAP=3.03365;AB=0.230769;ABP=256.738;RUN=1;RPP=5.83555;RPPR=39.3229;RPL=41.0;RPR=52.0;EPP=5.83555;EPPR=3.26247;DPRA=0.0;ODDS=136.308;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990323;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1315;Dels=0.0;FS=0.0;HaplotypeScore=11 [...]
+chr2 215632192 . G A 1034.0900000000001 REJECT NS=2;DP=271;DPB=304.0;AC=2;AN=4;AF=0.5;RO=246;AO=57;PRO=0.0;PAO=0.0;QR=9443;QA=2208;PQR=0.0;PQA=0.0;SRF=192;SRR=54;SAF=43;SAR=14;SRP=171.114;SAP=35.049;AB=0.1875;ABP=260.873;RUN=1;RPP=16.763;RPPR=94.8477;RPL=19.0;RPR=38.0;EPP=4.877;EPPR=4.74042;DPRA=0.0;ODDS=76.0641;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.3509;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995935;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.796;Dels=0.0;FS=3.5815;Haplotype [...]
+chr2 215632255 . C T 1084.27 PASS DP=213;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=1.256;Dels=0.0;FS=8.323;HaplotypeScore=4.9239;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.4;QD=8.535;ReadPosRankSum=0.9145;SOR=1.2965;ClippingRankSum=0.108 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:52,43:95:99.0:1451,0,1789:43:45:95:1:.:.:.:.:.:-0.00174608 0/1:290,40:331:99.0:774,0,11664:40:12:330:.:1:.:.:.:.:3.01261e-05
+chr2 215632255 . CA TG 13191.6 REJECT NS=2;DP=421;DPB=424.5;AC=2;AN=2;AF=0.5;RO=0;AO=80;PRO=2.0;PAO=2.0;QR=0;QA=3000;PQR=76.0;PQA=70.0;SRF=0;SRR=0;SAF=56;SAR=24;SRP=0.0;SAP=30.8051;AB=0.190024;ABP=354.371;RUN=1;RPP=3.98746;RPPR=0.0;RPL=43.0;RPR=37.0;EPP=11.8048;EPPR=0.0;DPRA=0.0;ODDS=103.013;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=2;MEANALT=3.0;LEN=2;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB [...]
+chr2 215632256 . A G 13191.6 REJECT NS=2;DP=374;DPB=424.5;AC=2;AN=2;AF=0.75;RO=0;AO=339;PRO=2.0;PAO=3.0;QR=0;QA=13004;PQR=76.0;PQA=111.0;SRF=0;SRR=0;SAF=189;SAR=150;SRP=0.0;SAP=12.7531;AB=0.805226;ABP=343.684;RUN=1;RPP=5.32269;RPPR=0.0;RPL=179.0;RPR=160.0;EPP=60.8201;EPPR=0.0;DPRA=0.0;ODDS=103.013;GTI=0;TYPE=snp;CIGAR=1M1X;NUMALT=2;MEANALT=3.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99705;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.9238;MLEAC=2;M [...]
+chr2 215634055 . C T 922.6044999999999 REJECT NS=2;DP=259;DPB=293.0;AC=2;AN=4;AF=0.5;RO=236;AO=57;PRO=0.0;PAO=0.0;QR=8958;QA=2084;PQR=0.0;PQA=0.0;SRF=49;SRR=187;SAF=13;SAR=44;SRP=178.237;SAP=39.6206;AB=0.194539;ABP=240.472;RUN=1;RPP=6.09608;RPPR=24.2098;RPL=33.0;RPR=24.0;EPP=4.877;EPPR=13.6468;DPRA=0.0;ODDS=51.2547;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.964912;PAIREDR=0.995763;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.7785;Dels=0.0;FS=1.712;Hap [...]
+chr2 215645464 . C G 5428.835 REJECT NS=2;DP=362;DPB=412.0;AC=2;AN=4;AF=0.5;RO=216;AO=195;PRO=0.0;PAO=0.0;QR=8248;QA=7392;PQR=0.0;PQA=0.0;SRF=116;SRR=100;SAF=93;SAR=102;SRP=5.5839;SAP=3.9123;AB=0.473301;ABP=5.56125;RUN=1;RPP=3.02144;RPPR=8.80089;RPL=97.0;RPR=98.0;EPP=3.9123;EPPR=3.6537;DPRA=0.0;ODDS=291.719;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994872;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.2345;Dels=0.0;FS=5.492;HaplotypeScore=8 [...]
+chr2 215674224 . G A 1474.64 REJECT NS=1;DP=121;DPB=121.0;AC=1;AN=4;AF=0.5;RO=65;AO=55;PRO=0.0;PAO=0.0;QR=2430;QA=2069;PQR=0.0;PQA=0.0;SRF=21;SRR=44;SAF=24;SAR=31;SRP=20.6827;SAP=4.94488;AB=0.454545;ABP=5.18177;RUN=1;RPP=7.78754;RPPR=4.64726;RPL=33.0;RPR=22.0;EPP=9.68264;EPPR=3.31097;DPRA=0.0;ODDS=339.549;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984615;technology.ILLUMINA=1.0;BaseQRankSum=0.578;FS=5.881;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum [...]
+chr2 223161889 . A G 14622.2 REJECT NS=2;DP=388;DPB=448.0;AC=4;AN=4;AF=1.0;RO=0;AO=448;PRO=0.0;PAO=0.0;QR=0;QA=17067;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=167;SAR=281;SRP=0.0;SAP=66.0024;AB=0.0;ABP=0.0;RUN=1;RPP=6.2869;RPPR=0.0;RPL=237.0;RPR=211.0;EPP=55.4358;EPPR=0.0;DPRA=0.0;ODDS=78.5297;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997768;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=9.7209;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.665;SOR=1. [...]
+chr2 225020875 . C A 5997.01 REJECT NS=2;DP=220;DPB=253.0;AC=2;AN=4;AF=0.5;RO=55;AO=197;PRO=0.0;PAO=0.0;QR=2095;QA=7625;PQR=0.0;PQA=0.0;SRF=22;SRR=33;SAF=66;SAR=131;SRP=7.78754;SAP=49.5812;AB=0.778656;ABP=173.647;RUN=1;RPP=55.4894;RPPR=23.8959;RPL=133.0;RPR=64.0;EPP=23.3913;EPPR=9.68264;DPRA=0.0;ODDS=79.5679;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.981818;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1565;Dels=0.0;FS=4.47;HaplotypeScore=2. [...]
+chr2 225346646 . T C 3430.86 PASS SOMATIC;NS=2;DP=435;DPB=435.0;AC=1;AN=3;AF=0.25;RO=308;AO=127;PRO=0.0;PAO=0.0;QR=11836;QA=4821;PQR=0.0;PQA=0.0;SRF=175;SRR=133;SAF=72;SAR=55;SRP=15.4469;SAP=7.95168;AB=0.409677;ABP=24.9772;RUN=1;RPP=9.18275;RPPR=3.46152;RPL=73.0;RPR=54.0;EPP=4.39525;EPPR=3.0385;DPRA=2.48;ODDS=78.9829;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984252;PAIREDR=0.99026;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.802;Dels=0.0;FS=0.8 [...]
+chr2 225362478 . C T 2382.7 PASS SOMATIC;NS=2;DP=364;DPB=364.0;AC=1;AN=3;AF=0.25;RO=270;AO=94;PRO=0.0;PAO=0.0;QR=10273;QA=3625;PQR=0.0;PQA=0.0;SRF=168;SRR=102;SAF=66;SAR=28;SRP=38.0434;SAP=36.3678;AB=0.327526;ABP=77.1657;RUN=1;RPP=18.6264;RPPR=8.44702;RPL=34.0;RPR=60.0;EPP=3.1027;EPPR=4.58663;DPRA=3.72727;ODDS=49.0513;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.562;Dels=0.0;FS=6.271;Haplo [...]
+chr2 225365056 . A G 1892.8 PASS SOMATIC;NS=2;DP=277;DPB=277.0;AC=1;AN=3;AF=0.25;RO=201;AO=76;PRO=0.0;PAO=0.0;QR=7700;QA=2877;PQR=0.0;PQA=0.0;SRF=133;SRR=68;SAF=56;SAR=20;SRP=48.6544;SAP=40.0396;AB=0.389744;ABP=23.6003;RUN=1;RPP=74.4403;RPPR=60.5813;RPL=13.0;RPR=63.0;EPP=5.8675;EPPR=8.72527;DPRA=2.37805;ODDS=52.167;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.493;Dels=0.0;FS=7.914;Haploty [...]
+chr2 225367669 . C T 1994.72 PASS SOMATIC;NS=2;DP=318;DPB=318.0;AC=1;AN=3;AF=0.25;RO=239;AO=78;PRO=0.0;PAO=0.0;QR=9179;QA=3061;PQR=0.0;PQA=0.0;SRF=162;SRR=77;SAF=47;SAR=31;SRP=68.6542;SAP=10.1372;AB=0.320988;ABP=70.6476;RUN=1;RPP=43.2104;RPPR=41.3972;RPL=20.0;RPR=58.0;EPP=4.79202;EPPR=7.01708;DPRA=3.24;ODDS=47.158;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987448;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.961;Dels=0.0;FS=6.068;Hapl [...]
+chr2 225434445 . A G 7868.45 REJECT NS=2;DP=376;DPB=426.0;AC=3;AN=4;AF=0.75;RO=139;AO=286;PRO=0.0;PAO=0.0;QR=5345;QA=10872;PQR=0.0;PQA=0.0;SRF=64;SRR=75;SAF=126;SAR=160;SRP=4.90057;SAP=11.7873;AB=0.573171;ABP=18.2636;RUN=1;RPP=3.49622;RPPR=6.52527;RPL=147.0;RPR=139.0;EPP=26.8206;EPPR=12.7741;DPRA=0.0;ODDS=62.1381;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=59.9928;PAIRED=0.986014;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.844;Dels=0.0;FS=0.0;HaplotypeSc [...]
+chr2 228002144 . T C 2796.41 REJECT NS=1;DP=86;DPB=86.0;AC=2;AN=4;AF=1.0;RO=0;AO=86;PRO=0.0;PAO=0.0;QR=0;QA=3205;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=30;SAR=56;SRP=0.0;SAP=20.0791;AB=0.0;ABP=0.0;RUN=1;RPP=39.4708;RPPR=0.0;RPL=62.0;RPR=24.0;EPP=5.53527;EPPR=0.0;DPRA=0.0;ODDS=58.2301;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.988372;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.63;SOR=1.501 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr2 231110582 . C T 1873.365 REJECT NS=2;DP=308;DPB=356.0;AC=2;AN=4;AF=0.5;RO=262;AO=94;PRO=0.0;PAO=0.0;QR=10022;QA=3536;PQR=0.0;PQA=0.0;SRF=151;SRR=111;SAF=55;SAR=39;SRP=16.2712;SAP=8.9241;AB=0.264045;ABP=175.167;RUN=1;RPP=14.1911;RPPR=30.8913;RPL=36.0;RPR=58.0;EPP=32.9489;EPPR=13.7516;DPRA=0.0;ODDS=164.324;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992366;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.301;Dels=0.0;FS=4.2725;HaplotypeScore= [...]
+chr2 231115790 . G A 1500.03 REJECT NS=2;DP=260;DPB=295.0;AC=2;AN=4;AF=0.5;RO=220;AO=75;PRO=0.0;PAO=0.0;QR=8449;QA=2840;PQR=0.0;PQA=0.0;SRF=78;SRR=142;SAF=28;SAR=47;SRP=43.4392;SAP=13.4623;AB=0.254237;ABP=157.774;RUN=1;RPP=9.52472;RPPR=22.1193;RPL=45.0;RPR=30.0;EPP=15.7786;EPPR=25.7515;DPRA=0.0;ODDS=140.021;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1565;Dels=0.0;FS=1.695;HaplotypeScore=6.8544; [...]
+chr2 231120255 . CG C 8157.405 REJECT NS=2;DP=252;DPB=254.133;AC=2;AN=2;AF=0.5;RO=0;AO=62;PRO=5.5;PAO=11.5;QR=0;QA=2159;PQR=198.083;PQA=389.083;SRF=0;SRR=0;SAF=13;SAR=49;SRP=0.0;SAP=48.4011;AB=0.236641;ABP=160.848;RUN=1;RPP=5.25182;RPPR=0.0;RPL=35.0;RPR=27.0;EPP=9.87495;EPPR=0.0;DPRA=0.0;ODDS=179.499;GTI=0;TYPE=del;CIGAR=1M1D13M;NUMALT=3;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;ALERT;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.93;QD=30 [...]
+chr2 231120255 . CGG C 8157.405 REJECT NS=2;DP=252;DPB=254.133;AC=2;AN=2;AF=0.25;RO=0;AO=3;PRO=5.5;PAO=4.5;QR=0;QA=112;PQR=198.083;PQA=160.583;SRF=0;SRR=0;SAF=0;SAR=3;SRP=0.0;SAP=9.52472;AB=0.0566038;ABP=93.5156;RUN=1;RPP=9.52472;RPPR=0.0;RPL=0.0;RPR=3.0;EPP=9.52472;EPPR=0.0;DPRA=0.0;ODDS=179.499;GTI=0;TYPE=del;CIGAR=1M2D12M;NUMALT=3;MEANALT=4.0;LEN=2;MQM=56.3333;MQMR=0.0;PAIRED=0.666667;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;ALERT;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.93;Q [...]
+chr2 231120256 . GGG T 8333.08 REJECT NS=2;DP=262;DPB=254.133;AC=2;AN=2;AF=0.5;RO=0;AO=192;PRO=5.5;PAO=32.5;QR=0;QA=7078;PQR=198.083;PQA=1125.25;SRF=0;SRR=0;SAF=62;SAR=130;SRP=0.0;SAP=55.3066;AB=0.732824;ABP=126.37;RUN=1;RPP=38.4777;RPPR=0.0;RPL=124.0;RPR=68.0;EPP=11.8771;EPPR=0.0;DPRA=0.0;ODDS=179.499;GTI=0;TYPE=complex;CIGAR=1M2D1X11M;NUMALT=3;MEANALT=5.0;LEN=13;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMIC [...]
+chr2 231120258 . G T 3810.2700000000004 PASS DP=152;AC=2;AN=4;AF=0.5;MQ0=0;ALERT;BaseQRankSum=1.7645;Dels=0.0;FS=2.9735;HaplotypeScore=65.4872;MLEAC=1;MLEAF=0.5;MQ=59.93;MQRankSum=-0.006;QD=21.36;ReadPosRankSum=2.283;SOR=0.8175;ClippingRankSum=1.676 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:39,30:69:99.0:1045,0,1459:30:43:69:1:.:.:.:.:.:-0.00174608 0/1:65,171:236:99.0:6632,0,2064:171:72:236:.:1:.:.:.:.:3.01261e-05
+chr2 231149108 . G A 14041.599999999999 REJECT NS=2;DP=366;DPB=415.0;AC=4;AN=4;AF=1.0;RO=1;AO=414;PRO=0.0;PAO=0.0;QR=40;QA=16078;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=208;SAR=206;SRP=5.18177;SAP=3.03128;AB=0.0;ABP=0.0;RUN=1;RPP=13.1648;RPPR=5.18177;RPL=229.0;RPR=185.0;EPP=40.0197;EPPR=5.18177;DPRA=0.0;ODDS=64.2156;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8164;MQMR=60.0;PAIRED=0.995169;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.349;Dels=0.0;FS=1.5745;HaplotypeSco [...]
+chr2 231157512 . A G 1124.02 REJECT NS=2;DP=286;DPB=330.0;AC=2;AN=4;AF=0.5;RO=266;AO=64;PRO=0.0;PAO=0.0;QR=10165;QA=2336;PQR=0.0;PQA=0.0;SRF=92;SRR=174;SAF=18;SAR=46;SRP=57.9012;SAP=29.6108;AB=0.193939;ABP=271.51;RUN=1;RPP=5.18177;RPPR=12.4472;RPL=36.0;RPR=28.0;EPP=5.18177;EPPR=12.4472;DPRA=0.0;ODDS=45.5925;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.6562;MQMR=59.9549;PAIRED=0.984375;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.3245;Dels=0.0;FS=4.544;HaplotypeS [...]
+chr2 231157527 . G A 8393.28 REJECT NS=2;DP=236;DPB=271.0;AC=4;AN=4;AF=1.0;RO=0;AO=270;PRO=0.0;PAO=0.0;QR=0;QA=9896;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=86;SAR=184;SRP=0.0;SAP=80.2504;AB=0.0;ABP=0.0;RUN=1;RPP=54.4822;RPPR=0.0;RPL=175.0;RPR=95.0;EPP=3.13898;EPPR=0.0;DPRA=0.0;ODDS=47.3011;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9778;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=59.96;QD=30.53;SOR=1.95 G [...]
+chr2 231175549 . T C 1473.05 REJECT NS=1;DP=128;DPB=128.0;AC=1;AN=4;AF=0.5;RO=65;AO=62;PRO=0.0;PAO=0.0;QR=2470;QA=2372;PQR=0.0;PQA=0.0;SRF=27;SRR=38;SAF=23;SAR=39;SRP=7.05258;SAP=11.9764;AB=0.484375;ABP=3.28173;RUN=1;RPP=3.0103;RPPR=4.64726;RPL=31.0;RPR=31.0;EPP=6.51267;EPPR=8.65613;DPRA=0.0;ODDS=339.182;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=37.3226;MQMR=38.1385;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=2.113;FS=1.548;MLEAC=1;MLEAF=0.5;MQ=39.17;MQRankSu [...]
+chr2 234087815 . C CCCT 3191.63 REJECT NS=2;DP=239;DPB=401.667;AC=2;AN=4;AF=0.5;RO=142;AO=127;PRO=8.5;PAO=8.5;QR=5421;QA=4521;PQR=295.5;PQA=295.5;SRF=37;SRR=105;SAF=32;SAR=95;SRP=73.7208;SAP=70.8731;AB=0.472119;ABP=4.82659;RUN=1;RPP=9.18275;RPPR=18.6694;RPL=73.0;RPR=54.0;EPP=17.3899;EPPR=3.56081;DPRA=0.0;ODDS=217.52;GTI=0;TYPE=ins;CIGAR=1M3I2M;NUMALT=1;MEANALT=1.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=0.992126;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=234087815;HOMLEN=0;SVLEN=3;SVTYPE=INS; [...]
+chr2 234590527 . T G 9962.58 REJECT NS=2;DP=364;DPB=415.0;AC=2;AN=4;AF=0.5;RO=87;AO=328;PRO=0.0;PAO=0.0;QR=3339;QA=12433;PQR=0.0;PQA=0.0;SRF=43;SRR=44;SAF=174;SAR=154;SRP=3.03526;SAP=5.65844;AB=0.790361;ABP=306.917;RUN=1;RPP=6.82362;RPPR=3.63429;RPL=152.0;RPR=176.0;EPP=30.1272;EPPR=3.63429;DPRA=0.0;ODDS=100.353;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993902;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1465;Dels=0.0;FS=0.3795;HaplotypeSco [...]
+chr2 234590969 . A G 4239.77 PASS SOMATIC;DP=275;AC=1;AN=4;AF=0.5;MQ0=1;BaseQRankSum=-0.196;Dels=0.0;FS=1.472;HaplotypeScore=147.73;MLEAC=1;MLEAF=0.5;MQ=52.96;MQRankSum=-0.625;QD=15.42;ReadPosRankSum=3.211;SOR=0.585 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00174608 0/1:153,122:275:99.0:4268,0,5638:122:44:275:.:1:.:.:.:.:3.01261e-05
+chr2 234590969 . AT GG 2178.77 PASS DP=96;AC=1;AN=4;AF=0.5;JOINED;BaseQRankSum=0.262;FS=6.647;MLEAC=1;MLEAF=0.5;MQ=55.77;MQRankSum=-4.258;QD=22.7;ReadPosRankSum=0.181;SOR=0.305;ClippingRankSum=-0.86 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:42,54:96:99.0:2207,0,2813:54:56:96:1:.:.:.:.:.:-0.00174608 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:3.01261e-05
+chr2 234590969 . ATGACCG GGGACAA 6052.01 REJECT NS=2;DP=345;DPB=354.857;AC=2;AN=3;AF=0.5;RO=87;AO=164;PRO=11.0;PAO=5.0;QR=3313;QA=6129;PQR=364.5;PQA=175.5;SRF=54;SRR=33;SAF=95;SAR=69;SRP=14.0174;SAP=11.961;AB=0.475362;ABP=4.8293;RUN=1;RPP=6.39992;RPPR=3.23494;RPL=90.0;RPR=74.0;EPP=9.41879;EPPR=7.22845;DPRA=0.0;ODDS=278.715;GTI=0;TYPE=complex;CIGAR=2X3M2X;NUMALT=2;MEANALT=2.0;LEN=7;MQM=50.1037;MQMR=59.4253;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO: [...]
+chr2 234590970 . T G 8283.77 PASS SOMATIC;DP=268;AC=1;AN=4;AF=0.5;MQ0=1;BaseQRankSum=-2.13;Dels=0.0;FS=1.268;HaplotypeScore=148.72;MLEAC=1;MLEAF=0.5;MQ=52.76;MQRankSum=-4.823;QD=30.91;ReadPosRankSum=2.633;SOR=0.823 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00174608 0/1:47,221:268:99.0:8312,0,1290:221:82:268:.:1:.:.:.:.:3.01261e-05
+chr2 234590970 . TGACCG GGACAA 6052.01 PASS SOMATIC;NS=2;DP=345;DPB=354.857;AC=2;AN=2;AF=0.25;RO=87;AO=93;PRO=11.0;PAO=11.0;QR=3313;QA=3424;PQR=364.5;PQA=408.0;SRF=54;SRR=33;SAF=55;SAR=38;SRP=14.0174;SAP=9.75821;AB=0.357692;ABP=48.7448;RUN=1;RPP=6.95631;RPPR=3.23494;RPL=40.0;RPR=53.0;EPP=8.26386;EPPR=7.22845;DPRA=0.0;ODDS=278.715;GTI=0;TYPE=complex;CIGAR=1M1X3M2X;NUMALT=2;MEANALT=2.0;LEN=7;MQM=49.2366;MQMR=59.4253;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP: [...]
+chr2 234590974 . CG AA 5151.27 PASS DP=181;AC=2;AN=4;AF=0.5;MQ0=1;JOINED;BaseQRankSum=1.9515;Dels=0.0;FS=2.924;HaplotypeScore=157.749;MLEAC=1;MLEAF=0.5;MQ=54.26;MQRankSum=-3.396;QD=26.545;ReadPosRankSum=2.1795;SOR=0.552;ClippingRankSum=1.347 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:41,56:97:99.0:2219,0,2832:56:58:97:1:.:.:.:.:.:-0.00174608 0/1:52,214:266:99.0:8140,0,1399:214:80:266:.:1:.:.:.:.:3.01261e-05
+chr2 234665659 . T G 7052.58 REJECT NS=2;DP=411;DPB=466.0;AC=2;AN=4;AF=0.5;RO=216;AO=250;PRO=0.0;PAO=0.0;QR=8233;QA=9447;PQR=0.0;PQA=0.0;SRF=97;SRR=119;SAF=114;SAR=136;SRP=7.87601;SAP=7.21427;AB=0.536481;ABP=8.39704;RUN=1;RPP=3.5662;RPPR=13.3047;RPL=121.0;RPR=129.0;EPP=3.14927;EPPR=4.01561;DPRA=0.0;ODDS=313.353;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.988;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990741;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.038;Dels=0.0;FS=0.774;HaplotypeSc [...]
+chr2 234665782 . G A 4474.0 REJECT NS=2;DP=340;DPB=390.0;AC=2;AN=4;AF=0.5;RO=217;AO=173;PRO=0.0;PAO=0.0;QR=8155;QA=6493;PQR=0.0;PQA=0.0;SRF=103;SRR=114;SAF=65;SAR=108;SRP=4.22112;SAP=26.2187;AB=0.44359;ABP=13.7897;RUN=1;RPP=12.1606;RPPR=3.26047;RPL=100.0;RPR=73.0;EPP=13.5664;EPPR=3.26047;DPRA=0.0;ODDS=298.752;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.2775;MQMR=59.8525;PAIRED=0.988439;PAIREDR=0.986175;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9295;Dels=0.0;FS=6.32;Haplo [...]
+chr2 234668879 . C CAT 2459.91 REJECT NS=2;DP=252;DPB=329.278;AC=2;AN=4;AF=0.5;RO=146;AO=96;PRO=62.0;PAO=62.0;QR=5539;QA=3520;PQR=2245.0;PQA=2242.0;SRF=57;SRR=89;SAF=35;SAR=61;SRP=18.2404;SAP=18.3011;AB=0.365019;ABP=44.6316;RUN=1;RPP=10.339;RPPR=40.193;RPL=57.0;RPR=39.0;EPP=3.37221;EPPR=11.5772;DPRA=0.0;ODDS=150.241;GTI=0;TYPE=ins;CIGAR=1M2I17M;NUMALT=1;MEANALT=7.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.6535;FS=1.6325;MLEAC=1;MLEAF=0 [...]
+chr2 235501364 . A G 1166.6 REJECT NS=2;DP=238;DPB=266.0;AC=2;AN=4;AF=0.5;RO=205;AO=61;PRO=0.0;PAO=0.0;QR=7911;QA=2334;PQR=0.0;PQA=0.0;SRF=63;SRR=142;SAF=22;SAR=39;SRP=69.1184;SAP=13.2981;AB=0.229323;ABP=172.287;RUN=1;RPP=18.709;RPPR=79.5415;RPL=41.0;RPR=20.0;EPP=7.31765;EPPR=3.02089;DPRA=0.0;ODDS=112.497;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995122;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0845;Dels=0.0;FS=2.6215;HaplotypeScore=3. [...]
+chr2 240003870 . G A 1905.66 REJECT NS=2;DP=355;DPB=408.0;AC=2;AN=4;AF=0.5;RO=312;AO=96;PRO=0.0;PAO=0.0;QR=11954;QA=3595;PQR=0.0;PQA=0.0;SRF=174;SRR=138;SAF=53;SAR=43;SRP=12.0303;SAP=5.27225;AB=0.235294;ABP=251.325;RUN=1;RPP=3.37221;RPPR=7.71516;RPL=50.0;RPR=46.0;EPP=10.339;EPPR=13.0603;DPRA=0.0;ODDS=140.863;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99359;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.071;Dels=0.0;FS=1.6;HaplotypeScore=6.898 [...]
+chr2 240016771 . C T 1572.08 PASS SOMATIC;NS=2;DP=238;DPB=238.0;AC=1;AN=3;AF=0.25;RO=173;AO=65;PRO=0.0;PAO=0.0;QR=6630;QA=2438;PQR=0.0;PQA=0.0;SRF=32;SRR=141;SAF=14;SAR=51;SRP=152.139;SAP=48.7448;AB=0.343915;ABP=43.0045;RUN=1;RPP=3.84548;RPPR=15.0726;RPL=35.0;RPR=30.0;EPP=15.0703;EPPR=5.13156;DPRA=3.85714;ODDS=31.5735;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99422;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.04;Dels=0.0;FS=0.0;Hap [...]
+chr2 240029736 . T C 2794.25 REJECT NS=1;DP=87;DPB=87.0;AC=2;AN=4;AF=1.0;RO=0;AO=87;PRO=0.0;PAO=0.0;QR=0;QA=3195;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=58;SAR=29;SRP=0.0;SAP=24.0012;AB=0.0;ABP=0.0;RUN=1;RPP=26.9963;RPPR=0.0;RPL=28.0;RPR=59.0;EPP=3.23494;EPPR=0.0;DPRA=0.0;ODDS=57.8537;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9655;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.26;SOR=1.501 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICO [...]
+chr2 240061400 . C T 5610.6 REJECT NS=2;DP=345;DPB=394.0;AC=2;AN=4;AF=0.5;RO=197;AO=197;PRO=0.0;PAO=0.0;QR=7511;QA=7550;PQR=0.0;PQA=0.0;SRF=123;SRR=74;SAF=117;SAR=80;SRP=29.4758;SAP=18.1004;AB=0.5;ABP=3.0103;RUN=1;RPP=3.55041;RPPR=4.87314;RPL=102.0;RPR=95.0;EPP=3.55041;EPPR=13.6031;DPRA=0.0;ODDS=290.04;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994924;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1665;Dels=0.0;FS=2.8125;HaplotypeScore=2.9992 [...]
+chr2 240066417 . A G 8360.03 REJECT NS=2;DP=223;DPB=256.0;AC=4;AN=4;AF=1.0;RO=0;AO=256;PRO=0.0;PAO=0.0;QR=0;QA=9833;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=50;SAR=206;SRP=0.0;SAP=209.436;AB=0.0;ABP=0.0;RUN=1;RPP=54.6167;RPPR=0.0;RPL=167.0;RPR=89.0;EPP=5.75857;EPPR=0.0;DPRA=0.0;ODDS=45.5235;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996094;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.77;SOR=2.775 [...]
+chr2 241713646 . A G 5790.43 REJECT NS=2;DP=325;DPB=361.0;AC=2;AN=4;AF=0.5;RO=159;AO=202;PRO=0.0;PAO=0.0;QR=6135;QA=7694;PQR=0.0;PQA=0.0;SRF=50;SRR=109;SAF=72;SAR=130;SRP=50.5505;SAP=39.1728;AB=0.559557;ABP=14.1323;RUN=1;RPP=3.0103;RPPR=9.03306;RPL=101.0;RPR=101.0;EPP=7.31025;EPPR=19.7402;DPRA=0.0;ODDS=145.916;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2865;Dels=0.0;FS=1.386;HaplotypeScore=7.92 [...]
+chr3 10074145 . G T 594.711 REJECT NS=2;DP=40;DPB=47.0;AC=2;AN=4;AF=0.5;RO=18;AO=29;PRO=0.0;PAO=0.0;QR=496;QA=1025;PQR=0.0;PQA=0.0;SRF=3;SRR=15;SAF=3;SAR=26;SRP=20.3821;SAP=42.621;AB=0.617021;ABP=8.60069;RUN=1;RPP=57.5966;RPPR=15.074;RPL=28.0;RPR=1.0;EPP=49.8093;EPPR=20.3821;DPRA=0.0;ODDS=15.1346;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.944444;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.359;Dels=0.0;FS=0.0;HaplotypeScore=1.9443;MLEAC=1;M [...]
+chr3 10074152 . AT GG 719.034 REJECT SOMATIC;NS=2;DP=41;DPB=41.0;AC=1;AN=3;AF=0.0;RO=9;AO=2;PRO=0.0;PAO=0.0;QR=299;QA=28;PQR=0.0;PQA=0.0;SRF=2;SRR=7;SAF=0;SAR=2;SRP=9.04217;SAP=7.35324;AB=0.0689655;ABP=49.8093;RUN=1;RPP=7.35324;RPPR=9.04217;RPL=0.0;RPR=2.0;EPP=7.35324;EPPR=22.5536;DPRA=2.41667;ODDS=3.79834;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=2;MEANALT=2.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:Call [...]
+chr3 10074153 . T G 719.034 REJECT NS=2;DP=35;DPB=41.0;AC=3;AN=4;AF=0.625;RO=9;AO=30;PRO=0.0;PAO=0.0;QR=299;QA=1057;PQR=0.0;PQA=0.0;SRF=2;SRR=7;SAF=4;SAR=26;SRP=9.04217;SAP=38.0434;AB=0.655172;ABP=9.07545;RUN=1;RPP=38.0434;RPPR=9.04217;RPL=26.0;RPR=4.0;EPP=26.4622;EPPR=22.5536;DPRA=0.0;ODDS=3.79834;GTI=0;TYPE=snp;CIGAR=1M1X;NUMALT=2;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.966667;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.374;Dels=0.0;FS=4.326;Haploty [...]
+chr3 10076842 . CTT C 4047.835 REJECT NS=2;DP=265;DPB=321.333;AC=2;AN=4;AF=0.5;RO=128;AO=150;PRO=54.5;PAO=45.5;QR=4789;QA=5680;PQR=1878.0;PQA=1548.0;SRF=92;SRR=36;SAF=106;SAR=44;SRP=56.2114;SAP=58.6579;AB=0.498339;ABP=3.01751;RUN=1;RPP=28.5468;RPPR=30.1537;RPL=54.0;RPR=96.0;EPP=28.5468;EPPR=4.09604;DPRA=0.0;ODDS=252.018;GTI=0;TYPE=del;CIGAR=1M2D12M;NUMALT=1;MEANALT=6.5;LEN=2;MQM=60.4;MQMR=60.0;PAIRED=0.993333;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.295;FS=0.759;MLEAC=1;M [...]
+chr3 10077955 . A G 5246.795 REJECT NS=2;DP=312;DPB=356.0;AC=2;AN=4;AF=0.5;RO=165;AO=188;PRO=0.0;PAO=0.0;QR=6153;QA=7067;PQR=0.0;PQA=0.0;SRF=102;SRR=63;SAF=126;SAR=62;SRP=23.0273;SAP=50.3207;AB=0.52809;ABP=5.45016;RUN=1;RPP=17.9796;RPPR=14.0782;RPL=76.0;RPR=112.0;EPP=4.67356;EPPR=11.2356;DPRA=0.0;ODDS=247.151;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984043;PAIREDR=0.993939;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1155;Dels=0.0;FS=2.5985;Haplotype [...]
+chr3 10081545 . G C 5413.14 REJECT NS=2;DP=362;DPB=418.0;AC=2;AN=4;AF=0.5;RO=219;AO=199;PRO=0.0;PAO=0.0;QR=8468;QA=7617;PQR=0.0;PQA=0.0;SRF=82;SRR=137;SAF=70;SAR=129;SRP=33.0044;SAP=40.9947;AB=0.476077;ABP=5.08826;RUN=1;RPP=8.78271;RPPR=16.5845;RPL=111.0;RPR=88.0;EPP=4.85441;EPPR=3.49615;DPRA=0.0;ODDS=356.487;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.974874;PAIREDR=0.995434;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.122;Dels=0.0;FS=6.7715;Haplotype [...]
+chr3 10084224 . C T 3727.66 REJECT NS=2;DP=254;DPB=293.0;AC=2;AN=4;AF=0.5;RO=151;AO=142;PRO=0.0;PAO=0.0;QR=5719;QA=5372;PQR=0.0;PQA=0.0;SRF=78;SRR=73;SAF=91;SAR=51;SRP=3.36982;SAP=27.4776;AB=0.484642;ABP=3.6106;RUN=1;RPP=50.9662;RPPR=40.4143;RPL=43.0;RPR=99.0;EPP=25.092;EPPR=53.0692;DPRA=0.0;ODDS=227.784;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986755;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1265;Dels=0.0;FS=7.4865;HaplotypeScore=9.7 [...]
+chr3 10085536 . A G 2418.87 REJECT NS=2;DP=364;DPB=393.0;AC=2;AN=4;AF=0.5;RO=271;AO=122;PRO=0.0;PAO=0.0;QR=10504;QA=4637;PQR=0.0;PQA=0.0;SRF=132;SRR=139;SAF=38;SAR=84;SRP=3.40293;SAP=40.6729;AB=0.310433;ABP=125.679;RUN=1;RPP=16.9647;RPPR=55.5824;RPL=75.0;RPR=47.0;EPP=16.9647;EPPR=63.6593;DPRA=0.0;ODDS=158.892;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=41.2951;MQMR=47.3948;PAIRED=1.0;PAIREDR=0.99262;technology.ILLUMINA=1.0;MQ0=29;BaseQRankSum=0.2145;Dels=0.0;FS=15.4935;Haploty [...]
+chr3 10088239 . G A 701.77 PASS DP=117;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.285;Dels=0.0;FS=3.681;HaplotypeScore=1.9243;MLEAC=1;MLEAF=0.5;MQ=58.05;MQRankSum=-4.5975;QD=5.955;ReadPosRankSum=-0.8895;SOR=1.588;ClippingRankSum=-0.986 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:49,13:62:99.0:395,0,2055:13:21:62:1:.:.:.:.:.:-0.002757 0/1:134,39:173:99.0:1065,0,5336:39:23:173:.:1:.:.:.:.:-0.0187789
+chr3 10088239 . GTTG ATTA 1063.24 REJECT NS=2;DP=236;DPB=241.0;AC=2;AN=4;AF=0.5;RO=184;AO=52;PRO=7.0;PAO=5.0;QR=7097;QA=1929;PQR=181.0;PQA=168.0;SRF=141;SRR=43;SAF=42;SAR=10;SRP=116.352;SAP=45.7716;AB=0.220339;ABP=163.331;RUN=1;RPP=69.8248;RPPR=82.3635;RPL=6.0;RPR=46.0;EPP=19.7139;EPPR=6.03148;DPRA=0.0;ODDS=56.0769;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=1;MEANALT=1.0;LEN=4;MQM=47.7692;MQMR=60.0;PAIRED=0.826923;PAIREDR=0.994565;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr3 10088242 . G A 770.27 PASS DP=123;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-1.3655;Dels=0.0;FS=3.647;HaplotypeScore=1.9243;MLEAC=1;MLEAF=0.5;MQ=58.135;MQRankSum=-3.4705;QD=6.21;ReadPosRankSum=-1.2015;SOR=1.625;ClippingRankSum=0.12 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:51,14:65:99.0:428,0,2085:14:22:65:1:.:.:.:.:.:-0.002757 0/1:139,43:182:99.0:1169,0,5574:43:24:182:.:1:.:.:.:.:-0.0187789
+chr3 10088266 . G T 2308.03 REJECT NS=2;DP=315;DPB=363.0;AC=2;AN=4;AF=0.5;RO=257;AO=106;PRO=0.0;PAO=0.0;QR=9825;QA=4120;PQR=0.0;PQA=0.0;SRF=180;SRR=77;SAF=74;SAR=32;SRP=92.649;SAP=39.1469;AB=0.292011;ABP=139.406;RUN=1;RPP=62.7463;RPPR=13.3607;RPL=26.0;RPR=80.0;EPP=3.74778;EPPR=7.47998;DPRA=0.0;ODDS=86.5067;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=49.2075;MQMR=59.8444;PAIRED=0.773585;PAIREDR=0.992218;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.401;Dels=0.0;FS=2.0965;Haploty [...]
+chr3 10088299 . C T 2788.21 REJECT NS=2;DP=367;DPB=424.0;AC=2;AN=4;AF=0.5;RO=282;AO=142;PRO=0.0;PAO=0.0;QR=10587;QA=5467;PQR=0.0;PQA=0.0;SRF=164;SRR=118;SAF=84;SAR=58;SRP=19.304;SAP=13.3477;AB=0.334906;ABP=103.39;RUN=1;RPP=4.53951;RPPR=3.0411;RPL=66.0;RPR=76.0;EPP=13.3477;EPPR=22.2609;DPRA=0.0;ODDS=118.238;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=42.3169;MQMR=55.2872;PAIRED=0.683099;PAIREDR=0.992908;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.503;Dels=0.0;FS=7.036;Haplotyp [...]
+chr3 10088308 . T C 2718.42 REJECT NS=2;DP=381;DPB=440.0;AC=2;AN=4;AF=0.5;RO=294;AO=146;PRO=0.0;PAO=0.0;QR=11164;QA=5525;PQR=0.0;PQA=0.0;SRF=166;SRR=128;SAF=81;SAR=65;SRP=13.6756;SAP=6.81781;AB=0.331818;ABP=111.11;RUN=1;RPP=3.06979;RPPR=3.27619;RPL=74.0;RPR=72.0;EPP=18.2404;EPPR=16.0391;DPRA=0.0;ODDS=104.978;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=41.363;MQMR=54.0136;PAIRED=0.671233;PAIREDR=0.996599;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.2995;Dels=0.0;FS=5.248;Haplo [...]
+chr3 10088343 . A G 2107.17 REJECT NS=2;DP=382;DPB=437.0;AC=2;AN=4;AF=0.5;RO=302;AO=135;PRO=0.0;PAO=0.0;QR=11519;QA=5203;PQR=0.0;PQA=0.0;SRF=138;SRR=164;SAF=61;SAR=74;SRP=7.87095;SAP=5.72866;AB=0.308924;ABP=141.592;RUN=1;RPP=14.7363;RPPR=3.47048;RPL=81.0;RPR=54.0;EPP=11.5193;EPPR=10.3732;DPRA=0.0;ODDS=90.0873;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=34.7037;MQMR=48.1192;PAIRED=0.674074;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=9;BaseQRankSum=2.0305;Dels=0.0;FS=5.185;Haplotype [...]
+chr3 10088404 . C T 552.27 PASS DP=150;AC=2;AN=4;AF=0.5;MQ0=24;BaseQRankSum=-0.296;Dels=0.0;FS=5.2825;HaplotypeScore=84.3551;MLEAC=1;MLEAF=0.5;MQ=39.395;MQRankSum=-2.807;QD=4.57;ReadPosRankSum=0.182;SOR=0.7205;ClippingRankSum=0.903 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:60,17:77:99.0:522,0,2502:17:22:77:1:.:.:.:.:.:-0.002757 0/1:181,43:224:99.0:639,0,6139:43:19:224:.:1:.:.:.:.:-0.0187789
+chr3 10088404 . CTTAGTAAG TTTAT 424.691 REJECT NS=2;DP=242;DPB=243.667;AC=2;AN=4;AF=0.5;RO=200;AO=42;PRO=32.0;PAO=6.0;QR=7704;QA=1510;PQR=1188.0;PQA=168.0;SRF=61;SRR=139;SAF=11;SAR=31;SRP=69.0665;SAP=23.691;AB=0.173554;ABP=227.013;RUN=1;RPP=8.18047;RPPR=42.0968;RPL=26.0;RPR=16.0;EPP=6.31921;EPPR=5.13834;DPRA=0.0;ODDS=34.5694;GTI=0;TYPE=complex;CIGAR=1X2M4D1M1X;NUMALT=1;MEANALT=1.0;LEN=5;MQM=35.1667;MQMR=39.67;PAIRED=0.97619;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr3 10088407 . AG A 481.73 PASS DP=77;AC=1;AN=4;AF=0.5;ALERT;BaseQRankSum=-0.031;FS=9.225;MLEAC=1;MLEAF=0.5;MQ=40.43;MQRankSum=-2.731;QD=6.26;ReadPosRankSum=-0.96;SOR=0.142;ClippingRankSum=2.555 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:61,16:77:99.0:519,0,2544:16:21:77:1:.:.:.:.:.:-0.002757 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0187789
+chr3 10088409 . TAAG T 450.73 PASS DP=77;AC=1;AN=4;AF=0.5;ALERT;BaseQRankSum=0.245;FS=9.225;MLEAC=1;MLEAF=0.5;MQ=40.43;MQRankSum=-2.128;QD=5.85;ReadPosRankSum=-0.96;SOR=0.142;ClippingRankSum=0.421 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:61,16:77:99.0:488,0,2513:16:21:77:1:.:.:.:.:.:-0.002757 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0187789
+chr3 10088412 . G T 523.77 PASS SOMATIC;DP=203;AC=1;AN=4;AF=0.5;MQ0=25;BaseQRankSum=0.045;Dels=0.0;FS=3.096;HaplotypeScore=1.933;MLEAC=1;MLEAF=0.5;MQ=36.9;MQRankSum=-1.653;QD=2.58;ReadPosRankSum=2.326;SOR=1.137 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.002757 0/1:165,38:203:99.0:552,0,5493:38:19:203:.:1:.:.:.:.:-0.0187789
+chr3 10088422 . C T 531.734 REJECT NS=2;DP=197;DPB=217.0;AC=2;AN=4;AF=0.5;RO=175;AO=42;PRO=0.0;PAO=0.0;QR=6644;QA=1614;PQR=0.0;PQA=0.0;SRF=48;SRR=127;SAF=11;SAR=31;SRP=80.4512;SAP=23.691;AB=0.193548;ABP=180.02;RUN=1;RPP=19.7617;RPPR=72.8076;RPL=30.0;RPR=12.0;EPP=3.83753;EPPR=3.12198;DPRA=0.0;ODDS=35.9131;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=35.1667;MQMR=37.84;PAIRED=0.97619;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=25;BaseQRankSum=0.3675;Dels=0.0;FS=5.9875;HaplotypeScore= [...]
+chr3 10088443 . C A 307.77 PASS DP=81;AC=2;AN=4;AF=0.5;MQ0=16;BaseQRankSum=1.0385;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=1;MLEAF=0.5;MQ=36.445;MQRankSum=-0.2195;QD=4.045;ReadPosRankSum=-0.605;SOR=0.536;ClippingRankSum=0.796 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:35,8:43:99.0:227,0,1420:8:19:43:1:.:.:.:.:.:-0.002757 0/1:95,25:120:99.0:445,0,3050:25:21:120:.:1:.:.:.:.:-0.0187789
+chr3 10088443 . CA AG 232.403 REJECT NS=2;DP=145;DPB=146.5;AC=2;AN=4;AF=0.5;RO=117;AO=28;PRO=3.0;PAO=0.0;QR=4475;QA=1063;PQR=105.0;PQA=0.0;SRF=30;SRR=87;SAF=7;SAR=21;SRP=63.3104;SAP=18.2106;AB=0.193103;ABP=121.633;RUN=1;RPP=63.8115;RPPR=101.914;RPL=28.0;RPR=0.0;EPP=18.2106;EPPR=8.37402;DPRA=0.0;ODDS=12.8704;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=1;MEANALT=1.0;LEN=2;MQM=34.9643;MQMR=37.3932;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:C [...]
+chr3 10088444 . A G 324.77 PASS DP=80;AC=2;AN=4;AF=0.5;MQ0=16;BaseQRankSum=2.136;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=1;MLEAF=0.5;MQ=36.385;MQRankSum=0.4025;QD=4.365;ReadPosRankSum=-0.8175;SOR=0.5705;ClippingRankSum=-0.389 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:32,8:40:99.0:227,0,1420:8:20:40:1:.:.:.:.:.:-0.002757 0/1:95,25:120:99.0:479,0,3097:25:21:120:.:1:.:.:.:.:-0.0187789
+chr3 10089723 . G A 2626.55 REJECT NS=2;DP=306;DPB=351.0;AC=2;AN=4;AF=0.5;RO=242;AO=109;PRO=0.0;PAO=0.0;QR=9303;QA=4142;PQR=0.0;PQA=0.0;SRF=84;SRR=158;SAF=38;SAR=71;SRP=52.1466;SAP=24.7051;AB=0.310541;ABP=112.444;RUN=1;RPP=15.4614;RPPR=14.6393;RPL=67.0;RPR=42.0;EPP=13.5489;EPPR=14.6393;DPRA=0.0;ODDS=137.974;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=57.6055;MQMR=60.0;PAIRED=0.93578;PAIREDR=0.995868;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.673;Dels=0.0;FS=1.946;HaplotypeSc [...]
+chr3 10089738 . A G 1818.55 REJECT NS=2;DP=262;DPB=296.0;AC=2;AN=4;AF=0.5;RO=215;AO=81;PRO=0.0;PAO=0.0;QR=8279;QA=3089;PQR=0.0;PQA=0.0;SRF=64;SRR=151;SAF=23;SAR=58;SRP=79.4562;SAP=35.8505;AB=0.273649;ABP=134.737;RUN=1;RPP=35.8505;RPPR=16.837;RPL=58.0;RPR=23.0;EPP=3.03711;EPPR=8.35313;DPRA=0.0;ODDS=96.0939;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=56.7778;MQMR=60.0;PAIRED=0.938272;PAIREDR=0.995349;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5985;Dels=0.0;FS=0.626;HaplotypeSc [...]
+chr3 10089749 . T C 1718.42 REJECT NS=2;DP=218;DPB=245.0;AC=2;AN=4;AF=0.5;RO=171;AO=74;PRO=0.0;PAO=0.0;QR=6548;QA=2830;PQR=0.0;PQA=0.0;SRF=47;SRR=124;SAF=21;SAR=53;SRP=78.3007;SAP=33.0588;AB=0.302041;ABP=86.4037;RUN=1;RPP=41.0404;RPPR=12.2676;RPL=55.0;RPR=19.0;EPP=3.12768;EPPR=12.2676;DPRA=0.0;ODDS=83.8482;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=56.473;MQMR=60.0;PAIRED=0.945946;PAIREDR=0.994152;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.793;Dels=0.0;FS=0.0;HaplotypeScore [...]
+chr3 10091035 . T C 1506.29 REJECT NS=2;DP=146;DPB=147.0;AC=2;AN=4;AF=0.5;RO=65;AO=82;PRO=0.0;PAO=0.0;QR=2475;QA=2997;PQR=0.0;PQA=0.0;SRF=44;SRR=21;SAF=63;SAR=19;SRP=20.6827;SAP=54.2782;AB=0.557823;ABP=7.27939;RUN=1;RPP=74.6159;RPPR=27.3642;RPL=15.0;RPR=67.0;EPP=20.9117;EPPR=3.31097;DPRA=0.0;ODDS=10.7702;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=31.4634;MQMR=54.3692;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=39;BaseQRankSum=-0.3735;Dels=0.0;FS=0.0;HaplotypeScore=0.96 [...]
+chr3 10091049 . C T 313.92449999999997 REJECT NS=2;DP=215;DPB=228.0;AC=2;AN=4;AF=0.5;RO=182;AO=46;PRO=0.0;PAO=0.0;QR=6916;QA=1612;PQR=0.0;PQA=0.0;SRF=124;SRR=58;SAF=36;SAR=10;SRP=54.9825;SAP=34.9215;AB=0.201754;ABP=179.166;RUN=1;RPP=40.0197;RPPR=87.1966;RPL=9.0;RPR=37.0;EPP=21.8927;EPPR=3.77389;DPRA=0.0;ODDS=38.3694;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=30.2174;MQMR=42.456;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=40;BaseQRankSum=-0.542;Dels=0.0;FS=3.2415;Haplot [...]
+chr3 10091153 . C T 320.473 REJECT NS=2;DP=354;DPB=394.0;AC=2;AN=4;AF=0.5;RO=342;AO=52;PRO=0.0;PAO=0.0;QR=12951;QA=2009;PQR=0.0;PQA=0.0;SRF=140;SRR=202;SAF=49;SAR=3;SRP=27.4171;SAP=91.3725;AB=0.13198;ABP=466.515;RUN=1;RPP=3.17734;RPPR=7.98818;RPL=27.0;RPR=25.0;EPP=3.67845;EPPR=3.41666;DPRA=0.0;ODDS=17.7361;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=35.9615;MQMR=42.1287;PAIRED=1.0;PAIREDR=0.988304;technology.ILLUMINA=1.0;MQ0=21;BaseQRankSum=3.0615;Dels=0.0;FS=64.074;HaplotypeS [...]
+chr3 10094206 . A AT 1279.45 REJECT NS=2;DP=155;DPB=207.889;AC=2;AN=4;AF=0.5;RO=61;AO=61;PRO=25.6667;PAO=23.1667;QR=2265;QA=2172;PQR=903.917;PQA=812.417;SRF=18;SRR=43;SAF=15;SAR=46;SRP=25.259;SAP=37.2199;AB=0.393548;ABP=18.2666;RUN=1;RPP=21.8416;RPPR=62.8504;RPL=42.0;RPR=19.0;EPP=3.33068;EPPR=3.90025;DPRA=0.0;ODDS=63.7064;GTI=0;TYPE=ins;CIGAR=1M1I17M;NUMALT=3;MEANALT=6.0;LEN=1;MQM=57.918;MQMR=59.1639;PAIRED=1.0;PAIREDR=0.967213;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum [...]
+chr3 10094206 . A ATT 1610.17 REJECT NS=2;DP=155;DPB=207.889;AC=2;AN=2;AF=0.0;RO=61;AO=11;PRO=25.6667;PAO=21.1667;QR=2265;QA=361;PQR=903.917;PQA=738.417;SRF=18;SRR=43;SAF=4;SAR=7;SRP=25.259;SAP=4.78696;AB=0.0709677;ABP=250.824;RUN=1;RPP=12.6832;RPPR=62.8504;RPL=9.0;RPR=2.0;EPP=4.78696;EPPR=3.90025;DPRA=0.0;ODDS=63.7064;GTI=0;TYPE=ins;CIGAR=1M2I17M;NUMALT=3;MEANALT=6.0;LEN=2;MQM=57.1818;MQMR=59.1639;PAIRED=1.0;PAIREDR=0.967213;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr3 10094206 . AT A 1610.17 REJECT NS=2;DP=155;DPB=207.889;AC=2;AN=2;AF=0.0;RO=61;AO=16;PRO=25.6667;PAO=20.0;QR=2265;QA=599;PQR=903.917;PQA=670.25;SRF=18;SRR=43;SAF=4;SAR=12;SRP=25.259;SAP=11.6962;AB=0.103226;ABP=214.96;RUN=1;RPP=11.6962;RPPR=62.8504;RPL=12.0;RPR=4.0;EPP=5.18177;EPPR=3.90025;DPRA=0.0;ODDS=63.7064;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=3;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=59.1639;PAIRED=1.0;PAIREDR=0.967213;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr3 10103811 . TA T 2614.21 PASS SOMATIC;NS=2;DP=309;DPB=324.538;AC=1;AN=4;AF=0.25;RO=201;AO=100;PRO=27.0;PAO=24.0;QR=7607;QA=3767;PQR=996.0;PQA=879.0;SRF=128;SRR=73;SAF=69;SAR=31;SRP=35.6904;SAP=34.3664;AB=0.421941;ABP=15.5535;RUN=1;RPP=41.3151;RPPR=73.891;RPL=29.0;RPR=71.0;EPP=6.13722;EPPR=38.1104;DPRA=3.29167;ODDS=44.0678;GTI=0;TYPE=del;CIGAR=1M1D11M;NUMALT=1;MEANALT=5.0;LEN=1;MQM=59.36;MQMR=59.0348;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.998;FS=2.384;MLEA [...]
+chr3 10106144 . C T 65.9522 REJECT NS=2;DP=327;DPB=327.0;AC=1;AN=4;AF=0.25;RO=293;AO=32;PRO=0.0;PAO=0.0;QR=11317;QA=1221;PQR=0.0;PQA=0.0;SRF=120;SRR=173;SAF=25;SAR=7;SRP=23.8283;SAP=24.9965;AB=0.180723;ABP=76.5003;RUN=1;RPP=20.3821;RPPR=94.3233;RPL=24.0;RPR=8.0;EPP=5.45321;EPPR=3.37345;DPRA=0.0;ODDS=15.186;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=25.5938;MQMR=58.3208;PAIRED=1.0;PAIREDR=0.993174;technology.ILLUMINA=1.0;BaseQRankSum=1.887;FS=31.183;MLEAC=1;MLEAF=0.5;MQ=54.92; [...]
+chr3 10106532 . C T 3479.49 REJECT NS=2;DP=347;DPB=397.0;AC=2;AN=4;AF=0.5;RO=248;AO=149;PRO=0.0;PAO=0.0;QR=9426;QA=5727;PQR=0.0;PQA=0.0;SRF=97;SRR=151;SAF=67;SAR=82;SRP=28.5426;SAP=6.28937;AB=0.375315;ABP=56.6189;RUN=1;RPP=17.0156;RPPR=34.5317;RPL=90.0;RPR=59.0;EPP=3.02487;EPPR=4.72646;DPRA=0.0;ODDS=160.129;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=39.8523;MQMR=53.9274;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=4;BaseQRankSum=0.9195;Dels=0.0;FS=4.8385;HaplotypeScore= [...]
+chr3 10107520 . G T 3683.815 REJECT NS=2;DP=228;DPB=265.0;AC=2;AN=4;AF=0.5;RO=128;AO=137;PRO=0.0;PAO=0.0;QR=4916;QA=5188;PQR=0.0;PQA=0.0;SRF=78;SRR=50;SAF=86;SAR=51;SRP=16.3106;SAP=22.4268;AB=0.516981;ABP=3.67403;RUN=1;RPP=96.9859;RPPR=35.8538;RPL=30.0;RPR=107.0;EPP=3.02615;EPPR=3.0103;DPRA=0.0;ODDS=213.028;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=50.8102;MQMR=52.1094;PAIRED=1.0;PAIREDR=0.984375;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.6205;Dels=0.0;FS=4.554;HaplotypeS [...]
+chr3 10133949 . A G 4420.16 REJECT NS=2;DP=306;DPB=349.0;AC=2;AN=4;AF=0.5;RO=190;AO=159;PRO=0.0;PAO=0.0;QR=7224;QA=6101;PQR=0.0;PQA=0.0;SRF=74;SRR=116;SAF=50;SAR=109;SRP=23.1707;SAP=50.5505;AB=0.455587;ABP=8.98963;RUN=1;RPP=16.1347;RPPR=19.5135;RPL=95.0;RPR=64.0;EPP=6.08314;EPPR=4.15318;DPRA=0.0;ODDS=221.362;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.5785;Dels=0.0;FS=4.6055;HaplotypeScore=4.857 [...]
+chr3 10138069 . T G 6165.995000000001 REJECT NS=2;DP=375;DPB=427.0;AC=2;AN=4;AF=0.5;RO=205;AO=222;PRO=0.0;PAO=0.0;QR=7838;QA=8591;PQR=0.0;PQA=0.0;SRF=112;SRR=93;SAF=138;SAR=84;SRP=6.83421;SAP=31.5329;AB=0.519906;ABP=4.47999;RUN=1;RPP=3.36243;RPPR=14.5456;RPL=108.0;RPR=114.0;EPP=27.4638;EPPR=6.83421;DPRA=0.0;ODDS=254.151;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990991;PAIREDR=0.990244;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.528;Dels=0.0;FS=5.4995 [...]
+chr3 10138189 . T C 3224.22 REJECT NS=2;DP=192;DPB=214.0;AC=2;AN=4;AF=0.5;RO=100;AO=114;PRO=0.0;PAO=0.0;QR=3732;QA=4404;PQR=0.0;PQA=0.0;SRF=30;SRR=70;SAF=35;SAR=79;SRP=37.7539;SAP=39.8872;AB=0.53271;ABP=4.99913;RUN=1;RPP=62.7448;RPPR=45.05;RPL=85.0;RPR=29.0;EPP=6.74371;EPPR=3.35774;DPRA=0.0;ODDS=139.502;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8055;Dels=0.01;FS=0.0;HaplotypeScore=5.8016;MLEAC [...]
+chr3 12009829 . G A 2053.2200000000003 REJECT NS=2;DP=382;DPB=432.0;AC=2;AN=4;AF=0.5;RO=331;AO=101;PRO=0.0;PAO=0.0;QR=12762;QA=3889;PQR=0.0;PQA=0.0;SRF=149;SRR=182;SAF=42;SAR=59;SRP=10.1545;SAP=9.22372;AB=0.233796;ABP=268.915;RUN=1;RPP=4.75178;RPPR=3.06934;RPL=46.0;RPR=55.0;EPP=6.64375;EPPR=3.17431;DPRA=0.0;ODDS=159.211;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990099;PAIREDR=0.996979;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.5445;Dels=0.0;FS=9.03 [...]
+chr3 12641518 . A G 11906.0 REJECT NS=2;DP=453;DPB=516.0;AC=2;AN=4;AF=0.5;RO=128;AO=387;PRO=0.0;PAO=0.0;QR=4926;QA=14875;PQR=0.0;PQA=0.0;SRF=57;SRR=71;SAF=177;SAR=210;SRP=6.33537;SAP=9.12072;AB=0.75;ABP=283.13;RUN=1;RPP=9.12072;RPPR=3.62103;RPL=210.0;RPR=177.0;EPP=4.63189;EPPR=5.45321;DPRA=0.0;ODDS=258.278;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997416;PAIREDR=0.976562;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.231;Dels=0.0;FS=1.5445;HaplotypeScor [...]
+chr3 12642949 . T C 4012.28 PASS SOMATIC;NS=2;DP=539;DPB=539.0;AC=1;AN=3;AF=0.25;RO=390;AO=149;PRO=0.0;PAO=0.0;QR=15071;QA=5748;PQR=0.0;PQA=0.0;SRF=208;SRR=182;SAF=71;SAR=78;SRP=6.77419;SAP=3.72441;AB=0.366995;ABP=65.3947;RUN=1;RPP=5.47325;RPPR=3.09939;RPL=68.0;RPR=81.0;EPP=3.37464;EPPR=3.36664;DPRA=3.05263;ODDS=83.9998;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.573;Dels=0.0;FS=4.254;Hap [...]
+chr3 12643013 . A G 3382.39 PASS SOMATIC;NS=2;DP=492;DPB=492.0;AC=1;AN=3;AF=0.25;RO=361;AO=131;PRO=0.0;PAO=0.0;QR=13999;QA=4950;PQR=0.0;PQA=0.0;SRF=188;SRR=173;SAF=61;SAR=70;SRP=4.36371;SAP=4.35297;AB=0.351206;ABP=74.7387;RUN=1;RPP=5.01601;RPPR=3.16068;RPL=71.0;RPR=60.0;EPP=5.81167;EPPR=3.01632;DPRA=3.13445;ODDS=75.2695;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99169;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.748;Dels=0.0;FS=4.135 [...]
+chr3 12644335 . G C 3213.77 PASS SOMATIC;NS=2;DP=478;DPB=478.0;AC=1;AN=3;AF=0.25;RO=355;AO=123;PRO=0.0;PAO=0.0;QR=13540;QA=4717;PQR=0.0;PQA=0.0;SRF=189;SRR=166;SAF=57;SAR=66;SRP=6.2461;SAP=4.44029;AB=0.348442;ABP=73.4386;RUN=1;RPP=14.0442;RPPR=3.16322;RPL=74.0;RPR=49.0;EPP=10.7958;EPPR=4.38659;DPRA=2.824;ODDS=78.9658;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997183;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.066;Dels=0.0;FS=5.022;H [...]
+chr3 12645007 . C T 3409.55 PASS SOMATIC;NS=2;DP=524;DPB=524.0;AC=1;AN=3;AF=0.25;RO=387;AO=136;PRO=0.0;PAO=0.0;QR=14456;QA=5083;PQR=0.0;PQA=0.0;SRF=170;SRR=217;SAF=70;SAR=66;SRP=15.4051;SAP=3.26577;AB=0.334975;ABP=99.0471;RUN=1;RPP=7.09778;RPPR=17.6046;RPL=60.0;RPR=76.0;EPP=15.5282;EPPR=3.0608;DPRA=3.44068;ODDS=74.5657;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=59.8529;MQMR=60.0;PAIRED=1.0;PAIREDR=0.98708;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.546;Dels=0.0;FS=5.3 [...]
+chr3 12646000 . T C 2978.54 PASS SOMATIC;NS=2;DP=470;DPB=470.0;AC=1;AN=3;AF=0.25;RO=354;AO=116;PRO=0.0;PAO=0.0;QR=13456;QA=4446;PQR=0.0;PQA=0.0;SRF=168;SRR=186;SAF=50;SAR=66;SRP=4.99775;SAP=7.80251;AB=0.330484;ABP=90.6178;RUN=1;RPP=9.07545;RPPR=3.0103;RPL=67.0;RPR=49.0;EPP=9.07545;EPPR=5.46394;DPRA=2.94958;ODDS=75.1923;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991379;PAIREDR=0.991525;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.828;Dels=0.0;FS= [...]
+chr3 12646357 . AC A 3455.06 PASS SOMATIC;NS=2;DP=475;DPB=531.944;AC=1;AN=4;AF=0.25;RO=332;AO=129;PRO=80.5;PAO=54.5;QR=12416;QA=4683;PQR=2748.5;PQA=1844.5;SRF=176;SRR=156;SAF=61;SAR=68;SRP=5.62653;SAP=3.83512;AB=0.36338;ABP=60.5635;RUN=1;RPP=4.37378;RPPR=18.0798;RPL=60.0;RPR=69.0;EPP=11.915;EPPR=3.11495;DPRA=2.95833;ODDS=78.9883;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=1;MEANALT=8.0;LEN=1;MQM=60.2326;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993976;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.099;FS=0. [...]
+chr3 12646749 . A ATG 761.476 REJECT NS=2;DP=82;DPB=189.057;AC=2;AN=2;AF=0.5;RO=8;AO=16;PRO=35.6;PAO=36.1;QR=301;QA=470;PQR=1288.6;PQA=1306.85;SRF=2;SRR=6;SAF=0;SAR=16;SRP=7.35324;SAP=37.7539;AB=0.195122;ABP=69.2137;RUN=1;RPP=5.18177;RPPR=7.35324;RPL=10.0;RPR=6.0;EPP=5.18177;EPPR=7.35324;DPRA=0.0;ODDS=3.82925;GTI=1;TYPE=ins;CIGAR=1M2I34M;NUMALT=4;MEANALT=10.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-3.017;FS=3.947;MLEAC [...]
+chr3 12646749 . A ATGTG 761.476 REJECT NS=2;DP=82;DPB=189.057;AC=1;AN=3;AF=0.25;RO=8;AO=17;PRO=35.6;PAO=36.1;QR=301;QA=479;PQR=1288.6;PQA=1306.85;SRF=2;SRR=6;SAF=2;SAR=15;SRP=7.35324;SAP=24.5973;AB=0.207317;ABP=64.0234;RUN=1;RPP=4.1599;RPPR=7.35324;RPL=7.0;RPR=10.0;EPP=4.1599;EPPR=7.35324;DPRA=0.0;ODDS=3.82925;GTI=1;TYPE=ins;CIGAR=1M4I34M;NUMALT=4;MEANALT=10.0;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr3 12646749 . A ATGTGTG 761.476 REJECT NS=2;DP=82;DPB=189.057;AC=2;AN=3;AF=0.375;RO=8;AO=21;PRO=35.6;PAO=36.1;QR=301;QA=590;PQR=1288.6;PQA=1306.85;SRF=2;SRR=6;SAF=2;SAR=19;SRP=7.35324;SAP=32.8939;AB=0.256098;ABP=45.3805;RUN=1;RPP=5.59539;RPPR=7.35324;RPL=13.0;RPR=8.0;EPP=11.386;EPPR=7.35324;DPRA=0.0;ODDS=3.82925;GTI=1;TYPE=ins;CIGAR=1M6I34M;NUMALT=4;MEANALT=10.0;LEN=6;MQM=59.5238;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-2.227;FS=1.9 [...]
+chr3 12646749 . A ATGTGTGTGTGTGTGTG 761.476 REJECT NS=2;DP=82;DPB=189.057;AC=0;AN=4;AF=0.0;RO=8;AO=6;PRO=35.6;PAO=36.1;QR=301;QA=156;PQR=1288.6;PQA=1306.85;SRF=2;SRR=6;SAF=0;SAR=6;SRP=7.35324;SAP=16.0391;AB=0.105263;ABP=80.1547;RUN=1;RPP=4.45795;RPPR=7.35324;RPL=2.0;RPR=4.0;EPP=4.45795;EPPR=7.35324;DPRA=0.0;ODDS=3.82925;GTI=1;TYPE=ins;CIGAR=1M16I34M;NUMALT=4;MEANALT=14.0;LEN=16;MQM=40.6667;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr3 12647547 . T TG 9876.62 REJECT NS=2;DP=401;DPB=575.667;AC=2;AN=4;AF=0.5;RO=125;AO=325;PRO=14.5;PAO=19.5;QR=4784;QA=12254;PQR=389.5;PQA=571.5;SRF=54;SRR=71;SAF=151;SAR=174;SRP=8.03074;SAP=6.54479;AB=0.720621;ABP=193.681;RUN=1;RPP=3.5515;RPPR=3.02767;RPL=158.0;RPR=167.0;EPP=13.1728;EPPR=3.44459;DPRA=0.0;ODDS=261.34;GTI=0;TYPE=ins;CIGAR=1M1I2M;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.3077;MQMR=60.0;PAIRED=0.993846;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=12647547;HOMLEN=0;SVLEN=1;SVTYPE= [...]
+chr3 12648156 . A G 610.396 PASS SOMATIC;NS=2;DP=136;DPB=136.0;AC=1;AN=3;AF=0.25;RO=105;AO=30;PRO=0.0;PAO=0.0;QR=3825;QA=1124;PQR=0.0;PQA=0.0;SRF=5;SRR=100;SAF=0;SAR=30;SRP=189.654;SAP=68.1545;AB=0.294118;ABP=40.564;RUN=1;RPP=4.16842;RPPR=6.50534;RPL=13.0;RPR=17.0;EPP=4.16842;EPPR=5.51266;DPRA=3.0;ODDS=22.2288;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990476;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.464;Dels=0.0;FS=5.013;Haplotyp [...]
+chr3 12648238 . T C 919.97 REJECT NS=2;DP=57;DPB=65.0;AC=2;AN=4;AF=0.5;RO=31;AO=34;PRO=0.0;PAO=0.0;QR=1173;QA=1296;PQR=0.0;PQA=0.0;SRF=5;SRR=26;SAF=15;SAR=19;SRP=33.9012;SAP=4.03217;AB=0.523077;ABP=3.31097;RUN=1;RPP=3.0103;RPPR=14.8483;RPL=17.0;RPR=17.0;EPP=23.7032;EPPR=18.771;DPRA=0.0;ODDS=43.0344;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.4118;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3445;Dels=0.0;FS=11.7105;HaplotypeScore=0.9998;MLE [...]
+chr3 12649446 . T TC 335.79 REJECT NS=2;DP=72;DPB=79.0;AC=2;AN=3;AF=0.25;RO=45;AO=16;PRO=1.66667;PAO=2.66667;QR=1483;QA=430;PQR=17.6667;PQA=46.1667;SRF=45;SRR=0;SAF=15;SAR=1;SRP=100.727;SAP=29.6108;AB=0.571429;ABP=4.25114;RUN=1;RPP=7.89611;RPPR=38.1882;RPL=11.0;RPR=5.0;EPP=11.6962;EPPR=38.1882;DPRA=0.0;ODDS=0.0867204;GTI=1;TYPE=ins;CIGAR=1M1I4M;NUMALT=2;MEANALT=5.0;LEN=1;MQM=59.6875;MQMR=57.0;PAIRED=0.9375;PAIREDR=0.955556;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr3 12649449 . A C 335.79 REJECT NS=2;DP=72;DPB=79.0;AC=2;AN=3;AF=0.25;RO=45;AO=6;PRO=1.66667;PAO=2.66667;QR=1483;QA=211;PQR=17.6667;PQA=46.1667;SRF=45;SRR=0;SAF=5;SAR=1;SRP=100.727;SAP=8.80089;AB=0.0833333;ABP=111.584;RUN=1;RPP=3.0103;RPPR=38.1882;RPL=3.0;RPR=3.0;EPP=4.45795;EPPR=38.1882;DPRA=0.0;ODDS=0.0867204;GTI=1;TYPE=snp;CIGAR=3M1X1M;NUMALT=2;MEANALT=4.0;LEN=1;MQM=55.5;MQMR=57.0;PAIRED=1.0;PAIREDR=0.955556;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr3 12649576 . A G 3020.11 PASS SOMATIC;NS=2;DP=407;DPB=407.0;AC=1;AN=3;AF=0.25;RO=296;AO=111;PRO=0.0;PAO=0.0;QR=11468;QA=4270;PQR=0.0;PQA=0.0;SRF=192;SRR=104;SAF=68;SAR=43;SRP=59.8207;SAP=15.2371;AB=0.397849;ABP=28.2974;RUN=1;RPP=3.02986;RPPR=10.5224;RPL=56.0;RPR=55.0;EPP=3.18637;EPPR=14.748;DPRA=2.17969;ODDS=80.8388;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.972973;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.99;Dels=0.0;FS=3.551; [...]
+chr3 12649857 . G C 12955.6 REJECT NS=2;DP=458;DPB=525.0;AC=2;AN=4;AF=0.5;RO=103;AO=420;PRO=0.0;PAO=0.0;QR=3841;QA=16072;PQR=0.0;PQA=0.0;SRF=51;SRR=52;SAF=237;SAR=183;SRP=3.03138;SAP=18.0865;AB=0.8;ABP=413.419;RUN=1;RPP=4.33386;RPPR=6.5732;RPL=218.0;RPR=202.0;EPP=5.51266;EPPR=4.04333;DPRA=0.0;ODDS=10.6794;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992857;PAIREDR=0.990291;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.3035;Dels=0.0;FS=2.143;HaplotypeScore [...]
+chr3 12649937 . C T 3612.64 PASS SOMATIC;NS=2;DP=513;DPB=513.0;AC=1;AN=3;AF=0.25;RO=374;AO=137;PRO=0.0;PAO=0.0;QR=14067;QA=5248;PQR=0.0;PQA=0.0;SRF=167;SRR=207;SAF=58;SAR=79;SRP=12.3;SAP=10.0002;AB=0.356021;ABP=71.7925;RUN=1;RPP=4.92817;RPPR=6.93521;RPL=74.0;RPR=63.0;EPP=3.15295;EPPR=4.49666;DPRA=0.0;ODDS=79.0212;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992701;PAIREDR=0.991979;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.892;Dels=0.0;FS=0.812; [...]
+chr3 17077268 . C T 9253.035 REJECT NS=2;DP=370;DPB=426.0;AC=3;AN=4;AF=0.75;RO=100;AO=325;PRO=0.0;PAO=0.0;QR=3823;QA=12473;PQR=0.0;PQA=0.0;SRF=43;SRR=57;SAF=174;SAR=151;SRP=7.26639;SAP=6.54479;AB=0.68038;ABP=92.3155;RUN=1;RPP=9.43118;RPPR=3.35774;RPL=178.0;RPR=147.0;EPP=21.7785;EPPR=3.79203;DPRA=0.0;ODDS=69.6535;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990769;PAIREDR=0.99;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.391;Dels=0.0;FS=5.295;HaplotypeSco [...]
+chr3 24001078 . C T 10808.8 REJECT NS=2;DP=380;DPB=428.0;AC=2;AN=4;AF=0.5;RO=80;AO=348;PRO=0.0;PAO=0.0;QR=2981;QA=13404;PQR=0.0;PQA=0.0;SRF=41;SRR=39;SAF=189;SAR=159;SRP=3.11887;SAP=8.62618;AB=0.813084;ABP=367.412;RUN=1;RPP=3.03526;RPPR=4.74748;RPL=173.0;RPR=175.0;EPP=22.5785;EPPR=3.11887;DPRA=0.0;ODDS=102.338;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997126;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8905;Dels=0.0;FS=2.834;HaplotypeScore [...]
+chr3 30686414 . A G 2053.16 PASS SOMATIC;NS=2;DP=310;DPB=310.0;AC=1;AN=3;AF=0.25;RO=230;AO=80;PRO=0.0;PAO=0.0;QR=8764;QA=3092;PQR=0.0;PQA=0.0;SRF=49;SRR=181;SAF=16;SAR=64;SRP=167.513;SAP=65.5487;AB=0.36036;ABP=40.61;RUN=1;RPP=13.8677;RPPR=69.6273;RPL=50.0;RPR=30.0;EPP=3.0103;EPPR=11.5074;DPRA=2.52273;ODDS=55.8843;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995652;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.562;Dels=0.0;FS=1.334;Haplo [...]
+chr3 30713126 . T A 970.45 REJECT NS=2;DP=200;DPB=224.0;AC=2;AN=4;AF=0.5;RO=173;AO=51;PRO=0.0;PAO=0.0;QR=6584;QA=1920;PQR=0.0;PQA=0.0;SRF=114;SRR=59;SAF=43;SAR=8;SRP=40.9797;SAP=55.1682;AB=0.227679;ABP=147.297;RUN=1;RPP=3.05288;RPPR=20.1938;RPL=25.0;RPR=26.0;EPP=3.3935;EPPR=16.6793;DPRA=0.0;ODDS=74.8639;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99422;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3545;Dels=0.0;FS=5.7105;HaplotypeScore=2.932 [...]
+chr3 37053568 . A G 2531.25 PASS SOMATIC;NS=2;DP=403;DPB=403.0;AC=1;AN=3;AF=0.25;RO=304;AO=99;PRO=0.0;PAO=0.0;QR=11660;QA=3828;PQR=0.0;PQA=0.0;SRF=110;SRR=194;SAF=33;SAR=66;SRP=53.4113;SAP=26.8965;AB=0.321429;ABP=88.3181;RUN=1;RPP=4.08507;RPPR=30.468;RPL=53.0;RPR=46.0;EPP=3.55865;EPPR=3.26745;DPRA=3.24211;ODDS=60.227;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.43;Dels=0.0;FS=0.981;Haploty [...]
+chr3 37067127 . GAC AAT 121.574 REJECT NS=2;DP=165;DPB=171.667;AC=2;AN=4;AF=0.5;RO=153;AO=3;PRO=14.0;PAO=0.0;QR=4832;QA=49;PQR=179.0;PQA=0.0;SRF=102;SRR=51;SAF=3;SAR=0;SRP=39.9253;SAP=9.52472;AB=0.0181818;ABP=335.719;RUN=1;RPP=3.73412;RPPR=203.992;RPL=1.0;RPR=2.0;EPP=3.73412;EPPR=11.8807;DPRA=0.0;ODDS=5.42423;GTI=0;TYPE=complex;CIGAR=1X1M1X;NUMALT=1;MEANALT=4.5;LEN=3;MQM=58.6667;MQMR=59.732;PAIRED=1.0;PAIREDR=0.993464;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:C [...]
+chr3 37083740 . A G 2193.94 PASS SOMATIC;NS=2;DP=379;DPB=379.0;AC=1;AN=3;AF=0.25;RO=290;AO=89;PRO=0.0;PAO=0.0;QR=10917;QA=3417;PQR=0.0;PQA=0.0;SRF=192;SRR=98;SAF=59;SAR=30;SRP=69.1728;SAP=23.5295;AB=0.309028;ABP=94.2423;RUN=1;RPP=18.2594;RPPR=11.6662;RPL=32.0;RPR=57.0;EPP=15.9171;EPPR=6.63441;DPRA=3.16484;ODDS=57.6522;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986207;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.516;Dels=0.0;FS=2.335 [...]
+chr3 37627112 . T C 12763.9 REJECT NS=2;DP=341;DPB=389.0;AC=4;AN=4;AF=1.0;RO=0;AO=389;PRO=0.0;PAO=0.0;QR=0;QA=14772;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=169;SAR=220;SRP=0.0;SAP=17.5296;AB=0.0;ABP=0.0;RUN=1;RPP=5.96328;RPPR=0.0;RPL=183.0;RPR=206.0;EPP=7.70492;EPPR=0.0;DPRA=0.0;ODDS=64.2585;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994859;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.26;SOR=0.95 [...]
+chr3 37627149 . G A 8912.54 REJECT NS=2;DP=318;DPB=368.0;AC=2;AN=4;AF=0.5;RO=81;AO=287;PRO=0.0;PAO=0.0;QR=3119;QA=11140;PQR=0.0;PQA=0.0;SRF=28;SRR=53;SAF=111;SAR=176;SRP=19.7655;SAP=34.9771;AB=0.779891;ABP=253.414;RUN=1;RPP=9.3734;RPPR=3.03711;RPL=158.0;RPR=129.0;EPP=13.3683;EPPR=9.04217;DPRA=0.0;ODDS=116.022;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989547;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.163;Dels=0.0;FS=4.4825;HaplotypeScore= [...]
+chr3 46537849 . C T 6918.01 REJECT NS=2;DP=316;DPB=350.0;AC=3;AN=4;AF=0.75;RO=110;AO=240;PRO=0.0;PAO=0.0;QR=4209;QA=9207;PQR=0.0;PQA=0.0;SRF=45;SRR=65;SAF=84;SAR=156;SRP=10.9066;SAP=49.9141;AB=0.609929;ABP=32.6101;RUN=1;RPP=58.0571;RPPR=16.355;RPL=159.0;RPR=81.0;EPP=18.9706;EPPR=48.4928;DPRA=0.0;ODDS=43.4595;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995833;PAIREDR=0.990909;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.189;Dels=0.0;FS=2.562;HaplotypeSc [...]
+chr3 46960742 . A G 13365.95 REJECT NS=2;DP=358;DPB=407.0;AC=4;AN=4;AF=1.0;RO=2;AO=405;PRO=0.0;PAO=0.0;QR=79;QA=15399;PQR=0.0;PQA=0.0;SRF=2;SRR=0;SAF=189;SAR=216;SRP=7.35324;SAP=6.91895;AB=0.0;ABP=0.0;RUN=1;RPP=5.84662;RPPR=7.35324;RPL=214.0;RPR=191.0;EPP=12.924;EPPR=7.35324;DPRA=0.0;ODDS=63.2863;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997531;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.605;Dels=0.0;FS=3.253;HaplotypeScore=2.9238;MLEAC= [...]
+chr3 46960797 . C G 9131.355 REJECT NS=2;DP=244;DPB=280.0;AC=4;AN=4;AF=1.0;RO=0;AO=279;PRO=0.0;PAO=0.0;QR=0;QA=10655;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=92;SAR=187;SRP=0.0;SAP=73.2524;AB=0.0;ABP=0.0;RUN=1;RPP=54.0749;RPPR=0.0;RPL=180.0;RPR=99.0;EPP=3.39167;EPPR=0.0;DPRA=0.0;ODDS=48.645;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996416;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9973;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.725;SOR=1.53 [...]
+chr3 46967040 . G A 11787.75 REJECT NS=2;DP=317;DPB=366.0;AC=4;AN=4;AF=1.0;RO=0;AO=366;PRO=0.0;PAO=0.0;QR=0;QA=13945;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=90;SAR=276;SRP=0.0;SAP=208.268;AB=0.0;ABP=0.0;RUN=1;RPP=42.9037;RPPR=0.0;RPL=224.0;RPR=142.0;EPP=20.3109;EPPR=0.0;DPRA=0.0;ODDS=64.8092;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994536;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8325;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.75;SOR=2.4 [...]
+chr3 47103861 . G GT 2393.26 REJECT NS=2;DP=130;DPB=163.815;AC=1;AN=3;AF=0.0;RO=16;AO=2;PRO=17.0333;PAO=16.0333;QR=590;QA=55;PQR=614.983;PQA=577.983;SRF=6;SRR=10;SAF=1;SAR=1;SRP=5.18177;SAP=3.0103;AB=0.0714286;ABP=47.6806;RUN=1;RPP=7.35324;RPPR=16.582;RPL=2.0;RPR=0.0;EPP=3.0103;EPPR=3.55317;DPRA=0.0;ODDS=13.1042;GTI=0;TYPE=ins;CIGAR=1M1I26M;NUMALT=4;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr3 47103861 . GT G 2393.26 REJECT NS=2;DP=130;DPB=163.815;AC=2;AN=2;AF=0.25;RO=16;AO=14;PRO=17.0333;PAO=21.0333;QR=590;QA=372;PQR=614.983;PQA=758.983;SRF=6;SRR=10;SAF=4;SAR=10;SRP=5.18177;SAP=8.59409;AB=0.107692;ABP=176.795;RUN=1;RPP=5.49198;RPPR=16.582;RPL=9.0;RPR=5.0;EPP=5.49198;EPPR=3.55317;DPRA=0.0;ODDS=13.1042;GTI=0;TYPE=del;CIGAR=1M1D25M;NUMALT=4;MEANALT=7.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.328;FS=1.215 [...]
+chr3 47103861 . GTT G 2393.26 REJECT NS=2;DP=130;DPB=163.815;AC=2;AN=3;AF=0.5;RO=16;AO=81;PRO=17.0333;PAO=32.7;QR=590;QA=2473;PQR=614.983;PQA=1132.65;SRF=6;SRR=10;SAF=23;SAR=58;SRP=5.18177;SAP=35.8505;AB=0.623077;ABP=20.1148;RUN=1;RPP=43.7857;RPPR=16.582;RPL=60.0;RPR=21.0;EPP=5.18177;EPPR=3.55317;DPRA=0.0;ODDS=13.1042;GTI=0;TYPE=del;CIGAR=1M2D24M;NUMALT=4;MEANALT=7.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.126;FS=1.56 [...]
+chr3 47103861 . GTTT G 2393.26 PASS SOMATIC;NS=2;DP=130;DPB=163.815;AC=1;AN=3;AF=0.0;RO=16;AO=10;PRO=17.0333;PAO=11.2;QR=590;QA=314;PQR=614.983;PQA=401.4;SRF=6;SRR=10;SAF=2;SAR=8;SRP=5.18177;SAP=10.8276;AB=0.0769231;ABP=205.124;RUN=1;RPP=6.48466;RPPR=16.582;RPL=7.0;RPR=3.0;EPP=3.0103;EPPR=3.55317;DPRA=0.0;ODDS=13.1042;GTI=0;TYPE=del;CIGAR=1M3D23M;NUMALT=4;MEANALT=7.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr3 47125385 . G A 10031.6 REJECT NS=2;DP=365;DPB=423.0;AC=2;AN=4;AF=0.5;RO=89;AO=333;PRO=0.0;PAO=0.0;QR=3328;QA=12495;PQR=0.0;PQA=0.0;SRF=46;SRR=43;SAF=161;SAR=172;SRP=3.22989;SAP=3.79933;AB=0.787234;ABP=306.139;RUN=1;RPP=3.17332;RPPR=3.0347;RPL=164.0;RPR=169.0;EPP=4.47751;EPPR=3.0347;DPRA=0.0;ODDS=102.574;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993994;PAIREDR=0.988764;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8025;Dels=0.0;FS=4.523;HaplotypeSc [...]
+chr3 47147393 . CAA C 301.877 REJECT NS=2;DP=48;DPB=129.057;AC=2;AN=3;AF=0.5;RO=5;AO=9;PRO=56.8167;PAO=46.8167;QR=166;QA=316;PQR=1991.25;PQA=1637.25;SRF=4;SRR=1;SAF=9;SAR=0;SRP=6.91895;SAP=22.5536;AB=0.1875;ABP=43.7254;RUN=1;RPP=14.8328;RPPR=6.91895;RPL=1.0;RPR=8.0;EPP=14.8328;EPPR=3.44459;DPRA=0.0;ODDS=4.31111;GTI=0;TYPE=del;CIGAR=1M2D32M;NUMALT=4;MEANALT=15.5;LEN=2;MQM=63.3333;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.751;FS=0.0;MLEAC=1;M [...]
+chr3 47147393 . CAAA C 301.877 REJECT NS=2;DP=48;DPB=129.057;AC=2;AN=2;AF=0.25;RO=5;AO=5;PRO=56.8167;PAO=42.9833;QR=166;QA=177;PQR=1991.25;PQA=1505.25;SRF=4;SRR=1;SAF=4;SAR=1;SRP=6.91895;SAP=6.91895;AB=0.104167;ABP=68.3354;RUN=1;RPP=6.91895;RPPR=6.91895;RPL=1.0;RPR=4.0;EPP=13.8677;EPPR=3.44459;DPRA=0.0;ODDS=4.31111;GTI=0;TYPE=del;CIGAR=1M3D31M;NUMALT=4;MEANALT=15.5;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr3 47147393 . CAAAA C 301.877 REJECT NS=2;DP=48;DPB=129.057;AC=1;AN=3;AF=0.0;RO=5;AO=3;PRO=56.8167;PAO=41.65;QR=166;QA=104;PQR=1991.25;PQA=1459.25;SRF=4;SRR=1;SAF=3;SAR=0;SRP=6.91895;SAP=9.52472;AB=0.0625;ABP=82.8119;RUN=1;RPP=9.52472;RPPR=6.91895;RPL=0.0;RPR=3.0;EPP=9.52472;EPPR=3.44459;DPRA=0.0;ODDS=4.31111;GTI=0;TYPE=del;CIGAR=1M4D30M;NUMALT=4;MEANALT=15.5;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr3 47147414 . AATCAAATCAGT TCAAATCAGA 301.877 REJECT NS=2;DP=48;DPB=129.057;AC=1;AN=3;AF=0.0;RO=5;AO=2;PRO=56.8167;PAO=5.73333;QR=166;QA=32;PQR=1991.25;PQA=181.0;SRF=4;SRR=1;SAF=2;SAR=0;SRP=6.91895;SAP=7.35324;AB=0.0555556;ABP=64.7766;RUN=1;RPP=7.35324;RPPR=6.91895;RPL=0.0;RPR=2.0;EPP=7.35324;EPPR=3.44459;DPRA=0.0;ODDS=4.31111;GTI=0;TYPE=complex;CIGAR=1M2D29M1X2M;NUMALT=4;MEANALT=24.0;LEN=33;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO [...]
+chr3 47161214 . T C 6709.48 REJECT NS=2;DP=244;DPB=286.0;AC=2;AN=4;AF=0.5;RO=57;AO=229;PRO=0.0;PAO=0.0;QR=2142;QA=8715;PQR=0.0;PQA=0.0;SRF=46;SRR=11;SAF=186;SAR=43;SRP=49.6779;SAP=196.916;AB=0.800699;ABP=227.629;RUN=1;RPP=78.1205;RPPR=11.5819;RPL=70.0;RPR=159.0;EPP=3.09564;EPPR=4.877;DPRA=0.0;ODDS=54.413;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.2576;MQMR=60.0;PAIRED=0.995633;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.02;Dels=0.0;FS=1.166;HaplotypeScore=9.75 [...]
+chr3 47162661 . A G 9964.81 REJECT NS=2;DP=364;DPB=414.0;AC=2;AN=4;AF=0.5;RO=90;AO=324;PRO=0.0;PAO=0.0;QR=3386;QA=12405;PQR=0.0;PQA=0.0;SRF=39;SRR=51;SAF=155;SAR=169;SRP=6.48466;SAP=4.32391;AB=0.782609;ABP=290.211;RUN=1;RPP=3.0103;RPPR=5.42305;RPL=162.0;RPR=162.0;EPP=10.7579;EPPR=4.55446;DPRA=0.0;ODDS=105.943;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.8295;Dels=0.0;FS=1.0775;HaplotypeScore=2.89 [...]
+chr3 47292183 . T C 9827.64 REJECT NS=2;DP=379;DPB=439.0;AC=2;AN=4;AF=0.5;RO=116;AO=323;PRO=0.0;PAO=0.0;QR=4457;QA=12352;PQR=0.0;PQA=0.0;SRF=57;SRR=59;SAF=145;SAR=178;SRP=3.08518;SAP=10.3315;AB=0.735763;ABP=214.959;RUN=1;RPP=3.01702;RPPR=4.88226;RPL=161.0;RPR=162.0;EPP=26.4125;EPPR=3.30981;DPRA=0.0;ODDS=184.851;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991379;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.359;Dels=0.0;FS=2.5735;HaplotypeSco [...]
+chr3 47300755 . G A 6701.775 REJECT NS=2;DP=188;DPB=214.0;AC=4;AN=4;AF=1.0;RO=1;AO=213;PRO=0.0;PAO=0.0;QR=40;QA=7939;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=130;SAR=83;SRP=5.18177;SAP=25.5304;AB=0.0;ABP=0.0;RUN=1;RPP=247.938;RPPR=5.18177;RPL=29.0;RPR=184.0;EPP=7.50617;EPPR=5.18177;DPRA=0.0;ODDS=29.9499;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.672;Dels=0.0;FS=0.0;HaplotypeScore=3.8994;MLEAC=2;MLEAF=1 [...]
+chr3 47305025 . C T 3016.94 PASS SOMATIC;NS=2;DP=418;DPB=418.0;AC=1;AN=3;AF=0.25;RO=296;AO=122;PRO=0.0;PAO=0.0;QR=11222;QA=4339;PQR=0.0;PQA=0.0;SRF=144;SRR=152;SAF=56;SAR=66;SRP=3.47981;SAP=4.7902;AB=0.401316;ABP=28.7251;RUN=1;RPP=3.0815;RPPR=3.03964;RPL=60.0;RPR=62.0;EPP=11.625;EPPR=4.44817;DPRA=2.66667;ODDS=72.0111;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996622;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-3.126;Dels=0.0;FS=0.0;Ha [...]
+chr3 49398505 . C CA 37.73 PASS DP=51;AC=1;AN=4;AF=0.5;BaseQRankSum=-0.102;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.56;MQRankSum=0.034;QD=0.74;ReadPosRankSum=-0.102;SOR=0.368;ClippingRankSum=-1.877 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:33,10:43:75.0:75,0,867:10:23:43:1:.:.:.:.:.:-0.00035518 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0187789
+chr3 49398505 . CAAAAAAAAC AAAAAAAAAA 2212.47 REJECT NS=1;DP=68;DPB=122.897;AC=0;AN=4;AF=0.0;RO=0;AO=12;PRO=21.8333;PAO=31.3333;QR=0;QA=105;PQR=776.0;PQA=1119.17;SRF=0;SRR=0;SAF=0;SAR=12;SRP=0.0;SAP=29.068;AB=0.0;ABP=0.0;RUN=1;RPP=21.1059;RPPR=0.0;RPL=1.0;RPR=11.0;EPP=21.1059;EPPR=0.0;DPRA=0.0;ODDS=30.1164;GTI=0;TYPE=complex;CIGAR=1X8M1X29M;NUMALT=3;MEANALT=39.0;LEN=39;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr3 49398514 . C A 2212.47 REJECT NS=1;DP=68;DPB=122.897;AC=2;AN=4;AF=1.0;RO=0;AO=6;PRO=21.8333;PAO=40.3333;QR=0;QA=235;PQR=776.0;PQA=1412.0;SRF=0;SRR=0;SAF=2;SAR=4;SRP=0.0;SAP=4.45795;AB=0.0;ABP=0.0;RUN=1;RPP=16.0391;RPPR=0.0;RPL=0.0;RPR=6.0;EPP=4.45795;EPPR=0.0;DPRA=0.0;ODDS=30.1164;GTI=0;TYPE=snp;CIGAR=9M1X29M;NUMALT=3;MEANALT=39.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.023;FS=3.728;MLEAC=1;MLEAF=0.5;MQ=59.75;MQRankSum [...]
+chr3 49398514 . CAAAACAAAAAAAAAAAAC AAAAACAAAAAAAAAAAAA 2212.47 REJECT NS=1;DP=68;DPB=122.897;AC=0;AN=4;AF=0.0;RO=0;AO=4;PRO=21.8333;PAO=16.5;QR=0;QA=56;PQR=776.0;PQA=520.833;SRF=0;SRR=0;SAF=4;SAR=0;SRP=0.0;SAP=11.6962;AB=0.0;ABP=0.0;RUN=1;RPP=11.6962;RPPR=0.0;RPL=0.0;RPR=4.0;EPP=11.6962;EPPR=0.0;DPRA=0.0;ODDS=30.1164;GTI=0;TYPE=complex;CIGAR=9M1X17M1X11M;NUMALT=3;MEANALT=39.0;LEN=39;MQM=59.25;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr3 52342529 . T G 5709.64 REJECT NS=2;DP=379;DPB=432.0;AC=2;AN=4;AF=0.5;RO=222;AO=210;PRO=0.0;PAO=0.0;QR=8546;QA=8049;PQR=0.0;PQA=0.0;SRF=92;SRR=130;SAF=106;SAR=104;SRP=17.1347;SAP=3.05166;AB=0.486111;ABP=3.73412;RUN=1;RPP=3.67208;RPPR=7.7445;RPL=101.0;RPR=109.0;EPP=26.8345;EPPR=3.04943;DPRA=0.0;ODDS=305.286;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995495;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.396;Dels=0.0;FS=6.758;HaplotypeScore= [...]
+chr3 52584431 . T TCTC 1867.55 PASS SOMATIC;NS=2;DP=285;DPB=365.667;AC=1;AN=4;AF=0.25;RO=209;AO=76;PRO=3.0;PAO=5.0;QR=7840;QA=2793;PQR=37.0;PQA=103.0;SRF=155;SRR=54;SAF=58;SAR=18;SRP=108.997;SAP=48.7255;AB=0.353488;ABP=43.0967;RUN=1;RPP=22.325;RPPR=7.59221;RPL=25.0;RPR=51.0;EPP=3.12459;EPPR=12.9949;DPRA=3.07143;ODDS=44.6811;GTI=0;TYPE=ins;CIGAR=1M3I2M;NUMALT=1;MEANALT=1.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=52584431;HOMLEN=2;HOMSEQ=CT;SVLEN=3 [...]
+chr3 52584715 . A G 2477.02 PASS SOMATIC;NS=2;DP=408;DPB=408.0;AC=1;AN=3;AF=0.25;RO=310;AO=98;PRO=0.0;PAO=0.0;QR=11572;QA=3701;PQR=0.0;PQA=0.0;SRF=163;SRR=147;SAF=54;SAR=44;SRP=4.80352;SAP=5.22609;AB=0.335616;ABP=71.5455;RUN=1;RPP=10.1895;RPPR=5.27984;RPL=58.0;RPR=40.0;EPP=3.80798;EPPR=21.9511;DPRA=2.51724;ODDS=73.2999;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.404;Dels=0.0;FS=0.0;Haplot [...]
+chr3 52584787 . T C 2615.8 PASS SOMATIC;NS=2;DP=406;DPB=406.0;AC=1;AN=3;AF=0.25;RO=306;AO=100;PRO=0.0;PAO=0.0;QR=11562;QA=3832;PQR=0.0;PQA=0.0;SRF=153;SRR=153;SAF=57;SAR=43;SRP=3.0103;SAP=7.26639;AB=0.350877;ABP=58.059;RUN=1;RPP=5.18177;RPPR=3.46446;RPL=55.0;RPR=45.0;EPP=4.40004;EPPR=11.2136;DPRA=2.35537;ODDS=76.4105;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.709;Dels=0.0;FS=2.727;Haplot [...]
+chr3 52610651 . T A 2835.72 PASS SOMATIC;NS=2;DP=404;DPB=404.0;AC=1;AN=3;AF=0.25;RO=296;AO=108;PRO=0.0;PAO=0.0;QR=11536;QA=4117;PQR=0.0;PQA=0.0;SRF=142;SRR=154;SAF=55;SAR=53;SRP=4.06669;SAP=3.09072;AB=0.363946;ABP=50.2804;RUN=1;RPP=6.95112;RPPR=3.74391;RPL=61.0;RPR=47.0;EPP=4.2971;EPPR=11.4908;DPRA=0.0;ODDS=66.5047;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8981;MQMR=60.0;PAIRED=0.990741;PAIREDR=0.993243;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.131;Dels=0.0;FS= [...]
+chr3 52643307 . A G 3143.28 PASS SOMATIC;NS=2;DP=362;DPB=362.0;AC=1;AN=3;AF=0.25;RO=248;AO=114;PRO=0.0;PAO=0.0;QR=9604;QA=4431;PQR=0.0;PQA=0.0;SRF=172;SRR=76;SAF=68;SAR=46;SRP=83.705;SAP=12.2295;AB=0.401408;ABP=26.9882;RUN=1;RPP=4.9151;RPPR=45.9144;RPL=52.0;RPR=62.0;EPP=12.2295;EPPR=3.04532;DPRA=3.64103;ODDS=49.6768;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.487;Dels=0.0;FS=7.852;Haploty [...]
+chr3 52643685 . T C 3166.83 PASS SOMATIC;NS=2;DP=417;DPB=417.0;AC=1;AN=3;AF=0.25;RO=298;AO=118;PRO=0.0;PAO=0.0;QR=11561;QA=4493;PQR=0.0;PQA=0.0;SRF=162;SRR=136;SAF=52;SAR=66;SRP=7.93619;SAP=6.61715;AB=0.389439;ABP=35.1811;RUN=1;RPP=3.0103;RPPR=15.8643;RPL=59.0;RPR=59.0;EPP=3.0103;EPPR=9.56844;DPRA=2.65789;ODDS=72.1291;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986577;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.399;Dels=0.0;FS=17.46; [...]
+chr3 52676065 . C T 1212.6 PASS SOMATIC;NS=2;DP=214;DPB=247.45;AC=2;AN=3;AF=0.25;RO=78;AO=37;PRO=11.7;PAO=12.5;QR=2894;QA=1050;PQR=410.483;PQA=395.0;SRF=14;SRR=64;SAF=7;SAR=30;SRP=72.6088;SAP=34.0565;AB=0.211429;ABP=129.589;RUN=1;RPP=16.2152;RPPR=4.01252;RPL=26.0;RPR=11.0;EPP=3.06899;EPPR=5.79424;DPRA=0.0;ODDS=13.7637;GTI=0;TYPE=snp;CIGAR=1X19M;NUMALT=8;MEANALT=18.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987179;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;ALERT;BaseQRankSum=1.6 [...]
+chr3 52676065 . C A 1212.6 REJECT NS=2;DP=214;DPB=247.45;AC=2;AN=2;AF=0.0;RO=78;AO=16;PRO=11.7;PAO=4.0;QR=2894;QA=292;PQR=410.483;PQA=81.0;SRF=14;SRR=64;SAF=2;SAR=14;SRP=72.6088;SAP=22.5536;AB=0.0747664;ABP=339.122;RUN=1;RPP=3.55317;RPPR=4.01252;RPL=7.0;RPR=9.0;EPP=7.89611;EPPR=5.79424;DPRA=0.0;ODDS=13.7637;GTI=0;TYPE=snp;CIGAR=1X19M;NUMALT=8;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987179;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr3 52676065 . C CA 1212.6 REJECT NS=2;DP=214;DPB=247.45;AC=2;AN=3;AF=0.25;RO=78;AO=14;PRO=11.7;PAO=9.2;QR=2894;QA=353;PQR=410.483;PQA=288.983;SRF=14;SRR=64;SAF=2;SAR=12;SRP=72.6088;SAP=18.5208;AB=0.0654206;ABP=354.058;RUN=1;RPP=3.0103;RPPR=4.01252;RPL=7.0;RPR=7.0;EPP=3.0103;EPPR=5.79424;DPRA=0.0;ODDS=13.7637;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=8;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987179;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr3 52676065 . CA C 1212.6 PASS SOMATIC;NS=2;DP=214;DPB=247.45;AC=2;AN=2;AF=0.0;RO=78;AO=27;PRO=11.7;PAO=8.7;QR=2894;QA=738;PQR=410.483;PQA=288.733;SRF=14;SRR=64;SAF=4;SAR=23;SRP=72.6088;SAP=32.0437;AB=0.126168;ABP=262.775;RUN=1;RPP=3.73412;RPPR=4.01252;RPL=15.0;RPR=12.0;EPP=5.02092;EPPR=5.79424;DPRA=0.0;ODDS=13.7637;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=8;MEANALT=13.0;LEN=1;MQM=60.3704;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987179;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;ALERT;BaseQRankSu [...]
+chr3 52676065 . CA T 1212.6 PASS SOMATIC;NS=2;DP=214;DPB=247.45;AC=2;AN=2;AF=0.0;RO=78;AO=15;PRO=11.7;PAO=10.5;QR=2894;QA=434;PQR=410.483;PQA=333.0;SRF=14;SRR=64;SAF=2;SAR=13;SRP=72.6088;SAP=20.5268;AB=0.0857143;ABP=263.897;RUN=1;RPP=6.62942;RPPR=4.01252;RPL=10.0;RPR=5.0;EPP=3.15506;EPPR=5.79424;DPRA=0.0;ODDS=13.7637;GTI=0;TYPE=complex;CIGAR=1X1D18M;NUMALT=8;MEANALT=18.0;LEN=19;MQM=70.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987179;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr3 52676065 . CAA C 1212.6 REJECT NS=2;DP=214;DPB=247.45;AC=2;AN=2;AF=0.0;RO=78;AO=7;PRO=11.7;PAO=6.5;QR=2894;QA=180;PQR=410.483;PQA=228.333;SRF=14;SRR=64;SAF=0;SAR=7;SRP=72.6088;SAP=18.2106;AB=0.0327103;ABP=408.893;RUN=1;RPP=3.32051;RPPR=4.01252;RPL=4.0;RPR=3.0;EPP=3.32051;EPPR=5.79424;DPRA=0.0;ODDS=13.7637;GTI=0;TYPE=del;CIGAR=1M2D17M;NUMALT=8;MEANALT=13.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987179;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr3 52676078 . AG A 1212.6 REJECT NS=2;DP=214;DPB=247.45;AC=2;AN=2;AF=0.0;RO=78;AO=2;PRO=11.7;PAO=7.2;QR=2894;QA=53;PQR=410.483;PQA=252.983;SRF=14;SRR=64;SAF=1;SAR=1;SRP=72.6088;SAP=3.0103;AB=0.0512821;ABP=71.2168;RUN=1;RPP=3.0103;RPPR=4.01252;RPL=1.0;RPR=1.0;EPP=7.35324;EPPR=5.79424;DPRA=0.0;ODDS=13.7637;GTI=0;TYPE=del;CIGAR=14M1D5M;NUMALT=8;MEANALT=8.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987179;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr3 52676080 . C A 1212.6 REJECT NS=2;DP=214;DPB=247.45;AC=2;AN=2;AF=0.0;RO=78;AO=3;PRO=11.7;PAO=7.7;QR=2894;QA=48;PQR=410.483;PQA=271.483;SRF=14;SRR=64;SAF=3;SAR=0;SRP=72.6088;SAP=9.52472;AB=0.0140187;ABP=442.013;RUN=1;RPP=9.52472;RPPR=4.01252;RPL=3.0;RPR=0.0;EPP=9.52472;EPPR=5.79424;DPRA=0.0;ODDS=13.7637;GTI=0;TYPE=snp;CIGAR=15M1X4M;NUMALT=8;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987179;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr3 52692359 . C G 1936.4 PASS SOMATIC;NS=2;DP=255;DPB=255.0;AC=1;AN=3;AF=0.25;RO=182;AO=73;PRO=0.0;PAO=0.0;QR=6963;QA=2852;PQR=0.0;PQA=0.0;SRF=46;SRR=136;SAF=21;SAR=52;SRP=99.6528;SAP=31.5964;AB=0.374359;ABP=29.7472;RUN=1;RPP=18.746;RPPR=95.4053;RPL=48.0;RPR=25.0;EPP=9.70319;EPPR=3.2012;DPRA=3.25;ODDS=38.4694;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.983516;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.045;Dels=0.0;FS=2.98;Haplotyp [...]
+chr3 61511324 . G A 6563.71 REJECT NS=2;DP=396;DPB=452.0;AC=2;AN=4;AF=0.5;RO=222;AO=230;PRO=0.0;PAO=0.0;QR=8377;QA=8790;PQR=0.0;PQA=0.0;SRF=92;SRR=130;SAF=93;SAR=137;SRP=17.1347;SAP=21.2884;AB=0.50885;ABP=3.31777;RUN=1;RPP=6.06924;RPPR=6.17948;RPL=124.0;RPR=106.0;EPP=18.1162;EPPR=4.92746;DPRA=0.0;ODDS=341.322;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990991;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.4245;Dels=0.0;FS=0.1995;HaplotypeScore [...]
+chr3 66001741 . A AT 2229.85 REJECT NS=2;DP=401;DPB=443.0;AC=2;AN=4;AF=0.5;RO=302;AO=99;PRO=8.5;PAO=8.5;QR=11555;QA=3748;PQR=186.0;PQA=186.0;SRF=167;SRR=135;SAF=50;SAR=49;SRP=10.3732;SAP=3.03223;AB=0.246883;ABP=226.163;RUN=1;RPP=3.03223;RPPR=4.85102;RPL=49.0;RPR=50.0;EPP=3.55865;EPPR=3.03906;DPRA=0.0;ODDS=191.591;GTI=0;TYPE=ins;CIGAR=1M1I2M;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986755;technology.ILLUMINA=1.0;END=66001741;HOMLEN=1;HOMSEQ=T;SVLEN=1;SVTYPE=INS;B [...]
+chr3 69691682 . G A 5140.845 REJECT NS=2;DP=355;DPB=408.0;AC=2;AN=4;AF=0.5;RO=214;AO=194;PRO=0.0;PAO=0.0;QR=8154;QA=7401;PQR=0.0;PQA=0.0;SRF=142;SRR=72;SAF=138;SAR=56;SRP=52.7309;SAP=78.2731;AB=0.47549;ABP=5.13919;RUN=1;RPP=71.1095;RPPR=49.9303;RPL=58.0;RPR=136.0;EPP=3.05507;EPPR=10.9656;DPRA=0.0;ODDS=327.651;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0467;PAIRED=0.994845;PAIREDR=0.990654;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9405;Dels=0.01;FS=2.444;Haplot [...]
+chr3 69691954 . C T 6382.34 REJECT NS=2;DP=359;DPB=410.0;AC=2;AN=4;AF=0.5;RO=185;AO=225;PRO=0.0;PAO=0.0;QR=7085;QA=8590;PQR=0.0;PQA=0.0;SRF=79;SRR=106;SAF=91;SAR=134;SRP=11.5671;SAP=20.855;AB=0.54878;ABP=11.4843;RUN=1;RPP=3.4832;RPPR=3.02204;RPL=109.0;RPR=116.0;EPP=3.79203;EPPR=4.43056;DPRA=0.0;ODDS=283.082;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991111;PAIREDR=0.989189;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4255;Dels=0.0;FS=1.5795;HaplotypeSc [...]
+chr3 70110627 . T G 7523.625 REJECT NS=2;DP=347;DPB=401.0;AC=3;AN=4;AF=0.75;RO=119;AO=282;PRO=0.0;PAO=0.0;QR=4615;QA=10556;PQR=0.0;PQA=0.0;SRF=77;SRR=42;SAF=160;SAR=122;SRP=25.3637;SAP=14.1295;AB=0.59661;ABP=26.9259;RUN=1;RPP=3.50312;RPPR=7.11603;RPL=145.0;RPR=137.0;EPP=4.11914;EPPR=7.11603;DPRA=0.0;ODDS=66.9837;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8319;PAIRED=0.996454;PAIREDR=0.983193;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.479;Dels=0.0;FS=3.238;Hapl [...]
+chr3 70110821 . C A 13012.349999999999 REJECT NS=2;DP=350;DPB=411.0;AC=4;AN=4;AF=1.0;RO=0;AO=411;PRO=0.0;PAO=0.0;QR=0;QA=15498;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=223;SAR=188;SRP=0.0;SAP=9.48245;AB=0.0;ABP=0.0;RUN=1;RPP=10.2433;RPPR=0.0;RPL=187.0;RPR=224.0;EPP=8.76391;EPPR=0.0;DPRA=0.0;ODDS=79.6912;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992701;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8796;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31 [...]
+chr3 70115600 . T G 14617.099999999999 REJECT NS=2;DP=390;DPB=446.0;AC=4;AN=4;AF=1.0;RO=0;AO=446;PRO=0.0;PAO=0.0;QR=0;QA=16899;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=233;SAR=213;SRP=0.0;SAP=4.95781;AB=0.0;ABP=0.0;RUN=1;RPP=19.3888;RPPR=0.0;RPL=194.0;RPR=252.0;EPP=34.1704;EPPR=0.0;DPRA=0.0;ODDS=73.5686;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997758;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8574;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27 [...]
+chr3 71015021 . G T 1351.115 REJECT NS=2;DP=275;DPB=311.0;AC=2;AN=4;AF=0.5;RO=237;AO=74;PRO=0.0;PAO=0.0;QR=9157;QA=2804;PQR=0.0;PQA=0.0;SRF=158;SRR=79;SAF=55;SAR=19;SRP=60.1924;SAP=41.0404;AB=0.237942;ABP=188.521;RUN=1;RPP=19.9126;RPPR=49.1976;RPL=25.0;RPR=49.0;EPP=3.12768;EPPR=14.2342;DPRA=0.0;ODDS=182.243;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.486;Dels=0.0;FS=3.783;HaplotypeScore=4.9323; [...]
+chr3 71247572 . A T 804.5025 REJECT NS=2;DP=83;DPB=94.0;AC=2;AN=4;AF=0.5;RO=43;AO=48;PRO=0.0;PAO=0.0;QR=1387;QA=1401;PQR=0.0;PQA=0.0;SRF=20;SRR=23;SAF=34;SAR=14;SRP=3.46479;SAP=21.1059;AB=0.510638;ABP=3.1027;RUN=1;RPP=90.593;RPPR=87.8997;RPL=46.0;RPR=2.0;EPP=21.1059;EPPR=4.27278;DPRA=0.0;ODDS=27.2774;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=59.9583;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.7585;Dels=0.0;FS=8.958;HaplotypeScore=22.0157;ML [...]
+chr3 72033035 . G C 5080.52 REJECT NS=2;DP=314;DPB=358.0;AC=2;AN=4;AF=0.5;RO=177;AO=181;PRO=0.0;PAO=0.0;QR=6859;QA=6878;PQR=0.0;PQA=0.0;SRF=118;SRR=59;SAF=124;SAR=57;SRP=45.7159;SAP=56.8652;AB=0.505587;ABP=3.10735;RUN=1;RPP=21.2579;RPPR=18.0389;RPL=71.0;RPR=110.0;EPP=7.34125;EPPR=9.50018;DPRA=0.0;ODDS=231.29;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99435;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6645;Dels=0.0;FS=0.241;HaplotypeScore=5. [...]
+chr3 78663956 . G A 5249.675 REJECT NS=2;DP=144;DPB=173.435;AC=2;AN=3;AF=0.5;RO=24;AO=64;PRO=10.6667;PAO=22.75;QR=875;QA=2157;PQR=365.333;PQA=769.167;SRF=2;SRR=22;SAF=6;SAR=58;SRP=39.2015;SAP=94.755;AB=0.444444;ABP=6.8707;RUN=1;RPP=3.14602;RPPR=3.37221;RPL=33.0;RPR=31.0;EPP=4.23175;EPPR=3.37221;DPRA=0.0;ODDS=12.5826;GTI=0;TYPE=snp;CIGAR=1X22M;NUMALT=6;MEANALT=12.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;ALERT;BaseQRankSum=6.839;Dels [...]
+chr3 78663956 . GAG AAA 6540.58 REJECT SOMATIC;NS=2;DP=144;DPB=173.435;AC=1;AN=3;AF=0.0;RO=24;AO=7;PRO=10.6667;PAO=2.25;QR=875;QA=73;PQR=365.333;PQA=79.5;SRF=2;SRR=22;SAF=0;SAR=7;SRP=39.2015;SAP=18.2106;AB=0.0486111;ABP=257.857;RUN=1;RPP=10.7656;RPPR=3.37221;RPL=1.0;RPR=6.0;EPP=10.7656;EPPR=3.37221;DPRA=0.0;ODDS=12.5826;GTI=0;TYPE=complex;CIGAR=1X1M1X20M;NUMALT=6;MEANALT=12.0;LEN=23;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr3 78663956 . GAG AAGA 6540.58 REJECT SOMATIC;NS=2;DP=144;DPB=173.435;AC=1;AN=3;AF=0.0;RO=24;AO=7;PRO=10.6667;PAO=21.75;QR=875;QA=166;PQR=365.333;PQA=662.167;SRF=2;SRR=22;SAF=1;SAR=6;SRP=39.2015;SAP=10.7656;AB=0.0486111;ABP=257.857;RUN=1;RPP=3.32051;RPPR=3.37221;RPL=4.0;RPR=3.0;EPP=3.32051;EPPR=3.37221;DPRA=0.0;ODDS=12.5826;GTI=0;TYPE=complex;CIGAR=1X2M1I20M;NUMALT=6;MEANALT=12.0;LEN=24;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:A [...]
+chr3 78663956 . GAGA AAG 6540.58 REJECT NS=2;DP=144;DPB=173.435;AC=2;AN=2;AF=0.25;RO=24;AO=12;PRO=10.6667;PAO=19.25;QR=875;QA=340;PQR=365.333;PQA=667.167;SRF=2;SRR=22;SAF=1;SAR=11;SRP=39.2015;SAP=21.1059;AB=0.0833333;ABP=220.158;RUN=1;RPP=3.0103;RPPR=3.37221;RPL=6.0;RPR=6.0;EPP=3.73412;EPPR=3.37221;DPRA=0.0;ODDS=12.5826;GTI=0;TYPE=complex;CIGAR=1X2M1D19M;NUMALT=6;MEANALT=12.0;LEN=22;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr3 78663958 . G A 6540.58 REJECT SOMATIC;NS=2;DP=144;DPB=173.435;AC=1;AN=3;AF=0.0;RO=24;AO=5;PRO=10.6667;PAO=2.66667;QR=875;QA=109;PQR=365.333;PQA=92.3333;SRF=2;SRR=22;SAF=0;SAR=5;SRP=39.2015;SAP=13.8677;AB=0.0347222;ABP=273.781;RUN=1;RPP=6.91895;RPPR=3.37221;RPL=1.0;RPR=4.0;EPP=6.91895;EPPR=3.37221;DPRA=0.0;ODDS=12.5826;GTI=0;TYPE=snp;CIGAR=2M1X20M;NUMALT=6;MEANALT=12.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr3 78663958 . GA G 6540.58 REJECT NS=2;DP=144;DPB=173.435;AC=2;AN=3;AF=0.0;RO=24;AO=6;PRO=10.6667;PAO=9.66667;QR=875;QA=144;PQR=365.333;PQA=329.333;SRF=2;SRR=22;SAF=1;SAR=5;SRP=39.2015;SAP=8.80089;AB=0.0530973;ABP=199.039;RUN=1;RPP=3.0103;RPPR=3.37221;RPL=3.0;RPR=3.0;EPP=4.45795;EPPR=3.37221;DPRA=0.0;ODDS=12.5826;GTI=0;TYPE=del;CIGAR=3M1D19M;NUMALT=6;MEANALT=15.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;ALERT;BaseQRankSum=0.274;FS=0.0;ML [...]
+chr3 78666765 . T C 3788.95 REJECT NS=2;DP=168;DPB=194.0;AC=3;AN=4;AF=0.75;RO=53;AO=141;PRO=0.0;PAO=0.0;QR=2027;QA=5317;PQR=0.0;PQA=0.0;SRF=40;SRR=13;SAF=106;SAR=35;SRP=32.8783;SAP=80.6443;AB=0.629371;ABP=23.7987;RUN=1;RPP=56.6195;RPPR=17.8009;RPL=41.0;RPR=100.0;EPP=12.6356;EPPR=4.03458;DPRA=0.0;ODDS=32.8076;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.981132;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.992;Dels=0.0;FS=0.0;HaplotypeScore=1.96 [...]
+chr3 78676467 . A G 9556.24 REJECT NS=2;DP=254;DPB=293.0;AC=4;AN=4;AF=1.0;RO=0;AO=293;PRO=0.0;PAO=0.0;QR=0;QA=11286;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=231;SAR=62;SRP=0.0;SAP=214.681;AB=0.0;ABP=0.0;RUN=1;RPP=42.5044;RPPR=0.0;RPL=110.0;RPR=183.0;EPP=3.19558;EPPR=0.0;DPRA=0.0;ODDS=53.032;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993174;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.025;SOR=2.5565 [...]
+chr3 78685024 . C T 2970.3 PASS SOMATIC;NS=2;DP=393;DPB=393.0;AC=1;AN=3;AF=0.25;RO=283;AO=110;PRO=0.0;PAO=0.0;QR=10814;QA=4270;PQR=0.0;PQA=0.0;SRF=158;SRR=125;SAF=48;SAR=62;SRP=11.3662;SAP=6.87947;AB=0.367893;ABP=48.3352;RUN=1;RPP=3.72096;RPPR=3.20213;RPL=52.0;RPR=58.0;EPP=6.87947;EPPR=11.3662;DPRA=3.18085;ODDS=59.6008;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996466;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.443;Dels=0.0;FS=10.35 [...]
+chr3 89462238 . ATTGT A . PASS SOMATIC;AC=1;AN=4 GT:AD:DP:MM:MQS:NQSBQ:NQSMM:REnd:RStart:SC:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:35,0:35:0.2,0.0:60.0,0.0:36.8025,0.0:0.00617284,0.0:0,0:0,0:30,5,0,0:0:0:35:.:.:.:.:0:.:-0.00035518 0/1:60,45:105:0.0666667,0.0222222:60.0,60.4444:37.8261,38.7557:0.0,0.0:78,9:22,9:52,8,33,12:45:43:105:.:.:.:.:1:.:-0.0187789
+chr3 89521602 . T TC 1261.06 REJECT NS=2;DP=311;DPB=332.333;AC=2;AN=4;AF=0.5;RO=244;AO=64;PRO=13.5;PAO=13.5;QR=9325;QA=2423;PQR=460.0;PQA=460.0;SRF=145;SRR=99;SAF=44;SAR=20;SRP=21.8416;SAP=22.5536;AB=0.205788;ABP=236.838;RUN=1;RPP=14.0034;RPPR=92.0051;RPL=23.0;RPR=41.0;EPP=4.23175;EPPR=3.33068;DPRA=0.0;ODDS=88.4115;GTI=0;TYPE=ins;CIGAR=1M1I8M;NUMALT=1;MEANALT=2.5;LEN=1;MQM=60.4688;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;END=89521602;HOMLEN=0;SVLEN=1;SVTYPE=INS;BaseQRankS [...]
+chr3 89521664 . G A 2697.17 PASS SOMATIC;NS=2;DP=424;DPB=424.0;AC=1;AN=3;AF=0.25;RO=320;AO=104;PRO=0.0;PAO=0.0;QR=12099;QA=3967;PQR=0.0;PQA=0.0;SRF=168;SRR=152;SAF=51;SAR=53;SRP=4.74748;SAP=3.09382;AB=0.345515;ABP=65.4059;RUN=1;RPP=7.10269;RPPR=3.25459;RPL=59.0;RPR=45.0;EPP=3.34437;EPPR=5.20892;DPRA=2.44715;ODDS=77.6534;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.1562;PAIRED=1.0;PAIREDR=0.996875;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.911;Dels=0.0;FS=0 [...]
+chr3 89521693 . T C 5050.9400000000005 REJECT NS=2;DP=361;DPB=422.0;AC=2;AN=4;AF=0.5;RO=227;AO=195;PRO=0.0;PAO=0.0;QR=8736;QA=7448;PQR=0.0;PQA=0.0;SRF=103;SRR=124;SAF=82;SAR=113;SRP=7.22889;SAP=13.7118;AB=0.462085;ABP=8.27947;RUN=1;RPP=7.03031;RPPR=3.47903;RPL=107.0;RPR=88.0;EPP=6.22853;EPPR=7.22889;DPRA=0.0;ODDS=382.046;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.1538;MQMR=60.0;PAIRED=0.994872;PAIREDR=0.995595;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.485;Dels=0.0;FS=2 [...]
+chr3 89521725 . T C 1763.705 REJECT NS=2;DP=343;DPB=398.0;AC=2;AN=4;AF=0.5;RO=308;AO=88;PRO=0.0;PAO=0.0;QR=11419;QA=3259;PQR=0.0;PQA=0.0;SRF=120;SRR=188;SAF=33;SAR=55;SRP=35.6106;SAP=14.9534;AB=0.221106;ABP=271.902;RUN=1;RPP=19.6912;RPPR=4.02553;RPL=57.0;RPR=31.0;EPP=6.56362;EPPR=14.2907;DPRA=0.0;ODDS=64.4094;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988636;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1765;Dels=0.0;FS=0.8005;HaplotypeScore [...]
+chr3 89613568 . G A 1096.28 REJECT NS=1;DP=83;DPB=83.0;AC=1;AN=4;AF=0.5;RO=41;AO=42;PRO=0.0;PAO=0.0;QR=1541;QA=1537;PQR=0.0;PQA=0.0;SRF=20;SRR=21;SAF=22;SAR=20;SRP=3.06326;SAP=3.21711;AB=0.506024;ABP=3.03646;RUN=1;RPP=13.1438;RPPR=9.41879;RPL=14.0;RPR=28.0;EPP=8.18047;EPPR=5.60547;DPRA=0.0;ODDS=252.428;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.732;FS=1.789;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.52; [...]
+chr3 89613664 . G A 1035.23 REJECT NS=1;DP=79;DPB=79.0;AC=1;AN=4;AF=0.5;RO=41;AO=38;PRO=0.0;PAO=0.0;QR=1536;QA=1481;PQR=0.0;PQA=0.0;SRF=13;SRR=28;SAF=16;SAR=22;SRP=14.9269;SAP=5.06748;AB=0.481013;ABP=3.25768;RUN=1;RPP=3.9246;RPPR=18.3165;RPL=21.0;RPR=17.0;EPP=35.9253;EPPR=7.30028;DPRA=0.0;ODDS=238.371;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-1.181;FS=4.54;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.801;Q [...]
+chr3 89625902 . C T 5794.6 REJECT NS=2;DP=388;DPB=449.0;AC=2;AN=4;AF=0.5;RO=233;AO=216;PRO=0.0;PAO=0.0;QR=8864;QA=8259;PQR=0.0;PQA=0.0;SRF=131;SRR=102;SAF=122;SAR=94;SRP=10.8481;SAP=10.8919;AB=0.481069;ABP=4.40797;RUN=1;RPP=6.26751;RPPR=5.70367;RPL=99.0;RPR=117.0;EPP=28.1431;EPPR=5.10722;DPRA=0.0;ODDS=370.947;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990741;PAIREDR=0.991416;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4845;Dels=0.0;FS=6.4585;Haplotyp [...]
+chr3 97517472 . C T 5785.05 REJECT NS=2;DP=215;DPB=243.0;AC=2;AN=4;AF=0.5;RO=48;AO=195;PRO=0.0;PAO=0.0;QR=1840;QA=7492;PQR=0.0;PQA=0.0;SRF=32;SRR=16;SAF=133;SAR=62;SRP=14.5915;SAP=59.1456;AB=0.802469;ABP=196.11;RUN=1;RPP=171.483;RPPR=4.6389;RPL=36.0;RPR=159.0;EPP=3.11052;EPPR=7.5342;DPRA=0.0;ODDS=81.6959;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984615;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4955;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLE [...]
+chr3 100529408 . AT A 931.232 REJECT NS=2;DP=227;DPB=259.824;AC=2;AN=4;AF=0.5;RO=180;AO=46;PRO=49.5;PAO=26.5;QR=6862;QA=1639;PQR=1793.0;PQA=918.0;SRF=45;SRR=135;SAF=12;SAR=34;SRP=100.727;SAP=25.858;AB=0.202643;ABP=177.35;RUN=1;RPP=7.73089;RPPR=16.956;RPL=28.0;RPR=18.0;EPP=12.2627;EPPR=22.3123;DPRA=0.0;ODDS=21.4531;GTI=0;TYPE=del;CIGAR=1M1D15M;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.978261;PAIREDR=0.994444;technology.ILLUMINA=1.0;BaseQRankSum=-0.614;FS=0.0;MLEAC=1;MLEAF=0.5 [...]
+chr3 105422844 . C T 11215.65 REJECT NS=2;DP=301;DPB=344.0;AC=4;AN=4;AF=1.0;RO=0;AO=344;PRO=0.0;PAO=0.0;QR=0;QA=13013;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=243;SAR=101;SRP=0.0;SAP=130.294;AB=0.0;ABP=0.0;RUN=1;RPP=27.2752;RPPR=0.0;RPL=141.0;RPR=203.0;EPP=4.62628;EPPR=0.0;DPRA=0.0;ODDS=56.6602;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9826;MQMR=0.0;PAIRED=0.991279;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8325;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.02;SO [...]
+chr3 114030477 . C CA 107.788 REJECT NS=2;DP=192;DPB=223.938;AC=2;AN=3;AF=0.25;RO=150;AO=21;PRO=30.8333;PAO=16.8333;QR=5686;QA=702;PQR=1135.33;PQA=609.333;SRF=38;SRR=112;SAF=6;SAR=15;SRP=82.2835;SAP=11.386;AB=0.109375;ABP=257.48;RUN=1;RPP=11.386;RPPR=51.7092;RPL=15.0;RPR=6.0;EPP=3.94093;EPPR=4.45795;DPRA=0.0;ODDS=5.00321;GTI=0;TYPE=ins;CIGAR=1M1I15M;NUMALT=2;MEANALT=4.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986667;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr3 114030477 . CA C 107.788 REJECT NS=2;DP=192;DPB=223.938;AC=2;AN=3;AF=0.25;RO=150;AO=13;PRO=30.8333;PAO=15.3333;QR=5686;QA=465;PQR=1135.33;PQA=564.333;SRF=38;SRR=112;SAF=2;SAR=11;SRP=82.2835;SAP=16.5402;AB=0.0677083;ABP=314.662;RUN=1;RPP=16.5402;RPPR=51.7092;RPL=11.0;RPR=2.0;EPP=7.18621;EPPR=4.45795;DPRA=0.0;ODDS=5.00321;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=2;MEANALT=4.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986667;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr3 118509389 . G C 1185.55 REJECT NS=2;DP=377;DPB=426.0;AC=2;AN=4;AF=0.5;RO=356;AO=70;PRO=0.0;PAO=0.0;QR=13553;QA=2665;PQR=0.0;PQA=0.0;SRF=183;SRR=173;SAF=35;SAR=35;SRP=3.62026;SAP=3.0103;AB=0.164319;ABP=419.953;RUN=1;RPP=3.50664;RPPR=18.2594;RPL=33.0;RPR=37.0;EPP=6.1124;EPPR=17.0639;DPRA=0.0;ODDS=44.1813;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994382;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4455;Dels=0.0;FS=5.1145;HaplotypeScore=4 [...]
+chr3 121151812 . G C 5157.045 REJECT NS=2;DP=349;DPB=407.0;AC=2;AN=4;AF=0.5;RO=212;AO=195;PRO=0.0;PAO=0.0;QR=8102;QA=7452;PQR=0.0;PQA=0.0;SRF=107;SRR=105;SAF=98;SAR=97;SRP=3.05127;SAP=3.02144;AB=0.479115;ABP=4.55221;RUN=1;RPP=44.4464;RPPR=5.63246;RPL=67.0;RPR=128.0;EPP=3.02144;EPPR=5.01789;DPRA=0.0;ODDS=349.458;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989744;PAIREDR=0.995283;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9375;Dels=0.0;FS=0.564;Haplotyp [...]
+chr3 121154974 . T C 5137.92 REJECT NS=2;DP=327;DPB=369.0;AC=2;AN=4;AF=0.5;RO=187;AO=182;PRO=0.0;PAO=0.0;QR=7283;QA=6968;PQR=0.0;PQA=0.0;SRF=107;SRR=80;SAF=126;SAR=56;SRP=11.4756;SAP=61.473;AB=0.493225;ABP=3.15742;RUN=1;RPP=8.78498;RPPR=4.97275;RPL=80.0;RPR=102.0;EPP=8.78498;EPPR=28.6615;DPRA=0.0;ODDS=218.837;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994505;PAIREDR=0.983957;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0535;Dels=0.0;FS=8.169;Haplotype [...]
+chr3 121186422 . G A 5656.645 REJECT NS=2;DP=360;DPB=415.0;AC=2;AN=4;AF=0.5;RO=217;AO=198;PRO=0.0;PAO=0.0;QR=8215;QA=7721;PQR=0.0;PQA=0.0;SRF=111;SRR=106;SAF=102;SAR=96;SRP=3.26047;SAP=3.40511;AB=0.477108;ABP=4.89922;RUN=1;RPP=3.0103;RPPR=3.02031;RPL=99.0;RPR=99.0;EPP=4.58955;EPPR=18.2306;DPRA=0.0;ODDS=333.84;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.2185;Dels=0.0;FS=0.0;HaplotypeScore=3.924;M [...]
+chr3 121186451 . T C 5368.790000000001 REJECT NS=2;DP=365;DPB=418.0;AC=2;AN=4;AF=0.5;RO=223;AO=195;PRO=0.0;PAO=0.0;QR=8503;QA=7459;PQR=0.0;PQA=0.0;SRF=91;SRR=132;SAF=72;SAR=123;SRP=19.3791;SAP=31.9744;AB=0.466507;ABP=7.08311;RUN=1;RPP=4.89224;RPPR=5.20125;RPL=104.0;RPR=91.0;EPP=8.90111;EPPR=24.5205;DPRA=0.0;ODDS=326.84;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6865;Dels=0.0;FS=1.9355;Haplotype [...]
+chr3 121202433 . T TA 480.53 REJECT NS=2;DP=132;DPB=176.806;AC=2;AN=2;AF=0.0;RO=74;AO=9;PRO=38.8333;PAO=23.8333;QR=2791;QA=245;PQR=1390.0;PQA=779.0;SRF=1;SRR=73;SAF=0;SAR=9;SRP=155.131;SAP=22.5536;AB=0.0681818;ABP=216.802;RUN=1;RPP=5.18177;RPPR=3.12768;RPL=3.0;RPR=6.0;EPP=5.18177;EPPR=3.47981;DPRA=0.0;ODDS=23.6641;GTI=0;TYPE=ins;CIGAR=1M1I30M;NUMALT=3;MEANALT=8.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986486;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr3 121202433 . TA T 480.53 REJECT NS=2;DP=132;DPB=176.806;AC=2;AN=4;AF=0.5;RO=74;AO=21;PRO=38.8333;PAO=30.3333;QR=2791;QA=628;PQR=1390.0;PQA=1030.0;SRF=1;SRR=73;SAF=0;SAR=21;SRP=155.131;SAP=48.6112;AB=0.159091;ABP=136.26;RUN=1;RPP=3.1137;RPPR=3.12768;RPL=10.0;RPR=11.0;EPP=3.1137;EPPR=3.47981;DPRA=0.0;ODDS=23.6641;GTI=0;TYPE=del;CIGAR=1M1D29M;NUMALT=3;MEANALT=8.5;LEN=1;MQM=60.4762;MQMR=60.0;PAIRED=0.952381;PAIREDR=0.986486;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr3 121202433 . TAA T 480.53 PASS SOMATIC;NS=2;DP=132;DPB=176.806;AC=2;AN=2;AF=0.0;RO=74;AO=11;PRO=38.8333;PAO=17.0;QR=2791;QA=361;PQR=1390.0;PQA=595.0;SRF=1;SRR=73;SAF=2;SAR=9;SRP=155.131;SAP=12.6832;AB=0.105769;ABP=143.404;RUN=1;RPP=4.78696;RPPR=3.12768;RPL=7.0;RPR=4.0;EPP=4.78696;EPPR=3.47981;DPRA=0.0;ODDS=23.6641;GTI=0;TYPE=del;CIGAR=1M2D28M;NUMALT=3;MEANALT=11.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986486;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr3 121208833 . G C 4366.28 REJECT NS=2;DP=316;DPB=376.0;AC=2;AN=4;AF=0.5;RO=206;AO=170;PRO=0.0;PAO=0.0;QR=7911;QA=6502;PQR=0.0;PQA=0.0;SRF=98;SRR=108;SAF=77;SAR=93;SRP=4.06441;SAP=6.28028;AB=0.452128;ABP=10.4949;RUN=1;RPP=3.47014;RPPR=3.05246;RPL=88.0;RPR=82.0;EPP=10.3678;EPPR=3.05246;DPRA=0.0;ODDS=392.935;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995146;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0075;Dels=0.0;FS=2.9045;HaplotypeScore [...]
+chr3 121228960 . G A 6267.945 REJECT NS=2;DP=377;DPB=434.0;AC=2;AN=4;AF=0.5;RO=201;AO=232;PRO=0.0;PAO=0.0;QR=7665;QA=8469;PQR=0.0;PQA=0.0;SRF=95;SRR=106;SAF=100;SAR=132;SRP=4.3175;SAP=12.5947;AB=0.534562;ABP=7.51335;RUN=1;RPP=3.16006;RPPR=3.10753;RPL=118.0;RPR=114.0;EPP=24.5753;EPPR=4.3175;DPRA=0.0;ODDS=346.704;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99569;PAIREDR=0.9801;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.6755;Dels=0.0;FS=2.5265;Haplotype [...]
+chr3 121238749 . G A 10767.15 REJECT NS=2;DP=284;DPB=330.0;AC=4;AN=4;AF=1.0;RO=0;AO=329;PRO=0.0;PAO=0.0;QR=0;QA=12659;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=216;SAR=113;SRP=0.0;SAP=73.032;AB=0.0;ABP=0.0;RUN=1;RPP=7.82186;RPPR=0.0;RPL=151.0;RPR=178.0;EPP=11.0956;EPPR=0.0;DPRA=0.0;ODDS=61.113;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99696;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9469;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.71;SOR=1.76 [...]
+chr3 121252048 . T G 4303.09 REJECT NS=2;DP=297;DPB=337.0;AC=2;AN=4;AF=0.5;RO=173;AO=164;PRO=0.0;PAO=0.0;QR=6561;QA=5990;PQR=0.0;PQA=0.0;SRF=40;SRR=133;SAF=38;SAR=126;SRP=111.571;SAP=105.546;AB=0.486647;ABP=3.53223;RUN=1;RPP=3.48696;RPPR=30.7374;RPL=85.0;RPR=79.0;EPP=9.41879;EPPR=4.52908;DPRA=0.0;ODDS=190.119;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988439;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.819;Dels=0.0;FS=2.0585;HaplotypeScore [...]
+chr3 121263720 . C A 14657.5 REJECT NS=2;DP=385;DPB=436.0;AC=4;AN=4;AF=1.0;RO=0;AO=435;PRO=0.0;PAO=0.0;QR=0;QA=16675;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=169;SAR=266;SRP=0.0;SAP=49.979;AB=0.0;ABP=0.0;RUN=1;RPP=14.9958;RPPR=0.0;RPL=242.0;RPR=193.0;EPP=4.45296;EPPR=0.0;DPRA=0.0;ODDS=66.7532;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995402;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=16.4766;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.4;SOR=1.5 [...]
+chr3 128202523 . CT C 127.119 REJECT NS=2;DP=430;DPB=435.667;AC=1;AN=4;AF=0.25;RO=411;AO=19;PRO=18.0;PAO=4.0;QR=15671;QA=695;PQR=555.5;PQA=51.5;SRF=164;SRR=247;SAF=11;SAR=8;SRP=39.4076;SAP=4.03889;AB=0.138614;ABP=117.582;RUN=1;RPP=3.12459;RPPR=6.86189;RPL=10.0;RPR=9.0;EPP=5.8675;EPPR=5.80521;DPRA=0.0;ODDS=29.2702;GTI=0;TYPE=del;CIGAR=1M1D1M;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997567;technology.ILLUMINA=1.0;END=128202524;HOMLEN=0;SVLEN=-1;SVTYPE=DEL;BaseQRan [...]
+chr3 128205860 . G C 3424.11 REJECT NS=2;DP=229;DPB=263.0;AC=2;AN=4;AF=0.5;RO=138;AO=124;PRO=0.0;PAO=0.0;QR=5311;QA=4811;PQR=0.0;PQA=0.0;SRF=21;SRR=117;SAF=21;SAR=103;SRP=148.027;SAP=120.76;AB=0.471483;ABP=4.86802;RUN=1;RPP=5.53201;RPPR=4.01736;RPL=68.0;RPR=56.0;EPP=11.486;EPPR=17.1721;DPRA=0.0;ODDS=192.618;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991935;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1085;Dels=0.0;FS=0.708;HaplotypeScore=7. [...]
+chr3 134644636 . G T 1299.375 REJECT NS=2;DP=284;DPB=321.0;AC=2;AN=4;AF=0.5;RO=254;AO=67;PRO=0.0;PAO=0.0;QR=9711;QA=2542;PQR=0.0;PQA=0.0;SRF=168;SRR=86;SAF=52;SAR=15;SRP=60.4945;SAP=47.3796;AB=0.208723;ABP=239.565;RUN=1;RPP=8.4876;RPPR=24.3831;RPL=27.0;RPR=40.0;EPP=3.82055;EPPR=7.14807;DPRA=0.0;ODDS=42.4421;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.955224;PAIREDR=0.996063;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1435;Dels=0.0;FS=10.447;HaplotypeSc [...]
+chr3 134670524 . C T 2541.9300000000003 REJECT NS=2;DP=400;DPB=457.0;AC=2;AN=4;AF=0.5;RO=341;AO=116;PRO=0.0;PAO=0.0;QR=13032;QA=4504;PQR=0.0;PQA=0.0;SRF=177;SRR=164;SAF=62;SAR=54;SRP=4.08648;SAP=4.20835;AB=0.253829;ABP=243.559;RUN=1;RPP=10.4981;RPPR=4.44309;RPL=48.0;RPR=68.0;EPP=7.80251;EPPR=11.728;DPRA=0.0;ODDS=171.007;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997067;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.222;Dels=0.0;FS=1.32;Haplot [...]
+chr3 134967368 . G A 7192.68 REJECT NS=2;DP=269;DPB=317.0;AC=2;AN=4;AF=0.5;RO=80;AO=237;PRO=0.0;PAO=0.0;QR=3050;QA=9175;PQR=0.0;PQA=0.0;SRF=27;SRR=53;SAF=83;SAR=154;SRP=21.3592;SAP=49.1976;AB=0.747634;ABP=171.858;RUN=1;RPP=72.36;RPPR=13.8677;RPL=162.0;RPR=75.0;EPP=26.8415;EPPR=5.72464;DPRA=0.0;ODDS=30.7372;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.745;Dels=0.0;FS=2.3225;HaplotypeScore=4.8993;M [...]
+chr3 137743508 . A T 5825.39 REJECT NS=2;DP=378;DPB=441.0;AC=2;AN=4;AF=0.5;RO=237;AO=204;PRO=0.0;PAO=0.0;QR=9060;QA=7966;PQR=0.0;PQA=0.0;SRF=125;SRR=112;SAF=108;SAR=96;SRP=4.55873;SAP=4.5431;AB=0.462585;ABP=8.37251;RUN=1;RPP=12.5903;RPPR=3.23936;RPL=87.0;RPR=117.0;EPP=43.9277;EPPR=54.5484;DPRA=0.0;ODDS=311.804;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995098;PAIREDR=0.995781;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.6695;Dels=0.0;FS=3.787;Haplotype [...]
+chr3 137749839 . A G 4209.620000000001 REJECT NS=2;DP=286;DPB=325.0;AC=2;AN=4;AF=0.5;RO=169;AO=155;PRO=0.0;PAO=0.0;QR=6394;QA=5866;PQR=0.0;PQA=0.0;SRF=116;SRR=53;SAF=115;SAR=40;SRP=54.0078;SAP=81.8137;AB=0.476923;ABP=4.51363;RUN=1;RPP=39.449;RPPR=6.72365;RPL=52.0;RPR=103.0;EPP=3.69677;EPPR=3.6399;DPRA=0.0;ODDS=241.35;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993548;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1035;Dels=0.0;FS=2.478;Haploty [...]
+chr3 137750056 . T C 5862.405000000001 REJECT NS=2;DP=375;DPB=424.0;AC=2;AN=4;AF=0.5;RO=214;AO=210;PRO=0.0;PAO=0.0;QR=8205;QA=8092;PQR=0.0;PQA=0.0;SRF=112;SRR=102;SAF=106;SAR=104;SRP=4.02501;SAP=3.05166;AB=0.495283;ABP=3.09224;RUN=1;RPP=3.38255;RPPR=4.02501;RPL=108.0;RPR=102.0;EPP=3.05166;EPPR=4.99913;DPRA=0.0;ODDS=258.187;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995238;PAIREDR=0.995327;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.767;Dels=0.0;FS=0.3 [...]
+chr3 137750586 . C A 5981.46 REJECT NS=2;DP=383;DPB=443.0;AC=2;AN=4;AF=0.5;RO=225;AO=218;PRO=0.0;PAO=0.0;QR=8665;QA=8361;PQR=0.0;PQA=0.0;SRF=108;SRR=117;SAF=115;SAR=103;SRP=3.79203;SAP=4.44467;AB=0.492099;ABP=3.25049;RUN=1;RPP=18.9477;RPPR=13.5202;RPL=129.0;RPR=89.0;EPP=7.83137;EPPR=3.01995;DPRA=0.0;ODDS=379.068;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995413;PAIREDR=0.991111;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7325;Dels=0.0;FS=7.466;Haploty [...]
+chr3 137750672 . G A 5738.09 REJECT NS=2;DP=361;DPB=423.0;AC=2;AN=4;AF=0.5;RO=207;AO=215;PRO=0.0;PAO=0.0;QR=7588;QA=8069;PQR=0.0;PQA=0.0;SRF=79;SRR=128;SAF=81;SAR=134;SRP=28.1973;SAP=31.3808;AB=0.508274;ABP=3.26184;RUN=1;RPP=18.3722;RPPR=6.04197;RPL=127.0;RPR=88.0;EPP=3.2628;EPPR=4.78314;DPRA=0.0;ODDS=384.394;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0483;PAIRED=0.986047;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.084;Dels=0.0;FS=0.2175;HaplotypeSco [...]
+chr3 137750882 . C G 5180.120000000001 REJECT NS=2;DP=343;DPB=389.0;AC=2;AN=4;AF=0.5;RO=202;AO=187;PRO=0.0;PAO=0.0;QR=7685;QA=7164;PQR=0.0;PQA=0.0;SRF=76;SRR=126;SAF=77;SAR=110;SRP=29.885;SAP=15.6559;AB=0.48072;ABP=4.26629;RUN=1;RPP=7.20229;RPPR=15.4371;RPL=84.0;RPR=103.0;EPP=8.13126;EPPR=6.49326;DPRA=0.0;ODDS=277.041;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989305;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.879;Dels=0.0;FS=1.86;Haplotyp [...]
+chr3 137751000 . G A 1227.27 PASS SOMATIC;NS=2;DP=177;DPB=177.0;AC=1;AN=3;AF=0.25;RO=128;AO=49;PRO=0.0;PAO=0.0;QR=4924;QA=1887;PQR=0.0;PQA=0.0;SRF=17;SRR=111;SAF=9;SAR=40;SRP=152.91;SAP=45.5977;AB=0.352518;ABP=29.2711;RUN=1;RPP=4.11819;RPPR=8.50684;RPL=27.0;RPR=22.0;EPP=4.11819;EPPR=3.0103;DPRA=3.65789;ODDS=24.7279;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.979592;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.816;Dels=0.0;FS=4.97;Hap [...]
+chr3 137751020 . G C 1769.38 REJECT NS=2;DP=139;DPB=157.0;AC=2;AN=4;AF=0.5;RO=87;AO=70;PRO=0.0;PAO=0.0;QR=3370;QA=2687;PQR=0.0;PQA=0.0;SRF=9;SRR=78;SAF=7;SAR=63;SRP=121.842;SAP=100.292;AB=0.44586;ABP=7.00747;RUN=1;RPP=15.4187;RPPR=3.03526;RPL=45.0;RPR=25.0;EPP=6.1124;EPPR=6.03039;DPRA=0.0;ODDS=96.3426;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8545;Dels=0.0;FS=0.0;HaplotypeScore=0.9999;MLEAC=1; [...]
+chr3 137751136 . C A 2314.2650000000003 REJECT NS=2;DP=86;DPB=105.0;AC=2;AN=4;AF=0.5;RO=27;AO=78;PRO=0.0;PAO=0.0;QR=1027;QA=2994;PQR=0.0;PQA=0.0;SRF=16;SRR=11;SAF=39;SAR=39;SRP=5.02092;SAP=3.0103;AB=0.742857;ABP=56.8008;RUN=1;RPP=3.0103;RPPR=3.09072;RPL=39.0;RPR=39.0;EPP=43.2104;EPPR=12.7417;DPRA=0.0;ODDS=28.0751;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987179;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0805;Dels=0.0;FS=3.9625;HaplotypeS [...]
+chr3 137751330 . T TA 1381.38 REJECT NS=2;DP=247;DPB=331.952;AC=2;AN=4;AF=0.5;RO=101;AO=71;PRO=42.25;PAO=34.75;QR=3644;QA=2604;PQR=1495.17;PQA=1225.67;SRF=73;SRR=28;SAF=49;SAR=22;SRP=46.5472;SAP=25.3061;AB=0.275194;ABP=116.264;RUN=1;RPP=6.71098;RPPR=4.75178;RPL=41.0;RPR=30.0;EPP=4.50892;EPPR=10.7717;DPRA=0.0;ODDS=131.289;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=3;MEANALT=17.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985915;PAIREDR=0.970297;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum [...]
+chr3 137751330 . T TAA 1839.03 REJECT NS=2;DP=258;DPB=331.952;AC=2;AN=2;AF=0.0;RO=101;AO=20;PRO=42.25;PAO=34.75;QR=3644;QA=692;PQR=1495.17;PQA=1225.67;SRF=73;SRR=28;SAF=15;SAR=5;SRP=46.5472;SAP=13.8677;AB=0.0775194;ABP=402.999;RUN=1;RPP=13.8677;RPPR=4.75178;RPL=5.0;RPR=15.0;EPP=4.74748;EPPR=10.7717;DPRA=0.0;ODDS=131.289;GTI=0;TYPE=ins;CIGAR=1M2I20M;NUMALT=3;MEANALT=17.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.970297;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr3 137751330 . TA T 1839.03 REJECT NS=2;DP=258;DPB=331.952;AC=2;AN=2;AF=0.0;RO=101;AO=21;PRO=42.25;PAO=33.25;QR=3644;QA=772;PQR=1495.17;PQA=1159.5;SRF=73;SRR=28;SAF=16;SAR=5;SRP=46.5472;SAP=15.5221;AB=0.0813953;ABP=395.693;RUN=1;RPP=8.07707;RPPR=4.75178;RPL=14.0;RPR=7.0;EPP=5.59539;EPPR=10.7717;DPRA=0.0;ODDS=131.289;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=3;MEANALT=17.5;LEN=1;MQM=59.3333;MQMR=60.0;PAIRED=1.0;PAIREDR=0.970297;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr3 137751420 . A G 8295.62 REJECT NS=2;DP=305;DPB=350.0;AC=2;AN=4;AF=0.5;RO=76;AO=274;PRO=0.0;PAO=0.0;QR=2932;QA=10400;PQR=0.0;PQA=0.0;SRF=38;SRR=38;SAF=124;SAR=150;SRP=3.0103;SAP=8.36766;AB=0.782857;ABP=246.24;RUN=1;RPP=44.0939;RPPR=4.03889;RPL=173.0;RPR=101.0;EPP=6.18033;EPPR=12.2676;DPRA=0.0;ODDS=105.213;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9854;MQMR=60.0;PAIRED=0.981752;PAIREDR=0.973684;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5445;Dels=0.0;FS=2.8925;Haplot [...]
+chr3 137752004 . C G 2687.99 PASS SOMATIC;NS=2;DP=458;DPB=458.0;AC=1;AN=3;AF=0.25;RO=352;AO=106;PRO=0.0;PAO=0.0;QR=13617;QA=4063;PQR=0.0;PQA=0.0;SRF=181;SRR=171;SAF=47;SAR=59;SRP=3.6272;SAP=5.96022;AB=0.315476;ABP=102.381;RUN=1;RPP=4.32138;RPPR=5.00904;RPL=49.0;RPR=57.0;EPP=3.09224;EPPR=22.3561;DPRA=2.7541;ODDS=77.1178;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990566;PAIREDR=0.988636;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.136;Dels=0.0;FS [...]
+chr3 142070013 . A G 6197.6 REJECT NS=2;DP=380;DPB=447.0;AC=2;AN=4;AF=0.5;RO=217;AO=228;PRO=0.0;PAO=0.0;QR=8180;QA=8696;PQR=0.0;PQA=0.0;SRF=140;SRR=77;SAF=155;SAR=73;SRP=42.7272;SAP=67.0497;AB=0.510067;ABP=3.40379;RUN=1;RPP=37.2967;RPPR=23.274;RPL=84.0;RPR=144.0;EPP=19.8106;EPPR=62.3405;DPRA=0.0;ODDS=412.685;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=59.9263;PAIRED=0.986842;PAIREDR=0.976959;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.9155;Dels=0.0;FS=6.399;Haplotyp [...]
+chr3 142071932 . A G 5648.56 REJECT NS=2;DP=372;DPB=431.0;AC=2;AN=4;AF=0.5;RO=221;AO=209;PRO=0.0;PAO=0.0;QR=8421;QA=7957;PQR=0.0;PQA=0.0;SRF=97;SRR=124;SAF=96;SAR=113;SRP=10.1732;SAP=6.01296;AB=0.484919;ABP=3.86176;RUN=1;RPP=4.76618;RPPR=3.80618;RPL=98.0;RPR=111.0;EPP=27.9563;EPPR=64.3323;DPRA=0.0;ODDS=378.814;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995215;PAIREDR=0.995475;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1475;Dels=0.0;FS=2.561;Haplotype [...]
+chr3 142076059 . A G 6082.25 REJECT NS=2;DP=363;DPB=422.0;AC=2;AN=4;AF=0.5;RO=207;AO=215;PRO=0.0;PAO=0.0;QR=7905;QA=8262;PQR=0.0;PQA=0.0;SRF=88;SRR=119;SAF=95;SAR=120;SRP=13.0914;SAP=9.32272;AB=0.509479;ABP=3.33962;RUN=1;RPP=4.71718;RPPR=20.6443;RPL=114.0;RPR=101.0;EPP=4.71718;EPPR=3.52432;DPRA=0.0;ODDS=358.345;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986047;PAIREDR=0.995169;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.555;Dels=0.0;FS=3.862;Haplotype [...]
+chr3 142078215 . G A 5243.615 REJECT NS=2;DP=376;DPB=433.0;AC=2;AN=4;AF=0.5;RO=243;AO=190;PRO=0.0;PAO=0.0;QR=9180;QA=7276;PQR=0.0;PQA=0.0;SRF=106;SRR=137;SAF=80;SAR=110;SRP=11.5979;SAP=13.2962;AB=0.438799;ABP=17.0973;RUN=1;RPP=3.19316;RPPR=3.73412;RPL=97.0;RPR=93.0;EPP=14.7134;EPPR=13.957;DPRA=0.0;ODDS=287.491;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994737;PAIREDR=0.995885;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.154;Dels=0.0;FS=2.849;HaplotypeS [...]
+chr3 142168331 . C T 9338.885 REJECT NS=2;DP=377;DPB=432.0;AC=3;AN=4;AF=0.75;RO=108;AO=324;PRO=0.0;PAO=0.0;QR=4188;QA=12543;PQR=0.0;PQA=0.0;SRF=67;SRR=41;SAF=181;SAR=143;SRP=16.6021;SAP=12.6881;AB=0.664596;ABP=78.7825;RUN=1;RPP=7.5409;RPPR=3.0103;RPL=175.0;RPR=149.0;EPP=21.1327;EPPR=9.52472;DPRA=0.0;ODDS=69.595;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.13;Dels=0.0;FS=1.989;HaplotypeScore=2.890 [...]
+chr3 142178144 . C T 5272.645 REJECT NS=2;DP=336;DPB=384.0;AC=2;AN=4;AF=0.5;RO=187;AO=197;PRO=0.0;PAO=0.0;QR=7112;QA=7448;PQR=0.0;PQA=0.0;SRF=93;SRR=94;SAF=95;SAR=102;SRP=3.02191;SAP=3.55041;AB=0.513021;ABP=3.57579;RUN=1;RPP=3.90314;RPPR=4.97275;RPL=94.0;RPR=103.0;EPP=6.9895;EPPR=7.20229;DPRA=0.0;ODDS=221.701;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984772;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.7375;Dels=0.0;FS=2.0095;HaplotypeScor [...]
+chr3 142188337 . A C 5625.99 REJECT NS=2;DP=363;DPB=414.0;AC=2;AN=4;AF=0.5;RO=215;AO=199;PRO=0.0;PAO=0.0;QR=8311;QA=7586;PQR=0.0;PQA=0.0;SRF=70;SRR=145;SAF=85;SAR=114;SRP=59.8221;SAP=12.1872;AB=0.480676;ABP=4.35305;RUN=1;RPP=3.2831;RPPR=7.46434;RPL=102.0;RPR=97.0;EPP=9.83025;EPPR=4.71718;DPRA=0.0;ODDS=271.751;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990698;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.112;Dels=0.0;FS=7.434;HaplotypeScore= [...]
+chr3 142215171 . T C 2035.17 REJECT NS=2;DP=105;DPB=105.0;AC=2;AN=4;AF=0.5;RO=23;AO=82;PRO=0.0;PAO=0.0;QR=849;QA=2797;PQR=0.0;PQA=0.0;SRF=6;SRR=17;SAF=48;SAR=34;SRP=14.4341;SAP=8.20065;AB=0.780952;ABP=74.9998;RUN=1;RPP=125.46;RPPR=30.2953;RPL=7.0;RPR=75.0;EPP=3.434;EPPR=18.9659;DPRA=0.0;ODDS=19.8874;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9565;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.867;Dels=0.0;FS=15.195;HaplotypeScore=0.9665;MLEA [...]
+chr3 142215178 . A C 2800.81 REJECT NS=2;DP=152;DPB=152.0;AC=2;AN=4;AF=0.5;RO=49;AO=102;PRO=0.0;PAO=0.0;QR=1739;QA=3746;PQR=0.0;PQA=0.0;SRF=28;SRR=21;SAF=60;SAR=42;SRP=5.18177;SAP=9.90792;AB=0.671053;ABP=41.6397;RUN=1;RPP=95.7449;RPPR=92.7497;RPL=18.0;RPR=84.0;EPP=3.7767;EPPR=5.18177;DPRA=0.0;ODDS=61.1684;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=59.9796;PAIRED=0.990196;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.328;Dels=0.0;FS=3.774;HaplotypeScore=1. [...]
+chr3 142217537 . A G 1655.31 REJECT NS=2;DP=383;DPB=437.0;AC=2;AN=4;AF=0.5;RO=352;AO=84;PRO=0.0;PAO=0.0;QR=13595;QA=3214;PQR=0.0;PQA=0.0;SRF=181;SRR=171;SAF=43;SAR=41;SRP=3.6272;SAP=3.1137;AB=0.19222;ABP=362.575;RUN=1;RPP=3.0103;RPPR=3.03498;RPL=42.0;RPR=42.0;EPP=3.94093;EPPR=3.89863;DPRA=0.0;ODDS=62.8734;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997159;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.138;Dels=0.0;FS=1.118;HaplotypeScore=1.93 [...]
+chr3 142241692 . G GA 113.19 REJECT NS=2;DP=170;DPB=205.952;AC=2;AN=3;AF=0.25;RO=121;AO=16;PRO=33.1667;PAO=15.1667;QR=4465;QA=528;PQR=1161.75;PQA=516.75;SRF=23;SRR=98;SAF=1;SAR=15;SRP=103.957;SAP=29.6108;AB=0.0941176;ABP=246.266;RUN=1;RPP=7.89611;RPPR=65.4805;RPL=11.0;RPR=5.0;EPP=11.6962;EPPR=10.9245;DPRA=0.0;ODDS=9.84943;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=3;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr3 142241692 . G GAA 113.19 REJECT NS=2;DP=170;DPB=205.952;AC=2;AN=2;AF=0.0;RO=121;AO=2;PRO=33.1667;PAO=12.1667;QR=4465;QA=30;PQR=1161.75;PQA=422.75;SRF=23;SRR=98;SAF=1;SAR=1;SRP=103.957;SAP=3.0103;AB=0.05;ABP=73.366;RUN=1;RPP=7.35324;RPPR=65.4805;RPL=2.0;RPR=0.0;EPP=3.0103;EPPR=10.9245;DPRA=0.0;ODDS=9.84943;GTI=0;TYPE=ins;CIGAR=1M2I20M;NUMALT=3;MEANALT=6.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr3 142241692 . GA G 113.19 REJECT NS=2;DP=170;DPB=205.952;AC=2;AN=3;AF=0.25;RO=121;AO=19;PRO=33.1667;PAO=15.5;QR=4465;QA=594;PQR=1161.75;PQA=509.75;SRF=23;SRR=98;SAF=2;SAR=17;SRP=103.957;SAP=28.7251;AB=0.111765;ABP=225.573;RUN=1;RPP=22.325;RPPR=65.4805;RPL=16.0;RPR=3.0;EPP=12.2676;EPPR=10.9245;DPRA=0.0;ODDS=9.84943;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=3;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr3 142277575 . A T 5189.885 REJECT NS=2;DP=357;DPB=410.0;AC=2;AN=4;AF=0.5;RO=216;AO=194;PRO=0.0;PAO=0.0;QR=8486;QA=7404;PQR=0.0;PQA=0.0;SRF=91;SRR=125;SAF=72;SAR=122;SRP=14.6317;SAP=30.9932;AB=0.473171;ABP=5.5737;RUN=1;RPP=5.87575;RPPR=7.87601;RPL=89.0;RPR=105.0;EPP=17.5166;EPPR=10.8919;DPRA=0.0;ODDS=318.26;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994845;PAIREDR=0.990741;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.2385;Dels=0.0;FS=2.3205;Haplotyp [...]
+chr3 142281612 . A G 5691.91 REJECT NS=2;DP=375;DPB=430.0;AC=2;AN=4;AF=0.5;RO=227;AO=203;PRO=0.0;PAO=0.0;QR=8727;QA=7722;PQR=0.0;PQA=0.0;SRF=124;SRR=103;SAF=95;SAR=108;SRP=7.22889;SAP=4.81808;AB=0.472093;ABP=5.91906;RUN=1;RPP=6.10171;RPPR=5.77486;RPL=110.0;RPR=93.0;EPP=3.53445;EPPR=3.09639;DPRA=0.0;ODDS=292.414;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985222;PAIREDR=0.991189;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7;Dels=0.0;FS=4.9845;HaplotypeS [...]
+chr3 142503605 . G A 10274.0 REJECT NS=2;DP=376;DPB=425.0;AC=2;AN=4;AF=0.5;RO=94;AO=331;PRO=0.0;PAO=0.0;QR=3544;QA=12808;PQR=0.0;PQA=0.0;SRF=51;SRR=43;SAF=184;SAR=147;SRP=4.48875;SAP=11.9914;AB=0.778824;ABP=289.997;RUN=1;RPP=7.11051;RPPR=3.37991;RPL=178.0;RPR=153.0;EPP=25.8468;EPPR=14.1911;DPRA=0.0;ODDS=121.704;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996979;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.737;Dels=0.0;FS=1.885;HaplotypeScore [...]
+chr3 147016796 . G A 11722.0 REJECT NS=2;DP=308;DPB=356.0;AC=4;AN=4;AF=1.0;RO=0;AO=356;PRO=0.0;PAO=0.0;QR=0;QA=13690;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=141;SAR=215;SRP=0.0;SAP=36.4119;AB=0.0;ABP=0.0;RUN=1;RPP=9.25633;RPPR=0.0;RPL=194.0;RPR=162.0;EPP=8.49998;EPPR=0.0;DPRA=0.0;ODDS=64.2138;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997191;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8657;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.755;SOR=1 [...]
+chr3 150013987 . C T 4977.69 REJECT NS=2;DP=349;DPB=396.0;AC=2;AN=4;AF=0.5;RO=214;AO=182;PRO=0.0;PAO=0.0;QR=8055;QA=6795;PQR=0.0;PQA=0.0;SRF=93;SRR=121;SAF=96;SAR=86;SRP=10.9656;SAP=4.20342;AB=0.459596;ABP=8.62542;RUN=1;RPP=4.72839;RPPR=13.4009;RPL=97.0;RPR=85.0;EPP=3.77389;EPPR=3.05089;DPRA=0.0;ODDS=212.251;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995327;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1465;Dels=0.0;FS=5.8285;HaplotypeScore= [...]
+chr3 151500916 . C A 8962.619999999999 REJECT NS=2;DP=383;DPB=440.0;AC=3;AN=4;AF=0.75;RO=122;AO=317;PRO=0.0;PAO=0.0;QR=4682;QA=12197;PQR=0.0;PQA=0.0;SRF=55;SRR=67;SAF=166;SAR=151;SRP=5.57335;SAP=4.55157;AB=0.632836;ABP=54.3543;RUN=1;RPP=3.18155;RPPR=11.625;RPL=156.0;RPR=161.0;EPP=84.396;EPPR=31.4886;DPRA=0.0;ODDS=66.5094;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9274;MQMR=60.0;PAIRED=0.977918;PAIREDR=0.967213;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.197;Dels=0.0;FS=4. [...]
+chr3 151899661 . T C 4867.165000000001 REJECT NS=2;DP=317;DPB=363.0;AC=2;AN=4;AF=0.5;RO=183;AO=180;PRO=0.0;PAO=0.0;QR=7023;QA=6904;PQR=0.0;PQA=0.0;SRF=109;SRR=74;SAF=107;SAR=73;SRP=17.5461;SAP=16.956;AB=0.495868;ABP=3.06414;RUN=1;RPP=26.3657;RPPR=33.8737;RPL=68.0;RPR=112.0;EPP=24.2907;EPPR=12.9896;DPRA=0.0;ODDS=250.018;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994444;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9985;Dels=0.0;FS=0.0;Haploty [...]
+chr3 151899704 . T A 14170.65 REJECT NS=2;DP=373;DPB=425.0;AC=4;AN=4;AF=1.0;RO=2;AO=423;PRO=0.0;PAO=0.0;QR=56;QA=16310;PQR=0.0;PQA=0.0;SRF=1;SRR=1;SAF=221;SAR=202;SRP=3.0103;SAP=4.8635;AB=0.0;ABP=0.0;RUN=1;RPP=7.9436;RPPR=7.35324;RPL=227.0;RPR=196.0;EPP=4.8635;EPPR=3.0103;DPRA=0.0;ODDS=61.7475;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992908;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.667;Dels=0.0;FS=0.0;HaplotypeScore=3.866;MLEAC=2;MLEAF [...]
+chr3 171016279 . T G 9426.15 REJECT NS=2;DP=369;DPB=411.0;AC=2;AN=4;AF=0.5;RO=100;AO=310;PRO=0.0;PAO=0.0;QR=3823;QA=11788;PQR=0.0;PQA=0.0;SRF=46;SRR=54;SAF=150;SAR=160;SRP=4.40004;SAP=3.71077;AB=0.754258;ABP=233.794;RUN=1;RPP=3.71077;RPPR=10.0459;RPL=160.0;RPR=150.0;EPP=5.27984;EPPR=7.26639;DPRA=0.0;ODDS=207.732;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993548;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.237;Dels=0.0;FS=1.856;HaplotypeScor [...]
+chr3 171016302 . C G 8705.76 REJECT NS=2;DP=334;DPB=374.0;AC=2;AN=4;AF=0.5;RO=86;AO=287;PRO=0.0;PAO=0.0;QR=3264;QA=10920;PQR=0.0;PQA=0.0;SRF=38;SRR=48;SAF=125;SAR=162;SRP=5.53527;SAP=13.3683;AB=0.76738;ABP=235.253;RUN=1;RPP=15.7289;RPPR=17.5541;RPL=164.0;RPR=123.0;EPP=24.2635;EPPR=17.5541;DPRA=0.0;ODDS=156.963;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993031;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.862;Dels=0.0;FS=2.363;HaplotypeScore= [...]
+chr3 178768011 . A G 1002.03 REJECT NS=1;DP=82;DPB=82.0;AC=1;AN=4;AF=0.5;RO=44;AO=38;PRO=0.0;PAO=0.0;QR=1698;QA=1431;PQR=0.0;PQA=0.0;SRF=20;SRR=24;SAF=13;SAR=25;SRP=3.79993;SAP=11.239;AB=0.463415;ABP=3.96363;RUN=1;RPP=8.7247;RPPR=12.6832;RPL=24.0;RPR=14.0;EPP=6.66752;EPPR=12.6832;DPRA=0.0;ODDS=230.727;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.894737;PAIREDR=0.931818;technology.ILLUMINA=1.0;BaseQRankSum=-0.934;FS=4.481;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankS [...]
+chr3 178780691 . G A 10413.8 REJECT NS=2;DP=378;DPB=436.0;AC=2;AN=4;AF=0.5;RO=102;AO=334;PRO=0.0;PAO=0.0;QR=3891;QA=12986;PQR=0.0;PQA=0.0;SRF=39;SRR=63;SAF=167;SAR=167;SRP=15.2727;SAP=3.0103;AB=0.766055;ABP=271.078;RUN=1;RPP=7.40526;RPPR=3.0103;RPL=154.0;RPR=180.0;EPP=20.5901;EPPR=5.13919;DPRA=0.0;ODDS=126.87;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9461;MQMR=60.0;PAIRED=0.997006;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9025;Dels=0.0;FS=8.5895;HaplotypeSc [...]
+chr3 178782021 . C T 2336.41 PASS SOMATIC;NS=2;DP=409;DPB=409.0;AC=1;AN=3;AF=0.25;RO=315;AO=94;PRO=0.0;PAO=0.0;QR=12013;QA=3544;PQR=0.0;PQA=0.0;SRF=138;SRR=177;SAF=44;SAR=50;SRP=13.4954;SAP=3.84193;AB=0.325175;ABP=78.9359;RUN=1;RPP=7.53805;RPPR=10.5174;RPL=40.0;RPR=54.0;EPP=10.4949;EPPR=8.80779;DPRA=0.0;ODDS=74.7632;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990476;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.786;Dels=0.0;FS=3.511;Ha [...]
+chr3 178917005 . A G 4576.28 REJECT NS=2;DP=178;DPB=200.0;AC=2;AN=4;AF=0.5;RO=45;AO=155;PRO=0.0;PAO=0.0;QR=1740;QA=5985;PQR=0.0;PQA=0.0;SRF=13;SRR=32;SAF=49;SAR=106;SRP=20.4303;SAP=48.5272;AB=0.775;ABP=134.384;RUN=1;RPP=151.637;RPPR=33.1696;RPL=129.0;RPR=26.0;EPP=5.37791;EPPR=3.44459;DPRA=0.0;ODDS=100.042;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987097;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0805;Dels=0.0;FS=3.0515;HaplotypeScore=0. [...]
+chr3 178922274 . C A 10240.735 REJECT NS=2;DP=271;DPB=311.0;AC=4;AN=4;AF=1.0;RO=0;AO=311;PRO=0.0;PAO=0.0;QR=0;QA=12042;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=231;SAR=80;SRP=0.0;SAP=162.212;AB=0.0;ABP=0.0;RUN=1;RPP=77.0847;RPPR=0.0;RPL=104.0;RPR=207.0;EPP=3.57586;EPPR=0.0;DPRA=0.0;ODDS=54.2793;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.545;SOR=2.299 GT [...]
+chr3 178927410 . A G 3212.19 PASS SOMATIC;NS=2;DP=424;DPB=424.0;AC=1;AN=3;AF=0.25;RO=305;AO=119;PRO=0.0;PAO=0.0;QR=11742;QA=4596;PQR=0.0;PQA=0.0;SRF=178;SRR=127;SAF=65;SAR=54;SRP=21.5283;SAP=5.21827;AB=0.375394;ABP=45.7616;RUN=1;RPP=3.02855;RPPR=6.77656;RPL=60.0;RPR=59.0;EPP=11.0575;EPPR=47.4436;DPRA=2.96262;ODDS=67.734;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983193;PAIREDR=0.986885;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.186;Dels=0.0;FS [...]
+chr3 178938747 . A T 4931.54 REJECT NS=2;DP=184;DPB=213.0;AC=2;AN=4;AF=0.5;RO=45;AO=168;PRO=0.0;PAO=0.0;QR=1727;QA=6499;PQR=0.0;PQA=0.0;SRF=32;SRR=13;SAF=132;SAR=36;SRP=20.4303;SAP=122.131;AB=0.788732;ABP=157.246;RUN=1;RPP=89.9209;RPPR=38.1882;RPL=43.0;RPR=125.0;EPP=17.9521;EPPR=4.21667;DPRA=0.0;ODDS=37.465;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=56.4762;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.3915;Dels=0.0;FS=0.615;HaplotypeScore=4.85 [...]
+chr3 180004571 . C T 1146.725 REJECT NS=2;DP=243;DPB=278.0;AC=2;AN=4;AF=0.5;RO=216;AO=62;PRO=0.0;PAO=0.0;QR=8251;QA=2326;PQR=0.0;PQA=0.0;SRF=143;SRR=73;SAF=40;SAR=22;SRP=52.2706;SAP=14.358;AB=0.223022;ABP=188.257;RUN=1;RPP=34.5317;RPPR=115.967;RPL=16.0;RPR=46.0;EPP=6.51267;EPPR=4.45795;DPRA=0.0;ODDS=92.6167;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.967742;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.5985;Dels=0.0;FS=3.817;HaplotypeScore=2 [...]
+chr3 181330688 . A T 1624.48 REJECT NS=2;DP=337;DPB=384.0;AC=2;AN=4;AF=0.5;RO=296;AO=88;PRO=0.0;PAO=0.0;QR=11304;QA=3384;PQR=0.0;PQA=0.0;SRF=137;SRR=159;SAF=32;SAR=56;SRP=6.56095;SAP=17.2236;AB=0.229167;ABP=247.663;RUN=1;RPP=3.0103;RPPR=3.47981;RPL=44.0;RPR=44.0;EPP=3.0103;EPPR=9.61275;DPRA=0.0;ODDS=182.937;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989865;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1255;Dels=0.0;FS=6.3335;HaplotypeScore=0 [...]
+chr3 181330770 . G A 5442.085 REJECT NS=2;DP=238;DPB=271.0;AC=3;AN=4;AF=0.75;RO=74;AO=197;PRO=0.0;PAO=0.0;QR=2735;QA=7495;PQR=0.0;PQA=0.0;SRF=39;SRR=35;SAF=51;SAR=146;SRP=3.47981;SAP=102.49;AB=0.640777;ABP=38.4707;RUN=1;RPP=78.9457;RPPR=29.4201;RPL=140.0;RPR=57.0;EPP=9.89949;EPPR=14.748;DPRA=0.0;ODDS=41.5625;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984772;PAIREDR=0.959459;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.59;Dels=0.0;FS=19.5685;HaplotypeSc [...]
+chr3 183211906 . A G 9000.485 REJECT NS=2;DP=378;DPB=436.0;AC=3;AN=4;AF=0.75;RO=116;AO=319;PRO=0.0;PAO=0.0;QR=4478;QA=12327;PQR=0.0;PQA=0.0;SRF=56;SRR=60;SAF=185;SAR=134;SRP=3.30981;SAP=20.7156;AB=0.639752;ABP=57.6343;RUN=1;RPP=3.56168;RPPR=15.6647;RPL=155.0;RPR=164.0;EPP=6.61127;EPPR=3.68421;DPRA=0.0;ODDS=71.4737;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984326;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.068;Dels=0.0;FS=4.0085;HaplotypeS [...]
+chr3 183212026 . C T 1967.54 REJECT NS=2;DP=336;DPB=381.0;AC=2;AN=4;AF=0.5;RO=286;AO=95;PRO=0.0;PAO=0.0;QR=11026;QA=3640;PQR=0.0;PQA=0.0;SRF=87;SRR=199;SAF=16;SAR=79;SRP=98.2514;SAP=93.7321;AB=0.249344;ABP=210.93;RUN=1;RPP=4.86177;RPPR=15.1584;RPL=52.0;RPR=43.0;EPP=3.21602;EPPR=4.49844;DPRA=0.0;ODDS=138.647;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.98951;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7945;Dels=0.0;FS=16.556;HaplotypeScore=4. [...]
+chr3 183226114 . G T 2557.795 REJECT NS=2;DP=392;DPB=450.0;AC=2;AN=4;AF=0.5;RO=337;AO=113;PRO=0.0;PAO=0.0;QR=12708;QA=4399;PQR=0.0;PQA=0.0;SRF=167;SRR=170;SAF=56;SAR=57;SRP=3.06829;SAP=3.02952;AB=0.251111;ABP=245.134;RUN=1;RPP=3.02952;RPPR=5.33642;RPL=56.0;RPR=57.0;EPP=3.49071;EPPR=4.09926;DPRA=0.0;ODDS=183.711;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99115;PAIREDR=0.997033;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.425;Dels=0.0;FS=3.225;HaplotypeS [...]
+chr3 187447032 . G A 14466.5 REJECT NS=2;DP=391;DPB=453.0;AC=4;AN=4;AF=1.0;RO=0;AO=453;PRO=0.0;PAO=0.0;QR=0;QA=16858;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=225;SAR=228;SRP=0.0;SAP=3.05344;AB=0.0;ABP=0.0;RUN=1;RPP=8.88238;RPPR=0.0;RPL=209.0;RPR=244.0;EPP=4.08885;EPPR=0.0;DPRA=0.0;ODDS=80.8962;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997792;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=7.8458;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.265;SOR=0 [...]
+chr3 187451609 . A G 5797.665000000001 REJECT NS=2;DP=162;DPB=187.0;AC=4;AN=4;AF=1.0;RO=0;AO=186;PRO=0.0;PAO=0.0;QR=0;QA=7078;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=30;SAR=156;SRP=0.0;SAP=188.356;AB=0.0;ABP=0.0;RUN=1;RPP=212.639;RPPR=0.0;RPL=160.0;RPR=26.0;EPP=81.5102;EPPR=0.0;DPRA=0.0;ODDS=34.9247;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9238;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.35;SOR= [...]
+chr4 1801511 . C T 5671.5650000000005 REJECT NS=2;DP=381;DPB=436.0;AC=2;AN=4;AF=0.5;RO=226;AO=210;PRO=0.0;PAO=0.0;QR=8579;QA=7907;PQR=0.0;PQA=0.0;SRF=114;SRR=112;SAF=102;SAR=108;SRP=3.04873;SAP=3.38255;AB=0.481651;ABP=4.28529;RUN=1;RPP=7.14644;RPPR=5.47002;RPL=95.0;RPR=115.0;EPP=3.17575;EPPR=3.16403;DPRA=0.0;ODDS=350.884;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2465;Dels=0.0;FS=4.9135;Haploty [...]
+chr4 1807894 . G A 14752.65 REJECT NS=2;DP=387;DPB=444.0;AC=4;AN=4;AF=1.0;RO=0;AO=444;PRO=0.0;PAO=0.0;QR=0;QA=17078;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=201;SAR=243;SRP=0.0;SAP=11.6375;AB=0.0;ABP=0.0;RUN=1;RPP=9.34865;RPPR=0.0;RPL=240.0;RPR=204.0;EPP=3.49937;EPPR=0.0;DPRA=0.0;ODDS=74.1887;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.988739;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8794;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.57;SOR=0.9 [...]
+chr4 1954945 . A G 13037.3 REJECT NS=2;DP=343;DPB=401.0;AC=4;AN=4;AF=1.0;RO=0;AO=401;PRO=0.0;PAO=0.0;QR=0;QA=15444;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=222;SAR=179;SRP=0.0;SAP=13.0229;AB=0.0;ABP=0.0;RUN=1;RPP=8.90739;RPPR=0.0;RPL=184.0;RPR=217.0;EPP=58.2502;EPPR=0.0;DPRA=0.0;ODDS=75.4868;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.990025;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.7934;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.73;SOR=0.88 [...]
+chr4 1980346 . A T 5483.96 REJECT NS=2;DP=316;DPB=360.0;AC=2;AN=4;AF=0.5;RO=170;AO=190;PRO=0.0;PAO=0.0;QR=6490;QA=7358;PQR=0.0;PQA=0.0;SRF=100;SRR=70;SAF=123;SAR=67;SRP=14.5063;SAP=38.851;AB=0.527778;ABP=5.42305;RUN=1;RPP=62.2572;RPPR=69.2274;RPL=59.0;RPR=131.0;EPP=6.71323;EPPR=10.3678;DPRA=0.0;ODDS=277.618;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988235;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.2705;Dels=0.0;FS=2.915;HaplotypeScore=0. [...]
+chr4 16514073 . CA C . PASS SOMATIC;AC=1;AN=4 GT:AD:DP:MM:MQS:NQSBQ:NQSMM:REnd:RStart:SC:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:35,0:35:0.314286,0.0:60.0,0.0:37.8839,0.0:0.00595238,0.0:0,0:0,0:30,5,0,0:0:0:35:.:.:.:.:0:.:2.36041e-06 0/1:46,34:80:0.152174,0.0:60.0,60.5882:38.7551,38.4592:0.0,0.0:81,10:19,10:40,6,29,5:34:43:80:.:.:.:.:1:.:-0.0106171
+chr4 20256722 . G A 794.014 REJECT NS=1;DP=60;DPB=60.0;AC=1;AN=4;AF=0.5;RO=29;AO=31;PRO=0.0;PAO=0.0;QR=1077;QA=1169;PQR=0.0;PQA=0.0;SRF=3;SRR=26;SAF=4;SAR=27;SRP=42.621;SAP=40.0654;AB=0.516667;ABP=3.15506;RUN=1;RPP=8.68415;RPPR=3.08518;RPL=20.0;RPR=11.0;EPP=8.68415;EPPR=4.88226;DPRA=0.0;ODDS=165.151;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=0.77;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-2.124;QD=18. [...]
+chr4 20492380 . A G 3527.05 PASS SOMATIC;NS=2;DP=426;DPB=426.0;AC=1;AN=3;AF=0.25;RO=295;AO=130;PRO=0.0;PAO=0.0;QR=11379;QA=4974;PQR=0.0;PQA=0.0;SRF=169;SRR=126;SAF=65;SAR=65;SRP=16.6206;SAP=3.0103;AB=0.402477;ABP=29.6932;RUN=1;RPP=11.0949;RPPR=8.37641;RPL=54.0;RPR=76.0;EPP=16.1059;EPPR=11.0263;DPRA=3.13592;ODDS=65.2422;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99661;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.695;Dels=0.0;FS=7.674; [...]
+chr4 20492417 . G T 8641.64 REJECT NS=2;DP=381;DPB=427.0;AC=3;AN=4;AF=0.75;RO=127;AO=300;PRO=0.0;PAO=0.0;QR=4936;QA=11495;PQR=0.0;PQA=0.0;SRF=53;SRR=74;SAF=156;SAR=144;SRP=10.5506;SAP=4.05261;AB=0.623145;ABP=47.3998;RUN=1;RPP=4.05261;RPPR=7.95168;RPL=156.0;RPR=144.0;EPP=3.47355;EPPR=3.16418;DPRA=0.0;ODDS=57.1719;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996667;PAIREDR=0.992126;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.722;Dels=0.0;FS=4.703;Haplotyp [...]
+chr4 20520993 . T C 10752.849999999999 REJECT NS=2;DP=287;DPB=332.0;AC=4;AN=4;AF=1.0;RO=0;AO=332;PRO=0.0;PAO=0.0;QR=0;QA=12715;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=226;SAR=106;SRP=0.0;SAP=97.1946;AB=0.0;ABP=0.0;RUN=1;RPP=85.0553;RPPR=0.0;RPL=110.0;RPR=222.0;EPP=49.1606;EPPR=0.0;DPRA=0.0;ODDS=59.2258;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996988;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8239;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27 [...]
+chr4 20533700 . A AT 4524.93 REJECT NS=2;DP=239;DPB=297.188;AC=3;AN=4;AF=0.75;RO=53;AO=177;PRO=44.0;PAO=48.0;QR=2020;QA=6548;PQR=1583.5;PQA=1766.5;SRF=11;SRR=42;SAF=41;SAR=136;SRP=42.3836;SAP=113.731;AB=0.685393;ABP=56.1504;RUN=1;RPP=48.6603;RPPR=4.03458;RPL=119.0;RPR=58.0;EPP=3.61144;EPPR=9.93443;DPRA=0.0;ODDS=19.3779;GTI=0;TYPE=ins;CIGAR=1M1I15M;NUMALT=1;MEANALT=4.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4515;FS=0.348;MLEAC=1;MLEAF= [...]
+chr4 20552510 . A C 5194.780000000001 REJECT NS=2;DP=386;DPB=439.0;AC=2;AN=4;AF=0.5;RO=238;AO=200;PRO=0.0;PAO=0.0;QR=8996;QA=7385;PQR=0.0;PQA=0.0;SRF=132;SRR=106;SAF=108;SAR=92;SRP=9.17801;SAP=5.78978;AB=0.455581;ABP=10.5338;RUN=1;RPP=18.6883;RPPR=25.8199;RPL=119.0;RPR=81.0;EPP=44.746;EPPR=38.0823;DPRA=0.0;ODDS=312.827;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985;PAIREDR=0.995798;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0225;Dels=0.0;FS=0.375;Ha [...]
+chr4 20569254 . A G 8308.0 REJECT NS=2;DP=298;DPB=342.0;AC=2;AN=4;AF=0.5;RO=69;AO=273;PRO=0.0;PAO=0.0;QR=2629;QA=10536;PQR=0.0;PQA=0.0;SRF=23;SRR=46;SAF=82;SAR=191;SRP=19.6583;SAP=97.5131;AB=0.798246;ABP=267.244;RUN=1;RPP=66.0148;RPPR=12.1053;RPL=181.0;RPR=92.0;EPP=23.6989;EPPR=8.32883;DPRA=0.0;ODDS=55.7397;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989011;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.206;Dels=0.0;FS=2.0895;HaplotypeScore=6. [...]
+chr4 20569259 . C T 8053.21 REJECT NS=2;DP=281;DPB=324.0;AC=2;AN=4;AF=0.5;RO=62;AO=262;PRO=0.0;PAO=0.0;QR=2401;QA=10199;PQR=0.0;PQA=0.0;SRF=19;SRR=43;SAF=80;SAR=182;SRP=23.184;SAP=89.2393;AB=0.808642;ABP=271.093;RUN=1;RPP=79.3931;RPPR=17.0198;RPL=179.0;RPR=83.0;EPP=19.056;EPPR=4.27115;DPRA=0.0;ODDS=29.3747;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992366;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1195;Dels=0.0;FS=2.7785;HaplotypeScore=4 [...]
+chr4 25507545 . C A 14106.3 REJECT NS=2;DP=367;DPB=421.0;AC=4;AN=4;AF=1.0;RO=0;AO=421;PRO=0.0;PAO=0.0;QR=0;QA=16312;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=231;SAR=190;SRP=0.0;SAP=11.6807;AB=0.0;ABP=0.0;RUN=1;RPP=27.567;RPPR=0.0;RPL=176.0;RPR=245.0;EPP=12.5472;EPPR=0.0;DPRA=0.0;ODDS=70.4754;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992874;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8966;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.865;SOR=0.9 [...]
+chr4 27162478 . T G 5340.265 REJECT NS=2;DP=369;DPB=425.0;AC=2;AN=4;AF=0.5;RO=227;AO=198;PRO=0.0;PAO=0.0;QR=8768;QA=7510;PQR=0.0;PQA=0.0;SRF=108;SRR=119;SAF=80;SAR=118;SRP=4.16778;SAP=18.8467;AB=0.465882;ABP=7.30726;RUN=1;RPP=4.107;RPPR=4.16778;RPL=104.0;RPR=94.0;EPP=3.40511;EPPR=5.16264;DPRA=0.0;ODDS=336.77;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994949;PAIREDR=0.991189;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.009;Dels=0.0;FS=8.1365;HaplotypeSc [...]
+chr4 41749668 . C T 2495.63 REJECT NS=2;DP=438;DPB=507.0;AC=2;AN=4;AF=0.5;RO=380;AO=127;PRO=0.0;PAO=0.0;QR=14393;QA=4731;PQR=0.0;PQA=0.0;SRF=196;SRR=184;SAF=67;SAR=60;SRP=3.83317;SAP=3.84811;AB=0.250493;ABP=277.16;RUN=1;RPP=6.8574;RPPR=3.03316;RPL=56.0;RPR=71.0;EPP=3.0274;EPPR=19.6735;DPRA=0.0;ODDS=246.494;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992126;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7955;Dels=0.0;FS=1.07;HaplotypeScore=6.86 [...]
+chr4 45001171 . G A 14476.6 REJECT NS=2;DP=380;DPB=425.0;AC=4;AN=4;AF=1.0;RO=0;AO=425;PRO=0.0;PAO=0.0;QR=0;QA=16279;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=260;SAR=165;SRP=0.0;SAP=49.1222;AB=0.0;ABP=0.0;RUN=1;RPP=18.4661;RPPR=0.0;RPL=185.0;RPR=240.0;EPP=65.9626;EPPR=0.0;DPRA=0.0;ODDS=57.9733;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.990588;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8905;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.3;SOR=1.16 [...]
+chr4 45001191 . C T 15511.75 REJECT NS=2;DP=410;DPB=456.0;AC=4;AN=4;AF=1.0;RO=0;AO=454;PRO=0.0;PAO=0.0;QR=0;QA=17373;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=246;SAR=208;SRP=0.0;SAP=9.91692;AB=0.0;ABP=0.0;RUN=1;RPP=3.02943;RPPR=0.0;RPL=226.0;RPR=228.0;EPP=48.946;EPPR=0.0;DPRA=0.0;ODDS=59.8465;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993392;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8572;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.695;SOR=0. [...]
+chr4 45001226 . A G 8686.285 PASS DP=200;AC=4;AN=4;AF=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.9293;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.02;SOR=0.9395 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:0,95:95:99.0:4253,286,0:95:100:95:1:.:.:.:.:.:2.36041e-06 1/1:0,305:305:99.0:13176,909,0:305:100:305:.:1:.:.:.:.:-0.0106171
+chr4 45001226 . ATGA GTGC 13618.8 REJECT NS=2;DP=388;DPB=396.25;AC=4;AN=4;AF=1.0;RO=0;AO=386;PRO=0.0;PAO=17.0;QR=0;QA=14569;PQR=0.0;PQA=641.0;SRF=0;SRR=0;SAF=170;SAR=216;SRP=0.0;SAP=14.914;AB=0.0;ABP=0.0;RUN=1;RPP=13.9014;RPPR=0.0;RPL=215.0;RPR=171.0;EPP=3.37034;EPPR=0.0;DPRA=0.0;ODDS=62.3289;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=1;MEANALT=2.0;LEN=4;MQM=60.0;MQMR=0.0;PAIRED=0.989637;PAIREDR=0.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:Cal [...]
+chr4 45001229 . A C 8541.785 PASS DP=196;AC=4;AN=4;AF=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.8201;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.895;SOR=1.012 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:0,90:90:99.0:4260,286,0:90:100:90:1:.:.:.:.:.:2.36041e-06 1/1:0,300:301:99.0:12880,891,0:300:100:300:.:1:.:.:.:.:-0.0106171
+chr4 45001235 . C T 13004.45 REJECT NS=2;DP=342;DPB=388.0;AC=4;AN=4;AF=1.0;RO=0;AO=388;PRO=0.0;PAO=0.0;QR=0;QA=14907;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=162;SAR=226;SRP=0.0;SAP=25.9339;AB=0.0;ABP=0.0;RUN=1;RPP=42.4998;RPPR=0.0;RPL=236.0;RPR=152.0;EPP=3.09985;EPPR=0.0;DPRA=0.0;ODDS=59.2717;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.989691;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.7785;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.385;SOR=1 [...]
+chr4 55130078 . T C 1805.51 REJECT NS=2;DP=401;DPB=451.0;AC=2;AN=4;AF=0.5;RO=357;AO=93;PRO=0.0;PAO=0.0;QR=13649;QA=3443;PQR=0.0;PQA=0.0;SRF=151;SRR=206;SAF=39;SAR=54;SRP=21.41;SAP=8.26386;AB=0.206208;ABP=341.129;RUN=1;RPP=4.15441;RPPR=10.4614;RPL=43.0;RPR=50.0;EPP=3.22044;EPPR=6.22797;DPRA=0.0;ODDS=78.5143;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=59.9608;PAIRED=0.989247;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3365;Dels=0.0;FS=0.3905;HaplotypeScore [...]
+chr4 55130154 . G A 783.537 REJECT NS=2;DP=212;DPB=237.0;AC=2;AN=4;AF=0.5;RO=187;AO=49;PRO=0.0;PAO=0.0;QR=6446;QA=1714;PQR=0.0;PQA=0.0;SRF=66;SRR=121;SAF=18;SAR=31;SRP=38.1371;SAP=10.4997;AB=0.206751;ABP=180.036;RUN=1;RPP=63.6786;RPPR=233.871;RPL=43.0;RPR=6.0;EPP=4.11819;EPPR=12.7761;DPRA=0.0;ODDS=32.2554;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=59.9786;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5155;Dels=0.0;FS=0.63;HaplotypeScore=62.9861 [...]
+chr4 55133726 . T G 1322.99 REJECT NS=2;DP=347;DPB=393.0;AC=2;AN=4;AF=0.5;RO=319;AO=74;PRO=0.0;PAO=0.0;QR=12106;QA=2745;PQR=0.0;PQA=0.0;SRF=167;SRR=152;SAF=34;SAR=40;SRP=4.5419;SAP=4.06669;AB=0.188295;ABP=334.671;RUN=1;RPP=4.88833;RPPR=18.0472;RPL=33.0;RPR=41.0;EPP=10.5224;EPPR=3.18048;DPRA=0.0;ODDS=59.2102;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.419;Dels=0.0;FS=2.697;HaplotypeScore=2.9661;M [...]
+chr4 55133936 . C T 984.54 REJECT NS=2;DP=181;DPB=209.0;AC=2;AN=4;AF=0.5;RO=155;AO=54;PRO=0.0;PAO=0.0;QR=5931;QA=2054;PQR=0.0;PQA=0.0;SRF=57;SRR=98;SAF=17;SAR=37;SRP=26.5603;SAP=19.0953;AB=0.258373;ABP=108.997;RUN=1;RPP=55.1256;RPPR=86.0726;RPL=45.0;RPR=9.0;EPP=10.8919;EPPR=4.14507;DPRA=0.0;ODDS=131.1;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.014;Dels=0.0;FS=5.7425;HaplotypeScore=0.9665;MLEAC [...]
+chr4 55139771 . T C 2230.7349999999997 REJECT NS=2;DP=381;DPB=441.0;AC=2;AN=4;AF=0.5;RO=332;AO=107;PRO=0.0;PAO=0.0;QR=12306;QA=4077;PQR=0.0;PQA=0.0;SRF=186;SRR=146;SAF=56;SAR=51;SRP=13.4752;SAP=3.51765;AB=0.24263;ABP=256.738;RUN=1;RPP=15.6941;RPPR=3.11495;RPL=41.0;RPR=66.0;EPP=20.0777;EPPR=15.6729;DPRA=0.0;ODDS=157.736;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996988;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.806;Dels=0.0;FS=6.6205;Haplo [...]
+chr4 55141055 . A G 14387.95 REJECT NS=2;DP=383;DPB=445.0;AC=4;AN=4;AF=1.0;RO=0;AO=443;PRO=0.0;PAO=0.0;QR=0;QA=16983;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=244;SAR=199;SRP=0.0;SAP=12.9363;AB=0.0;ABP=0.0;RUN=1;RPP=5.60332;RPPR=0.0;RPL=233.0;RPR=210.0;EPP=3.0152;EPPR=0.0;DPRA=0.0;ODDS=81.7029;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997743;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9243;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.49;SOR=0.9 [...]
+chr4 55143577 . G A 1885.29 REJECT NS=2;DP=384;DPB=434.0;AC=2;AN=4;AF=0.5;RO=342;AO=92;PRO=0.0;PAO=0.0;QR=13085;QA=3516;PQR=0.0;PQA=0.0;SRF=176;SRR=166;SAF=43;SAR=49;SRP=3.64523;SAP=3.86001;AB=0.211982;ABP=315.722;RUN=1;RPP=3.0103;RPPR=8.7247;RPL=46.0;RPR=46.0;EPP=3.10471;EPPR=3.23888;DPRA=0.0;ODDS=88.0366;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997076;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.758;Dels=0.0;FS=5.082;HaplotypeScore=0.94 [...]
+chr4 55152040 . C T 1456.1799999999998 REJECT NS=2;DP=330;DPB=378.0;AC=2;AN=4;AF=0.5;RO=298;AO=79;PRO=0.0;PAO=0.0;QR=11354;QA=2928;PQR=0.0;PQA=0.0;SRF=197;SRR=101;SAF=45;SAR=34;SRP=70.1656;SAP=6.33623;AB=0.208995;ABP=281.051;RUN=1;RPP=6.33623;RPPR=8.72317;RPL=34.0;RPR=45.0;EPP=15.1321;EPPR=21.2274;DPRA=0.0;ODDS=93.8528;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.1342;PAIRED=1.0;PAIREDR=0.993289;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0255;Dels=0.0;FS=3.963;Ha [...]
+chr4 55161254 . C T 3654.49 REJECT NS=2;DP=145;DPB=169.0;AC=2;AN=4;AF=0.5;RO=41;AO=128;PRO=0.0;PAO=0.0;QR=1582;QA=4837;PQR=0.0;PQA=0.0;SRF=35;SRR=6;SAF=95;SAR=33;SRP=47.552;SAP=68.2223;AB=0.757396;ABP=100.264;RUN=1;RPP=106.223;RPPR=36.112;RPL=25.0;RPR=103.0;EPP=9.79615;EPPR=18.3165;DPRA=0.0;ODDS=26.2356;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.95122;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.7535;Dels=0.0;FS=3.396;HaplotypeScore=1.9664 [...]
+chr4 55161391 . T C 15104.95 REJECT NS=2;DP=397;DPB=458.0;AC=4;AN=4;AF=1.0;RO=0;AO=457;PRO=0.0;PAO=0.0;QR=0;QA=17616;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=230;SAR=227;SRP=0.0;SAP=3.05306;AB=0.0;ABP=0.0;RUN=1;RPP=5.98004;RPPR=0.0;RPL=216.0;RPR=241.0;EPP=12.6323;EPPR=0.0;DPRA=0.0;ODDS=80.4296;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997812;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9664;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.815;SOR=0 [...]
+chr4 55260358 . T G 9275.375 REJECT NS=2;DP=251;DPB=296.0;AC=4;AN=4;AF=1.0;RO=0;AO=296;PRO=0.0;PAO=0.0;QR=0;QA=11193;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=189;SAR=107;SRP=0.0;SAP=52.3379;AB=0.0;ABP=0.0;RUN=1;RPP=108.649;RPPR=0.0;RPL=88.0;RPR=208.0;EPP=3.74391;EPPR=0.0;DPRA=0.0;ODDS=59.1888;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.983108;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8152;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.745;SOR=1. [...]
+chr4 55264280 . C T 7727.74 REJECT NS=2;DP=329;DPB=379.0;AC=3;AN=4;AF=0.75;RO=102;AO=277;PRO=0.0;PAO=0.0;QR=3908;QA=10615;PQR=0.0;PQA=0.0;SRF=36;SRR=66;SAF=116;SAR=161;SRP=22.1704;SAP=18.8848;AB=0.634409;ABP=46.79;RUN=1;RPP=5.27584;RPPR=15.2727;RPL=147.0;RPR=130.0;EPP=10.5438;EPPR=3.35092;DPRA=0.0;ODDS=63.3488;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99639;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.488;Dels=0.0;FS=1.083;HaplotypeScore=3 [...]
+chr4 55424289 . T G 9701.61 REJECT NS=2;DP=373;DPB=429.0;AC=2;AN=4;AF=0.5;RO=108;AO=321;PRO=0.0;PAO=0.0;QR=4125;QA=12163;PQR=0.0;PQA=0.0;SRF=57;SRR=51;SAF=159;SAR=162;SRP=3.73412;SAP=3.07118;AB=0.748252;ABP=232.655;RUN=1;RPP=3.55824;RPPR=3.09072;RPL=165.0;RPR=156.0;EPP=16.7088;EPPR=8.15749;DPRA=0.0;ODDS=250.157;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996885;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.148;Dels=0.0;FS=0.636;HaplotypeScore [...]
+chr4 55424655 . A G 9743.11 REJECT NS=2;DP=365;DPB=413.0;AC=2;AN=4;AF=0.5;RO=95;AO=318;PRO=0.0;PAO=0.0;QR=3679;QA=12151;PQR=0.0;PQA=0.0;SRF=38;SRR=57;SAF=167;SAR=151;SRP=11.2619;SAP=4.7584;AB=0.769976;ABP=264.476;RUN=1;RPP=3.44733;RPPR=3.21602;RPL=155.0;RPR=163.0;EPP=6.31531;EPPR=19.6735;DPRA=0.0;ODDS=177.059;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.957895;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.298;Dels=0.0;FS=6.787;HaplotypeScore= [...]
+chr4 55426538 . T C 5590.425 REJECT NS=2;DP=369;DPB=428.0;AC=2;AN=4;AF=0.5;RO=220;AO=207;PRO=0.0;PAO=0.0;QR=8315;QA=7905;PQR=0.0;PQA=0.0;SRF=115;SRR=105;SAF=106;SAR=101;SRP=3.99733;SAP=3.27256;AB=0.483645;ABP=4.00471;RUN=1;RPP=4.27961;RPPR=11.8936;RPL=98.0;RPR=109.0;EPP=3.86001;EPPR=3.16823;DPRA=0.0;ODDS=372.055;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990338;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.964;Dels=0.0;FS=5.0975;HaplotypeSco [...]
+chr4 55426561 . C T 10392.6 REJECT NS=2;DP=388;DPB=447.0;AC=2;AN=4;AF=0.5;RO=108;AO=339;PRO=0.0;PAO=0.0;QR=4087;QA=12980;PQR=0.0;PQA=0.0;SRF=51;SRR=57;SAF=167;SAR=172;SRP=3.73412;SAP=3.17044;AB=0.758389;ABP=262.232;RUN=1;RPP=7.67993;RPPR=3.332;RPL=156.0;RPR=183.0;EPP=7.01375;EPPR=16.6021;DPRA=0.0;ODDS=194.156;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.9941;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.3265;Dels=0.0;FS=6.4565;HaplotypeScore=7 [...]
+chr4 55426618 . A C 3656.66 PASS SOMATIC;NS=2;DP=415;DPB=415.0;AC=1;AN=3;AF=0.25;RO=278;AO=135;PRO=0.0;PAO=0.0;QR=10362;QA=5104;PQR=0.0;PQA=0.0;SRF=114;SRR=164;SAF=58;SAR=77;SRP=22.5379;SAP=8.81698;AB=0.421875;ABP=19.9749;RUN=1;RPP=13.0634;RPPR=14.2895;RPL=80.0;RPR=55.0;EPP=4.31318;EPPR=3.2915;DPRA=3.36842;ODDS=59.579;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996403;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.739;Dels=0.0;FS=0.0;Ha [...]
+chr4 55524252 . G A 1288.83 REJECT NS=1;DP=90;DPB=90.0;AC=1;AN=4;AF=0.5;RO=43;AO=47;PRO=0.0;PAO=0.0;QR=1669;QA=1785;PQR=0.0;PQA=0.0;SRF=20;SRR=23;SAF=19;SAR=28;SRP=3.46479;SAP=6.75262;AB=0.522222;ABP=3.39634;RUN=1;RPP=8.60069;RPPR=4.27278;RPL=29.0;RPR=18.0;EPP=19.6891;EPPR=5.48477;DPRA=0.0;ODDS=277.908;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.973;FS=1.752;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.388 [...]
+chr4 55602765 . G C 1940.625 REJECT NS=2;DP=370;DPB=419.0;AC=2;AN=4;AF=0.5;RO=314;AO=104;PRO=0.0;PAO=0.0;QR=12031;QA=3957;PQR=0.0;PQA=0.0;SRF=152;SRR=162;SAF=46;SAR=58;SRP=3.70185;SAP=6.01695;AB=0.24821;ABP=233.741;RUN=1;RPP=5.09825;RPPR=6.99364;RPL=57.0;RPR=47.0;EPP=9.77527;EPPR=8.43207;DPRA=0.0;ODDS=238.797;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.42;Dels=0.0;FS=1.7525;HaplotypeScore=5.845 [...]
+chr4 55703218 . A G 14939.65 REJECT NS=2;DP=398;DPB=454.0;AC=4;AN=4;AF=1.0;RO=0;AO=453;PRO=0.0;PAO=0.0;QR=0;QA=17208;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=200;SAR=253;SRP=0.0;SAP=16.4753;AB=0.0;ABP=0.0;RUN=1;RPP=7.61689;RPPR=0.0;RPL=242.0;RPR=211.0;EPP=14.5196;EPPR=0.0;DPRA=0.0;ODDS=73.5411;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993377;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.7221;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.685;SOR=0 [...]
+chr4 55703257 . C T 8887.88 REJECT NS=2;DP=345;DPB=394.0;AC=2;AN=4;AF=0.5;RO=96;AO=298;PRO=0.0;PAO=0.0;QR=3697;QA=11219;PQR=0.0;PQA=0.0;SRF=40;SRR=56;SAF=103;SAR=195;SRP=8.80089;SAP=64.6859;AB=0.756345;ABP=227.895;RUN=1;RPP=9.56844;RPPR=4.45795;RPL=164.0;RPR=134.0;EPP=8.72317;EPPR=3.37221;DPRA=0.0;ODDS=214.207;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0671;MQMR=60.1042;PAIRED=0.996644;PAIREDR=0.979167;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.1375;Dels=0.0;FS=4.99;Hap [...]
+chr4 55704161 . C T 14464.5 REJECT NS=2;DP=394;DPB=456.0;AC=4;AN=4;AF=1.0;RO=0;AO=456;PRO=0.0;PAO=0.0;QR=0;QA=17117;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=248;SAR=208;SRP=0.0;SAP=10.6295;AB=0.0;ABP=0.0;RUN=1;RPP=19.0297;RPPR=0.0;RPL=257.0;RPR=199.0;EPP=52.5542;EPPR=0.0;DPRA=0.0;ODDS=81.6503;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9328;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.955;SOR=0.866 G [...]
+chr4 55706827 . T C 13320.65 REJECT NS=2;DP=356;DPB=408.0;AC=4;AN=4;AF=1.0;RO=0;AO=408;PRO=0.0;PAO=0.0;QR=0;QA=15441;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=192;SAR=216;SRP=0.0;SAP=6.07591;AB=0.0;ABP=0.0;RUN=1;RPP=7.80031;RPPR=0.0;RPL=189.0;RPR=219.0;EPP=4.7347;EPPR=0.0;DPRA=0.0;ODDS=68.6004;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995098;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9134;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.925;SOR=0. [...]
+chr4 55946081 . A G 7791.145 REJECT NS=2;DP=207;DPB=240.0;AC=4;AN=4;AF=1.0;RO=1;AO=239;PRO=0.0;PAO=0.0;QR=27;QA=9182;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=156;SAR=83;SRP=5.18177;SAP=51.4278;AB=0.0;ABP=0.0;RUN=1;RPP=68.6542;RPPR=5.18177;RPL=77.0;RPR=162.0;EPP=3.09207;EPPR=5.18177;DPRA=0.0;ODDS=44.2728;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991632;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.673;Dels=0.0;FS=2.206;HaplotypeScore=6.8076;MLEAC=2;M [...]
+chr4 55948108 . A G 9158.51 REJECT NS=2;DP=243;DPB=277.0;AC=4;AN=4;AF=1.0;RO=0;AO=276;PRO=0.0;PAO=0.0;QR=0;QA=10601;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=192;SAR=84;SRP=0.0;SAP=94.7786;AB=0.0;ABP=0.0;RUN=1;RPP=35.2362;RPPR=0.0;RPL=106.0;RPR=170.0;EPP=24.2844;EPPR=0.0;DPRA=0.0;ODDS=46.7816;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996377;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.866;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.36;SOR=1.91 [...]
+chr4 55968053 . A C 6770.26 REJECT NS=2;DP=259;DPB=297.0;AC=2;AN=4;AF=0.5;RO=68;AO=229;PRO=0.0;PAO=0.0;QR=2493;QA=8650;PQR=0.0;PQA=0.0;SRF=52;SRR=16;SAF=170;SAR=59;SRP=44.396;SAP=119.843;AB=0.771044;ABP=192.528;RUN=1;RPP=27.6741;RPPR=28.0461;RPL=89.0;RPR=140.0;EPP=4.15767;EPPR=7.60871;DPRA=0.0;ODDS=78.4305;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0505;Dels=0.0;FS=2.2715;HaplotypeScore=13.7223 [...]
+chr4 58507747 . C T 2298.61 PASS SOMATIC;NS=2;DP=432;DPB=432.0;AC=1;AN=3;AF=0.25;RO=341;AO=91;PRO=0.0;PAO=0.0;QR=13170;QA=3564;PQR=0.0;PQA=0.0;SRF=142;SRR=199;SAF=38;SAR=53;SRP=23.6998;SAP=8.37933;AB=0.293548;ABP=117.776;RUN=1;RPP=4.94315;RPPR=4.44309;RPL=50.0;RPR=41.0;EPP=15.6335;EPPR=23.6998;DPRA=2.54098;ODDS=77.1192;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991202;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.92;Dels=0.0;FS=0.0;Ha [...]
+chr4 64502837 . T C 7711.945 REJECT NS=2;DP=208;DPB=242.0;AC=4;AN=4;AF=1.0;RO=0;AO=241;PRO=0.0;PAO=0.0;QR=0;QA=9179;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=191;SAR=50;SRP=0.0;SAP=182.143;AB=0.0;ABP=0.0;RUN=1;RPP=87.7878;RPPR=0.0;RPL=72.0;RPR=169.0;EPP=5.61426;EPPR=0.0;DPRA=0.0;ODDS=46.1023;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995851;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9638;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.135;SOR=2.61 [...]
+chr4 66197804 . C T 8179.02 REJECT NS=2;DP=330;DPB=374.0;AC=2;AN=4;AF=0.5;RO=91;AO=283;PRO=0.0;PAO=0.0;QR=3314;QA=10379;PQR=0.0;PQA=0.0;SRF=28;SRR=63;SAF=92;SAR=191;SRP=32.2417;SAP=78.2138;AB=0.756684;ABP=217.045;RUN=1;RPP=4.73674;RPPR=11.6246;RPL=149.0;RPR=134.0;EPP=11.3662;EPPR=20.4059;DPRA=0.0;ODDS=147.85;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992933;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.973;Dels=0.0;FS=0.9435;HaplotypeScore=7 [...]
+chr4 66218728 . C T 10004.0 REJECT NS=2;DP=266;DPB=296.0;AC=4;AN=4;AF=1.0;RO=0;AO=296;PRO=0.0;PAO=0.0;QR=0;QA=11320;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=186;SAR=110;SRP=0.0;SAP=45.3834;AB=0.0;ABP=0.0;RUN=1;RPP=79.3346;RPPR=0.0;RPL=97.0;RPR=199.0;EPP=24.4022;EPPR=0.0;DPRA=0.0;ODDS=41.7828;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993243;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.54;SOR=1.365 G [...]
+chr4 66280171 . C T 10683.95 REJECT NS=2;DP=283;DPB=323.0;AC=4;AN=4;AF=1.0;RO=0;AO=323;PRO=0.0;PAO=0.0;QR=0;QA=12440;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=111;SAR=212;SRP=0.0;SAP=71.5898;AB=0.0;ABP=0.0;RUN=1;RPP=111.443;RPPR=0.0;RPL=225.0;RPR=98.0;EPP=3.33972;EPPR=0.0;DPRA=0.0;ODDS=52.4128;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.990712;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9243;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.05;SOR=1.5 [...]
+chr4 66509085 . T G 2306.75 PASS SOMATIC;NS=2;DP=376;DPB=376.0;AC=1;AN=3;AF=0.25;RO=283;AO=92;PRO=0.0;PAO=0.0;QR=10609;QA=3518;PQR=0.0;PQA=0.0;SRF=170;SRR=113;SAF=51;SAR=41;SRP=27.94;SAP=5.3706;AB=0.316151;ABP=88.4439;RUN=1;RPP=6.40913;RPPR=43.9;RPL=40.0;RPR=52.0;EPP=18.9659;EPPR=7.80595;DPRA=3.42353;ODDS=54.0017;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=59.9293;PAIRED=0.98913;PAIREDR=0.996466;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.81;Dels=0.0;FS=5.176 [...]
+chr4 90032048 . T C 3647.34 REJECT NS=1;DP=109;DPB=109.0;AC=2;AN=4;AF=1.0;RO=0;AO=109;PRO=0.0;PAO=0.0;QR=0;QA=4115;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=47;SAR=62;SRP=0.0;SAP=7.4927;AB=0.0;ABP=0.0;RUN=1;RPP=15.4614;RPPR=0.0;RPL=67.0;RPR=42.0;EPP=8.76769;EPPR=0.0;DPRA=0.0;ODDS=72.5463;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.15;SOR=0.981 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV: [...]
+chr4 91530823 . T C 2779.96 PASS SOMATIC;NS=2;DP=401;DPB=401.0;AC=1;AN=3;AF=0.25;RO=295;AO=106;PRO=0.0;PAO=0.0;QR=11466;QA=4094;PQR=0.0;PQA=0.0;SRF=162;SRR=133;SAF=62;SAR=44;SRP=9.20084;SAP=9.64763;AB=0.345277;ABP=66.8459;RUN=1;RPP=5.05886;RPPR=19.2706;RPL=48.0;RPR=58.0;EPP=12.9253;EPPR=8.37641;DPRA=3.26596;ODDS=59.6343;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.634;Dels=0.0;FS=0.441;Hap [...]
+chr4 99035867 . G GCA . PASS SOMATIC;AC=1;AN=4 GT:AD:DP:MM:MQS:NQSBQ:NQSMM:REnd:RStart:SC:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:12,0:12:1.66667,0.0:60.0,0.0:37.9174,0.0:0.0,0.0:0,0:0,0:12,0,0,0:0:0:12:.:.:.:.:0:.:-6.58513e-05 0/1:22,11:33:1.5,2.09091:60.0,60.0:36.8061,39.2273:0.0181818,0.1:81,2:17,2:21,1,11,0:11:33:33:.:.:.:.:1:.:-0.00190096
+chr4 106196951 . A G 6055.43 REJECT NS=2;DP=376;DPB=435.0;AC=2;AN=4;AF=0.5;RO=215;AO=220;PRO=0.0;PAO=0.0;QR=8162;QA=8427;PQR=0.0;PQA=0.0;SRF=100;SRR=115;SAF=110;SAR=110;SRP=5.28277;SAP=3.0103;AB=0.505747;ABP=3.1351;RUN=1;RPP=9.68264;RPPR=7.46434;RPL=97.0;RPR=123.0;EPP=4.94488;EPPR=5.28277;DPRA=0.0;ODDS=360.776;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995349;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.735;Dels=0.0;FS=1.5035;HaplotypeScore [...]
+chr4 108999366 . G A 8030.95 REJECT NS=2;DP=215;DPB=252.0;AC=4;AN=4;AF=1.0;RO=0;AO=252;PRO=0.0;PAO=0.0;QR=0;QA=9617;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=178;SAR=74;SRP=0.0;SAP=96.2113;AB=0.0;ABP=0.0;RUN=1;RPP=85.7675;RPPR=0.0;RPL=77.0;RPR=175.0;EPP=7.18091;EPPR=0.0;DPRA=0.0;ODDS=50.4697;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996032;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.855;SOR=1.8465 [...]
+chr4 109086280 . C T 5822.860000000001 REJECT NS=2;DP=359;DPB=407.0;AC=2;AN=4;AF=0.5;RO=198;AO=208;PRO=0.0;PAO=0.0;QR=7543;QA=7969;PQR=0.0;PQA=0.0;SRF=91;SRR=107;SAF=119;SAR=89;SRP=5.81786;SAP=12.4061;AB=0.511057;ABP=3.44246;RUN=1;RPP=3.67845;RPPR=3.71219;RPL=108.0;RPR=100.0;EPP=21.4261;EPPR=34.9902;DPRA=0.0;ODDS=273.601;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990385;PAIREDR=0.994949;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1625;Dels=0.0;FS=10.6 [...]
+chr4 111009123 . C T 5487.545 REJECT NS=2;DP=343;DPB=399.0;AC=2;AN=4;AF=0.5;RO=206;AO=193;PRO=0.0;PAO=0.0;QR=7875;QA=7444;PQR=0.0;PQA=0.0;SRF=99;SRR=107;SAF=90;SAR=103;SRP=3.68493;SAP=4.91174;AB=0.483709;ABP=3.93005;RUN=1;RPP=3.11156;RPPR=5.07636;RPL=98.0;RPR=95.0;EPP=12.4725;EPPR=13.8044;DPRA=0.0;ODDS=307.768;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990291;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7345;Dels=0.0;FS=1.996;HaplotypeScore [...]
+chr4 139510390 . T A 8746.05 REJECT NS=2;DP=328;DPB=370.0;AC=2;AN=4;AF=0.5;RO=80;AO=290;PRO=0.0;PAO=0.0;QR=3027;QA=10943;PQR=0.0;PQA=0.0;SRF=42;SRR=38;SAF=160;SAR=130;SRP=3.44459;SAP=9.74935;AB=0.783784;ABP=261.826;RUN=1;RPP=20.2623;RPPR=13.8677;RPL=121.0;RPR=169.0;EPP=12.7145;EPPR=9.95901;DPRA=0.0;ODDS=180.414;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996552;PAIREDR=0.9625;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.155;Dels=0.0;FS=11.486;HaplotypeS [...]
+chr4 142849228 . T G 13677.55 REJECT NS=2;DP=367;DPB=420.0;AC=4;AN=4;AF=1.0;RO=0;AO=420;PRO=0.0;PAO=0.0;QR=0;QA=15782;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=196;SAR=224;SRP=0.0;SAP=7.06372;AB=0.0;ABP=0.0;RUN=1;RPP=107.262;RPPR=0.0;RPL=281.0;RPR=139.0;EPP=48.6939;EPPR=0.0;DPRA=0.0;ODDS=69.7695;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9976;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8754;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.05;SOR=0.7 [...]
+chr4 142849240 . G A 12035.099999999999 REJECT NS=2;DP=316;DPB=360.0;AC=4;AN=4;AF=1.0;RO=0;AO=360;PRO=0.0;PAO=0.0;QR=0;QA=13907;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=157;SAR=203;SRP=0.0;SAP=15.7737;AB=0.0;ABP=0.0;RUN=1;RPP=101.836;RPPR=0.0;RPL=244.0;RPR=116.0;EPP=86.998;EPPR=0.0;DPRA=0.0;ODDS=58.6486;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9917;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.7224;MLEAC=2;MLEAF=1.0;MQ=59.995;QD=31 [...]
+chr4 142849725 . A G 6722.45 REJECT NS=2;DP=184;DPB=203.0;AC=4;AN=4;AF=1.0;RO=0;AO=203;PRO=0.0;PAO=0.0;QR=0;QA=7799;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=142;SAR=61;SRP=0.0;SAP=73.1927;AB=0.0;ABP=0.0;RUN=1;RPP=175.541;RPPR=0.0;RPL=38.0;RPR=165.0;EPP=6.10171;EPPR=0.0;DPRA=0.0;ODDS=28.0622;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995074;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.77;SOR=1.769 [...]
+chr4 142851087 . G A 8978.78 REJECT NS=2;DP=242;DPB=274.0;AC=4;AN=4;AF=1.0;RO=0;AO=274;PRO=0.0;PAO=0.0;QR=0;QA=10435;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=231;SAR=43;SRP=0.0;SAP=283.114;AB=0.0;ABP=0.0;RUN=1;RPP=24.4397;RPPR=0.0;RPL=111.0;RPR=163.0;EPP=10.1429;EPPR=0.0;DPRA=0.0;ODDS=44.1871;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=57.8029;MQMR=0.0;PAIRED=0.99635;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=58.12;QD=28.23;SOR=3.5 [...]
+chr4 142851140 . A G 13907.95 REJECT NS=2;DP=374;DPB=426.0;AC=4;AN=4;AF=1.0;RO=0;AO=425;PRO=0.0;PAO=0.0;QR=0;QA=16030;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=265;SAR=160;SRP=0.0;SAP=59.3408;AB=0.0;ABP=0.0;RUN=1;RPP=39.9253;RPPR=0.0;RPL=170.0;RPR=255.0;EPP=12.4575;EPPR=0.0;DPRA=0.0;ODDS=67.8921;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.76;MQMR=0.0;PAIRED=0.992941;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8659;MLEAC=2;MLEAF=1.0;MQ=59.82;QD=32.735;SO [...]
+chr4 142853001 . C A 12577.45 REJECT NS=2;DP=331;DPB=376.0;AC=4;AN=4;AF=1.0;RO=0;AO=376;PRO=0.0;PAO=0.0;QR=0;QA=14466;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=225;SAR=151;SRP=0.0;SAP=34.6353;AB=0.0;ABP=0.0;RUN=1;RPP=6.33681;RPPR=0.0;RPL=200.0;RPR=176.0;EPP=22.438;EPPR=0.0;DPRA=0.0;ODDS=59.8933;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992021;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.955;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=25.16;SOR=1.0 [...]
+chr4 142853017 . A G 12433.349999999999 REJECT NS=2;DP=330;DPB=374.0;AC=4;AN=4;AF=1.0;RO=1;AO=373;PRO=0.0;PAO=0.0;QR=34;QA=14316;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=211;SAR=162;SRP=5.18177;SAP=16.9881;AB=0.0;ABP=0.0;RUN=1;RPP=7.9063;RPPR=5.18177;RPL=201.0;RPR=172.0;EPP=41.2061;EPPR=5.18177;DPRA=0.0;ODDS=58.6448;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989276;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.538;Dels=0.0;FS=0.0;HaplotypeScore=0.999 [...]
+chr4 142858190 . A G 13895.8 REJECT NS=2;DP=360;DPB=405.0;AC=4;AN=4;AF=1.0;RO=1;AO=404;PRO=0.0;PAO=0.0;QR=40;QA=15763;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=167;SAR=237;SRP=5.18177;SAP=29.3475;AB=0.0;ABP=0.0;RUN=1;RPP=19.8661;RPPR=5.18177;RPL=230.0;RPR=174.0;EPP=14.3837;EPPR=5.18177;DPRA=0.0;ODDS=59.2701;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990099;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.03;Dels=0.0;FS=0.0;HaplotypeScore=3.9645;MLEAC=2; [...]
+chr4 143007419 . A G 1866.44 PASS SOMATIC;NS=2;DP=277;DPB=277.0;AC=1;AN=3;AF=0.25;RO=204;AO=73;PRO=0.0;PAO=0.0;QR=7791;QA=2806;PQR=0.0;PQA=0.0;SRF=43;SRR=161;SAF=19;SAR=54;SRP=151.224;SAP=39.4494;AB=0.350962;ABP=43.1408;RUN=1;RPP=5.41974;RPPR=16.8055;RPL=41.0;RPR=32.0;EPP=8.03741;EPPR=3.05288;DPRA=3.01449;ODDS=44.0831;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.985294;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.763;Dels=0.0;FS=4.183; [...]
+chr4 143043340 . A G 1779.085 REJECT NS=2;DP=385;DPB=437.0;AC=2;AN=4;AF=0.5;RO=344;AO=93;PRO=0.0;PAO=0.0;QR=13168;QA=3480;PQR=0.0;PQA=0.0;SRF=172;SRR=172;SAF=40;SAR=53;SRP=3.0103;SAP=6.95631;AB=0.212815;ABP=316.065;RUN=1;RPP=3.03365;RPPR=11.1912;RPL=46.0;RPR=47.0;EPP=3.03365;EPPR=6.64625;DPRA=0.0;ODDS=125.131;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991279;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3;Dels=0.0;FS=4.1745;HaplotypeScore=5 [...]
+chr4 143043404 . C T 5092.535 REJECT NS=2;DP=289;DPB=342.0;AC=2;AN=4;AF=0.5;RO=157;AO=185;PRO=0.0;PAO=0.0;QR=5951;QA=7142;PQR=0.0;PQA=0.0;SRF=53;SRR=104;SAF=70;SAR=115;SRP=38.9848;SAP=26.7791;AB=0.540936;ABP=7.98818;RUN=1;RPP=49.5972;RPPR=6.12228;RPL=124.0;RPR=61.0;EPP=4.99397;EPPR=8.0033;DPRA=0.0;ODDS=323.031;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994595;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.679;Dels=0.0;FS=2.7825;HaplotypeScore [...]
+chr4 143044427 . T C 801.4965 REJECT NS=2;DP=259;DPB=289.0;AC=2;AN=4;AF=0.5;RO=236;AO=53;PRO=0.0;PAO=0.0;QR=9172;QA=1982;PQR=0.0;PQA=0.0;SRF=192;SRR=44;SAF=45;SAR=8;SRP=204.552;SAP=59.0998;AB=0.183391;ABP=254.638;RUN=1;RPP=12.2288;RPPR=67.9336;RPL=19.0;RPR=34.0;EPP=3.05127;EPPR=8.31016;DPRA=0.0;ODDS=82.6922;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3555;Dels=0.0;FS=2.796;HaplotypeScore=2.8995 [...]
+chr4 143067054 . G A 5330.205 REJECT NS=2;DP=343;DPB=395.0;AC=2;AN=4;AF=0.5;RO=204;AO=191;PRO=0.0;PAO=0.0;QR=7755;QA=7376;PQR=0.0;PQA=0.0;SRF=117;SRR=87;SAF=100;SAR=91;SRP=12.5903;SAP=3.93119;AB=0.483544;ABP=3.93936;RUN=1;RPP=28.1243;RPPR=4.5431;RPL=119.0;RPR=72.0;EPP=3.93119;EPPR=21.7871;DPRA=0.0;ODDS=341.488;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994764;PAIREDR=0.97549;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1055;Dels=0.0;FS=3.471;HaplotypeS [...]
+chr4 143130034 . A T 7755.34 REJECT NS=2;DP=293;DPB=323.0;AC=2;AN=4;AF=0.5;RO=57;AO=264;PRO=0.0;PAO=0.0;QR=2004;QA=9797;PQR=0.0;PQA=0.0;SRF=44;SRR=13;SAF=180;SAR=84;SRP=39.6206;SAP=78.8144;AB=0.817337;ABP=285.537;RUN=1;RPP=38.8396;RPPR=16.763;RPL=99.0;RPR=165.0;EPP=17.5197;EPPR=3.9627;DPRA=0.0;ODDS=42.1929;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.982456;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.949;Dels=0.0;FS=7.179;HaplotypeScore=34.8 [...]
+chr4 143181731 . TA T 2623.08 REJECT NS=2;DP=209;DPB=250.542;AC=1;AN=3;AF=0.0;RO=32;AO=11;PRO=21.9048;PAO=10.5714;QR=1186;QA=321;PQR=799.481;PQA=377.814;SRF=6;SRR=26;SAF=3;SAR=8;SRP=30.1537;SAP=7.94546;AB=0.0526316;ABP=366.332;RUN=1;RPP=3.20771;RPPR=3.0103;RPL=6.0;RPR=5.0;EPP=7.94546;EPPR=12.7819;DPRA=0.0;ODDS=14.5858;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=6;MEANALT=15.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr4 143181731 . TAA T 2623.08 REJECT NS=2;DP=209;DPB=250.542;AC=1;AN=3;AF=0.0;RO=32;AO=3;PRO=21.9048;PAO=8.57143;QR=1186;QA=92;PQR=799.481;PQA=314.714;SRF=6;SRR=26;SAF=0;SAR=3;SRP=30.1537;SAP=9.52472;AB=0.0612245;ABP=84.9501;RUN=1;RPP=3.73412;RPPR=3.0103;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=12.7819;DPRA=0.0;ODDS=14.5858;GTI=0;TYPE=del;CIGAR=1M2D21M;NUMALT=6;MEANALT=9.0;LEN=2;MQM=53.3333;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr4 143181745 . AAAT A 2623.08 PASS SOMATIC;NS=2;DP=209;DPB=250.542;AC=1;AN=3;AF=0.0;RO=32;AO=11;PRO=21.9048;PAO=7.57143;QR=1186;QA=376;PQR=799.481;PQA=274.714;SRF=6;SRR=26;SAF=6;SAR=5;SRP=30.1537;SAP=3.20771;AB=0.0526316;ABP=366.332;RUN=1;RPP=12.6832;RPPR=3.0103;RPL=9.0;RPR=2.0;EPP=7.94546;EPPR=12.7819;DPRA=0.0;ODDS=14.5858;GTI=0;TYPE=del;CIGAR=15M3D6M;NUMALT=6;MEANALT=15.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr4 143181746 . AAT A 2623.08 REJECT NS=2;DP=209;DPB=250.542;AC=1;AN=3;AF=0.0;RO=32;AO=17;PRO=21.9048;PAO=10.5714;QR=1186;QA=625;PQR=799.481;PQA=377.814;SRF=6;SRR=26;SAF=5;SAR=12;SRP=30.1537;SAP=9.26925;AB=0.0813397;ABP=321.199;RUN=1;RPP=9.26925;RPPR=3.0103;RPL=12.0;RPR=5.0;EPP=4.1599;EPPR=12.7819;DPRA=0.0;ODDS=14.5858;GTI=0;TYPE=del;CIGAR=16M2D6M;NUMALT=6;MEANALT=15.0;LEN=2;MQM=59.5882;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr4 143181747 . AT A 2623.08 REJECT NS=2;DP=209;DPB=250.542;AC=2;AN=3;AF=0.5;RO=32;AO=66;PRO=21.9048;PAO=21.9048;QR=1186;QA=2322;PQR=799.481;PQA=798.481;SRF=6;SRR=26;SAF=13;SAR=53;SRP=30.1537;SAP=55.6521;AB=0.315789;ABP=64.6115;RUN=1;RPP=3.1419;RPPR=3.0103;RPL=32.0;RPR=34.0;EPP=16.1707;EPPR=12.7819;DPRA=0.0;ODDS=14.5858;GTI=0;TYPE=del;CIGAR=17M1D6M;NUMALT=6;MEANALT=15.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984848;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr4 143181748 . T A 2623.08 REJECT NS=2;DP=209;DPB=250.542;AC=2;AN=2;AF=0.25;RO=32;AO=43;PRO=21.9048;PAO=13.9048;QR=1186;QA=1645;PQR=799.481;PQA=501.981;SRF=6;SRR=26;SAF=11;SAR=32;SRP=30.1537;SAP=25.2805;AB=0.205742;ABP=160.198;RUN=1;RPP=11.5447;RPPR=3.0103;RPL=28.0;RPR=15.0;EPP=7.10075;EPPR=12.7819;DPRA=0.0;ODDS=14.5858;GTI=0;TYPE=snp;CIGAR=17M1X6M;NUMALT=6;MEANALT=15.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr4 143268702 . A G 6006.96 REJECT NS=2;DP=362;DPB=404.0;AC=2;AN=4;AF=0.5;RO=190;AO=214;PRO=0.0;PAO=0.0;QR=7241;QA=8013;PQR=0.0;PQA=0.0;SRF=71;SRR=119;SAF=78;SAR=136;SRP=29.3423;SAP=37.145;AB=0.529703;ABP=6.10626;RUN=1;RPP=3.37559;RPPR=3.74174;RPL=110.0;RPR=104.0;EPP=14.7403;EPPR=16.222;DPRA=0.0;ODDS=265.958;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.971963;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.701;Dels=0.0;FS=0.0;HaplotypeScore=13. [...]
+chr4 143305189 . A T 1364.24 REJECT NS=2;DP=237;DPB=269.0;AC=2;AN=4;AF=0.5;RO=198;AO=71;PRO=0.0;PAO=0.0;QR=7649;QA=2708;PQR=0.0;PQA=0.0;SRF=135;SRR=63;SAF=44;SAR=27;SRP=59.8634;SAP=11.8491;AB=0.263941;ABP=133.21;RUN=1;RPP=14.0512;RPPR=15.6882;RPL=26.0;RPR=45.0;EPP=3.28556;EPPR=3.0103;DPRA=0.0;ODDS=175.846;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985915;PAIREDR=0.994949;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.218;Dels=0.0;FS=3.927;HaplotypeScore= [...]
+chr4 143324094 . G A 2338.48 PASS SOMATIC;NS=2;DP=333;DPB=333.0;AC=1;AN=3;AF=0.25;RO=243;AO=89;PRO=0.0;PAO=0.0;QR=9412;QA=3474;PQR=0.0;PQA=0.0;SRF=144;SRR=99;SAF=55;SAR=34;SRP=21.1059;SAP=13.7701;AB=0.339695;ABP=61.4909;RUN=1;RPP=15.9171;RPPR=9.52472;RPL=33.0;RPR=56.0;EPP=4.98658;EPPR=4.09157;DPRA=3.69014;ODDS=44.6828;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99177;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.775;Dels=0.0;FS=1.023;H [...]
+chr4 143344974 . T TA 390.846 REJECT NS=2;DP=329;DPB=392.938;AC=2;AN=4;AF=0.5;RO=253;AO=39;PRO=51.6667;PAO=44.6667;QR=9534;QA=1344;PQR=1858.67;PQA=1605.67;SRF=104;SRR=149;SAF=15;SAR=24;SRP=20.3907;SAP=7.52028;AB=0.118541;ABP=418.831;RUN=1;RPP=7.52028;RPPR=10.2285;RPL=24.0;RPR=15.0;EPP=7.52028;EPPR=3.08755;DPRA=0.0;ODDS=12.2008;GTI=0;TYPE=ins;CIGAR=1M1I15M;NUMALT=2;MEANALT=9.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.974359;PAIREDR=0.992095;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:Q [...]
+chr4 143344974 . TA T 390.846 REJECT NS=2;DP=329;DPB=392.938;AC=2;AN=2;AF=0.0;RO=253;AO=20;PRO=51.6667;PAO=40.6667;QR=9534;QA=681;PQR=1858.67;PQA=1466.67;SRF=104;SRR=149;SAF=6;SAR=14;SRP=20.3907;SAP=9.95901;AB=0.0607903;ABP=554.267;RUN=1;RPP=3.0103;RPPR=10.2285;RPL=10.0;RPR=10.0;EPP=3.0103;EPPR=3.08755;DPRA=0.0;ODDS=12.2008;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=2;MEANALT=9.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992095;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr4 143348680 . C T 2233.61 PASS SOMATIC;NS=2;DP=294;DPB=294.0;AC=1;AN=3;AF=0.25;RO=210;AO=84;PRO=0.0;PAO=0.0;QR=8087;QA=3243;PQR=0.0;PQA=0.0;SRF=74;SRR=136;SAF=24;SAR=60;SRP=42.7586;SAP=36.513;AB=0.390698;ABP=25.3209;RUN=1;RPP=17.9004;RPPR=62.7361;RPL=54.0;RPR=30.0;EPP=4.66476;EPPR=13.5988;DPRA=2.72152;ODDS=50.2937;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988095;PAIREDR=0.995238;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.088;Dels=0.0;FS=1. [...]
+chr4 143862981 . G GA 62.0647 REJECT NS=2;DP=328;DPB=410.857;AC=2;AN=3;AF=0.25;RO=226;AO=21;PRO=72.5;PAO=49.5;QR=8243;QA=726;PQR=2524.83;PQA=1734.83;SRF=92;SRR=134;SAF=15;SAR=6;SRP=19.9593;SAP=11.386;AB=0.0640244;ABP=544.528;RUN=1;RPP=8.07707;RPPR=12.8492;RPL=7.0;RPR=14.0;EPP=3.94093;EPPR=18.3836;DPRA=0.0;ODDS=3.15025;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=2;MEANALT=18.5;LEN=1;MQM=60.9524;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99115;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr4 143862981 . GA G 62.0647 REJECT NS=2;DP=328;DPB=410.857;AC=2;AN=3;AF=0.25;RO=226;AO=28;PRO=72.5;PAO=42.0;QR=8243;QA=894;PQR=2524.83;PQA=1454.33;SRF=92;SRR=134;SAF=14;SAR=14;SRP=19.9593;SAP=3.0103;AB=0.0853659;ABP=492.81;RUN=1;RPP=7.97367;RPPR=12.8492;RPL=18.0;RPR=10.0;EPP=7.97367;EPPR=18.3836;DPRA=0.0;ODDS=3.15025;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=2;MEANALT=18.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99115;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr4 143863671 . T C 7303.525000000001 REJECT NS=2;DP=357;DPB=408.0;AC=3;AN=4;AF=0.75;RO=125;AO=283;PRO=0.0;PAO=0.0;QR=4742;QA=10374;PQR=0.0;PQA=0.0;SRF=72;SRR=53;SAF=181;SAR=102;SRP=9.28151;SAP=50.8978;AB=0.592834;ABP=25.9911;RUN=1;RPP=19.9601;RPPR=4.41741;RPL=118.0;RPR=165.0;EPP=43.9;EPPR=32.2123;DPRA=0.0;ODDS=63.9497;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992933;PAIREDR=0.992;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.268;Dels=0.0;FS=1.3115;H [...]
+chr4 143863721 . A G 7777.34 REJECT NS=2;DP=358;DPB=406.0;AC=3;AN=4;AF=0.75;RO=125;AO=281;PRO=0.0;PAO=0.0;QR=4844;QA=10706;PQR=0.0;PQA=0.0;SRF=48;SRR=77;SAF=116;SAR=165;SRP=17.62;SAP=21.5644;AB=0.596774;ABP=28.2274;RUN=1;RPP=20.0807;RPPR=4.41741;RPL=164.0;RPR=117.0;EPP=28.1175;EPPR=3.86152;DPRA=0.0;ODDS=60.8535;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996441;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.129;Dels=0.0;FS=1.9225;HaplotypeSco [...]
+chr4 143866615 . G A 3318.75 REJECT NS=1;DP=98;DPB=98.0;AC=2;AN=4;AF=1.0;RO=0;AO=98;PRO=0.0;PAO=0.0;QR=0;QA=3726;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=50;SAR=48;SRP=0.0;SAP=3.09893;AB=0.0;ABP=0.0;RUN=1;RPP=3.09893;RPPR=0.0;RPL=50.0;RPR=48.0;EPP=5.22609;EPPR=0.0;DPRA=0.0;ODDS=65.748;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.49;SOR=0.757 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:AD [...]
+chr4 143866667 . C T 3110.19 REJECT NS=1;DP=93;DPB=93.0;AC=2;AN=4;AF=1.0;RO=0;AO=93;PRO=0.0;PAO=0.0;QR=0;QA=3512;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=37;SAR=56;SRP=0.0;SAP=11.4393;AB=0.0;ABP=0.0;RUN=1;RPP=3.03365;RPPR=0.0;RPL=47.0;RPR=46.0;EPP=13.3073;EPPR=0.0;DPRA=0.0;ODDS=62.6055;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.989247;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=35.58;SOR=1.191 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr4 153004679 . G A 1917.28 REJECT NS=2;DP=362;DPB=414.0;AC=2;AN=4;AF=0.5;RO=316;AO=97;PRO=0.0;PAO=0.0;QR=12081;QA=3702;PQR=0.0;PQA=0.0;SRF=140;SRR=176;SAF=49;SAR=48;SRP=11.9161;SAP=3.03269;AB=0.2343;ABP=256.873;RUN=1;RPP=6.79359;RPPR=21.5915;RPL=55.0;RPR=42.0;EPP=4.10723;EPPR=3.12025;DPRA=0.0;ODDS=169.439;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996835;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.3355;Dels=0.0;FS=4.0755;HaplotypeScore=3 [...]
+chr4 153143877 . C T 1883.685 REJECT NS=2;DP=358;DPB=414.0;AC=2;AN=4;AF=0.5;RO=323;AO=91;PRO=0.0;PAO=0.0;QR=12381;QA=3446;PQR=0.0;PQA=0.0;SRF=142;SRR=181;SAF=41;SAR=50;SRP=13.2357;SAP=4.94315;AB=0.219807;ABP=285.323;RUN=1;RPP=9.90651;RPPR=3.17837;RPL=54.0;RPR=37.0;EPP=9.90651;EPPR=63.6838;DPRA=0.0;ODDS=69.8514;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.978022;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.089;Dels=0.0;FS=1.187;HaplotypeScore [...]
+chr4 153149284 . G A 1801.73 REJECT NS=2;DP=350;DPB=398.0;AC=2;AN=4;AF=0.5;RO=300;AO=98;PRO=0.0;PAO=0.0;QR=11459;QA=3657;PQR=0.0;PQA=0.0;SRF=119;SRR=181;SAF=44;SAR=54;SRP=30.8341;SAP=5.22609;AB=0.246231;ABP=225.635;RUN=1;RPP=3.0103;RPPR=6.51361;RPL=49.0;RPR=49.0;EPP=3.36483;EPPR=29.068;DPRA=0.0;ODDS=211.248;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.979592;PAIREDR=0.993333;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.662;Dels=0.0;FS=3.3255;HaplotypeSc [...]
+chr4 153268227 . C A 203.5 REJECT NS=2;DP=100;DPB=147.2;AC=2;AN=2;AF=0.0;RO=36;AO=24;PRO=58.1667;PAO=15.0;QR=1342;QA=339;PQR=2045.67;PQA=260.0;SRF=2;SRR=34;SAF=0;SAR=24;SRP=64.7766;SAP=55.1256;AB=0.24;ABP=61.7269;RUN=1;RPP=3.37221;RPPR=11.6962;RPL=11.0;RPR=13.0;EPP=3.37221;EPPR=11.6962;DPRA=0.0;ODDS=18.1306;GTI=0;TYPE=snp;CIGAR=1X44M;NUMALT=3;MEANALT=10.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.958333;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr4 153268227 . C CA 203.5 REJECT NS=2;DP=100;DPB=147.2;AC=2;AN=2;AF=0.0;RO=36;AO=5;PRO=58.1667;PAO=31.1667;QR=1342;QA=103;PQR=2045.67;PQA=1033.67;SRF=2;SRR=34;SAF=0;SAR=5;SRP=64.7766;SAP=13.8677;AB=0.0694444;ABP=118.943;RUN=1;RPP=3.44459;RPPR=11.6962;RPL=3.0;RPR=2.0;EPP=3.44459;EPPR=11.6962;DPRA=0.0;ODDS=18.1306;GTI=0;TYPE=ins;CIGAR=1M1I44M;NUMALT=3;MEANALT=12.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr4 153268227 . CA C 203.5 REJECT NS=2;DP=100;DPB=147.2;AC=2;AN=4;AF=0.5;RO=36;AO=17;PRO=58.1667;PAO=32.6667;QR=1342;QA=323;PQR=2045.67;PQA=1098.67;SRF=2;SRR=34;SAF=1;SAR=16;SRP=64.7766;SAP=31.7504;AB=0.17;ABP=97.5996;RUN=1;RPP=3.13803;RPPR=11.6962;RPL=9.0;RPR=8.0;EPP=3.13803;EPPR=11.6962;DPRA=0.0;ODDS=18.1306;GTI=0;TYPE=del;CIGAR=1M1D43M;NUMALT=3;MEANALT=10.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.941176;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.82;FS=3.699;MLEAC= [...]
+chr4 153554397 . G A 11092.55 REJECT NS=2;DP=292;DPB=339.0;AC=4;AN=4;AF=1.0;RO=0;AO=339;PRO=0.0;PAO=0.0;QR=0;QA=13092;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=237;SAR=102;SRP=0.0;SAP=119.751;AB=0.0;ABP=0.0;RUN=1;RPP=14.8541;RPPR=0.0;RPL=148.0;RPR=191.0;EPP=4.09283;EPPR=0.0;DPRA=0.0;ODDS=62.3674;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99705;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9995;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.435;SOR=1 [...]
+chr4 153555774 . A G 13726.8 REJECT NS=2;DP=357;DPB=414.0;AC=4;AN=4;AF=1.0;RO=0;AO=414;PRO=0.0;PAO=0.0;QR=0;QA=16036;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=192;SAR=222;SRP=0.0;SAP=7.73089;AB=0.0;ABP=0.0;RUN=1;RPP=21.8927;RPPR=0.0;RPL=237.0;RPR=177.0;EPP=19.4589;EPPR=0.0;DPRA=0.0;ODDS=74.8043;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992754;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9469;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.715;SOR=0 [...]
+chr4 154513927 . G C 1649.575 REJECT NS=2;DP=325;DPB=376.0;AC=2;AN=4;AF=0.5;RO=297;AO=79;PRO=0.0;PAO=0.0;QR=11514;QA=3096;PQR=0.0;PQA=0.0;SRF=153;SRR=144;SAF=45;SAR=34;SRP=3.60252;SAP=6.33623;AB=0.210106;ABP=277.471;RUN=1;RPP=17.5509;RPPR=41.9725;RPL=28.0;RPR=51.0;EPP=26.1269;EPPR=28.4611;DPRA=0.0;ODDS=72.1674;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.983165;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.4155;Dels=0.0;FS=4.741;HaplotypeScore [...]
+chr4 156007856 . G C 4090.1 REJECT NS=2;DP=226;DPB=257.0;AC=2;AN=4;AF=0.5;RO=112;AO=145;PRO=0.0;PAO=0.0;QR=4165;QA=5516;PQR=0.0;PQA=0.0;SRF=67;SRR=45;SAF=86;SAR=59;SRP=12.3942;SAP=13.9276;AB=0.564202;ABP=12.2116;RUN=1;RPP=106.178;RPPR=109.18;RPL=31.0;RPR=114.0;EPP=3.14508;EPPR=3.0103;DPRA=0.0;ODDS=164.233;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993103;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.486;Dels=0.0;FS=2.323;HaplotypeScore=3.923 [...]
+chr4 156007879 . T C 5267.59 REJECT NS=2;DP=288;DPB=330.0;AC=2;AN=4;AF=0.5;RO=146;AO=184;PRO=0.0;PAO=0.0;QR=5543;QA=6988;PQR=0.0;PQA=0.0;SRF=90;SRR=56;SAF=112;SAR=72;SRP=20.2036;SAP=21.8927;AB=0.557576;ABP=12.5121;RUN=1;RPP=20.0516;RPPR=16.3961;RPL=73.0;RPR=111.0;EPP=5.32339;EPPR=3.06979;DPRA=0.0;ODDS=252.346;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.98913;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3125;Dels=0.0;FS=0.4185;HaplotypeScore= [...]
+chr4 156007965 . A G 1659.37 REJECT NS=2;DP=333;DPB=380.0;AC=2;AN=4;AF=0.5;RO=295;AO=85;PRO=0.0;PAO=0.0;QR=11401;QA=3217;PQR=0.0;PQA=0.0;SRF=105;SRR=190;SAF=39;SAR=46;SRP=56.193;SAP=4.26209;AB=0.223684;ABP=255.015;RUN=1;RPP=14.2764;RPPR=3.90097;RPL=53.0;RPR=32.0;EPP=30.8307;EPPR=22.1561;DPRA=0.0;ODDS=120.474;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.2353;MQMR=60.0;PAIRED=0.988235;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.629;Dels=0.0;FS=8.3975;HaplotypeSco [...]
+chr4 166509271 . A T 13287.55 REJECT NS=2;DP=357;DPB=406.0;AC=4;AN=4;AF=1.0;RO=0;AO=406;PRO=0.0;PAO=0.0;QR=0;QA=15280;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=186;SAR=220;SRP=0.0;SAP=9.19311;AB=0.0;ABP=0.0;RUN=1;RPP=3.78048;RPPR=0.0;RPL=197.0;RPR=209.0;EPP=19.7831;EPPR=0.0;DPRA=0.0;ODDS=64.8287;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995074;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.645;SOR=0 [...]
+chr4 171008696 . G A 14028.2 REJECT NS=2;DP=366;DPB=421.0;AC=4;AN=4;AF=1.0;RO=0;AO=421;PRO=0.0;PAO=0.0;QR=0;QA=16288;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=185;SAR=236;SRP=0.0;SAP=16.426;AB=0.0;ABP=0.0;RUN=1;RPP=5.28493;RPPR=0.0;RPL=221.0;RPR=200.0;EPP=40.2761;EPPR=0.0;DPRA=0.0;ODDS=72.3237;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997625;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.8059;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.22;SOR=0.9 [...]
+chr4 172516637 . G A 9329.435000000001 REJECT NS=2;DP=249;DPB=286.0;AC=4;AN=4;AF=1.0;RO=0;AO=286;PRO=0.0;PAO=0.0;QR=0;QA=10969;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=215;SAR=71;SRP=0.0;SAP=160.45;AB=0.0;ABP=0.0;RUN=1;RPP=131.325;RPPR=0.0;RPL=78.0;RPR=208.0;EPP=3.13178;EPPR=0.0;DPRA=0.0;ODDS=49.8425;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996503;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9663;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.94 [...]
+chr4 172516685 . A G 3192.75 PASS SOMATIC;NS=2;DP=422;DPB=422.0;AC=1;AN=3;AF=0.25;RO=299;AO=122;PRO=0.0;PAO=0.0;QR=11552;QA=4598;PQR=0.0;PQA=0.0;SRF=181;SRR=118;SAF=66;SAR=56;SRP=31.835;SAP=4.7902;AB=0.376543;ABP=45.9036;RUN=1;RPP=3.29508;RPPR=3.36616;RPL=63.0;RPR=59.0;EPP=13.2625;EPPR=41.7119;DPRA=3.30612;ODDS=61.5454;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993311;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.133;Dels=0.0;FS=4.534 [...]
+chr4 172516765 . C T 1857.4 PASS SOMATIC;NS=2;DP=315;DPB=315.0;AC=1;AN=3;AF=0.25;RO=237;AO=76;PRO=0.0;PAO=0.0;QR=9068;QA=2903;PQR=0.0;PQA=0.0;SRF=71;SRR=166;SAF=18;SAR=58;SRP=85.7003;SAP=48.7255;AB=0.312757;ABP=77.0101;RUN=1;RPP=7.12467;RPPR=85.7003;RPL=44.0;RPR=32.0;EPP=3.0103;EPPR=4.55873;DPRA=3.375;ODDS=45.9219;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.311;Dels=0.0;FS=8.76;Haplotype [...]
+chr4 184511265 . A G 1723.15 REJECT NS=2;DP=361;DPB=416.0;AC=2;AN=4;AF=0.5;RO=324;AO=91;PRO=0.0;PAO=0.0;QR=12471;QA=3490;PQR=0.0;PQA=0.0;SRF=182;SRR=142;SAF=51;SAR=40;SRP=13.7336;SAP=5.89764;AB=0.21875;ABP=288.83;RUN=1;RPP=4.17955;RPPR=3.25157;RPL=42.0;RPR=49.0;EPP=7.04303;EPPR=22.5536;DPRA=0.0;ODDS=162.756;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993827;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.2115;Dels=0.0;FS=1.3975;HaplotypeScore=3 [...]
+chr4 187511861 . G A 3747.025 REJECT NS=2;DP=270;DPB=313.0;AC=2;AN=4;AF=0.5;RO=176;AO=137;PRO=0.0;PAO=0.0;QR=6586;QA=5297;PQR=0.0;PQA=0.0;SRF=49;SRR=127;SAF=43;SAR=94;SRP=78.0742;SAP=44.2366;AB=0.4377;ABP=13.5624;RUN=1;RPP=10.0002;RPPR=50.4372;RPL=79.0;RPR=58.0;EPP=4.29416;EPPR=3.0103;DPRA=0.0;ODDS=224.358;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.978102;PAIREDR=0.994318;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.3455;Dels=0.0;FS=1.654;HaplotypeScor [...]
+chr4 187516880 . A G 5047.46 REJECT NS=2;DP=338;DPB=391.0;AC=2;AN=4;AF=0.5;RO=201;AO=190;PRO=0.0;PAO=0.0;QR=7744;QA=7159;PQR=0.0;PQA=0.0;SRF=122;SRR=79;SAF=122;SAR=68;SRP=22.9857;SAP=36.3367;AB=0.485934;ABP=3.68229;RUN=1;RPP=6.71323;RPPR=19.4422;RPL=86.0;RPR=104.0;EPP=6.71323;EPPR=5.44105;DPRA=0.0;ODDS=336.684;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8632;MQMR=60.0;PAIRED=0.989474;PAIREDR=0.995025;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.6555;Dels=0.0;FS=1.7175;Hapl [...]
+chr4 187518041 . T C 6859.635 REJECT NS=2;DP=433;DPB=494.0;AC=2;AN=4;AF=0.5;RO=246;AO=248;PRO=0.0;PAO=0.0;QR=9282;QA=9332;PQR=0.0;PQA=0.0;SRF=138;SRR=108;SAF=128;SAR=120;SRP=10.9547;SAP=3.57068;AB=0.502024;ABP=3.02788;RUN=1;RPP=8.05372;RPPR=3.32808;RPL=112.0;RPR=136.0;EPP=5.25182;EPPR=3.89301;DPRA=0.0;ODDS=383.644;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991935;PAIREDR=0.987805;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.937;Dels=0.0;FS=3.4765;Haplo [...]
+chr4 187518976 . C T 2174.27 PASS DP=122;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.98;Dels=0.0;FS=2.2685;HaplotypeScore=6.8864;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.1195;QD=16.535;ReadPosRankSum=0.1505;SOR=0.7215;ClippingRankSum=-0.182 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:40,25:65:99.0:924,0,3067:25:38:65:1:.:.:.:.:.:-0.000279671 0/1:85,94:179:99.0:3481,0,3083:94:53:179:.:1:.:.:.:.:-0.00190096
+chr4 187518976 . CTCAT TTCAC 3044.8 REJECT NS=2;DP=233;DPB=238.6;AC=2;AN=4;AF=0.5;RO=117;AO=112;PRO=8.0;PAO=6.0;QR=4387;QA=4066;PQR=276.0;PQA=216.0;SRF=47;SRR=70;SAF=43;SAR=69;SRP=12.8283;SAP=16.1167;AB=0.480687;ABP=3.76519;RUN=1;RPP=77.5383;RPPR=55.1442;RPL=87.0;RPR=25.0;EPP=5.80219;EPPR=7.18621;DPRA=0.0;ODDS=141.625;GTI=0;TYPE=complex;CIGAR=1X3M1X;NUMALT=1;MEANALT=3.0;LEN=5;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:Ca [...]
+chr4 187518980 . T C 2048.77 PASS DP=115;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.6705;Dels=0.0;FS=2.819;HaplotypeScore=5.878;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.7985;QD=16.39;ReadPosRankSum=-0.145;SOR=0.802;ClippingRankSum=0.867 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:40,24:64:99.0:884,0,3070:24:38:64:1:.:.:.:.:.:-0.000279671 0/1:78,89:167:99.0:3270,0,2806:89:53:167:.:1:.:.:.:.:-0.00190096
+chr4 187519206 . C G 13984.4 REJECT NS=2;DP=369;DPB=427.0;AC=4;AN=4;AF=1.0;RO=0;AO=427;PRO=0.0;PAO=0.0;QR=0;QA=16371;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=207;SAR=220;SRP=0.0;SAP=3.86974;AB=0.0;ABP=0.0;RUN=1;RPP=4.47999;RPPR=0.0;RPL=222.0;RPR=205.0;EPP=27.222;EPPR=0.0;DPRA=0.0;ODDS=76.0652;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.9657;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.51;SOR=0.7575 G [...]
+chr4 187521037 . C A 3875.975 REJECT NS=2;DP=242;DPB=286.0;AC=2;AN=4;AF=0.5;RO=141;AO=145;PRO=0.0;PAO=0.0;QR=5353;QA=5469;PQR=0.0;PQA=0.0;SRF=114;SRR=27;SAF=117;SAR=28;SRP=119.577;SAP=121.633;AB=0.506993;ABP=3.13178;RUN=1;RPP=10.9324;RPPR=3.76493;RPL=61.0;RPR=84.0;EPP=5.54119;EPPR=6.47542;DPRA=0.0;ODDS=246.685;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993103;PAIREDR=0.992908;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1745;Dels=0.0;FS=3.6775;Haplotyp [...]
+chr4 187525020 . A C 5298.48 REJECT NS=2;DP=339;DPB=390.0;AC=2;AN=4;AF=0.5;RO=199;AO=191;PRO=0.0;PAO=0.0;QR=7587;QA=7301;PQR=0.0;PQA=0.0;SRF=96;SRR=103;SAF=95;SAR=96;SRP=3.54498;SAP=3.02167;AB=0.489744;ABP=3.36664;RUN=1;RPP=15.3911;RPPR=3.89417;RPL=112.0;RPR=79.0;EPP=10.1159;EPPR=3.89417;DPRA=0.0;ODDS=316.817;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994764;PAIREDR=0.98995;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.691;Dels=0.0;FS=0.6995;HaplotypeSc [...]
+chr4 187530313 . C T 8583.645 REJECT NS=2;DP=229;DPB=270.0;AC=4;AN=4;AF=1.0;RO=0;AO=270;PRO=0.0;PAO=0.0;QR=0;QA=10369;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=170;SAR=100;SRP=0.0;SAP=42.4185;AB=0.0;ABP=0.0;RUN=1;RPP=107.531;RPPR=0.0;RPL=78.0;RPR=192.0;EPP=3.29983;EPPR=0.0;DPRA=0.0;ODDS=55.5046;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996296;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9243;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.18;SOR=1. [...]
+chr4 187531022 . A G 6053.385 REJECT NS=2;DP=344;DPB=398.0;AC=2;AN=4;AF=0.5;RO=185;AO=213;PRO=0.0;PAO=0.0;QR=7019;QA=8176;PQR=0.0;PQA=0.0;SRF=102;SRR=83;SAF=120;SAR=93;SRP=7.24761;SAP=10.4422;AB=0.535176;ABP=7.28777;RUN=1;RPP=3.26517;RPPR=4.99397;RPL=109.0;RPR=104.0;EPP=3.02049;EPPR=3.02204;DPRA=0.0;ODDS=341.026;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.973;PAIRED=0.995305;PAIREDR=0.983784;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.464;Dels=0.0;FS=4.1525;Haplo [...]
+chr4 187534363 . G A 9318.14 REJECT NS=2;DP=371;DPB=433.0;AC=2;AN=4;AF=0.5;RO=125;AO=308;PRO=0.0;PAO=0.0;QR=4864;QA=11750;PQR=0.0;PQA=0.0;SRF=72;SRR=53;SAF=161;SAR=147;SRP=9.28151;SAP=4.39215;AB=0.711316;ABP=170.956;RUN=1;RPP=16.6596;RPPR=4.41741;RPL=176.0;RPR=132.0;EPP=3.26411;EPPR=13.8677;DPRA=0.0;ODDS=284.864;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99026;PAIREDR=0.992;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.628;Dels=0.0;FS=7.5315;HaplotypeS [...]
+chr4 187534375 . A G 2292.77 PASS SOMATIC;NS=2;DP=420;DPB=420.0;AC=1;AN=3;AF=0.25;RO=328;AO=91;PRO=0.0;PAO=0.0;QR=12652;QA=3489;PQR=0.0;PQA=0.0;SRF=161;SRR=167;SAF=47;SAR=44;SRP=3.24863;SAP=3.22506;AB=0.31058;ABP=94.3233;RUN=1;RPP=3.22506;RPPR=5.65844;RPL=47.0;RPR=44.0;EPP=3.22506;EPPR=10.6634;DPRA=2.30709;ODDS=79.61;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.978022;PAIREDR=0.993902;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.631;Dels=0.0;FS=0. [...]
+chr4 187538133 . A G 4898.03 REJECT NS=2;DP=206;DPB=244.0;AC=2;AN=4;AF=0.5;RO=71;AO=173;PRO=0.0;PAO=0.0;QR=2693;QA=6530;PQR=0.0;PQA=0.0;SRF=50;SRR=21;SAF=130;SAR=43;SRP=28.7315;SAP=98.0154;AB=0.709016;ABP=95.6005;RUN=1;RPP=136.173;RPPR=25.3061;RPL=35.0;RPR=138.0;EPP=20.1938;EPPR=3.7749;DPRA=0.0;ODDS=78.571;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.982659;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.7525;Dels=0.0;FS=3.8955;HaplotypeScore=1 [...]
+chr4 187538330 . G A 2338.8 PASS SOMATIC;NS=2;DP=375;DPB=375.0;AC=1;AN=3;AF=0.25;RO=284;AO=91;PRO=0.0;PAO=0.0;QR=10798;QA=3511;PQR=0.0;PQA=0.0;SRF=112;SRR=172;SAF=38;SAR=53;SRP=30.536;SAP=8.37933;AB=0.330909;ABP=71.3051;RUN=1;RPP=8.37933;RPPR=3.49965;RPL=38.0;RPR=53.0;EPP=15.6335;EPPR=34.3284;DPRA=2.75;ODDS=63.3681;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.7802;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989437;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.808;Dels=0.0;FS=1.004; [...]
+chr4 187538942 . T G 7527.99 REJECT NS=2;DP=326;DPB=365.0;AC=2;AN=3;AF=0.5;RO=81;AO=190;PRO=0.0;PAO=0.0;QR=3130;QA=7257;PQR=0.0;PQA=0.0;SRF=44;SRR=37;SAF=111;SAR=79;SRP=4.32391;SAP=14.7134;AB=0.520548;ABP=4.34888;RUN=1;RPP=3.74174;RPPR=4.32391;RPL=99.0;RPR=91.0;EPP=3.42174;EPPR=6.2541;DPRA=0.0;ODDS=225.489;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=2;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994737;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.416;Dels=0.0;FS=0.755;H [...]
+chr4 187538942 . T A 7527.99 PASS SOMATIC;NS=2;DP=365;DPB=365.0;AC=2;AN=2;AF=0.25;RO=81;AO=94;PRO=0.0;PAO=0.0;QR=3130;QA=3652;PQR=0.0;PQA=0.0;SRF=44;SRR=37;SAF=57;SAR=37;SRP=4.32391;SAP=12.2506;AB=0.326389;ABP=78.4086;RUN=1;RPP=3.84193;RPPR=4.32391;RPL=50.0;RPR=44.0;EPP=3.0103;EPPR=6.2541;DPRA=0.0;ODDS=225.489;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=2;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.325;Dels=0.0;FS=0.656;Ha [...]
+chr4 187542755 . T C 6123.280000000001 REJECT NS=2;DP=369;DPB=426.0;AC=2;AN=4;AF=0.5;RO=208;AO=218;PRO=0.0;PAO=0.0;QR=7917;QA=8400;PQR=0.0;PQA=0.0;SRF=105;SRR=103;SAF=111;SAR=107;SRP=3.05206;SAP=3.16967;AB=0.511737;ABP=3.52004;RUN=1;RPP=6.23763;RPPR=3.67845;RPL=100.0;RPR=118.0;EPP=5.56029;EPPR=3.05206;DPRA=0.0;ODDS=352.855;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.981651;PAIREDR=0.995192;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.0115;Dels=0.0;FS=0. [...]
+chr4 187557893 . T C 11019.3 REJECT NS=2;DP=406;DPB=455.0;AC=2;AN=4;AF=0.5;RO=100;AO=355;PRO=0.0;PAO=0.0;QR=3879;QA=13702;PQR=0.0;PQA=0.0;SRF=44;SRR=56;SAF=184;SAR=171;SRP=6.13722;SAP=4.04404;AB=0.78022;ABP=313.34;RUN=1;RPP=8.88857;RPPR=15.518;RPL=193.0;RPR=162.0;EPP=4.77806;EPPR=3.0103;DPRA=0.0;ODDS=145.405;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.194;Dels=0.0;FS=11.988;HaplotypeScore=3.9462 [...]
+chr4 187584771 . C G 8630.96 REJECT NS=2;DP=237;DPB=265.0;AC=4;AN=4;AF=1.0;RO=1;AO=264;PRO=0.0;PAO=0.0;QR=15;QA=9939;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=61;SAR=203;SRP=5.18177;SAP=168.865;AB=0.0;ABP=0.0;RUN=1;RPP=95.4295;RPPR=5.18177;RPL=185.0;RPR=79.0;EPP=3.1419;EPPR=5.18177;DPRA=0.0;ODDS=38.6427;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.716;Dels=0.0;FS=0.0;HaplotypeScore=3.8795;MLEAC=2;MLEAF=1.0 [...]
+chr4 187627792 . T C 11346.349999999999 REJECT NS=2;DP=300;DPB=343.0;AC=4;AN=4;AF=1.0;RO=1;AO=342;PRO=0.0;PAO=0.0;QR=39;QA=13152;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=196;SAR=146;SRP=5.18177;SAP=18.8836;AB=0.0;ABP=0.0;RUN=1;RPP=6.66752;RPPR=5.18177;RPL=183.0;RPR=159.0;EPP=15.3026;EPPR=5.18177;DPRA=0.0;ODDS=56.7535;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991228;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.182;Dels=0.0;FS=1.683;HaplotypeScore=11 [...]
+chr4 187628398 . C G 13179.25 REJECT NS=2;DP=350;DPB=405.0;AC=4;AN=4;AF=1.0;RO=0;AO=405;PRO=0.0;PAO=0.0;QR=0;QA=15429;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=206;SAR=199;SRP=0.0;SAP=3.27302;AB=0.0;ABP=0.0;RUN=1;RPP=8.84915;RPPR=0.0;RPL=186.0;RPR=219.0;EPP=4.21667;EPPR=0.0;DPRA=0.0;ODDS=71.716;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992593;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8978;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.285;SOR=0 [...]
+chr4 187629140 . G C 11983.599999999999 REJECT NS=2;DP=314;DPB=355.0;AC=4;AN=4;AF=1.0;RO=0;AO=355;PRO=0.0;PAO=0.0;QR=0;QA=13618;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=173;SAR=182;SRP=0.0;SAP=3.50576;AB=0.0;ABP=0.0;RUN=1;RPP=4.38659;RPPR=0.0;RPL=185.0;RPR=170.0;EPP=3.06535;EPPR=0.0;DPRA=0.0;ODDS=54.8327;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991549;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8325;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=3 [...]
+chr4 187629497 . G A 12388.55 REJECT NS=2;DP=326;DPB=371.0;AC=4;AN=4;AF=1.0;RO=0;AO=371;PRO=0.0;PAO=0.0;QR=0;QA=14229;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=201;SAR=170;SRP=0.0;SAP=8.63506;AB=0.0;ABP=0.0;RUN=1;RPP=12.8492;RPPR=0.0;RPL=165.0;RPR=206.0;EPP=12.8492;EPPR=0.0;DPRA=0.0;ODDS=59.8488;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.775;SOR=0.958 [...]
+chr4 187629538 . C T 13621.05 REJECT NS=2;DP=357;DPB=411.0;AC=4;AN=4;AF=1.0;RO=0;AO=411;PRO=0.0;PAO=0.0;QR=0;QA=15774;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=222;SAR=189;SRP=0.0;SAP=8.76391;AB=0.0;ABP=0.0;RUN=1;RPP=3.26919;RPPR=0.0;RPL=202.0;RPR=209.0;EPP=8.08764;EPPR=0.0;DPRA=0.0;ODDS=71.0525;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997567;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9108;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.36;SOR=0 [...]
+chr4 187629770 . A C 14324.3 REJECT NS=2;DP=377;DPB=433.0;AC=4;AN=4;AF=1.0;RO=0;AO=433;PRO=0.0;PAO=0.0;QR=0;QA=16525;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=230;SAR=203;SRP=0.0;SAP=6.6662;AB=0.0;ABP=0.0;RUN=1;RPP=3.13567;RPPR=0.0;RPL=214.0;RPR=219.0;EPP=3.61711;EPPR=0.0;DPRA=0.0;ODDS=74.1536;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995381;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9328;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.955;SOR=0. [...]
+chr5 1295243 . G A 4617.97 REJECT NS=2;DP=332;DPB=384.0;AC=2;AN=4;AF=0.5;RO=194;AO=190;PRO=0.0;PAO=0.0;QR=6874;QA=6622;PQR=0.0;PQA=0.0;SRF=103;SRR=91;SAF=104;SAR=86;SRP=4.62211;SAP=6.71323;AB=0.494792;ABP=3.10078;RUN=1;RPP=5.25035;RPPR=3.18939;RPL=88.0;RPR=102.0;EPP=10.7362;EPPR=5.20416;DPRA=0.0;ODDS=256.433;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0515;PAIRED=1.0;PAIREDR=0.984536;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.2525;Dels=0.0;FS=2.76;HaplotypeScor [...]
+chr5 1296072 . A G 12382.4 REJECT NS=2;DP=331;DPB=378.0;AC=4;AN=4;AF=1.0;RO=0;AO=378;PRO=0.0;PAO=0.0;QR=0;QA=14279;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=216;SAR=162;SRP=0.0;SAP=19.7617;AB=0.0;ABP=0.0;RUN=1;RPP=10.4553;RPPR=0.0;RPL=171.0;RPR=207.0;EPP=12.2017;EPPR=0.0;DPRA=0.0;ODDS=63.0088;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994709;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8276;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.62;SOR=1.04 [...]
+chr5 1296486 . A G 18295.35 REJECT NS=2;DP=486;DPB=548.0;AC=4;AN=4;AF=1.0;RO=0;AO=546;PRO=0.0;PAO=0.0;QR=0;QA=20808;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=278;SAR=268;SRP=0.0;SAP=3.40801;AB=0.0;ABP=0.0;RUN=1;RPP=3.15347;RPPR=0.0;RPL=276.0;RPR=270.0;EPP=6.58965;EPPR=0.0;DPRA=0.0;ODDS=79.78;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992674;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.9649;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.74;SOR=0.829 [...]
+chr5 1296759 . C T 13775.4 REJECT NS=2;DP=511;DPB=580.0;AC=2;AN=4;AF=0.5;RO=135;AO=445;PRO=0.0;PAO=0.0;QR=5182;QA=17136;PQR=0.0;PQA=0.0;SRF=71;SRR=64;SAF=224;SAR=221;SRP=3.79846;SAP=3.05422;AB=0.767241;ABP=362.801;RUN=1;RPP=3.05422;RPPR=7.65886;RPL=221.0;RPR=224.0;EPP=3.60075;EPPR=5.72866;DPRA=0.0;ODDS=323.309;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993258;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5895;Dels=0.0;FS=2.0815;HaplotypeScor [...]
+chr5 1297258 . T C 7992.675 REJECT NS=2;DP=218;DPB=251.0;AC=4;AN=4;AF=1.0;RO=0;AO=249;PRO=0.0;PAO=0.0;QR=0;QA=9395;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=176;SAR=73;SRP=0.0;SAP=95.529;AB=0.0;ABP=0.0;RUN=1;RPP=69.0178;RPPR=0.0;RPL=81.0;RPR=168.0;EPP=4.06551;EPPR=0.0;DPRA=0.0;ODDS=43.6532;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991968;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=9.6086;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.5;SOR=1.8905 G [...]
+chr5 1297918 . T C 6109.93 REJECT NS=2;DP=166;DPB=192.0;AC=4;AN=4;AF=1.0;RO=0;AO=192;PRO=0.0;PAO=0.0;QR=0;QA=7221;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=98;SAR=94;SRP=0.0;SAP=3.19126;AB=0.0;ABP=0.0;RUN=1;RPP=5.9056;RPPR=0.0;RPL=88.0;RPR=104.0;EPP=49.335;EPPR=0.0;DPRA=0.0;ODDS=36.7581;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8698;MQMR=0.0;PAIRED=0.994792;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=59.92;QD=31.915;SOR=0.811 [...]
+chr5 1298645 . G A 11932.7 REJECT NS=2;DP=444;DPB=500.0;AC=2;AN=4;AF=0.5;RO=110;AO=389;PRO=0.0;PAO=0.0;QR=4178;QA=14842;PQR=0.0;PQA=0.0;SRF=68;SRR=42;SAF=202;SAR=187;SRP=16.355;SAP=4.26629;AB=0.778;ABP=338.65;RUN=1;RPP=3.01588;RPPR=28.5942;RPL=195.0;RPR=194.0;EPP=3.14985;EPPR=4.2737;DPRA=0.0;ODDS=238.946;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.196;Dels=0.0;FS=7.2335;HaplotypeScore=4.8899;MLE [...]
+chr5 1298782 . C T 1852.18 REJECT NS=2;DP=474;DPB=545.0;AC=2;AN=4;AF=0.5;RO=440;AO=105;PRO=0.0;PAO=0.0;QR=16299;QA=3739;PQR=0.0;PQA=0.0;SRF=234;SRR=206;SAF=54;SAR=51;SRP=6.87947;SAP=3.19643;AB=0.192661;ABP=450.154;RUN=1;RPP=3.03098;RPPR=7.45195;RPL=53.0;RPR=52.0;EPP=3.03098;EPPR=4.60929;DPRA=0.0;ODDS=68.8944;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.1905;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993182;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.1595;Dels=0.0;FS=4.6185;HaplotypeSc [...]
+chr5 1298805 . CT C 1548.38 REJECT NS=2;DP=563;DPB=534.333;AC=2;AN=4;AF=0.5;RO=442;AO=118;PRO=16.5;PAO=5.5;QR=15832;QA=3498;PQR=474.0;PQA=91.0;SRF=231;SRR=211;SAF=61;SAR=57;SRP=4.97543;SAP=3.30474;AB=0.209591;ABP=415.432;RUN=1;RPP=3.30474;RPPR=10.8708;RPL=57.0;RPR=61.0;EPP=3.08391;EPPR=3.02995;DPRA=0.0;ODDS=49.7031;GTI=0;TYPE=del;CIGAR=1M1D1M;NUMALT=1;MEANALT=2.5;LEN=1;MQM=60.8475;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995475;technology.ILLUMINA=1.0;END=1298806;HOMLEN=0;SVLEN=-1;SVTYPE=DEL;BaseQ [...]
+chr5 1299087 . C T 14676.0 REJECT NS=2;DP=527;DPB=596.0;AC=2;AN=4;AF=0.5;RO=125;AO=470;PRO=0.0;PAO=0.0;QR=4682;QA=18184;PQR=0.0;PQA=0.0;SRF=67;SRR=58;SAF=241;SAR=229;SRP=4.41741;SAP=3.6756;AB=0.788591;ABP=434.157;RUN=1;RPP=3.08422;RPPR=3.02767;RPL=237.0;RPR=233.0;EPP=3.91585;EPPR=3.86152;DPRA=0.0;ODDS=185.574;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993617;PAIREDR=0.992;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.3905;Dels=0.0;FS=1.949;HaplotypeScor [...]
+chr5 1299213 . A G 9469.16 REJECT NS=2;DP=362;DPB=409.0;AC=2;AN=4;AF=0.5;RO=90;AO=318;PRO=0.0;PAO=0.0;QR=3392;QA=11925;PQR=0.0;PQA=0.0;SRF=35;SRR=55;SAF=106;SAR=212;SRP=12.6613;SAP=79.7357;AB=0.777506;ABP=276.589;RUN=1;RPP=18.7432;RPPR=4.55446;RPL=183.0;RPR=135.0;EPP=3.44733;EPPR=10.8276;DPRA=0.0;ODDS=143.079;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993711;PAIREDR=0.988889;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.1115;Dels=0.0;FS=2.788;Haplotype [...]
+chr5 1299859 . G C 7413.285 PASS DP=228;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.4575;Dels=0.0;FS=1.123;HaplotypeScore=8.9575;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.873;QD=26.485;ReadPosRankSum=-0.0215;SOR=0.5745;ClippingRankSum=0.056 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:42,63:105:99.0:2519,0,3200:63:60:105:1:.:.:.:.:.:-0.0516987 0/1:40,312:352:99.0:12364,0,569:312:89:352:.:1:.:.:.:.:0.101192
+chr5 1299859 . GGAG CGAC 11689.8 REJECT NS=2;DP=439;DPB=457.75;AC=2;AN=4;AF=0.5;RO=80;AO=356;PRO=4.0;PAO=31.0;QR=2988;QA=13368;PQR=152.0;PQA=1131.0;SRF=43;SRR=37;SAF=184;SAR=172;SRP=3.98746;SAP=3.88865;AB=0.810934;ABP=371.661;RUN=1;RPP=11.8182;RPPR=3.44459;RPL=159.0;RPR=197.0;EPP=7.13366;EPPR=5.72464;DPRA=0.0;ODDS=81.2218;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=1;MEANALT=2.0;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=0.988764;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr5 1299862 . G C 7311.785 PASS DP=227;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.607;Dels=0.0;FS=0.373;HaplotypeScore=8.96;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.108;QD=29.355;ReadPosRankSum=-0.3775;SOR=0.623;ClippingRankSum=0.278 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:42,63:105:99.0:2554,0,3197:63:60:105:1:.:.:.:.:.:-0.0516987 0/1:42,306:349:99.0:12126,0,705:306:88:348:.:1:.:.:.:.:0.101192
+chr5 1300025 . G T 2729.0299999999997 REJECT NS=2;DP=517;DPB=582.0;AC=2;AN=4;AF=0.5;RO=447;AO=135;PRO=0.0;PAO=0.0;QR=17038;QA=5068;PQR=0.0;PQA=0.0;SRF=223;SRR=224;SAF=70;SAR=65;SRP=3.01516;SAP=3.41242;AB=0.231959;ABP=366.206;RUN=1;RPP=3.02638;RPPR=4.41423;RPL=67.0;RPR=68.0;EPP=3.02638;EPPR=4.41423;DPRA=0.0;ODDS=214.518;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985185;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.074;Dels=0.0;FS=3.068;Haplo [...]
+chr5 1300070 . A G 2716.025 REJECT NS=2;DP=484;DPB=550.0;AC=2;AN=4;AF=0.5;RO=423;AO=127;PRO=0.0;PAO=0.0;QR=16132;QA=4845;PQR=0.0;PQA=0.0;SRF=185;SRR=238;SAF=65;SAR=62;SRP=17.4303;SAP=3.16418;AB=0.230909;ABP=348.93;RUN=1;RPP=3.84811;RPPR=8.60069;RPL=67.0;RPR=60.0;EPP=3.84811;EPPR=19.6891;DPRA=0.0;ODDS=146.033;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9858;PAIRED=0.984252;PAIREDR=0.997636;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1825;Dels=0.0;FS=3.951;Haplotyp [...]
+chr5 1300310 . G T 10906.4 REJECT NS=2;DP=409;DPB=461.0;AC=2;AN=4;AF=0.5;RO=103;AO=358;PRO=0.0;PAO=0.0;QR=3934;QA=13598;PQR=0.0;PQA=0.0;SRF=52;SRR=51;SAF=190;SAR=168;SRP=3.03138;SAP=5.94603;AB=0.776573;ABP=309.301;RUN=1;RPP=6.50407;RPPR=3.53736;RPL=191.0;RPR=167.0;EPP=9.22144;EPPR=6.5732;DPRA=0.0;ODDS=189.229;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994413;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.403;Dels=0.0;FS=0.79;HaplotypeScore=5 [...]
+chr5 1300357 . GTCAGCC G 1148.77 REJECT NS=2;DP=386;DPB=406.643;AC=2;AN=4;AF=0.5;RO=311;AO=72;PRO=79.5;PAO=37.5;QR=11852;QA=2620;PQR=2680.5;PQA=1156.5;SRF=172;SRR=139;SAF=34;SAR=38;SRP=10.6139;SAP=3.49285;AB=0.186528;ABP=332.467;RUN=1;RPP=3.13094;RPPR=4.1903;RPL=35.0;RPR=37.0;EPP=6.02623;EPPR=3.07314;DPRA=0.0;ODDS=21.2623;GTI=0;TYPE=del;CIGAR=1M6D7M;NUMALT=1;MEANALT=2.5;LEN=6;MQM=60.1389;MQMR=60.0;PAIRED=0.986111;PAIREDR=0.996785;technology.ILLUMINA=1.0;END=1300363;HOMLEN=8;HOMSEQ=TCAGCC [...]
+chr5 1300401 . T C 2189.56 REJECT NS=2;DP=448;DPB=506.0;AC=2;AN=4;AF=0.5;RO=401;AO=104;PRO=0.0;PAO=0.0;QR=15454;QA=4061;PQR=0.0;PQA=0.0;SRF=222;SRR=179;SAF=55;SAR=49;SRP=13.0229;SAP=3.76196;AB=0.205534;ABP=384.108;RUN=1;RPP=3.09382;RPPR=5.87491;RPL=53.0;RPR=51.0;EPP=4.34659;EPPR=8.21425;DPRA=0.0;ODDS=101.835;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0962;MQMR=60.0;PAIRED=0.990385;PAIREDR=0.997506;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.815;Dels=0.0;FS=1.392;Haplotype [...]
+chr5 1300429 . T G 17203.15 REJECT NS=2;DP=462;DPB=525.0;AC=4;AN=4;AF=1.0;RO=3;AO=522;PRO=0.0;PAO=0.0;QR=107;QA=19827;PQR=0.0;PQA=0.0;SRF=2;SRR=1;SAF=279;SAR=243;SRP=3.73412;SAP=8.40154;AB=0.0;ABP=0.0;RUN=1;RPP=12.5947;RPPR=3.73412;RPL=237.0;RPR=285.0;EPP=7.81915;EPPR=3.73412;DPRA=0.0;ODDS=82.264;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0192;MQMR=60.0;PAIRED=0.996169;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.306;Dels=0.0;FS=0.0;HaplotypeScore=10.6809;MLEA [...]
+chr5 1300584 . C G 2426.3599999999997 REJECT NS=2;DP=529;DPB=598.0;AC=2;AN=4;AF=0.5;RO=475;AO=123;PRO=0.0;PAO=0.0;QR=18034;QA=4734;PQR=0.0;PQA=0.0;SRF=214;SRR=261;SAF=60;SAR=63;SRP=13.1088;SAP=3.16919;AB=0.205686;ABP=452.934;RUN=1;RPP=3.45166;RPPR=5.02634;RPL=64.0;RPR=59.0;EPP=12.3494;EPPR=3.12459;DPRA=0.0;ODDS=139.829;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995789;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8315;Dels=0.0;FS=0.6735;Hapl [...]
+chr5 1302113 . A AC 1021.815 REJECT NS=2;DP=30;DPB=41.0;AC=4;AN=4;AF=1.0;RO=0;AO=34;PRO=1.5;PAO=1.5;QR=0;QA=1182;PQR=52.5;PQA=52.5;SRF=0;SRR=0;SAF=25;SAR=9;SRP=0.0;SAP=19.3602;AB=0.0;ABP=0.0;RUN=1;RPP=4.03217;RPPR=0.0;RPL=15.0;RPR=19.0;EPP=3.26577;EPPR=0.0;DPRA=0.0;ODDS=9.36163;GTI=0;TYPE=ins;CIGAR=1M1I6M;NUMALT=1;MEANALT=1.5;LEN=1;MQM=57.7647;MQMR=0.0;PAIRED=0.941176;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=1302113;HOMLEN=2;HOMSEQ=CC;SVLEN=1;SVTYPE=INS;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=5 [...]
+chr5 1302144 . T C 1342.38 REJECT NS=2;DP=40;DPB=47.0;AC=4;AN=4;AF=1.0;RO=0;AO=47;PRO=0.0;PAO=0.0;QR=0;QA=1651;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=35;SAR=12;SRP=0.0;SAP=27.4509;AB=0.0;ABP=0.0;RUN=1;RPP=4.16534;RPPR=0.0;RPL=21.0;RPR=26.0;EPP=3.42611;EPPR=0.0;DPRA=0.0;ODDS=12.1847;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.1277;MQMR=0.0;PAIRED=0.893617;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.8995;MLEAC=2;MLEAF=1.0;MQ=58.865;QD=28.085;SOR=1.981 [...]
+chr5 1302914 . G A 3603.23 REJECT NS=2;DP=99;DPB=117.0;AC=4;AN=4;AF=1.0;RO=0;AO=117;PRO=0.0;PAO=0.0;QR=0;QA=4337;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=57;SAR=60;SRP=0.0;SAP=3.17734;AB=0.0;ABP=0.0;RUN=1;RPP=3.47429;RPPR=0.0;RPL=56.0;RPR=61.0;EPP=47.5719;EPPR=0.0;DPRA=0.0;ODDS=26.7629;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991453;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.155;SOR=0.949 GT:GQ: [...]
+chr5 1303901 . T C 1635.72 REJECT NS=2;DP=46;DPB=52.0;AC=4;AN=4;AF=1.0;RO=0;AO=52;PRO=0.0;PAO=0.0;QR=0;QA=1972;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=50;SAR=2;SRP=0.0;SAP=99.2232;AB=0.0;ABP=0.0;RUN=1;RPP=3.0103;RPPR=0.0;RPL=26.0;RPR=26.0;EPP=3.67845;EPPR=0.0;DPRA=0.0;ODDS=11.2467;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9995;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.31;SOR=4.7425 GT:GQ:DP:RO: [...]
+chr5 1306165 . T C 2916.505 REJECT NS=2;DP=79;DPB=93.0;AC=4;AN=4;AF=1.0;RO=0;AO=93;PRO=0.0;PAO=0.0;QR=0;QA=3474;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=34;SAR=59;SRP=0.0;SAP=17.6035;AB=0.0;ABP=0.0;RUN=1;RPP=3.22044;RPPR=0.0;RPL=48.0;RPR=45.0;EPP=4.90158;EPPR=0.0;DPRA=0.0;ODDS=20.5554;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.7849;MQMR=0.0;PAIRED=0.989247;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=59.875;QD=30.95;SOR=1.311 GT: [...]
+chr5 1306281 . A AT 77.1781 REJECT NS=2;DP=50;DPB=66.9565;AC=2;AN=2;AF=0.0;RO=25;AO=3;PRO=8.03333;PAO=6.03333;QR=913;QA=71;PQR=282.8;PQA=223.8;SRF=10;SRR=15;SAF=1;SAR=2;SRP=5.18177;SAP=3.73412;AB=0.075;ABP=65.7659;RUN=1;RPP=3.73412;RPPR=13.5202;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=5.18177;DPRA=0.0;ODDS=1.9031;GTI=1;TYPE=ins;CIGAR=1M1I22M;NUMALT=5;MEANALT=7.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV: [...]
+chr5 1306281 . A ATT 77.1781 REJECT NS=2;DP=50;DPB=66.9565;AC=2;AN=2;AF=0.0;RO=25;AO=2;PRO=8.03333;PAO=5.03333;QR=913;QA=55;PQR=282.8;PQA=184.8;SRF=10;SRR=15;SAF=1;SAR=1;SRP=5.18177;SAP=3.0103;AB=0.05;ABP=73.366;RUN=1;RPP=7.35324;RPPR=13.5202;RPL=2.0;RPR=0.0;EPP=3.0103;EPPR=5.18177;DPRA=0.0;ODDS=1.9031;GTI=1;TYPE=ins;CIGAR=1M2I22M;NUMALT=5;MEANALT=7.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:Cal [...]
+chr5 1306281 . A ATTT 77.1781 REJECT NS=2;DP=50;DPB=66.9565;AC=2;AN=2;AF=0.0;RO=25;AO=3;PRO=8.03333;PAO=5.03333;QR=913;QA=84;PQR=282.8;PQA=184.8;SRF=10;SRR=15;SAF=0;SAR=3;SRP=5.18177;SAP=9.52472;AB=0.06;ABP=87.0897;RUN=1;RPP=3.73412;RPPR=13.5202;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=5.18177;DPRA=0.0;ODDS=1.9031;GTI=1;TYPE=ins;CIGAR=1M3I22M;NUMALT=5;MEANALT=5.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV [...]
+chr5 1306281 . AT A 77.1781 REJECT NS=2;DP=50;DPB=66.9565;AC=2;AN=3;AF=0.25;RO=25;AO=10;PRO=8.03333;PAO=4.03333;QR=913;QA=303;PQR=282.8;PQA=146.8;SRF=10;SRR=15;SAF=3;SAR=7;SRP=5.18177;SAP=6.48466;AB=0.2;ABP=42.0968;RUN=1;RPP=16.9077;RPPR=13.5202;RPL=9.0;RPR=1.0;EPP=3.87889;EPPR=5.18177;DPRA=0.0;ODDS=1.9031;GTI=1;TYPE=del;CIGAR=1M1D21M;NUMALT=5;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.725;FS=1.316;MLEAC=1;M [...]
+chr5 1306281 . ATT A 77.1781 REJECT NS=2;DP=50;DPB=66.9565;AC=2;AN=3;AF=0.25;RO=25;AO=5;PRO=8.03333;PAO=3.83333;QR=913;QA=156;PQR=282.8;PQA=139.0;SRF=10;SRR=15;SAF=4;SAR=1;SRP=5.18177;SAP=6.91895;AB=0.1;ABP=72.4974;RUN=1;RPP=3.44459;RPPR=13.5202;RPL=3.0;RPR=2.0;EPP=6.91895;EPPR=5.18177;DPRA=0.0;ODDS=1.9031;GTI=1;TYPE=del;CIGAR=1M2D20M;NUMALT=5;MEANALT=5.0;LEN=2;MQM=56.0;MQMR=60.0;PAIRED=0.8;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV [...]
+chr5 1306331 . T C 1369.875 REJECT NS=2;DP=43;DPB=50.0;AC=4;AN=4;AF=1.0;RO=1;AO=48;PRO=0.0;PAO=0.0;QR=16;QA=1676;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=9;SAR=39;SRP=5.18177;SAP=43.7254;AB=0.0;ABP=0.0;RUN=1;RPP=3.0103;RPPR=5.18177;RPL=24.0;RPR=24.0;EPP=3.19126;EPPR=5.18177;DPRA=0.0;ODDS=11.7481;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=58.0;MQMR=60.0;PAIRED=0.979167;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.535;Dels=0.0;FS=0.0;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.0;M [...]
+chr5 1306765 . C G 9994.585 REJECT NS=2;DP=267;DPB=302.0;AC=4;AN=4;AF=1.0;RO=0;AO=302;PRO=0.0;PAO=0.0;QR=0;QA=11466;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=151;SAR=151;SRP=0.0;SAP=3.0103;AB=0.0;ABP=0.0;RUN=1;RPP=8.6475;RPPR=0.0;RPL=165.0;RPR=137.0;EPP=18.225;EPPR=0.0;DPRA=0.0;ODDS=46.7755;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993377;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9637;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.695;SOR=1.066 [...]
+chr5 1306796 . G A 4076.835 REJECT NS=2;DP=243;DPB=276.0;AC=2;AN=4;AF=0.5;RO=126;AO=149;PRO=0.0;PAO=0.0;QR=4714;QA=5640;PQR=0.0;PQA=0.0;SRF=56;SRR=70;SAF=63;SAR=86;SRP=6.38815;SAP=10.7198;AB=0.539855;ABP=6.81824;RUN=1;RPP=4.19076;RPPR=14.6604;RPL=79.0;RPR=70.0;EPP=22.9616;EPPR=3.63072;DPRA=0.0;ODDS=138.56;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992063;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.249;Dels=0.0;FS=1.058;HaplotypeScore=3.859 [...]
+chr5 1307434 . T A 4456.09 REJECT NS=2;DP=135;DPB=174.238;AC=0;AN=4;AF=0.0;RO=0;AO=7;PRO=20.3333;PAO=2.33333;QR=0;QA=270;PQR=707.0;PQA=82.0;SRF=0;SRR=0;SAF=0;SAR=7;SRP=0.0;SAP=18.2106;AB=0.0;ABP=0.0;RUN=1;RPP=18.2106;RPPR=0.0;RPL=0.0;RPR=7.0;EPP=18.2106;EPPR=0.0;DPRA=0.0;ODDS=31.766;GTI=0;TYPE=snp;CIGAR=1X20M;NUMALT=2;MEANALT=5.5;LEN=1;MQM=40.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallP [...]
+chr5 1307434 . T TTA 4456.09 REJECT NS=2;DP=135;DPB=174.238;AC=4;AN=4;AF=1.0;RO=0;AO=120;PRO=20.3333;PAO=37.3333;QR=0;QA=4502;PQR=707.0;PQA=1311.0;SRF=0;SRR=0;SAF=36;SAR=84;SRP=0.0;SAP=44.7026;AB=0.0;ABP=0.0;RUN=1;RPP=19.2963;RPPR=0.0;RPL=75.0;RPR=45.0;EPP=23.9288;EPPR=0.0;DPRA=0.0;ODDS=31.766;GTI=0;TYPE=ins;CIGAR=1M2I20M;NUMALT=2;MEANALT=5.5;LEN=2;MQM=57.4583;MQMR=0.0;PAIRED=0.966667;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;END=1307434;HOMLEN=7;HOMSEQ=TATATAT;SVLEN=2; [...]
+chr5 1307434 . T TTATATATATTTATATATATATGTATATACGTA . PASS SOMATIC;AC=1;AN=4;END=1307434;HOMLEN=7;HOMSEQ=TATATAT;SVLEN=32;SVTYPE=INS GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:-3.40649 0/1:41,28:28:41:69:.:.:.:1:.:.:-3.47473
+chr5 1307469 . C T 3278.98 REJECT NS=2;DP=104;DPB=104.0;AC=4;AN=4;AF=1.0;RO=0;AO=104;PRO=0.0;PAO=0.0;QR=0;QA=3987;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=18;SAR=86;SRP=0.0;SAP=99.5573;AB=0.0;ABP=0.0;RUN=1;RPP=47.1914;RPPR=0.0;RPL=75.0;RPR=29.0;EPP=5.09825;EPPR=0.0;DPRA=0.0;ODDS=23.0742;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=52.5385;MQMR=0.0;PAIRED=0.971154;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=4;Dels=0.01;FS=0.0;HaplotypeScore=3.9994;MLEAC=2;MLEAF=1.0;MQ=51.73;QD=32.38;SOR=2.99 [...]
+chr5 1307483 . C T 1899.77 PASS SOMATIC;DP=75;AC=1;AN=4;AF=0.5;MQ0=4;ALERT;BaseQRankSum=2.954;Dels=0.0;FS=2.462;HaplotypeScore=0.0;MLEAC=1;MLEAF=0.5;MQ=44.25;MQRankSum=5.26;QD=25.33;ReadPosRankSum=5.21;SOR=0.168 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.40649 0/1:22,53:75:99.0:1928,0,379:53:71:75:.:1:.:.:.:.:-3.47473
+chr5 1307483 . CG TT 1693.67 REJECT NS=2;DP=97;DPB=97.0;AC=2;AN=4;AF=0.5;RO=28;AO=69;PRO=0.0;PAO=0.0;QR=988;QA=2656;PQR=0.0;PQA=0.0;SRF=0;SRR=28;SAF=4;SAR=65;SRP=63.8115;SAP=120.112;AB=0.71134;ABP=40.6417;RUN=1;RPP=78.5712;RPPR=18.2106;RPL=59.0;RPR=10.0;EPP=55.9124;EPPR=18.2106;DPRA=0.0;ODDS=21.1133;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=1;MEANALT=1.0;LEN=2;MQM=49.6957;MQMR=29.1786;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:Ca [...]
+chr5 1307484 . G T 1875.77 PASS SOMATIC;DP=76;AC=1;AN=4;AF=0.5;MQ0=4;ALERT;BaseQRankSum=1.766;Dels=0.0;FS=2.44;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.5;MQ=44.01;MQRankSum=5.519;QD=24.68;ReadPosRankSum=5.409;SOR=0.154 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.40649 0/1:23,53:76:99.0:1904,0,398:53:70:76:.:1:.:.:.:.:-3.47473
+chr5 1307486 . A G 217.11 REJECT NS=2;DP=103;DPB=103.0;AC=2;AN=4;AF=0.5;RO=75;AO=28;PRO=0.0;PAO=0.0;QR=2891;QA=1023;PQR=0.0;PQA=0.0;SRF=4;SRR=71;SAF=0;SAR=28;SRP=132.98;SAP=63.8115;AB=0.271845;ABP=49.581;RUN=1;RPP=18.2106;RPPR=56.5443;RPL=7.0;RPR=21.0;EPP=18.2106;EPPR=38.4777;DPRA=0.0;ODDS=20.0957;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=29.1786;MQMR=47.48;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=4;ALERT;BaseQRankSum=0.018;Dels=0.0;FS=2.43;HaplotypeScore=3.9629;ML [...]
+chr5 1307494 . A G 1041.8 REJECT NS=2;DP=101;DPB=101.0;AC=2;AN=4;AF=0.5;RO=46;AO=55;PRO=0.0;PAO=0.0;QR=1737;QA=2061;PQR=0.0;PQA=0.0;SRF=0;SRR=46;SAF=1;SAR=54;SRP=102.898;SAP=113.913;AB=0.544554;ABP=4.75178;RUN=1;RPP=105.701;RPPR=45.4956;RPL=53.0;RPR=2.0;EPP=97.8049;EPPR=45.4956;DPRA=0.0;ODDS=44.6073;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=47.1273;MQMR=26.8913;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=5;BaseQRankSum=-0.829;Dels=0.0;FS=0.0;HaplotypeScore=119.669;MLE [...]
+chr5 1307498 . ACATT A 737.686 REJECT NS=2;DP=82;DPB=83.8333;AC=2;AN=2;AF=0.5;RO=0;AO=32;PRO=3.2;PAO=0.2;QR=0;QA=1149;PQR=110.333;PQA=7.0;SRF=0;SRR=0;SAF=0;SAR=32;SRP=0.0;SAP=72.4974;AB=0.390244;ABP=11.5903;RUN=1;RPP=72.4974;RPPR=0.0;RPL=0.0;RPR=32.0;EPP=72.4974;EPPR=0.0;DPRA=0.0;ODDS=2.80869;GTI=1;TYPE=del;CIGAR=1M4D1M;NUMALT=4;MEANALT=4.0;LEN=4;MQM=24.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;ALERT;BaseQRankSum=1.72;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=37 [...]
+chr5 1307499 . C T 737.686 REJECT NS=2;DP=82;DPB=83.8333;AC=0;AN=4;AF=0.0;RO=0;AO=14;PRO=3.2;PAO=0.2;QR=0;QA=411;PQR=110.333;PQA=7.0;SRF=0;SRR=0;SAF=0;SAR=14;SRP=0.0;SAP=33.4109;AB=0.170732;ABP=80.23;RUN=1;RPP=3.63072;RPPR=0.0;RPL=8.0;RPR=6.0;EPP=3.63072;EPPR=0.0;DPRA=0.0;ODDS=2.80869;GTI=1;TYPE=snp;CIGAR=1M1X4M;NUMALT=4;MEANALT=4.0;LEN=1;MQM=33.5;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:Ca [...]
+chr5 1307499 . C CGTAT 947.73 PASS SOMATIC;DP=71;AC=2;AN=4;AF=1.0;MQ0=0;ALERT;BaseQRankSum=-0.409;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=37.29;MQRankSum=-1.085;QD=10.01;ReadPosRankSum=3.684;SOR=3.056 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.40649 1/1:11,53:42:43.0:985,43,0:53:83:64:.:1:.:.:.:.:-3.47473
+chr5 1307500 . ATT GTA 737.686 REJECT NS=2;DP=82;DPB=83.8333;AC=0;AN=4;AF=0.0;RO=0;AO=6;PRO=3.2;PAO=3.2;QR=0;QA=223;PQR=110.333;PQA=110.333;SRF=0;SRR=0;SAF=0;SAR=6;SRP=0.0;SAP=16.0391;AB=0.0731707;ABP=132.769;RUN=1;RPP=16.0391;RPPR=0.0;RPL=6.0;RPR=0.0;EPP=16.0391;EPPR=0.0;DPRA=0.0;ODDS=2.80869;GTI=1;TYPE=complex;CIGAR=2M1X1M1X1M;NUMALT=4;MEANALT=4.0;LEN=6;MQM=59.3333;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:Cal [...]
+chr5 1307500 . ATT GTATATA 737.686 REJECT NS=2;DP=82;DPB=83.8333;AC=2;AN=2;AF=0.5;RO=0;AO=30;PRO=3.2;PAO=3.2;QR=0;QA=1037;PQR=110.333;PQA=110.333;SRF=0;SRR=0;SAF=0;SAR=30;SRP=0.0;SAP=68.1545;AB=0.365854;ABP=15.8273;RUN=1;RPP=68.1545;RPPR=0.0;RPL=30.0;RPR=0.0;EPP=68.1545;EPPR=0.0;DPRA=0.0;ODDS=2.80869;GTI=1;TYPE=complex;CIGAR=2M4I2M1X1M;NUMALT=4;MEANALT=4.0;LEN=10;MQM=37.8667;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr5 1307506 . A T 1190.79 REJECT NS=2;DP=76;DPB=78.6667;AC=2;AN=4;AF=0.5;RO=14;AO=62;PRO=2.0;PAO=2.0;QR=481;QA=2395;PQR=69.5;PQA=69.5;SRF=0;SRR=14;SAF=0;SAR=62;SRP=33.4109;SAP=137.642;AB=0.815789;ABP=68.8402;RUN=1;RPP=3.15039;RPPR=33.4109;RPL=30.0;RPR=32.0;EPP=3.15039;EPPR=33.4109;DPRA=0.0;ODDS=2.60908;GTI=0;TYPE=snp;CIGAR=2M1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=30.7097;MQMR=49.5714;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=5;BaseQRankSum=2.361;Dels=0.0;FS=0.0;HaplotypeScore=83.041 [...]
+chr5 1307516 . A G 2702.76 REJECT NS=2;DP=124;DPB=124.0;AC=4;AN=4;AF=1.0;RO=0;AO=124;PRO=0.0;PAO=0.0;QR=0;QA=4406;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=0;SAR=124;SRP=0.0;SAP=272.273;AB=0.0;ABP=0.0;RUN=1;RPP=79.292;RPPR=0.0;RPL=29.0;RPR=95.0;EPP=79.292;EPPR=0.0;DPRA=0.0;ODDS=22.9351;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=34.1694;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=7;Dels=0.0;FS=0.0;HaplotypeScore=3.9629;MLEAC=2;MLEAF=1.0;MQ=34.35;QD=30.54;SOR=9.108 GT:GQ: [...]
+chr5 1307529 . C T 3056.77 PASS SOMATIC;DP=92;AC=2;AN=4;AF=1.0;MQ0=6;Dels=0.0;FS=0.0;HaplotypeScore=0.9973;MLEAC=2;MLEAF=1.0;MQ=33.34;QD=33.23;SOR=8.932 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.40649 1/1:0,92:92:99.0:3085,250,0:92:100:92:.:1:.:.:.:.:-3.47473
+chr5 1307529 . CATG TATT 2593.81 REJECT NS=2;DP=112;DPB=112.25;AC=4;AN=4;AF=1.0;RO=0;AO=112;PRO=0.0;PAO=1.0;QR=0;QA=4220;PQR=0.0;PQA=35.0;SRF=0;SRR=0;SAF=0;SAR=112;SRP=0.0;SAP=246.215;AB=0.0;ABP=0.0;RUN=1;RPP=40.5458;RPPR=0.0;RPL=34.0;RPR=78.0;EPP=40.5458;EPPR=0.0;DPRA=0.0;ODDS=21.0938;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=1;MEANALT=1.0;LEN=4;MQM=32.5268;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallS [...]
+chr5 1307532 . G T 3026.77 PASS SOMATIC;DP=91;AC=2;AN=4;AF=1.0;MQ0=6;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=33.26;QD=33.26;SOR=8.909 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.40649 1/1:0,91:91:99.0:3055,247,0:91:100:91:.:1:.:.:.:.:-3.47473
+chr5 1307542 . A G 2346.28 REJECT NS=2;DP=102;DPB=102.0;AC=4;AN=4;AF=1.0;RO=0;AO=102;PRO=0.0;PAO=0.0;QR=0;QA=3839;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=0;SAR=102;SRP=0.0;SAP=224.5;AB=0.0;ABP=0.0;RUN=1;RPP=17.4016;RPPR=0.0;RPL=38.0;RPR=64.0;EPP=17.4016;EPPR=0.0;DPRA=0.0;ODDS=20.4438;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=32.4216;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=6;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=33.09;QD=31.96;SOR=8.688 GT:GQ:DP: [...]
+chr5 1307555 . C T 2743.77 PASS SOMATIC;DP=79;AC=2;AN=4;AF=1.0;MQ0=3;Dels=0.0;FS=0.0;HaplotypeScore=0.9947;MLEAC=2;MLEAF=1.0;MQ=33.71;QD=34.73;SOR=8.688 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.40649 1/1:0,79:79:99.0:2772,226,0:79:100:79:.:1:.:.:.:.:-3.47473
+chr5 1307555 . CATG TATT 1872.17 REJECT NS=2;DP=102;DPB=102.0;AC=4;AN=4;AF=1.0;RO=0;AO=101;PRO=0.0;PAO=0.0;QR=0;QA=3919;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=0;SAR=101;SRP=0.0;SAP=222.329;AB=0.0;ABP=0.0;RUN=1;RPP=213.729;RPPR=0.0;RPL=100.0;RPR=1.0;EPP=213.729;EPPR=0.0;DPRA=0.0;ODDS=20.4712;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=1;MEANALT=1.5;LEN=4;MQM=32.505;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID: [...]
+chr5 1307558 . G T 2739.77 PASS SOMATIC;DP=79;AC=2;AN=4;AF=1.0;MQ0=3;Dels=0.0;FS=0.0;HaplotypeScore=0.9947;MLEAC=2;MLEAF=1.0;MQ=33.71;QD=34.68;SOR=8.688 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.40649 1/1:0,79:79:99.0:2768,226,0:79:100:79:.:1:.:.:.:.:-3.47473
+chr5 1307568 . A G 1851.62 REJECT NS=2;DP=102;DPB=102.0;AC=4;AN=4;AF=1.0;RO=0;AO=102;PRO=0.0;PAO=0.0;QR=0;QA=4005;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=0;SAR=102;SRP=0.0;SAP=224.5;AB=0.0;ABP=0.0;RUN=1;RPP=224.5;RPPR=0.0;RPL=102.0;RPR=0.0;EPP=224.5;EPPR=0.0;DPRA=0.0;ODDS=20.4708;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=32.4216;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=2;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=33.92;QD=28.42;SOR=8.688 GT:GQ:DP:RO:Q [...]
+chr5 1307581 . C T 1823.77 PASS SOMATIC;DP=45;AC=2;AN=4;AF=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=39.41;QD=31.93;SOR=7.658 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.40649 1/1:0,45:45:99.0:1852,132,0:45:100:45:.:1:.:.:.:.:-3.47473
+chr5 1307581 . CATG TATT 1232.53 REJECT NS=2;DP=55;DPB=55.0;AC=4;AN=4;AF=1.0;RO=0;AO=55;PRO=0.0;PAO=0.0;QR=0;QA=2147;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=0;SAR=55;SRP=0.0;SAP=122.441;AB=0.0;ABP=0.0;RUN=1;RPP=122.441;RPPR=0.0;RPL=55.0;RPR=0.0;EPP=122.441;EPPR=0.0;DPRA=0.0;ODDS=10.5641;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=1;MEANALT=1.0;LEN=4;MQM=38.7818;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:Call [...]
+chr5 1307584 . G T 1818.77 PASS SOMATIC;DP=45;AC=2;AN=4;AF=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=39.41;QD=33.1;SOR=7.658 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.40649 1/1:0,45:45:99.0:1847,132,0:45:100:45:.:1:.:.:.:.:-3.47473
+chr5 1307603 . C T 61.74 PASS SOMATIC;DP=2;AC=2;AN=4;AF=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=52.61;QD=30.87;SOR=2.303 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.40649 1/1:0,2:2:6.0:89,6,0:2:100:2:.:1:.:.:.:.:-3.47473
+chr5 1307603 . CATG TATT 55.0825 REJECT SOMATIC;NS=1;DP=2;DPB=2.0;AC=2;AN=4;AF=1.0;RO=0;AO=2;PRO=0.0;PAO=0.0;QR=0;QA=78;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=0;SAR=2;SRP=0.0;SAP=7.35324;AB=0.0;ABP=0.0;RUN=1;RPP=7.35324;RPPR=0.0;RPL=0.0;RPR=2.0;EPP=7.35324;EPPR=0.0;DPRA=0.0;ODDS=5.92187;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=1;MEANALT=1.0;LEN=4;MQM=52.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU [...]
+chr5 1307606 . G T 100.28 PASS SOMATIC;DP=3;AC=2;AN=4;AF=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=55.18;QD=33.43;SOR=2.833 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.40649 1/1:0,3:3:9.0:128,9,0:3:100:3:.:1:.:.:.:.:-3.47473
+chr5 1307616 . A G 44.0299 REJECT SOMATIC;NS=1;DP=6;DPB=6.0;AC=1;AN=4;AF=0.5;RO=3;AO=3;PRO=0.0;PAO=0.0;QR=116;QA=119;PQR=0.0;PQA=0.0;SRF=0;SRR=3;SAF=0;SAR=3;SRP=9.52472;SAP=9.52472;AB=0.5;ABP=3.0103;RUN=1;RPP=9.52472;RPPR=9.52472;RPL=0.0;RPR=3.0;EPP=9.52472;EPPR=9.52472;DPRA=0.0;ODDS=9.80822;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=54.6667;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.537;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=1;MLEAF=0.5;M [...]
+chr5 1307621 . C T 83.77 PASS SOMATIC;DP=6;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.406;Dels=0.0;FS=0.0;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.5;MQ=57.64;MQRankSum=0.406;QD=13.96;ReadPosRankSum=-1.537;SOR=0.693 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.40649 0/1:3,3:6:99.0:112,0,111:3:50:6:.:1:.:.:.:.:-3.47473
+chr5 1307621 . CGTA TGTT 33.4651 REJECT SOMATIC;NS=1;DP=6;DPB=6.0;AC=1;AN=4;AF=0.5;RO=3;AO=3;PRO=0.0;PAO=0.0;QR=118;QA=106;PQR=0.0;PQA=0.0;SRF=0;SRR=3;SAF=0;SAR=3;SRP=9.52472;SAP=9.52472;AB=0.5;ABP=3.0103;RUN=1;RPP=9.52472;RPPR=9.52472;RPL=0.0;RPR=3.0;EPP=9.52472;EPPR=9.52472;DPRA=0.0;ODDS=7.70513;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=1;MEANALT=1.0;LEN=4;MQM=60.0;MQMR=54.6667;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB [...]
+chr5 1307624 . A T 76.77 PASS SOMATIC;DP=6;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-0.988;Dels=0.0;FS=0.0;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.5;MQ=57.64;MQRankSum=0.406;QD=12.79;ReadPosRankSum=-1.537;SOR=0.693 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.40649 0/1:3,3:6:99.0:105,0,116:3:50:6:.:1:.:.:.:.:-3.47473
+chr5 1307629 . C T 236.84 PASS SOMATIC;DP=6;AC=2;AN=4;AF=1.0;MQ0=0;ALERT;Dels=0.0;FS=0.0;HaplotypeScore=1.9996;MLEAC=2;MLEAF=1.0;MQ=57.64;QD=26.12;SOR=3.912 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.40649 1/1:0,6:6:18.0:265,18,0:6:100:6:.:1:.:.:.:.:-3.47473
+chr5 1307629 . CATGTA TACGTG 105.385 REJECT NS=2;DP=7;DPB=9.66667;AC=2;AN=3;AF=0.5;RO=0;AO=3;PRO=0.0;PAO=0.0;QR=0;QA=106;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=0;SAR=3;SRP=0.0;SAP=9.52472;AB=0.5;ABP=3.0103;RUN=1;RPP=9.52472;RPPR=0.0;RPL=0.0;RPR=3.0;EPP=9.52472;EPPR=0.0;DPRA=0.0;ODDS=0.0;GTI=0;TYPE=complex;CIGAR=1X1M1X2M1X;NUMALT=2;MEANALT=3.0;LEN=6;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB [...]
+chr5 1307629 . CATGTA TATTTATATACGTG 105.385 REJECT NS=2;DP=7;DPB=9.66667;AC=2;AN=2;AF=0.25;RO=0;AO=2;PRO=0.0;PAO=0.0;QR=0;QA=77;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=0;SAR=2;SRP=0.0;SAP=7.35324;AB=0.333333;ABP=4.45795;RUN=1;RPP=3.0103;RPPR=0.0;RPL=1.0;RPR=1.0;EPP=3.0103;EPPR=0.0;DPRA=0.0;ODDS=0.0;GTI=0;TYPE=complex;CIGAR=1X2M8I2M1X;NUMALT=2;MEANALT=3.0;LEN=14;MQM=52.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC: [...]
+chr5 1307631 . T C 80.77 PASS SOMATIC;DP=6;AC=1;AN=4;AF=0.5;MQ0=0;ALERT;BaseQRankSum=-1.537;Dels=0.0;FS=0.0;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.5;MQ=57.64;MQRankSum=0.406;QD=13.46;ReadPosRankSum=-1.537;SOR=0.693 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.40649 0/1:3,3:6:99.0:109,0,115:3:50:6:.:1:.:.:.:.:-3.47473
+chr5 1307634 . A G 169.78 PASS SOMATIC;DP=6;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.736;Dels=0.0;FS=0.0;HaplotypeScore=2.9994;MLEAC=1;MLEAF=0.5;MQ=57.64;MQRankSum=0.736;QD=28.3;ReadPosRankSum=0.736;SOR=2.303 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.40649 0/1:1,5:6:26.0:198,0,26:5:83:6:.:1:.:.:.:.:-3.47473
+chr5 1307983 . T A 17.61 LowQual SOMATIC;DP=1;AC=2;AN=4;AF=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=17.61;SOR=1.609 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.40649 1/1:0,1:1:3.0:44,3,0:1:100:1:.:1:.:.:.:.:-3.47473
+chr5 1308005 . T TTATATATG 52.2065 REJECT SOMATIC;NS=1;DP=2;DPB=3.6;AC=2;AN=4;AF=1.0;RO=0;AO=2;PRO=0.0;PAO=0.0;QR=0;QA=74;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=2;SAR=0;SRP=0.0;SAP=7.35324;AB=0.0;ABP=0.0;RUN=1;RPP=7.35324;RPPR=0.0;RPL=0.0;RPR=2.0;EPP=7.35324;EPPR=0.0;DPRA=0.0;ODDS=5.92177;GTI=0;TYPE=ins;CIGAR=1M8I9M;NUMALT=1;MEANALT=1.0;LEN=8;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:L [...]
+chr5 1309168 . T C 20612.25 REJECT NS=2;DP=549;DPB=631.0;AC=4;AN=4;AF=1.0;RO=0;AO=631;PRO=0.0;PAO=0.0;QR=0;QA=23902;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=286;SAR=345;SRP=0.0;SAP=14.9895;AB=0.0;ABP=0.0;RUN=1;RPP=3.7846;RPPR=0.0;RPL=323.0;RPR=308.0;EPP=17.5499;EPPR=0.0;DPRA=0.0;ODDS=105.246;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99683;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8634;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.61;SOR=0.885 [...]
+chr5 1309754 . G A 303.3975 REJECT NS=2;DP=73;DPB=84.0;AC=2;AN=4;AF=0.5;RO=66;AO=18;PRO=0.0;PAO=0.0;QR=2511;QA=697;PQR=0.0;PQA=0.0;SRF=36;SRR=30;SAF=10;SAR=8;SRP=4.19474;SAP=3.49285;AB=0.214286;ABP=62.5707;RUN=1;RPP=7.35324;RPPR=4.19474;RPL=12.0;RPR=6.0;EPP=7.35324;EPPR=4.19474;DPRA=0.0;ODDS=37.29;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.944444;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4265;Dels=0.0;FS=3.4865;HaplotypeScore=0.9995;MLEA [...]
+chr5 1309904 . G A 2622.295 REJECT NS=2;DP=72;DPB=81.0;AC=4;AN=4;AF=1.0;RO=0;AO=81;PRO=0.0;PAO=0.0;QR=0;QA=3018;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=28;SAR=53;SRP=0.0;SAP=19.7655;AB=0.0;ABP=0.0;RUN=1;RPP=3.68051;RPPR=0.0;RPL=38.0;RPR=43.0;EPP=10.7579;EPPR=0.0;DPRA=0.0;ODDS=15.59;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.6049;MQMR=0.0;PAIRED=0.987654;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=59.695;QD=28.35;SOR=1.2445 GT:G [...]
+chr5 1310152 . G A 9583.27 REJECT NS=2;DP=258;DPB=293.0;AC=4;AN=4;AF=1.0;RO=0;AO=293;PRO=0.0;PAO=0.0;QR=0;QA=11205;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=255;SAR=38;SRP=0.0;SAP=351.995;AB=0.0;ABP=0.0;RUN=1;RPP=59.1054;RPPR=0.0;RPL=103.0;RPR=190.0;EPP=6.93081;EPPR=0.0;DPRA=0.0;ODDS=46.7262;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.989761;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.445;SOR=3.7465 [...]
+chr5 1311105 . GA G 7747.675 REJECT NS=2;DP=274;DPB=313.824;AC=4;AN=4;AF=1.0;RO=7;AO=268;PRO=54.0;PAO=65.0;QR=249;QA=9700;PQR=1823.0;PQA=2246.0;SRF=3;SRR=4;SAF=85;SAR=183;SRP=3.32051;SAP=80.8268;AB=0.0;ABP=0.0;RUN=1;RPP=13.5112;RPPR=5.80219;RPL=152.0;RPR=116.0;EPP=34.1563;EPPR=10.7656;DPRA=0.0;ODDS=29.0046;GTI=0;TYPE=del;CIGAR=1M1D15M;NUMALT=1;MEANALT=4.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996269;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9635;FS=3.6675;MLEAC=2;MLEAF=1.0;MQ= [...]
+chr5 1311198 . C T 10940.099999999999 REJECT NS=2;DP=299;DPB=334.0;AC=4;AN=4;AF=1.0;RO=0;AO=333;PRO=0.0;PAO=0.0;QR=0;QA=12469;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=207;SAR=126;SRP=0.0;SAP=45.7942;AB=0.0;ABP=0.0;RUN=1;RPP=39.6906;RPPR=0.0;RPL=204.0;RPR=129.0;EPP=5.36436;EPPR=0.0;DPRA=0.0;ODDS=48.0446;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996997;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.7901;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30. [...]
+chr5 1311693 . T C 12174.9 REJECT NS=2;DP=323;DPB=370.0;AC=4;AN=4;AF=1.0;RO=0;AO=370;PRO=0.0;PAO=0.0;QR=0;QA=13983;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=192;SAR=178;SRP=0.0;SAP=4.16059;AB=0.0;ABP=0.0;RUN=1;RPP=3.1042;RPPR=0.0;RPL=187.0;RPR=183.0;EPP=5.35784;EPPR=0.0;DPRA=0.0;ODDS=62.2787;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9997;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.91;SOR=0.7785 GT: [...]
+chr5 1312020 . T C 14344.8 REJECT NS=2;DP=384;DPB=433.0;AC=4;AN=4;AF=1.0;RO=0;AO=432;PRO=0.0;PAO=0.0;QR=0;QA=16374;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=237;SAR=195;SRP=0.0;SAP=11.8771;AB=0.0;ABP=0.0;RUN=1;RPP=8.15749;RPPR=0.0;RPL=200.0;RPR=232.0;EPP=11.8771;EPPR=0.0;DPRA=0.0;ODDS=65.4554;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993056;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.9628;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.71;SOR=0.95 [...]
+chr5 1312457 . G A 10576.45 REJECT NS=2;DP=279;DPB=319.0;AC=4;AN=4;AF=1.0;RO=0;AO=318;PRO=0.0;PAO=0.0;QR=0;QA=12233;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=165;SAR=153;SRP=0.0;SAP=3.99361;AB=0.0;ABP=0.0;RUN=1;RPP=11.8601;RPPR=0.0;RPL=141.0;RPR=177.0;EPP=15.0558;EPPR=0.0;DPRA=0.0;ODDS=54.2527;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.987421;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.966;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.525;SOR=0.7 [...]
+chr5 1312935 . T C 4171.62 REJECT NS=2;DP=147;DPB=168.0;AC=4;AN=4;AF=1.0;RO=0;AO=168;PRO=0.0;PAO=0.0;QR=0;QA=5319;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=166;SAR=2;SRP=0.0;SAP=350.653;AB=0.0;ABP=0.0;RUN=1;RPP=6.31921;RPPR=0.0;RPL=92.0;RPR=76.0;EPP=8.18047;EPPR=0.0;DPRA=0.0;ODDS=30.3869;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.1131;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=59.035;QD=33.38;SOR=7.368 GT:G [...]
+chr5 1312987 . G A 1719.81 REJECT NS=2;DP=127;DPB=244.0;AC=0;AN=4;AF=0.0;RO=9;AO=9;PRO=38.8333;PAO=19.4333;QR=338;QA=199;PQR=1370.57;PQA=659.967;SRF=6;SRR=3;SAF=0;SAR=9;SRP=5.18177;SAP=22.5536;AB=0.0708661;ABP=206.154;RUN=1;RPP=14.8328;RPPR=22.5536;RPL=1.0;RPR=8.0;EPP=14.8328;EPPR=5.18177;DPRA=0.0;ODDS=11.2206;GTI=0;TYPE=snp;CIGAR=1X20M;NUMALT=5;MEANALT=14.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr5 1312987 . G GA 1719.81 REJECT NS=2;DP=127;DPB=244.0;AC=2;AN=2;AF=0.5;RO=9;AO=24;PRO=38.8333;PAO=39.5833;QR=338;QA=706;PQR=1370.57;PQA=1399.82;SRF=6;SRR=3;SAF=12;SAR=12;SRP=5.18177;SAP=3.0103;AB=0.188976;ABP=109.72;RUN=1;RPP=20.744;RPPR=22.5536;RPL=5.0;RPR=19.0;EPP=3.37221;EPPR=5.18177;DPRA=0.0;ODDS=11.2206;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=5;MEANALT=14.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-1.532;FS=1.201;MLE [...]
+chr5 1312987 . G GAA 1719.81 REJECT NS=2;DP=127;DPB=244.0;AC=2;AN=2;AF=0.5;RO=9;AO=45;PRO=38.8333;PAO=39.9167;QR=338;QA=1335;PQR=1370.57;PQA=1411.82;SRF=6;SRR=3;SAF=24;SAR=21;SRP=5.18177;SAP=3.44459;AB=0.354331;ABP=26.4177;RUN=1;RPP=76.4061;RPPR=22.5536;RPL=3.0;RPR=42.0;EPP=4.21667;EPPR=5.18177;DPRA=0.0;ODDS=11.2206;GTI=0;TYPE=ins;CIGAR=1M2I20M;NUMALT=5;MEANALT=14.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-1.8845;FS=4.0 [...]
+chr5 1312987 . G GAAA 1719.81 REJECT NS=2;DP=127;DPB=244.0;AC=0;AN=4;AF=0.0;RO=9;AO=7;PRO=38.8333;PAO=39.9167;QR=338;QA=187;PQR=1370.57;PQA=1411.82;SRF=6;SRR=3;SAF=3;SAR=4;SRP=5.18177;SAP=3.32051;AB=0.0551181;ABP=221.337;RUN=1;RPP=10.7656;RPPR=22.5536;RPL=1.0;RPR=6.0;EPP=3.32051;EPPR=5.18177;DPRA=0.0;ODDS=11.2206;GTI=0;TYPE=ins;CIGAR=1M3I20M;NUMALT=5;MEANALT=14.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr5 1313002 . G AAA 1719.81 REJECT NS=2;DP=127;DPB=244.0;AC=0;AN=4;AF=0.0;RO=9;AO=7;PRO=38.8333;PAO=26.3167;QR=338;QA=98;PQR=1370.57;PQA=907.017;SRF=6;SRR=3;SAF=7;SAR=0;SRP=5.18177;SAP=18.2106;AB=0.0551181;ABP=221.337;RUN=1;RPP=3.32051;RPPR=22.5536;RPL=3.0;RPR=4.0;EPP=3.32051;EPPR=5.18177;DPRA=0.0;ODDS=11.2206;GTI=0;TYPE=complex;CIGAR=1M2I14M1X5M;NUMALT=5;MEANALT=14.0;LEN=23;MQM=54.1429;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr5 1313701 . A G 13806.3 REJECT NS=2;DP=367;DPB=416.0;AC=4;AN=4;AF=1.0;RO=0;AO=416;PRO=0.0;PAO=0.0;QR=0;QA=15807;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=189;SAR=227;SRP=0.0;SAP=10.5478;AB=0.0;ABP=0.0;RUN=1;RPP=7.10269;RPPR=0.0;RPL=194.0;RPR=222.0;EPP=10.5478;EPPR=0.0;DPRA=0.0;ODDS=65.4718;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.9293;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.77;SOR=1.08 GT:G [...]
+chr5 1314009 . C T 5508.735000000001 REJECT NS=2;DP=146;DPB=167.0;AC=4;AN=4;AF=1.0;RO=0;AO=167;PRO=0.0;PAO=0.0;QR=0;QA=6458;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=39;SAR=128;SRP=0.0;SAP=106.006;AB=0.0;ABP=0.0;RUN=1;RPP=15.506;RPPR=0.0;RPL=99.0;RPR=68.0;EPP=5.93594;EPPR=0.0;DPRA=0.0;ODDS=30.5803;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.988024;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=59.825;QD=31.27;SOR= [...]
+chr5 1314254 . C CAA 66.645 REJECT NS=2;DP=20;DPB=97.4286;AC=2;AN=4;AF=0.5;RO=3;AO=3;PRO=54.0;PAO=51.5;QR=108;QA=89;PQR=1805.33;PQA=1722.83;SRF=3;SRR=0;SAF=2;SAR=1;SRP=9.52472;SAP=3.73412;AB=0.15;ABP=24.2907;RUN=1;RPP=3.73412;RPPR=9.52472;RPL=1.0;RPR=2.0;EPP=9.52472;EPPR=9.52472;DPRA=0.0;ODDS=1.59344;GTI=0;TYPE=ins;CIGAR=1M2I27M;NUMALT=2;MEANALT=7.5;LEN=2;MQM=53.3333;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:Ca [...]
+chr5 1314254 . C CAAA 66.645 REJECT NS=2;DP=20;DPB=97.4286;AC=2;AN=2;AF=0.0;RO=3;AO=3;PRO=54.0;PAO=51.5;QR=108;QA=55;PQR=1805.33;PQA=1722.83;SRF=3;SRR=0;SAF=1;SAR=2;SRP=9.52472;SAP=3.73412;AB=0.15;ABP=24.2907;RUN=1;RPP=3.73412;RPPR=9.52472;RPL=1.0;RPR=2.0;EPP=9.52472;EPPR=9.52472;DPRA=0.0;ODDS=1.59344;GTI=0;TYPE=ins;CIGAR=1M3I27M;NUMALT=2;MEANALT=7.5;LEN=3;MQM=52.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.747;FS=9.031;MLEAC=1;MLEAF=0.5;MQ= [...]
+chr5 1315343 . G A 15360.0 REJECT NS=2;DP=403;DPB=463.0;AC=4;AN=4;AF=1.0;RO=0;AO=463;PRO=0.0;PAO=0.0;QR=0;QA=17750;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=233;SAR=230;SRP=0.0;SAP=3.05251;AB=0.0;ABP=0.0;RUN=1;RPP=6.42931;RPPR=0.0;RPL=245.0;RPR=218.0;EPP=26.6526;EPPR=0.0;DPRA=0.0;ODDS=78.5507;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99568;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9664;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.935;SOR=0.71 [...]
+chr5 1315660 . G A 16622.9 REJECT NS=2;DP=437;DPB=500.0;AC=4;AN=4;AF=1.0;RO=0;AO=500;PRO=0.0;PAO=0.0;QR=0;QA=19148;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=247;SAR=253;SRP=0.0;SAP=3.16665;AB=0.0;ABP=0.0;RUN=1;RPP=3.02767;RPPR=0.0;RPL=249.0;RPR=251.0;EPP=5.51184;EPPR=0.0;DPRA=0.0;ODDS=79.7517;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.988;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9575;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.345;SOR=0.758 [...]
+chr5 1315884 . C T 6102.805 REJECT NS=2;DP=371;DPB=431.0;AC=2;AN=4;AF=0.5;RO=212;AO=219;PRO=0.0;PAO=0.0;QR=8194;QA=8466;PQR=0.0;PQA=0.0;SRF=87;SRR=125;SAF=100;SAR=119;SRP=17.8009;SAP=6.58976;AB=0.508121;ABP=3.25717;RUN=1;RPP=4.686;RPPR=3.05127;RPL=116.0;RPR=103.0;EPP=4.21006;EPPR=4.48526;DPRA=0.0;ODDS=365.555;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990566;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.925;Dels=0.0;FS=2.9565;HaplotypeScore= [...]
+chr5 1317102 . G A 16681.949999999997 REJECT NS=2;DP=441;DPB=509.0;AC=4;AN=4;AF=1.0;RO=1;AO=507;PRO=0.0;PAO=0.0;QR=16;QA=19383;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=242;SAR=265;SRP=5.18177;SAP=5.276;AB=0.0;ABP=0.0;RUN=1;RPP=7.67447;RPPR=5.18177;RPL=270.0;RPR=237.0;EPP=28.4041;EPPR=5.18177;DPRA=0.0;ODDS=86.0292;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994083;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.679;Dels=0.0;FS=0.0;HaplotypeScore=3.866;ML [...]
+chr5 1317481 . A G 1032.54 REJECT NS=2;DP=230;DPB=264.0;AC=2;AN=4;AF=0.5;RO=210;AO=54;PRO=0.0;PAO=0.0;QR=7957;QA=2006;PQR=0.0;PQA=0.0;SRF=66;SRR=144;SAF=21;SAR=33;SRP=65.921;SAP=8.80089;AB=0.204545;ABP=203.181;RUN=1;RPP=3.6537;RPPR=3.67208;RPL=29.0;RPR=25.0;EPP=3.17115;EPPR=3.67208;DPRA=0.0;ODDS=15.0745;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995238;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.02;Dels=0.0;FS=3.5585;HaplotypeScore=3.9327 [...]
+chr5 1317820 . A G 15059.6 REJECT NS=2;DP=564;DPB=636.0;AC=2;AN=4;AF=0.5;RO=149;AO=487;PRO=0.0;PAO=0.0;QR=5741;QA=18754;PQR=0.0;PQA=0.0;SRF=71;SRR=78;SAF=235;SAR=252;SRP=3.72441;SAP=4.29892;AB=0.765723;ABP=393.07;RUN=1;RPP=17.4972;RPPR=9.43728;RPL=215.0;RPR=272.0;EPP=5.36905;EPPR=5.47325;DPRA=0.0;ODDS=288.662;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9261;MQMR=60.0;PAIRED=0.997947;PAIREDR=0.986577;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8575;Dels=0.0;FS=3.3055;Haplot [...]
+chr5 1317949 . C T 18858.699999999997 REJECT NS=2;DP=513;DPB=585.0;AC=4;AN=4;AF=1.0;RO=0;AO=585;PRO=0.0;PAO=0.0;QR=0;QA=21760;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=289;SAR=296;SRP=0.0;SAP=3.19218;AB=0.0;ABP=0.0;RUN=1;RPP=3.19218;RPPR=0.0;RPL=296.0;RPR=289.0;EPP=4.3503;EPPR=0.0;DPRA=0.0;ODDS=92.1312;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.989744;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8659;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.2 [...]
+chr5 1319473 . T TG 2154.56 REJECT NS=2;DP=144;DPB=196.933;AC=2;AN=3;AF=0.5;RO=20;AO=89;PRO=24.5833;PAO=29.5833;QR=689;QA=2942;PQR=710.083;PQA=817.083;SRF=12;SRR=8;SAF=89;SAR=0;SRP=4.74748;SAP=196.271;AB=0.618056;ABP=20.4424;RUN=1;RPP=11.8182;RPPR=6.91895;RPL=54.0;RPR=35.0;EPP=11.8182;EPPR=3.44459;DPRA=0.0;ODDS=16.881;GTI=0;TYPE=ins;CIGAR=1M1I14M;NUMALT=3;MEANALT=6.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988764;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.397;FS [...]
+chr5 1319473 . T TGG 2202.39 REJECT NS=2;DP=144;DPB=196.933;AC=2;AN=2;AF=0.25;RO=20;AO=18;PRO=24.5833;PAO=23.5833;QR=689;QA=519;PQR=710.083;PQA=679.083;SRF=12;SRR=8;SAF=18;SAR=0;SRP=4.74748;SAP=42.0968;AB=0.125;ABP=178.9;RUN=1;RPP=15.074;RPPR=6.91895;RPL=14.0;RPR=4.0;EPP=15.074;EPPR=3.44459;DPRA=0.0;ODDS=16.881;GTI=0;TYPE=ins;CIGAR=1M2I14M;NUMALT=3;MEANALT=6.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=1.259;FS=4.313;MLEAC=1;MLE [...]
+chr5 1319483 . CA GGCC 2202.39 REJECT SOMATIC;NS=2;DP=144;DPB=196.933;AC=1;AN=3;AF=0.0;RO=20;AO=2;PRO=24.5833;PAO=14.25;QR=689;QA=16;PQR=710.083;PQA=381.75;SRF=12;SRR=8;SAF=2;SAR=0;SRP=4.74748;SAP=7.35324;AB=0.0571429;ABP=62.6327;RUN=1;RPP=7.35324;RPPR=6.91895;RPL=0.0;RPR=2.0;EPP=7.35324;EPPR=3.44459;DPRA=0.0;ODDS=16.881;GTI=0;TYPE=complex;CIGAR=1M2I10M1X3M;NUMALT=3;MEANALT=7.0;LEN=17;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr5 1319680 . C A 1869.2649999999999 REJECT NS=2;DP=317;DPB=368.0;AC=2;AN=4;AF=0.5;RO=279;AO=89;PRO=0.0;PAO=0.0;QR=10402;QA=3312;PQR=0.0;PQA=0.0;SRF=143;SRR=136;SAF=53;SAR=36;SRP=3.39167;SAP=10.0615;AB=0.241848;ABP=216.027;RUN=1;RPP=7.13366;RPPR=4.76149;RPL=51.0;RPR=38.0;EPP=3.62026;EPPR=10.4898;DPRA=0.0;ODDS=117.363;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988764;PAIREDR=0.996416;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3275;Dels=0.0;FS=2.4315; [...]
+chr5 1320136 . G A 1916.03 REJECT NS=2;DP=379;DPB=433.0;AC=2;AN=4;AF=0.5;RO=341;AO=92;PRO=0.0;PAO=0.0;QR=13094;QA=3500;PQR=0.0;PQA=0.0;SRF=163;SRR=178;SAF=48;SAR=44;SRP=4.44309;SAP=3.38795;AB=0.212471;ABP=313.942;RUN=1;RPP=4.52089;RPPR=4.85064;RPL=50.0;RPR=42.0;EPP=6.40913;EPPR=8.36575;DPRA=0.0;ODDS=69.8694;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.978261;PAIREDR=0.98827;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.09;Dels=0.0;FS=0.3615;HaplotypeScor [...]
+chr5 1320247 . G A 2284.185 REJECT NS=2;DP=417;DPB=480.0;AC=2;AN=4;AF=0.5;RO=374;AO=106;PRO=0.0;PAO=0.0;QR=14336;QA=4049;PQR=0.0;PQA=0.0;SRF=224;SRR=150;SAF=54;SAR=52;SRP=34.8044;SAP=3.09224;AB=0.220833;ABP=327.935;RUN=1;RPP=3.09224;RPPR=3.84637;RPL=52.0;RPR=54.0;EPP=5.05886;EPPR=4.49666;DPRA=0.0;ODDS=100.232;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990566;PAIREDR=0.997326;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.181;Dels=0.0;FS=4.2155;Haplotype [...]
+chr5 1320722 . C T 2563.725 REJECT NS=2;DP=395;DPB=453.0;AC=2;AN=4;AF=0.5;RO=336;AO=117;PRO=0.0;PAO=0.0;QR=12941;QA=4470;PQR=0.0;PQA=0.0;SRF=169;SRR=167;SAF=55;SAR=62;SRP=3.03615;SAP=3.91972;AB=0.258278;ABP=232.913;RUN=1;RPP=3.02886;RPPR=4.66476;RPL=59.0;RPR=58.0;EPP=5.25601;EPPR=6.13825;DPRA=0.0;ODDS=196.31;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991453;PAIREDR=0.997024;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9805;Dels=0.0;FS=1.3395;HaplotypeS [...]
+chr5 1322087 . C T 1849.03 REJECT NS=2;DP=394;DPB=460.0;AC=2;AN=4;AF=0.5;RO=367;AO=92;PRO=0.0;PAO=0.0;QR=13926;QA=3502;PQR=0.0;PQA=0.0;SRF=165;SRR=202;SAF=40;SAR=52;SRP=11.1104;SAP=6.40913;AB=0.2;ABP=362.606;RUN=1;RPP=3.38795;RPPR=5.14627;RPL=48.0;RPR=44.0;EPP=3.0103;EPPR=4.01024;DPRA=0.0;ODDS=55.3926;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991826;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.488;Dels=0.0;FS=2.8715;HaplotypeScore=15.4605; [...]
+chr5 1322468 . G A 1568.29 REJECT NS=2;DP=281;DPB=325.0;AC=2;AN=4;AF=0.5;RO=250;AO=75;PRO=0.0;PAO=0.0;QR=9361;QA=2786;PQR=0.0;PQA=0.0;SRF=131;SRR=119;SAF=36;SAR=39;SRP=4.26107;SAP=3.27088;AB=0.230769;ABP=207.63;RUN=1;RPP=3.27088;RPPR=6.48466;RPL=39.0;RPR=36.0;EPP=7.90335;EPPR=5.82453;DPRA=0.0;ODDS=52.8115;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0305;Dels=0.0;FS=0.0;HaplotypeScore=7.8875;ML [...]
+chr5 1322663 . T C 13015.5 REJECT NS=2;DP=341;DPB=392.0;AC=4;AN=4;AF=1.0;RO=0;AO=392;PRO=0.0;PAO=0.0;QR=0;QA=15084;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=193;SAR=199;SRP=0.0;SAP=3.20972;AB=0.0;ABP=0.0;RUN=1;RPP=11.0093;RPPR=0.0;RPL=215.0;RPR=177.0;EPP=17.989;EPPR=0.0;DPRA=0.0;ODDS=67.9636;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997449;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9242;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.265;SOR=0.75 [...]
+chr5 1323196 . T C 11943.45 REJECT NS=2;DP=318;DPB=360.0;AC=4;AN=4;AF=1.0;RO=0;AO=360;PRO=0.0;PAO=0.0;QR=0;QA=13686;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=176;SAR=184;SRP=0.0;SAP=3.39634;AB=0.0;ABP=0.0;RUN=1;RPP=26.1968;RPPR=0.0;RPL=211.0;RPR=149.0;EPP=4.96463;EPPR=0.0;DPRA=0.0;ODDS=56.1505;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9194;MQMR=0.0;PAIRED=0.991667;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.8825;MLEAC=2;MLEAF=1.0;MQ=59.87;QD=29.395;SO [...]
+chr5 1323212 . C T 1675.075 REJECT NS=2;DP=306;DPB=344.0;AC=2;AN=4;AF=0.5;RO=263;AO=80;PRO=0.0;PAO=0.0;QR=9938;QA=3031;PQR=0.0;PQA=0.0;SRF=134;SRR=129;SAF=37;SAR=43;SRP=3.21671;SAP=3.98746;AB=0.232558;ABP=216.724;RUN=1;RPP=16.1477;RPPR=5.99091;RPL=51.0;RPR=29.0;EPP=13.8677;EPPR=12.0017;DPRA=0.0;ODDS=96.4032;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=58.6125;MQMR=59.4905;PAIRED=1.0;PAIREDR=0.992395;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4605;Dels=0.0;FS=5.956;HaplotypeS [...]
+chr5 1324121 . G A 2114.4849999999997 REJECT NS=2;DP=329;DPB=382.0;AC=2;AN=4;AF=0.5;RO=286;AO=96;PRO=0.0;PAO=0.0;QR=10722;QA=3728;PQR=0.0;PQA=0.0;SRF=138;SRR=148;SAF=50;SAR=46;SRP=3.76956;SAP=3.37221;AB=0.251309;ABP=208.22;RUN=1;RPP=3.10078;RPPR=6.6851;RPL=47.0;RPR=49.0;EPP=3.10078;EPPR=19.0762;DPRA=0.0;ODDS=171.968;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993007;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.9485;Dels=0.0;FS=1.8185;Haploty [...]
+chr5 1325590 . T C 1700.38 REJECT NS=2;DP=349;DPB=402.0;AC=2;AN=4;AF=0.5;RO=319;AO=82;PRO=0.0;PAO=0.0;QR=12224;QA=3160;PQR=0.0;PQA=0.0;SRF=192;SRR=127;SAF=45;SAR=37;SRP=31.7704;SAP=4.70511;AB=0.20398;ABP=308.983;RUN=1;RPP=3.11623;RPPR=3.83396;RPL=42.0;RPR=40.0;EPP=3.434;EPPR=12.3293;DPRA=0.0;ODDS=38.2158;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996865;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5215;Dels=0.0;FS=1.699;HaplotypeScore=9.748 [...]
+chr5 1325803 . A G 2048.085 REJECT NS=2;DP=465;DPB=524.0;AC=2;AN=4;AF=0.5;RO=414;AO=110;PRO=0.0;PAO=0.0;QR=16018;QA=4140;PQR=0.0;PQA=0.0;SRF=212;SRR=202;SAF=62;SAR=48;SRP=3.53481;SAP=6.87947;AB=0.209924;ABP=385.985;RUN=1;RPP=3.32615;RPPR=14.1089;RPL=53.0;RPR=57.0;EPP=3.32615;EPPR=3.03128;DPRA=0.0;ODDS=154.394;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8818;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995169;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.7185;Dels=0.0;FS=2.0645;HaplotypeS [...]
+chr5 1326843 . GGGG AGAC 198.883 REJECT NS=2;DP=420;DPB=433.0;AC=2;AN=3;AF=0.25;RO=346;AO=23;PRO=19.5;PAO=3.5;QR=11491;QA=652;PQR=345.5;PQA=89.0;SRF=193;SRR=153;SAF=12;SAR=11;SRP=13.0518;SAP=3.10471;AB=0.132075;ABP=127.645;RUN=1;RPP=37.093;RPPR=7.93063;RPL=21.0;RPR=2.0;EPP=3.10471;EPPR=6.04785;DPRA=0.0;ODDS=37.3758;GTI=0;TYPE=complex;CIGAR=1X1M2X;NUMALT=2;MEANALT=7.5;LEN=4;MQM=35.8261;MQMR=57.1387;PAIRED=1.0;PAIREDR=0.99422;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr5 1326846 . G C 198.883 REJECT NS=2;DP=420;DPB=433.0;AC=2;AN=2;AF=0.0;RO=346;AO=16;PRO=19.5;PAO=7.0;QR=11491;QA=285;PQR=345.5;PQA=177.5;SRF=193;SRR=153;SAF=2;SAR=14;SRP=13.0518;SAP=22.5536;AB=0.0566038;ABP=184.021;RUN=1;RPP=22.5536;RPPR=7.93063;RPL=2.0;RPR=14.0;EPP=37.7539;EPPR=6.04785;DPRA=0.0;ODDS=37.3758;GTI=0;TYPE=snp;CIGAR=3M1X;NUMALT=2;MEANALT=7.5;LEN=1;MQM=57.4375;MQMR=57.1387;PAIRED=1.0;PAIREDR=0.99422;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr5 1327101 . C G 1290.545 REJECT NS=2;DP=359;DPB=412.0;AC=2;AN=4;AF=0.5;RO=296;AO=89;PRO=0.0;PAO=0.0;QR=9638;QA=2854;PQR=0.0;PQA=0.0;SRF=149;SRR=147;SAF=38;SAR=51;SRP=3.03964;SAP=7.13366;AB=0.216019;ABP=291.605;RUN=1;RPP=3.0347;RPPR=3.2744;RPL=45.0;RPR=44.0;EPP=3.22989;EPPR=4.88833;DPRA=0.0;ODDS=75.6723;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=2;MEANALT=2.5;LEN=1;MQM=53.382;MQMR=56.2736;PAIRED=0.988764;PAIREDR=0.989865;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.0815;Dels=0.0 [...]
+chr5 1327101 . C T 1389.32 REJECT NS=2;DP=412;DPB=412.0;AC=2;AN=2;AF=0.0;RO=296;AO=26;PRO=0.0;PAO=0.0;QR=9638;QA=597;PQR=0.0;PQA=0.0;SRF=149;SRR=147;SAF=19;SAR=7;SRP=3.03964;SAP=15.0369;AB=0.0631068;ABP=686.075;RUN=1;RPP=8.35546;RPPR=3.2744;RPL=17.0;RPR=9.0;EPP=11.3621;EPPR=4.88833;DPRA=0.0;ODDS=75.6723;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=2;MEANALT=2.5;LEN=1;MQM=35.4615;MQMR=56.2736;PAIRED=1.0;PAIREDR=0.989865;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr5 1327851 . C T 873.959 REJECT NS=2;DP=401;DPB=459.0;AC=2;AN=4;AF=0.5;RO=377;AO=81;PRO=0.0;PAO=0.0;QR=13654;QA=2605;PQR=0.0;PQA=0.0;SRF=196;SRR=181;SAF=41;SAR=40;SRP=4.30627;SAP=3.03711;AB=0.176471;ABP=420.316;RUN=1;RPP=3.03711;RPPR=3.1543;RPL=40.0;RPR=41.0;EPP=25.5561;EPPR=3.47685;DPRA=0.0;ODDS=33.3219;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=49.2593;MQMR=49.1114;PAIRED=0.987654;PAIREDR=0.994695;technology.ILLUMINA=1.0;MQ0=3;BaseQRankSum=-2.7855;Dels=0.0;FS=1.9925;Haplo [...]
+chr5 1328058 . G T 1035.84 REJECT NS=2;DP=101;DPB=101.0;AC=4;AN=4;AF=1.0;RO=11;AO=90;PRO=0.0;PAO=0.0;QR=275;QA=3178;PQR=0.0;PQA=0.0;SRF=7;SRR=4;SAF=36;SAR=54;SRP=4.78696;SAP=10.8276;AB=0.0;ABP=0.0;RUN=1;RPP=198.443;RPPR=12.6832;RPL=90.0;RPR=0.0;EPP=10.8276;EPPR=12.6832;DPRA=0.0;ODDS=13.753;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=20.5;MQMR=14.4545;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=43;BaseQRankSum=1.839;Dels=0.0;FS=0.0;HaplotypeScore=0.9332;MLEAC=2;MLEAF=1.0 [...]
+chr5 1328320 . A G 113.569 REJECT NS=2;DP=116;DPB=116.0;AC=2;AN=4;AF=0.5;RO=86;AO=22;PRO=0.0;PAO=0.0;QR=2805;QA=674;PQR=0.0;PQA=0.0;SRF=39;SRR=47;SAF=9;SAR=13;SRP=4.62628;SAP=4.58955;AB=0.189655;ABP=100.053;RUN=1;RPP=42.4916;RPPR=61.1856;RPL=1.0;RPR=21.0;EPP=6.56362;EPPR=3.1113;DPRA=0.0;ODDS=0.423635;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=2;MEANALT=2.0;LEN=1;MQM=31.2273;MQMR=32.8721;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=176;BaseQRankSum=-1.768;Dels=0.0;FS=0.0;Haplo [...]
+chr5 1328320 . A C 113.569 REJECT NS=2;DP=116;DPB=116.0;AC=2;AN=2;AF=0.0;RO=86;AO=8;PRO=0.0;PAO=0.0;QR=2805;QA=113;PQR=0.0;PQA=0.0;SRF=39;SRR=47;SAF=0;SAR=8;SRP=4.62628;SAP=20.3821;AB=0.0689655;ABP=190.206;RUN=1;RPP=20.3821;RPPR=61.1856;RPL=0.0;RPR=8.0;EPP=20.3821;EPPR=3.1113;DPRA=0.0;ODDS=0.423635;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=2;MEANALT=2.0;LEN=1;MQM=29.75;MQMR=32.8721;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:C [...]
+chr5 1328331 . T C 2821.55 REJECT NS=2;DP=153;DPB=153.0;AC=4;AN=4;AF=1.0;RO=21;AO=132;PRO=0.0;PAO=0.0;QR=623;QA=4486;PQR=0.0;PQA=0.0;SRF=9;SRR=12;SAF=53;SAR=79;SRP=3.94093;SAP=14.1309;AB=0.0;ABP=0.0;RUN=1;RPP=289.645;RPPR=48.6112;RPL=0.0;RPR=132.0;EPP=14.1309;EPPR=3.94093;DPRA=0.0;ODDS=21.8686;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=41.8485;MQMR=17.7143;PAIRED=0.992424;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=107;BaseQRankSum=1.9735;Dels=0.0;FS=0.0;HaplotypeScore=23.114;MLE [...]
+chr5 1328430 . ACTCCTCTACGGACACATTTCATCCAGCTC A 738.73 PASS DP=86;AC=1;AN=4;AF=0.5;BaseQRankSum=0.948;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.51;MQRankSum=-1.866;QD=8.59;ReadPosRankSum=0.304;SOR=0.85;ClippingRankSum=0.733 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:28,22:50:99.0:776,0,1074:22:44:50:1:.:.:.:.:.:0.138309 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0139599
+chr5 1328459 . C A 251.317 REJECT NS=2;DP=286;DPB=286.0;AC=1;AN=4;AF=0.25;RO=258;AO=28;PRO=0.0;PAO=0.0;QR=9457;QA=944;PQR=0.0;PQA=0.0;SRF=140;SRR=118;SAF=16;SAR=12;SRP=7.08391;SAP=4.25114;AB=0.272727;ABP=32.6213;RUN=1;RPP=63.8115;RPPR=3.3133;RPL=0.0;RPR=28.0;EPP=4.25114;EPPR=5.73727;DPRA=0.0;ODDS=57.8678;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=49.75;MQMR=52.1744;PAIRED=1.0;PAIREDR=0.996124;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:C [...]
+chr5 1328897 . C T 1425.9650000000001 REJECT NS=2;DP=315;DPB=364.0;AC=2;AN=4;AF=0.5;RO=269;AO=93;PRO=0.0;PAO=0.0;QR=9645;QA=3030;PQR=0.0;PQA=0.0;SRF=143;SRR=126;SAF=43;SAR=50;SRP=5.34322;SAP=4.15441;AB=0.255495;ABP=192.024;RUN=1;RPP=3.03365;RPPR=5.92443;RPL=46.0;RPR=47.0;EPP=4.90158;EPPR=4.37453;DPRA=0.0;ODDS=149.362;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=55.3763;MQMR=54.2565;PAIRED=0.989247;PAIREDR=0.98513;technology.ILLUMINA=1.0;MQ0=2;BaseQRankSum=-1.9305;Dels=0.0;FS=2. [...]
+chr5 1329886 . C A 13.8197 REJECT NS=2;DP=537;DPB=537.0;AC=1;AN=4;AF=0.25;RO=489;AO=47;PRO=0.0;PAO=0.0;QR=16804;QA=1521;PQR=0.0;PQA=0.0;SRF=237;SRR=252;SAF=34;SAR=13;SRP=4.00944;SAP=23.3852;AB=0.188976;ABP=109.72;RUN=1;RPP=47.41;RPPR=63.7982;RPL=8.0;RPR=39.0;EPP=10.8184;EPPR=33.6019;DPRA=0.0;ODDS=3.13973;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=21.8298;MQMR=31.3027;PAIRED=1.0;PAIREDR=0.993865;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG [...]
+chr5 1330253 . T C 2325.275 REJECT NS=2;DP=472;DPB=546.0;AC=2;AN=4;AF=0.5;RO=421;AO=125;PRO=0.0;PAO=0.0;QR=16242;QA=4653;PQR=0.0;PQA=0.0;SRF=211;SRR=210;SAF=57;SAR=68;SRP=3.01546;SAP=5.11229;AB=0.228938;ABP=351.464;RUN=1;RPP=6.91895;RPPR=3.6344;RPL=55.0;RPR=70.0;EPP=6.91895;EPPR=3.26304;DPRA=0.0;ODDS=224.709;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988124;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.203;Dels=0.0;FS=2.528;HaplotypeScore=6. [...]
+chr5 1330840 . T C 2885.77 REJECT NS=2;DP=542;DPB=615.0;AC=2;AN=4;AF=0.5;RO=470;AO=145;PRO=0.0;PAO=0.0;QR=18118;QA=5571;PQR=0.0;PQA=0.0;SRF=212;SRR=258;SAF=72;SAR=73;SRP=12.7865;SAP=3.02528;AB=0.235772;ABP=375.956;RUN=1;RPP=7.33827;RPPR=12.7865;RPL=64.0;RPR=81.0;EPP=3.14508;EPPR=4.50723;DPRA=0.0;ODDS=299.344;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993103;PAIREDR=0.991489;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6505;Dels=0.0;FS=1.415;HaplotypeSc [...]
+chr5 1331219 . A G 1936.215 REJECT NS=2;DP=438;DPB=494.0;AC=2;AN=4;AF=0.5;RO=391;AO=103;PRO=0.0;PAO=0.0;QR=13951;QA=3859;PQR=0.0;PQA=0.0;SRF=196;SRR=195;SAF=53;SAR=50;SRP=3.01585;SAP=3.20004;AB=0.208502;ABP=367.607;RUN=1;RPP=4.04333;RPPR=16.3446;RPL=55.0;RPR=48.0;EPP=3.03138;EPPR=7.0589;DPRA=0.0;ODDS=144.613;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990291;PAIREDR=0.997442;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.383;Dels=0.0;FS=0.352;HaplotypeSco [...]
+chr5 1331673 . CAGGCCCTGAGCTGTGCAGCCGCTGG C 3924.48 REJECT NS=2;DP=220;DPB=105.889;AC=2;AN=4;AF=0.5;RO=66;AO=175;PRO=69.0;PAO=5.0;QR=2498;QA=5378;PQR=2380.5;PQA=68.5;SRF=30;SRR=36;SAF=82;SAR=93;SRP=4.19474;SAP=4.51172;AB=0.72314;ABP=107.672;RUN=1;RPP=30.4205;RPPR=4.19474;RPL=111.0;RPR=64.0;EPP=5.10732;EPPR=13.6703;DPRA=0.0;ODDS=157.238;GTI=0;TYPE=del;CIGAR=1M25D1M;NUMALT=1;MEANALT=1.5;LEN=25;MQM=64.6286;MQMR=60.0;PAIRED=0.994286;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=1331698;HOMLE [...]
+chr5 1333077 . A G 2142.965 REJECT NS=2;DP=478;DPB=538.0;AC=2;AN=4;AF=0.5;RO=408;AO=129;PRO=0.0;PAO=0.0;QR=14702;QA=4622;PQR=0.0;PQA=0.0;SRF=181;SRR=227;SAF=52;SAR=77;SRP=14.2722;SAP=13.531;AB=0.239777;ABP=319.448;RUN=1;RPP=4.37378;RPPR=3.35092;RPL=69.0;RPR=60.0;EPP=3.1618;EPPR=5.58626;DPRA=0.0;ODDS=278.599;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=56.0233;MQMR=58.1373;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=2;BaseQRankSum=0.276;Dels=0.0;FS=0.346;HaplotypeScore=27 [...]
+chr5 1333231 . G T 58.7476 REJECT NS=2;DP=380;DPB=380.0;AC=2;AN=4;AF=0.5;RO=288;AO=70;PRO=0.0;PAO=0.0;QR=7910;QA=2228;PQR=0.0;PQA=0.0;SRF=177;SRR=111;SAF=61;SAR=9;SRP=35.8538;SAP=86.8912;AB=0.184211;ABP=332.16;RUN=1;RPP=80.5629;RPPR=61.3988;RPL=60.0;RPR=10.0;EPP=63.067;EPPR=21.8599;DPRA=0.0;ODDS=13.5271;GTI=1;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.5;LEN=1;MQM=8.2;MQMR=11.9688;PAIRED=0.985714;PAIREDR=0.996528;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG [...]
+chr5 1333260 . T G 49.77 PASS SOMATIC;DP=1537;AC=1;AN=4;AF=0.5;MQ0=858;BaseQRankSum=1.374;Dels=0.0;FS=0.991;HaplotypeScore=83.1669;MLEAC=1;MLEAF=0.5;MQ=8.94;MQRankSum=-0.012;QD=0.03;ReadPosRankSum=1.596;SOR=0.925 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:1.95593 0/1:1254,161:1537:78.0:78,0,1729:161:11:1415:.:1:.:.:.:.:2.05322
+chr5 1333396 . A G 1313.46 REJECT NS=2;DP=625;DPB=625.0;AC=2;AN=4;AF=0.5;RO=435;AO=185;PRO=0.0;PAO=0.0;QR=14570;QA=6631;PQR=0.0;PQA=0.0;SRF=208;SRR=227;SAF=154;SAR=31;SRP=4.81237;SAP=180.59;AB=0.296;ABP=228.93;RUN=1;RPP=263.599;RPPR=93.9875;RPL=18.0;RPR=167.0;EPP=180.59;EPPR=9.12537;DPRA=0.0;ODDS=146.087;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.5;LEN=1;MQM=25.3351;MQMR=39.1241;PAIRED=0.994595;PAIREDR=0.995402;technology.ILLUMINA=1.0;MQ0=75;BaseQRankSum=1.761;Dels=0.0;FS=67.073;Haplotyp [...]
+chr5 1333411 . GA G 89.0711 REJECT NS=2;DP=883;DPB=841.0;AC=2;AN=3;AF=0.25;RO=596;AO=195;PRO=22.0;PAO=11.5;QR=20568;QA=6367;PQR=491.667;PQA=122.667;SRF=367;SRR=229;SAF=111;SAR=84;SRP=72.3954;SAP=11.1283;AB=0.245337;ABP=395.636;RUN=1;RPP=237.14;RPPR=103.408;RPL=25.0;RPR=170.0;EPP=44.4464;EPPR=59.0314;DPRA=0.0;ODDS=20.5094;GTI=0;TYPE=del;CIGAR=1M1D1M;NUMALT=2;MEANALT=6.5;LEN=1;MQM=13.7692;MQMR=38.5386;PAIRED=0.994872;PAIREDR=0.996644;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR [...]
+chr5 1333412 . A G 89.0711 REJECT NS=2;DP=883;DPB=841.0;AC=2;AN=2;AF=0.0;RO=596;AO=80;PRO=22.0;PAO=11.5;QR=20568;QA=1033;PQR=491.667;PQA=122.667;SRF=367;SRR=229;SAF=56;SAR=24;SRP=72.3954;SAP=30.8051;AB=0.0846485;ABP=1047.44;RUN=1;RPP=55.5599;RPPR=103.408;RPL=18.0;RPR=62.0;EPP=3.0103;EPPR=59.0314;DPRA=0.0;ODDS=20.5094;GTI=0;TYPE=snp;CIGAR=1M1X1M;NUMALT=2;MEANALT=6.5;LEN=1;MQM=18.9875;MQMR=38.5386;PAIRED=1.0;PAIREDR=0.996644;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr5 1333463 . AC GG 11276.8 REJECT NS=2;DP=1258;DPB=1273.5;AC=2;AN=2;AF=0.0;RO=290;AO=125;PRO=7.5;PAO=10.5;QR=9756;QA=4151;PQR=130.5;PQA=340.5;SRF=133;SRR=157;SAF=81;SAR=44;SRP=7.32329;SAP=26.7923;AB=0.0993641;ABP=1756.87;RUN=1;RPP=3.86152;RPPR=3.13011;RPL=66.0;RPR=59.0;EPP=3.44459;EPPR=3.04025;DPRA=0.0;ODDS=202.033;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=2;MEANALT=6.5;LEN=2;MQM=13.448;MQMR=49.7759;PAIRED=1.0;PAIREDR=0.996552;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr5 1333464 . C G 11276.8 REJECT NS=2;DP=1258;DPB=1273.5;AC=2;AN=4;AF=0.5;RO=290;AO=823;PRO=7.5;PAO=13.0;QR=9756;QA=29063;PQR=130.5;PQA=401.0;SRF=133;SRR=157;SAF=549;SAR=274;SRP=7.32329;SAP=202.546;AB=0.654213;ABP=262.869;RUN=1;RPP=3.77282;RPPR=3.13011;RPL=403.0;RPR=420.0;EPP=13.4824;EPPR=3.04025;DPRA=0.0;ODDS=202.033;GTI=0;TYPE=snp;CIGAR=1M1X;NUMALT=2;MEANALT=6.5;LEN=1;MQM=22.8032;MQMR=49.7759;PAIRED=0.996355;PAIREDR=0.996552;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=168;BaseQRankS [...]
+chr5 1333497 . CA GG 2632.04 REJECT NS=2;DP=1605;DPB=1629.5;AC=2;AN=2;AF=0.0;RO=999;AO=105;PRO=28.0;PAO=2.5;QR=32798;QA=3051;PQR=509.5;PQA=88.5;SRF=493;SRR=506;SAF=52;SAR=53;SRP=3.37765;SAP=3.03098;AB=0.0654206;ABP=2635.87;RUN=1;RPP=79.9631;RPPR=137.779;RPL=22.0;RPR=83.0;EPP=3.03098;EPPR=9.58558;DPRA=0.0;ODDS=192.431;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=2;MEANALT=10.0;LEN=2;MQM=21.9143;MQMR=35.025;PAIRED=1.0;PAIREDR=0.98999;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr5 1333498 . A G 2632.04 REJECT NS=2;DP=1605;DPB=1629.5;AC=2;AN=4;AF=0.5;RO=999;AO=456;PRO=28.0;PAO=18.5;QR=32798;QA=15328;PQR=509.5;PQA=598.0;SRF=493;SRR=506;SAF=322;SAR=134;SRP=3.37765;SAP=171.318;AB=0.284112;ABP=652.759;RUN=1;RPP=281.892;RPPR=137.779;RPL=349.0;RPR=107.0;EPP=64.8973;EPPR=9.58558;DPRA=0.0;ODDS=192.431;GTI=0;TYPE=snp;CIGAR=1M1X;NUMALT=2;MEANALT=10.0;LEN=1;MQM=17.0417;MQMR=35.025;PAIRED=0.991228;PAIREDR=0.98999;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=327;BaseQRank [...]
+chr5 1333534 . G C 371.479 REJECT NS=2;DP=1584;DPB=1584.0;AC=2;AN=3;AF=0.25;RO=1225;AO=253;PRO=0.0;PAO=0.0;QR=39322;QA=8117;PQR=0.0;PQA=0.0;SRF=609;SRR=616;SAF=158;SAR=95;SRP=3.09716;SAP=37.0758;AB=0.171824;ABP=1151.76;RUN=1;RPP=399.755;RPPR=71.8043;RPL=19.0;RPR=234.0;EPP=20.3907;EPPR=23.3051;DPRA=0.0;ODDS=37.302;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=2;MEANALT=3.0;LEN=1;MQM=23.6087;MQMR=35.0376;PAIRED=0.992095;PAIREDR=0.991837;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=298;BaseQRankSum=2.273 [...]
+chr5 1333534 . G A 371.479 REJECT NS=2;DP=1584;DPB=1584.0;AC=2;AN=2;AF=0.0;RO=1225;AO=69;PRO=0.0;PAO=0.0;QR=39322;QA=2025;PQR=0.0;PQA=0.0;SRF=609;SRR=616;SAF=26;SAR=43;SRP=3.09716;SAP=12.1053;AB=0.0545603;ABP=2119.38;RUN=1;RPP=6.81824;RPPR=71.8043;RPL=29.0;RPR=40.0;EPP=16.8888;EPPR=23.3051;DPRA=0.0;ODDS=37.302;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=2;MEANALT=3.0;LEN=1;MQM=47.8406;MQMR=35.0376;PAIRED=0.956522;PAIREDR=0.991837;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr5 1333570 . GGATGAGGATAAGGGGGGACTATTGTATACACACCA G . PASS SOMATIC;AC=1;AN=4;END=1333605;HOMLEN=21;HOMSEQ=GATGAGGATAAGGGGGGACTA;SVLEN=-35;SVTYPE=DEL GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:1.95593 0/1:295,33:33:10:328:.:.:.:1:.:.:2.05322
+chr5 1333592 . T C 14258.8 REJECT NS=2;DP=2399;DPB=2399.0;AC=2;AN=4;AF=0.5;RO=1084;AO=1268;PRO=0.0;PAO=0.0;QR=34837;QA=43509;PQR=0.0;PQA=0.0;SRF=558;SRR=526;SAF=701;SAR=567;SRP=5.06158;SAP=33.7603;AB=0.528554;ABP=19.9992;RUN=1;RPP=12.388;RPPR=215.903;RPL=597.0;RPR=671.0;EPP=3.99671;EPPR=11.7363;DPRA=0.0;ODDS=720.158;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=3.0;LEN=1;MQM=21.5205;MQMR=41.1928;PAIRED=0.997634;PAIREDR=0.993542;technology.ILLUMINA=1.0;MQ0=383;BaseQRankSum=5.674;Dels=0.0;FS=0. [...]
+chr5 1333605 . A G 17.548 REJECT NS=2;DP=2800;DPB=2800.0;AC=2;AN=4;AF=0.5;RO=2236;AO=543;PRO=0.0;PAO=0.0;QR=70300;QA=16516;PQR=0.0;PQA=0.0;SRF=1137;SRR=1099;SAF=344;SAR=199;SRP=4.41263;SAP=87.0899;AB=0.193929;ABP=2281.35;RUN=1;RPP=87.0899;RPPR=277.867;RPL=199.0;RPR=344.0;EPP=6.37348;EPPR=4.72339;DPRA=0.0;ODDS=1.33683;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=17.4015;MQMR=30.805;PAIRED=1.0;PAIREDR=0.994186;technology.ILLUMINA=1.0;MQ0=511;BaseQRankSum=0.678;Dels=0.0;FS=1.845;H [...]
+chr5 1333640 . A G 11264.4 REJECT NS=2;DP=3480;DPB=3480.0;AC=2;AN=4;AF=0.5;RO=2236;AO=1219;PRO=0.0;PAO=0.0;QR=68637;QA=39242;PQR=0.0;PQA=0.0;SRF=1076;SRR=1160;SAF=692;SAR=527;SRP=9.86267;SAP=51.5077;AB=0.350287;ABP=680.512;RUN=1;RPP=88.4459;RPPR=167.856;RPL=500.0;RPR=719.0;EPP=3.02633;EPPR=6.50641;DPRA=0.0;ODDS=500.049;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=3.0;LEN=1;MQM=22.6079;MQMR=27.0854;PAIRED=0.994258;PAIREDR=0.992844;technology.ILLUMINA=1.0;MQ0=775;BaseQRankSum=9.954;Dels=0.0;FS [...]
+chr5 1333690 . GA G 7943.98 REJECT NS=2;DP=3028;DPB=2903.33;AC=2;AN=3;AF=0.25;RO=1448;AO=737;PRO=80.0;PAO=96.0;QR=49233;QA=23290;PQR=2239.33;PQA=2825.83;SRF=623;SRR=825;SAF=356;SAR=381;SRP=64.2014;SAP=4.85178;AB=0.243395;ABP=1734.82;RUN=1;RPP=79.3831;RPPR=5.65566;RPL=449.0;RPR=288.0;EPP=3.67323;EPPR=12.608;DPRA=0.0;ODDS=23.304;GTI=0;TYPE=del;CIGAR=1M1D1M;NUMALT=2;MEANALT=13.5;LEN=1;MQM=21.8711;MQMR=39.0815;PAIRED=0.995929;PAIREDR=0.986188;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:D [...]
+chr5 1333691 . A G 7943.98 REJECT NS=2;DP=3028;DPB=2903.33;AC=2;AN=3;AF=0.25;RO=1448;AO=743;PRO=80.0;PAO=96.0;QR=49233;QA=12643;PQR=2239.33;PQA=2825.83;SRF=623;SRR=825;SAF=447;SAR=296;SRP=64.2014;SAP=69.6479;AB=0.245376;ABP=1708.18;RUN=1;RPP=338.875;RPPR=5.65566;RPL=541.0;RPR=202.0;EPP=88.4693;EPPR=12.608;DPRA=0.0;ODDS=23.304;GTI=0;TYPE=snp;CIGAR=1M1X1M;NUMALT=2;MEANALT=13.5;LEN=1;MQM=21.3109;MQMR=39.0815;PAIRED=0.995962;PAIREDR=0.986188;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP [...]
+chr5 1333702 . T C 1046.77 PASS SOMATIC;DP=2439;AC=1;AN=4;AF=0.5;MQ0=299;BaseQRankSum=-3.092;Dels=0.0;FS=2.016;HaplotypeScore=340.723;MLEAC=1;MLEAF=0.5;MQ=34.84;MQRankSum=0.918;QD=0.43;ReadPosRankSum=2.128;SOR=0.569 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:1.95593 0/1:2099,259:2439:99.0:1075,0,42545:259:11:2358:.:1:.:.:.:.:2.05322
+chr5 1333748 . G T 505.77 PASS DP=181;AC=1;AN=4;AF=0.5;BaseQRankSum=-0.706;FS=3.062;MLEAC=1;MLEAF=0.5;MQ=46.63;MQRankSum=0.326;QD=2.79;ReadPosRankSum=3.671;SOR=0.381;ClippingRankSum=-0.738 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:155,26:181:99.0:534,0,5516:26:14:181:1:.:.:.:.:.:1.95593 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:2.05322
+chr5 1333753 . A AG 1293.5 REJECT NS=2;DP=1093;DPB=1308.5;AC=2;AN=4;AF=0.5;RO=714;AO=261;PRO=134.5;PAO=146.5;QR=25517;QA=5588;PQR=4307.5;PQA=4733.5;SRF=326;SRR=388;SAF=55;SAR=206;SRP=14.701;SAP=192.71;AB=0.238792;ABP=650.759;RUN=1;RPP=527.167;RPPR=224.719;RPL=256.0;RPR=5.0;EPP=187.719;EPPR=45.3571;DPRA=0.0;ODDS=31.2458;GTI=0;TYPE=ins;CIGAR=1M1I7M;NUMALT=2;MEANALT=15.0;LEN=1;MQM=23.2759;MQMR=41.5378;PAIRED=1.0;PAIREDR=0.992997;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr5 1333755 . GGGG CGGGA 1293.5 REJECT NS=2;DP=1093;DPB=1308.5;AC=2;AN=2;AF=0.0;RO=714;AO=56;PRO=134.5;PAO=43.0;QR=25517;QA=1394;PQR=4307.5;PQA=1320.0;SRF=326;SRR=388;SAF=30;SAR=26;SRP=14.701;SAP=3.63072;AB=0.0512351;ABP=1914.94;RUN=1;RPP=124.613;RPPR=224.719;RPL=0.0;RPR=56.0;EPP=3.63072;EPPR=45.3571;DPRA=0.0;ODDS=31.2458;GTI=0;TYPE=complex;CIGAR=2M1I3M1X2M;NUMALT=2;MEANALT=15.0;LEN=9;MQM=35.0179;MQMR=41.5378;PAIRED=1.0;PAIREDR=0.992997;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP [...]
+chr5 1333774 . CC TT 444.77 PASS DP=111;AC=1;AN=4;AF=0.5;JOINED;BaseQRankSum=-2.1;FS=10.101;MLEAC=1;MLEAF=0.5;MQ=48.4;MQRankSum=-0.618;QD=4.01;ReadPosRankSum=-1.339;SOR=0.365;ClippingRankSum=0.463 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:94,17:111:99.0:473,0,3887:17:15:111:1:.:.:.:.:.:1.95593 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:2.05322
+chr5 1333774 . CCGGC TTGGA 11084.6 REJECT NS=2;DP=862;DPB=906.0;AC=2;AN=2;AF=0.0;RO=192;AO=21;PRO=42.5;PAO=0.0;QR=6678;QA=675;PQR=1361.5;PQA=0.0;SRF=84;SRR=108;SAF=9;SAR=12;SRP=9.52472;SAP=3.94093;AB=0.0243619;ABP=1696.86;RUN=1;RPP=40.3389;RPPR=134.927;RPL=20.0;RPR=1.0;EPP=5.59539;EPPR=14.5915;DPRA=0.0;ODDS=118.945;GTI=0;TYPE=complex;CIGAR=2X2M1X;NUMALT=2;MEANALT=13.5;LEN=5;MQM=39.4762;MQMR=44.2969;PAIRED=1.0;PAIREDR=0.989583;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr5 1333778 . C A 11084.6 REJECT NS=2;DP=817;DPB=906.0;AC=2;AN=4;AF=0.5;RO=192;AO=598;PRO=42.5;PAO=43.5;QR=6678;QA=19524;PQR=1361.5;PQA=1388.5;SRF=84;SRR=108;SAF=289;SAR=309;SRP=9.52472;SAP=4.46279;AB=0.693735;ABP=284.032;RUN=1;RPP=163.147;RPPR=134.927;RPL=404.0;RPR=194.0;EPP=45.3649;EPPR=14.5915;DPRA=0.0;ODDS=118.945;GTI=0;TYPE=snp;CIGAR=4M1X;NUMALT=2;MEANALT=13.5;LEN=1;MQM=35.3194;MQMR=44.2969;PAIRED=0.996656;PAIREDR=0.989583;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=114;BaseQRank [...]
+chr5 1333779 . T A 1721.69 REJECT NS=2;DP=865;DPB=865.0;AC=2;AN=4;AF=0.5;RO=688;AO=167;PRO=0.0;PAO=0.0;QR=23306;QA=5044;PQR=0.0;PQA=0.0;SRF=308;SRR=380;SAF=97;SAR=70;SRP=19.3721;SAP=12.4894;AB=0.193064;ABP=710.838;RUN=1;RPP=219.39;RPPR=748.494;RPL=19.0;RPR=148.0;EPP=5.20778;EPPR=46.9574;DPRA=0.0;ODDS=116.13;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.5;LEN=1;MQM=42.6527;MQMR=35.0945;PAIRED=1.0;PAIREDR=0.994186;technology.ILLUMINA=1.0;MQ0=114;BaseQRankSum=-3.59;Dels=0.0;FS=1.453;HaplotypeS [...]
+chr5 1333803 . G T 3859.65 REJECT NS=2;DP=825;DPB=830.0;AC=2;AN=4;AF=0.5;RO=465;AO=317;PRO=0.0;PAO=0.0;QR=13946;QA=10148;PQR=0.0;PQA=0.0;SRF=244;SRR=221;SAF=138;SAR=179;SRP=5.48064;SAP=14.5253;AB=0.381928;ABP=103.515;RUN=1;RPP=167.583;RPPR=226.98;RPL=236.0;RPR=81.0;EPP=3.56516;EPPR=3.23912;DPRA=0.0;ODDS=195.135;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=3.0;LEN=1;MQM=29.0095;MQMR=34.1376;PAIRED=0.993691;PAIREDR=0.997849;technology.ILLUMINA=1.0;MQ0=207;BaseQRankSum=2.3725;Dels=0.0;FS=4.986; [...]
+chr5 1333810 . CGCAA GGGAT 3023.65 REJECT NS=2;DP=752;DPB=818.8;AC=2;AN=2;AF=0.0;RO=278;AO=43;PRO=34.1667;PAO=52.0;QR=9275;QA=1344;PQR=961.167;PQA=1378.0;SRF=162;SRR=116;SAF=29;SAR=14;SRP=19.5385;SAP=14.3727;AB=0.0571809;ABP=1283.82;RUN=1;RPP=39.8243;RPPR=5.54108;RPL=8.0;RPR=35.0;EPP=9.12072;EPPR=8.29057;DPRA=0.0;ODDS=84.6119;GTI=0;TYPE=complex;CIGAR=1X1M1X1M1X;NUMALT=3;MEANALT=25.5;LEN=5;MQM=10.093;MQMR=48.0;PAIRED=1.0;PAIREDR=0.992806;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP: [...]
+chr5 1333812 . C G 2411.21 REJECT NS=2;DP=752;DPB=818.8;AC=2;AN=2;AF=0.25;RO=278;AO=49;PRO=34.1667;PAO=35.6667;QR=9275;QA=600;PQR=961.167;PQA=923.167;SRF=162;SRR=116;SAF=14;SAR=35;SRP=19.5385;SAP=22.5536;AB=0.0651596;ABP=1238.08;RUN=1;RPP=22.5536;RPPR=5.54108;RPL=14.0;RPR=35.0;EPP=92.7497;EPPR=8.29057;DPRA=0.0;ODDS=84.6119;GTI=0;TYPE=snp;CIGAR=2M1X2M;NUMALT=3;MEANALT=25.5;LEN=1;MQM=20.8571;MQMR=48.0;PAIRED=1.0;PAIREDR=0.992806;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=236;ALERT;BaseQ [...]
+chr5 1333812 . CAA GAT 3023.65 REJECT NS=2;DP=752;DPB=818.8;AC=2;AN=4;AF=0.5;RO=278;AO=265;PRO=34.1667;PAO=70.1667;QR=9275;QA=7647;PQR=961.167;PQA=1933.67;SRF=162;SRR=116;SAF=120;SAR=145;SRP=19.5385;SAP=8.1317;AB=0.352394;ABP=145.323;RUN=1;RPP=403.225;RPPR=5.54108;RPL=22.0;RPR=243.0;EPP=16.7848;EPPR=8.29057;DPRA=0.0;ODDS=84.6119;GTI=0;TYPE=complex;CIGAR=2M1X1M1X;NUMALT=3;MEANALT=25.5;LEN=5;MQM=12.4755;MQMR=48.0;PAIRED=1.0;PAIREDR=0.992806;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:D [...]
+chr5 1333813 . A C 507.77 PASS DP=44;AC=1;AN=4;AF=0.5;ALERT;BaseQRankSum=-0.695;FS=6.828;MLEAC=1;MLEAF=0.5;MQ=50.78;MQRankSum=-3.013;QD=11.54;ReadPosRankSum=-2.037;SOR=1.821;ClippingRankSum=-0.085 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:28,16:44:99.0:536,0,1137:16:36:44:1:.:.:.:.:.:1.95593 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:2.05322
+chr5 1333814 . A T 931.77 PASS DP=465;AC=2;AN=4;AF=0.5;MQ0=253;ALERT;BaseQRankSum=1.1505;Dels=0.0;FS=1.6515;HaplotypeScore=231.164;MLEAC=1;MLEAF=0.5;MQ=39.33;MQRankSum=-9.302;QD=6.405;ReadPosRankSum=-5.1865;SOR=1.0395;ClippingRankSum=1.031 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:29,16:45:99.0:536,0,1137:16:36:45:1:.:.:.:.:.:1.95593 0/1:312,539:885:99.0:1384,0,6319:539:63:851:.:1:.:.:.:.:2.05322
+chr5 1333880 . C G 138.77 PASS SOMATIC;DP=3041;AC=1;AN=4;AF=0.5;MQ0=975;BaseQRankSum=-7.724;Dels=0.0;FS=0.859;HaplotypeScore=642.661;MLEAC=1;MLEAF=0.5;MQ=23.4;MQRankSum=-3.075;QD=0.05;ReadPosRankSum=1.944;SOR=0.618 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:1.95593 0/1:2480,391:3041:99.0:167,0,21182:391:14:2871:.:1:.:.:.:.:2.05322
+chr5 1334507 . GA G 9383.515 REJECT NS=2;DP=422;DPB=501.111;AC=2;AN=4;AF=0.5;RO=100;AO=326;PRO=74.0;PAO=94.0;QR=3768;QA=11875;PQR=2580.5;PQA=3353.5;SRF=36;SRR=64;SAF=130;SAR=196;SRP=20.0346;SAP=32.0254;AB=0.739229;ABP=222.231;RUN=1;RPP=5.67468;RPPR=3.09716;RPL=153.0;RPR=173.0;EPP=18.3571;EPPR=3.79203;DPRA=0.0;ODDS=141.868;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=1;MEANALT=5.0;LEN=1;MQM=60.1534;MQMR=60.0;PAIRED=0.993865;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.34;FS=2.2265;MLEA [...]
+chr5 1334729 . C T 856.9114999999999 REJECT NS=2;DP=130;DPB=150.0;AC=2;AN=4;AF=0.5;RO=108;AO=42;PRO=0.0;PAO=0.0;QR=4032;QA=1526;PQR=0.0;PQA=0.0;SRF=54;SRR=54;SAF=15;SAR=27;SRP=3.0103;SAP=10.4553;AB=0.28;ABP=66.0699;RUN=1;RPP=3.83753;RPPR=3.09072;RPL=23.0;RPR=19.0;EPP=8.18047;EPPR=45.5551;DPRA=0.0;ODDS=64.6719;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8148;PAIRED=1.0;PAIREDR=0.990741;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.68;Dels=0.0;FS=4.1425;HaplotypeSco [...]
+chr5 1334869 . A AAAAC 486.624 REJECT NS=2;DP=167;DPB=320.429;AC=2;AN=4;AF=0.5;RO=128;AO=25;PRO=156.5;PAO=145.5;QR=4839;QA=923;PQR=5666.0;PQA=5231.0;SRF=73;SRR=55;SAF=15;SAR=10;SRP=8.50684;SAP=5.18177;AB=0.149701;ABP=181.006;RUN=1;RPP=7.26639;RPPR=38.9075;RPL=9.0;RPR=16.0;EPP=5.18177;EPPR=7.35324;DPRA=0.0;ODDS=11.9685;GTI=0;TYPE=ins;CIGAR=1M4I41M;NUMALT=1;MEANALT=7.0;LEN=4;MQM=58.12;MQMR=60.0;PAIRED=0.96;PAIREDR=0.992188;technology.ILLUMINA=1.0;END=1334869;HOMLEN=30;HOMSEQ=AAACAAACAAACAA [...]
+chr5 1335385 . CTG C 1421.96 REJECT NS=2;DP=297;DPB=305.556;AC=2;AN=4;AF=0.5;RO=226;AO=69;PRO=33.0;PAO=28.0;QR=8411;QA=2504;PQR=1025.0;PQA=857.0;SRF=104;SRR=122;SAF=29;SAR=40;SRP=6.12338;SAP=6.81824;AB=0.232323;ABP=187.849;RUN=1;RPP=5.55942;RPPR=3.0103;RPL=30.0;RPR=39.0;EPP=14.3712;EPPR=6.85361;DPRA=0.0;ODDS=108.684;GTI=0;TYPE=del;CIGAR=1M2D6M;NUMALT=1;MEANALT=2.0;LEN=2;MQM=60.1449;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;END=1335387;HOMLEN=4;HOMSEQ=TGTG;SVLEN=-2;SVTYPE=D [...]
+chr5 1336178 . A T 1082.935 REJECT NS=2;DP=232;DPB=266.0;AC=2;AN=4;AF=0.5;RO=208;AO=58;PRO=0.0;PAO=0.0;QR=7921;QA=2195;PQR=0.0;PQA=0.0;SRF=89;SRR=119;SAF=33;SAR=25;SRP=12.4061;SAP=5.40641;AB=0.218045;ABP=186.687;RUN=1;RPP=3.16006;RPPR=3.67845;RPL=28.0;RPR=30.0;EPP=32.3626;EPPR=4.05428;DPRA=0.0;ODDS=98.81;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.985577;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.001;Dels=0.0;FS=3.5605;HaplotypeScore=9.656 [...]
+chr5 1336221 . T C 1089.125 REJECT NS=2;DP=223;DPB=258.0;AC=2;AN=4;AF=0.5;RO=203;AO=55;PRO=0.0;PAO=0.0;QR=7744;QA=2069;PQR=0.0;PQA=0.0;SRF=91;SRR=112;SAF=34;SAR=21;SRP=7.72764;SAP=9.68264;AB=0.213178;ABP=187.367;RUN=1;RPP=3.04978;RPPR=3.10657;RPL=28.0;RPR=27.0;EPP=17.2631;EPPR=3.87675;DPRA=0.0;ODDS=87.3007;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.980296;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.206;Dels=0.0;FS=5.1465;HaplotypeScore=1.9 [...]
+chr5 1336243 . A G 1052.19 REJECT NS=2;DP=231;DPB=267.0;AC=2;AN=4;AF=0.5;RO=215;AO=52;PRO=0.0;PAO=0.0;QR=8298;QA=2038;PQR=0.0;PQA=0.0;SRF=97;SRR=118;SAF=25;SAR=27;SRP=7.46434;SAP=3.17734;AB=0.194757;ABP=219.092;RUN=1;RPP=5.68288;RPPR=5.92916;RPL=30.0;RPR=22.0;EPP=7.18621;EPPR=6.65635;DPRA=0.0;ODDS=61.5446;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.981395;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7155;Dels=0.0;FS=4.431;HaplotypeScore=0.99 [...]
+chr5 1336459 . T C 1460.185 REJECT NS=2;DP=292;DPB=338.0;AC=2;AN=4;AF=0.5;RO=263;AO=75;PRO=0.0;PAO=0.0;QR=9853;QA=2813;PQR=0.0;PQA=0.0;SRF=139;SRR=124;SAF=35;SAR=40;SRP=4.86802;SAP=3.73412;AB=0.221893;ABP=230.077;RUN=1;RPP=3.73412;RPPR=3.41487;RPL=40.0;RPR=35.0;EPP=3.27088;EPPR=4.40566;DPRA=0.0;ODDS=85.0332;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986667;PAIREDR=0.996198;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3725;Dels=0.0;FS=0.765;HaplotypeSco [...]
+chr5 1336626 . T A 1897.815 REJECT NS=2;DP=349;DPB=399.0;AC=2;AN=4;AF=0.5;RO=305;AO=93;PRO=0.0;PAO=0.0;QR=11683;QA=3505;PQR=0.0;PQA=0.0;SRF=158;SRR=147;SAF=57;SAR=36;SRP=3.87177;SAP=13.3073;AB=0.233083;ABP=249.921;RUN=1;RPP=4.15441;RPPR=3.35916;RPL=43.0;RPR=50.0;EPP=13.3073;EPPR=5.58047;DPRA=0.0;ODDS=112.057;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4885;Dels=0.0;FS=5.878;HaplotypeScore=10.60 [...]
+chr5 1337070 . T C 2039.515 REJECT NS=2;DP=408;DPB=470.0;AC=2;AN=4;AF=0.5;RO=368;AO=101;PRO=0.0;PAO=0.0;QR=13889;QA=3800;PQR=0.0;PQA=0.0;SRF=186;SRR=182;SAF=46;SAR=55;SRP=3.10471;SAP=4.75178;AB=0.214894;ABP=334.848;RUN=1;RPP=6.64375;RPPR=11.531;RPL=44.0;RPR=57.0;EPP=5.61177;EPPR=4.16685;DPRA=0.0;ODDS=124.6;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.98913;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.452;Dels=0.0;FS=1.9505;HaplotypeScore=12.6 [...]
+chr5 1337106 . T A 2207.745 REJECT NS=2;DP=440;DPB=511.0;AC=2;AN=4;AF=0.5;RO=399;AO=111;PRO=0.0;PAO=0.0;QR=14933;QA=4109;PQR=0.0;PQA=0.0;SRF=208;SRR=191;SAF=51;SAR=60;SRP=4.58312;SAP=4.59489;AB=0.217221;ABP=357.929;RUN=1;RPP=6.31642;RPPR=3.45113;RPL=62.0;RPR=49.0;EPP=3.18637;EPPR=14.0309;DPRA=0.0;ODDS=129.112;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984962;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1905;Dels=0.0;FS=4.799;HaplotypeScore [...]
+chr5 1337906 . A T 2254.325 REJECT NS=2;DP=375;DPB=440.0;AC=2;AN=4;AF=0.5;RO=330;AO=110;PRO=0.0;PAO=0.0;QR=12428;QA=4036;PQR=0.0;PQA=0.0;SRF=167;SRR=163;SAF=57;SAR=53;SRP=3.11558;SAP=3.32615;AB=0.25;ABP=241.872;RUN=1;RPP=3.08926;RPPR=3.43143;RPL=54.0;RPR=56.0;EPP=4.2737;EPPR=14.6178;DPRA=0.0;ODDS=163.503;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990909;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.3375;Dels=0.0;FS=4.5535;HaplotypeScore=8.9 [...]
+chr5 1338523 . TG T 2253.12 REJECT NS=2;DP=414;DPB=458.308;AC=2;AN=4;AF=0.5;RO=292;AO=106;PRO=62.5;PAO=48.5;QR=10884;QA=3792;PQR=2055.5;PQA=1578.5;SRF=143;SRR=149;SAF=54;SAR=52;SRP=3.27802;SAP=3.09224;AB=0.256039;ABP=217.031;RUN=1;RPP=8.25461;RPPR=4.91406;RPL=45.0;RPR=61.0;EPP=19.071;EPPR=5.41974;DPRA=0.0;ODDS=226.029;GTI=0;TYPE=del;CIGAR=1M1D11M;NUMALT=1;MEANALT=6.0;LEN=1;MQM=60.283;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993151;technology.ILLUMINA=1.0;BaseQRankSum=-0.583;FS=0.0;MLEAC=1;MLEAF=0. [...]
+chr5 1339985 . C A 629.001 REJECT NS=2;DP=558;DPB=558.0;AC=1;AN=4;AF=0.25;RO=463;AO=94;PRO=0.0;PAO=0.0;QR=16879;QA=3238;PQR=0.0;PQA=0.0;SRF=218;SRR=245;SAF=47;SAR=47;SRP=6.42931;SAP=3.0103;AB=0.416058;ABP=11.395;RUN=1;RPP=3.84193;RPPR=8.11772;RPL=44.0;RPR=50.0;EPP=26.6655;EPPR=29.3916;DPRA=0.0;ODDS=81.0532;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=23.9043;MQMR=28.622;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-1.364;FS=0.865;MLEAC=1;MLEAF=0.5;MQ=35.75;MQRank [...]
+chr5 4510772 . C T 7913.425 REJECT NS=2;DP=329;DPB=371.0;AC=3;AN=4;AF=0.75;RO=96;AO=274;PRO=0.0;PAO=0.0;QR=3657;QA=10498;PQR=0.0;PQA=0.0;SRF=59;SRR=37;SAF=181;SAR=93;SRP=13.9581;SAP=64.3821;AB=0.666667;ABP=72.4974;RUN=1;RPP=6.18033;RPPR=3.10078;RPL=127.0;RPR=147.0;EPP=10.1429;EPPR=4.45795;DPRA=0.0;ODDS=44.4837;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99635;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.527;Dels=0.0;FS=3.345;HaplotypeScore=2 [...]
+chr5 25520017 . T A 3795.06 REJECT NS=2;DP=251;DPB=284.0;AC=2;AN=4;AF=0.5;RO=148;AO=136;PRO=0.0;PAO=0.0;QR=5692;QA=5331;PQR=0.0;PQA=0.0;SRF=40;SRR=108;SAF=41;SAR=95;SRP=70.8541;SAP=49.5692;AB=0.478873;ABP=4.11133;RUN=1;RPP=42.9271;RPPR=11.4614;RPL=93.0;RPR=43.0;EPP=7.09778;EPPR=6.76636;DPRA=0.0;ODDS=197.686;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992647;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.3935;Dels=0.0;FS=1.788;HaplotypeScore=2. [...]
+chr5 30031011 . C G 1816.0 REJECT NS=2;DP=396;DPB=444.0;AC=2;AN=4;AF=0.5;RO=350;AO=94;PRO=0.0;PAO=0.0;QR=13384;QA=3562;PQR=0.0;PQA=0.0;SRF=163;SRR=187;SAF=40;SAR=54;SRP=6.58392;SAP=7.53805;AB=0.211712;ABP=323.527;RUN=1;RPP=3.1027;RPPR=6.01314;RPL=46.0;RPR=48.0;EPP=10.4949;EPPR=11.051;DPRA=0.0;ODDS=112.401;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991429;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0025;Dels=0.0;FS=2.412;HaplotypeScore=4.84 [...]
+chr5 35857177 . G C 5995.325000000001 REJECT NS=2;DP=277;DPB=310.0;AC=3;AN=4;AF=0.75;RO=96;AO=214;PRO=0.0;PAO=0.0;QR=3635;QA=8162;PQR=0.0;PQA=0.0;SRF=38;SRR=58;SAF=69;SAR=145;SRP=12.0581;SAP=61.6198;AB=0.606557;ABP=27.0745;RUN=1;RPP=81.5892;RPPR=16.0391;RPL=151.0;RPR=63.0;EPP=3.37559;EPPR=8.80089;DPRA=0.0;ODDS=42.2111;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.7917;PAIRED=0.995327;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.793;Dels=0.0;FS=5.722;Hapl [...]
+chr5 35861068 . T C 8570.535 REJECT NS=2;DP=373;DPB=424.0;AC=3;AN=4;AF=0.75;RO=118;AO=306;PRO=0.0;PAO=0.0;QR=4535;QA=11530;PQR=0.0;PQA=0.0;SRF=46;SRR=72;SAF=121;SAR=185;SRP=15.4503;SAP=32.0768;AB=0.637771;ABP=56.2618;RUN=1;RPP=3.12384;RPPR=5.66023;RPL=151.0;RPR=155.0;EPP=20.7511;EPPR=7.72129;DPRA=0.0;ODDS=60.7379;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9525;Dels=0.0;FS=0.0;HaplotypeScore=7.8 [...]
+chr5 35871190 . G A 7215.59 REJECT NS=2;DP=352;DPB=402.0;AC=3;AN=4;AF=0.75;RO=125;AO=277;PRO=0.0;PAO=0.0;QR=4528;QA=10147;PQR=0.0;PQA=0.0;SRF=80;SRR=45;SAF=183;SAR=94;SRP=24.2907;SAP=65.105;AB=0.586093;ABP=22.4529;RUN=1;RPP=3.20628;RPPR=3.16665;RPL=136.0;RPR=141.0;EPP=30.2987;EPPR=35.1307;DPRA=0.0;ODDS=63.2891;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.98917;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.757;Dels=0.0;FS=0.467;HaplotypeScore=1 [...]
+chr5 35874575 . C T 1827.96 REJECT NS=2;DP=399;DPB=452.0;AC=2;AN=4;AF=0.5;RO=358;AO=94;PRO=0.0;PAO=0.0;QR=13846;QA=3562;PQR=0.0;PQA=0.0;SRF=185;SRR=173;SAF=49;SAR=45;SRP=3.88374;SAP=3.37991;AB=0.207965;ABP=337.84;RUN=1;RPP=5.32038;RPPR=8.46931;RPL=42.0;RPR=52.0;EPP=12.2506;EPPR=16.9854;DPRA=0.0;ODDS=120.512;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988827;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.116;Dels=0.0;FS=0.3035;HaplotypeScore=2 [...]
+chr5 35875593 . A T 9119.185000000001 REJECT NS=2;DP=383;DPB=437.0;AC=3;AN=4;AF=0.75;RO=118;AO=319;PRO=0.0;PAO=0.0;QR=4539;QA=12293;PQR=0.0;PQA=0.0;SRF=67;SRR=51;SAF=170;SAR=149;SRP=7.72129;SAP=6.01224;AB=0.644578;ABP=63.2883;RUN=1;RPP=6.01224;RPPR=4.18805;RPL=149.0;RPR=170.0;EPP=7.26475;EPPR=11.917;DPRA=0.0;ODDS=66.5142;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996865;PAIREDR=0.991525;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.096;Dels=0.0;FS=0.441 [...]
+chr5 35876274 . A G 5334.47 REJECT NS=2;DP=331;DPB=380.0;AC=2;AN=4;AF=0.5;RO=192;AO=188;PRO=0.0;PAO=0.0;QR=7289;QA=7254;PQR=0.0;PQA=0.0;SRF=89;SRR=103;SAF=95;SAR=93;SRP=5.22701;SAP=3.0565;AB=0.494737;ABP=3.10173;RUN=1;RPP=3.74952;RPPR=3.41745;RPL=90.0;RPR=98.0;EPP=8.60069;EPPR=3.73412;DPRA=0.0;ODDS=308.991;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8542;PAIRED=0.994681;PAIREDR=0.989583;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.5855;Dels=0.0;FS=2.315;HaplotypeS [...]
+chr5 36094363 . G A 1508.955 REJECT NS=2;DP=246;DPB=280.0;AC=2;AN=4;AF=0.5;RO=208;AO=71;PRO=0.0;PAO=0.0;QR=7923;QA=2773;PQR=0.0;PQA=0.0;SRF=133;SRR=75;SAF=54;SAR=17;SRP=38.1297;SAP=44.88;AB=0.253571;ABP=150.701;RUN=1;RPP=22.1254;RPPR=158.396;RPL=23.0;RPR=48.0;EPP=3.7749;EPPR=3.17734;DPRA=0.0;ODDS=133.325;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990385;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.7165;Dels=0.0;FS=6.5895;HaplotypeScore=2.93 [...]
+chr5 36094476 . C T 10364.335 REJECT NS=2;DP=276;DPB=320.0;AC=4;AN=4;AF=1.0;RO=0;AO=320;PRO=0.0;PAO=0.0;QR=0;QA=12250;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=105;SAR=215;SRP=0.0;SAP=85.1191;AB=0.0;ABP=0.0;RUN=1;RPP=36.261;RPPR=0.0;RPL=195.0;RPR=125.0;EPP=42.2054;EPPR=0.0;DPRA=0.0;ODDS=57.9759;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.9875;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.9657;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.1;SOR=1.604 [...]
+chr5 37051861 . A AT 267.29 REJECT NS=2;DP=269;DPB=328.8;AC=2;AN=2;AF=0.0;RO=217;AO=10;PRO=57.5;PAO=39.5;QR=8156;QA=365;PQR=2060.67;PQA=1367.67;SRF=189;SRR=28;SAF=9;SAR=1;SRP=262.396;SAP=16.9077;AB=0.0371747;ABP=503.506;RUN=1;RPP=16.9077;RPPR=19.8317;RPL=1.0;RPR=9.0;EPP=10.8276;EPPR=3.02031;DPRA=0.0;ODDS=30.4534;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=2;MEANALT=7.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr5 37051861 . AT A 267.29 REJECT NS=2;DP=269;DPB=328.8;AC=2;AN=4;AF=0.5;RO=217;AO=32;PRO=57.5;PAO=39.0;QR=8156;QA=1159;PQR=2060.67;PQA=1347.67;SRF=189;SRR=28;SAF=27;SAR=5;SRP=262.396;SAP=35.8538;AB=0.118959;ABP=342.252;RUN=1;RPP=3.28173;RPPR=19.8317;RPL=15.0;RPR=17.0;EPP=7.35324;EPPR=3.02031;DPRA=0.0;ODDS=30.4534;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=2;MEANALT=7.0;LEN=1;MQM=60.3125;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.688;FS=7.829;MLEA [...]
+chr5 38510481 . AC A . PASS SOMATIC;AC=1;AN=4 GT:AD:DP:MM:MQS:NQSBQ:NQSMM:REnd:RStart:SC:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:10,0:10:0.3,0.0:60.0,0.0:36.5217,0.0:0.0,0.0:0,0:0,0:10,0,0,0:0:0:10:.:.:.:.:0:.:0.000150648 0/1:15,8:23:0.0,0.0:60.0,61.25:37.0405,36.0921:0.0,0.0:90,2:10,2:15,0,8,0:8:35:23:.:.:.:.:1:.:-6.50323e-05
+chr5 38950776 . G A 12239.4 REJECT NS=2;DP=321;DPB=372.0;AC=4;AN=4;AF=1.0;RO=0;AO=372;PRO=0.0;PAO=0.0;QR=0;QA=14302;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=161;SAR=211;SRP=0.0;SAP=17.6035;AB=0.0;ABP=0.0;RUN=1;RPP=4.50465;RPPR=0.0;RPL=194.0;RPR=178.0;EPP=38.5244;EPPR=0.0;DPRA=0.0;ODDS=65.4797;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9839;MQMR=0.0;PAIRED=0.986559;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.866;MLEAC=2;MLEAF=1.0;MQ=59.99;QD=26.49;SOR= [...]
+chr5 38953665 . G GA 4971.45 REJECT NS=2;DP=221;DPB=266.438;AC=4;AN=4;AF=1.0;RO=10;AO=199;PRO=15.6667;PAO=23.1667;QR=379;QA=6634;PQR=558.333;PQA=816.333;SRF=2;SRR=8;SAF=35;SAR=164;SRP=10.8276;SAP=184.596;AB=0.0;ABP=0.0;RUN=1;RPP=51.9939;RPPR=3.0103;RPL=133.0;RPR=66.0;EPP=3.02121;EPPR=3.0103;DPRA=0.0;ODDS=29.0378;GTI=0;TYPE=ins;CIGAR=1M1I15M;NUMALT=2;MEANALT=4.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994975;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.374;FS=0.0; [...]
+chr5 38953665 . G GAA 5653.17 REJECT NS=2;DP=228;DPB=266.438;AC=0;AN=4;AF=0.0;RO=10;AO=14;PRO=15.6667;PAO=17.1667;QR=379;QA=428;PQR=558.333;PQA=617.333;SRF=2;SRR=8;SAF=1;SAR=13;SRP=10.8276;SAP=25.3454;AB=0.0;ABP=0.0;RUN=1;RPP=12.937;RPPR=3.0103;RPL=11.0;RPR=3.0;EPP=8.59409;EPPR=3.0103;DPRA=0.0;ODDS=29.0378;GTI=0;TYPE=ins;CIGAR=1M2I15M;NUMALT=2;MEANALT=4.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=0.928571;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr5 38955796 . G A 8571.86 REJECT NS=2;DP=323;DPB=369.0;AC=2;AN=4;AF=0.5;RO=85;AO=284;PRO=0.0;PAO=0.0;QR=3233;QA=10826;PQR=0.0;PQA=0.0;SRF=33;SRR=52;SAF=94;SAR=190;SRP=12.2327;SAP=73.4761;AB=0.769648;ABP=236.052;RUN=1;RPP=9.00479;RPPR=18.977;RPL=156.0;RPR=128.0;EPP=30.536;EPPR=3.03585;DPRA=0.0;ODDS=167.067;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992958;PAIREDR=0.976471;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.7015;Dels=0.0;FS=2.8125;HaplotypeS [...]
+chr5 38958750 . A G 1664.425 REJECT NS=2;DP=266;DPB=310.0;AC=2;AN=4;AF=0.5;RO=231;AO=79;PRO=0.0;PAO=0.0;QR=8931;QA=3035;PQR=0.0;PQA=0.0;SRF=146;SRR=85;SAF=49;SAR=30;SRP=37.9889;SAP=12.9331;AB=0.254839;ABP=164.848;RUN=1;RPP=10.954;RPPR=23.7756;RPL=31.0;RPR=48.0;EPP=5.23675;EPPR=3.24531;DPRA=0.0;ODDS=133.878;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995671;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4405;Dels=0.0;FS=4.115;HaplotypeScore=1.9 [...]
+chr5 38978758 . TA T 3135.3 REJECT NS=2;DP=232;DPB=291.0;AC=2;AN=4;AF=0.5;RO=108;AO=103;PRO=57.0;PAO=68.0;QR=3986;QA=3824;PQR=2068.0;PQA=2478.0;SRF=17;SRR=91;SAF=8;SAR=95;SRP=113.112;SAP=162.582;AB=0.443966;ABP=9.33752;RUN=1;RPP=5.56125;RPPR=16.6021;RPL=57.0;RPR=46.0;EPP=3.53736;EPPR=4.2971;DPRA=0.0;ODDS=191.557;GTI=0;TYPE=del;CIGAR=1M1D24M;NUMALT=1;MEANALT=7.0;LEN=1;MQM=60.1942;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0165;FS=2.9605;MLEAC=1;MLEAF=0.5 [...]
+chr5 39074296 . G C 1549.58 REJECT NS=1;DP=118;DPB=118.0;AC=1;AN=4;AF=0.5;RO=62;AO=56;PRO=0.0;PAO=0.0;QR=2247;QA=2152;PQR=0.0;PQA=0.0;SRF=39;SRR=23;SAF=38;SAR=18;SRP=11.9764;SAP=18.5208;AB=0.474576;ABP=3.67278;RUN=1;RPP=5.49198;RPPR=11.9764;RPL=24.0;RPR=32.0;EPP=3.63072;EPPR=6.51267;DPRA=0.0;ODDS=356.804;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=1.98;FS=1.553;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.467 [...]
+chr5 43509462 . T TC 11835.0 REJECT NS=2;DP=326;DPB=499.333;AC=4;AN=4;AF=1.0;RO=0;AO=361;PRO=11.5;PAO=15.5;QR=0;QA=13233;PQR=381.5;PQA=523.5;SRF=0;SRR=0;SAF=111;SAR=250;SRP=0.0;SAP=119.229;AB=0.0;ABP=0.0;RUN=1;RPP=35.0651;RPPR=0.0;RPL=217.0;RPR=144.0;EPP=8.06905;EPPR=0.0;DPRA=0.0;ODDS=60.4168;GTI=0;TYPE=ins;CIGAR=1M1I2M;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0277;MQMR=0.0;PAIRED=0.99723;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=43509462;HOMLEN=1;HOMSEQ=C;SVLEN=1;SVTYPE=INS;FS=0.0;MLEAC=2; [...]
+chr5 44305309 . C G 1911.3 PASS SOMATIC;NS=2;DP=260;DPB=260.0;AC=1;AN=3;AF=0.25;RO=187;AO=73;PRO=0.0;PAO=0.0;QR=7163;QA=2803;PQR=0.0;PQA=0.0;SRF=50;SRR=137;SAF=26;SAR=47;SRP=90.9027;SAP=16.1284;AB=0.398907;ABP=19.2548;RUN=1;RPP=48.2543;RPPR=116.821;RPL=56.0;RPR=17.0;EPP=8.03741;EPPR=5.62303;DPRA=2.37662;ODDS=49.049;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986301;PAIREDR=0.994652;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.59;Dels=0.0;FS=4.846 [...]
+chr5 49570855 . A G 14074.8 REJECT NS=2;DP=373;DPB=426.0;AC=4;AN=4;AF=1.0;RO=0;AO=426;PRO=0.0;PAO=0.0;QR=0;QA=16162;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=213;SAR=213;SRP=0.0;SAP=3.0103;AB=0.0;ABP=0.0;RUN=1;RPP=10.3709;RPPR=0.0;RPL=232.0;RPR=194.0;EPP=23.8891;EPPR=0.0;DPRA=0.0;ODDS=69.7703;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995305;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8967;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.28;SOR=0.97 [...]
+chr5 52512796 . C CT 779.466 REJECT NS=2;DP=254;DPB=304.9;AC=2;AN=3;AF=0.25;RO=135;AO=44;PRO=41.3333;PAO=35.3333;QR=4998;QA=1445;PQR=1424.0;PQA=1220.0;SRF=98;SRR=37;SAF=29;SAR=15;SRP=62.8625;SAP=12.6832;AB=0.173228;ABP=238.589;RUN=1;RPP=3.20771;RPPR=20.5268;RPL=21.0;RPR=23.0;EPP=15.6443;EPPR=5.72866;DPRA=0.0;ODDS=2.08008;GTI=1;TYPE=ins;CIGAR=1M1I19M;NUMALT=2;MEANALT=15.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.193;FS= [...]
+chr5 52512796 . CT C 779.466 REJECT NS=2;DP=254;DPB=304.9;AC=2;AN=3;AF=0.25;RO=135;AO=26;PRO=41.3333;PAO=31.3333;QR=4998;QA=888;PQR=1424.0;PQA=1068.0;SRF=98;SRR=37;SAF=19;SAR=7;SRP=62.8625;SAP=15.0369;AB=0.102362;ABP=351.848;RUN=1;RPP=15.0369;RPPR=20.5268;RPL=7.0;RPR=19.0;EPP=3.34437;EPPR=5.72866;DPRA=0.0;ODDS=2.08008;GTI=1;TYPE=del;CIGAR=1M1D18M;NUMALT=2;MEANALT=15.0;LEN=1;MQM=60.3846;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr5 56152416 . C A 3655.05 REJECT NS=2;DP=270;DPB=312.0;AC=2;AN=4;AF=0.5;RO=174;AO=138;PRO=0.0;PAO=0.0;QR=6536;QA=5197;PQR=0.0;PQA=0.0;SRF=129;SRR=45;SAF=106;SAR=32;SRP=91.0673;SAP=89.1768;AB=0.442308;ABP=12.0303;RUN=1;RPP=30.7674;RPPR=57.372;RPL=48.0;RPR=90.0;EPP=3.07324;EPPR=4.80738;DPRA=0.0;ODDS=196.655;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.927;Dels=0.0;FS=3.2565;HaplotypeScore=2.9995; [...]
+chr5 56161787 . G A 6765.125 REJECT NS=2;DP=300;DPB=345.0;AC=3;AN=4;AF=0.75;RO=102;AO=243;PRO=0.0;PAO=0.0;QR=3951;QA=9404;PQR=0.0;PQA=0.0;SRF=28;SRR=74;SAF=75;SAR=168;SRP=48.0577;SAP=80.2986;AB=0.6;ABP=25.1593;RUN=1;RPP=9.52472;RPPR=5.13919;RPL=135.0;RPR=108.0;EPP=6.23623;EPPR=3.7767;DPRA=0.0;ODDS=57.1368;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995885;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.717;Dels=0.0;FS=1.561;HaplotypeScore=4.899 [...]
+chr5 56177443 . G A 5212.75 REJECT NS=2;DP=344;DPB=395.0;AC=2;AN=4;AF=0.5;RO=204;AO=190;PRO=0.0;PAO=0.0;QR=7586;QA=7243;PQR=0.0;PQA=0.0;SRF=118;SRR=86;SAF=118;SAR=72;SRP=13.9102;SAP=27.1936;AB=0.481013;ABP=4.24721;RUN=1;RPP=4.65605;RPPR=10.206;RPL=89.0;RPR=101.0;EPP=3.74174;EPPR=12.5903;DPRA=0.0;ODDS=303.294;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994737;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.5145;Dels=0.0;FS=3.672;HaplotypeScore=2 [...]
+chr5 56177743 . G A 8647.525000000001 REJECT NS=2;DP=387;DPB=443.0;AC=3;AN=4;AF=0.75;RO=131;AO=311;PRO=0.0;PAO=0.0;QR=5005;QA=11877;PQR=0.0;PQA=0.0;SRF=59;SRR=72;SAF=137;SAR=174;SRP=5.81167;SAP=12.569;AB=0.605422;ABP=35.0591;RUN=1;RPP=8.88235;RPPR=4.35297;RPL=170.0;RPR=141.0;EPP=4.1903;EPPR=3.02688;DPRA=0.0;ODDS=69.5873;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996785;PAIREDR=0.992366;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.641;Dels=0.0;FS=0.0;H [...]
+chr5 56177848 . TCAA T 5595.3 REJECT NS=2;DP=275;DPB=362.214;AC=3;AN=4;AF=0.75;RO=69;AO=191;PRO=89.8333;PAO=84.8333;QR=2591;QA=6859;PQR=3256.33;PQA=3070.33;SRF=33;SRR=36;SAF=91;SAR=100;SRP=3.29354;SAP=3.93119;AB=0.594872;ABP=18.2551;RUN=1;RPP=6.29593;RPPR=3.29354;RPL=104.0;RPR=87.0;EPP=3.93119;EPPR=3.29354;DPRA=0.0;ODDS=33.214;GTI=0;TYPE=del;CIGAR=1M3D24M;NUMALT=2;MEANALT=4.5;LEN=3;MQM=60.3141;MQMR=60.0;PAIRED=0.989529;PAIREDR=0.971014;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;Base [...]
+chr5 56177848 . TCAACAA T 5595.3 REJECT SOMATIC;NS=2;DP=275;DPB=362.214;AC=1;AN=3;AF=0.0;RO=69;AO=10;PRO=89.8333;PAO=64.3333;QR=2591;QA=330;PQR=3256.33;PQA=2308.33;SRF=33;SRR=36;SAF=4;SAR=6;SRP=3.29354;SAP=3.87889;AB=0.025641;ABP=384.132;RUN=1;RPP=3.0103;RPPR=3.29354;RPL=5.0;RPR=5.0;EPP=3.0103;EPPR=3.29354;DPRA=0.0;ODDS=33.214;GTI=0;TYPE=del;CIGAR=1M6D21M;NUMALT=2;MEANALT=4.5;LEN=6;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.971014;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO: [...]
+chr5 56178217 . A C 7835.09 REJECT NS=2;DP=379;DPB=429.0;AC=3;AN=4;AF=0.75;RO=143;AO=286;PRO=0.0;PAO=0.0;QR=5514;QA=10781;PQR=0.0;PQA=0.0;SRF=70;SRR=73;SAF=144;SAR=142;SRP=3.14697;SAP=3.04067;AB=0.569277;ABP=16.8502;RUN=1;RPP=11.7873;RPPR=3.02549;RPL=160.0;RPR=126.0;EPP=9.8436;EPPR=3.38993;DPRA=0.0;ODDS=61.4746;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.98951;PAIREDR=0.993007;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.113;Dels=0.0;FS=1.187;Haplotype [...]
+chr5 56179341 . G A 1158.4 REJECT NS=2;DP=238;DPB=271.0;AC=2;AN=4;AF=0.5;RO=212;AO=59;PRO=0.0;PAO=0.0;QR=8175;QA=2235;PQR=0.0;PQA=0.0;SRF=155;SRR=57;SAF=47;SAR=12;SRP=101.382;SAP=48.096;AB=0.217712;ABP=190.582;RUN=1;RPP=19.2411;RPPR=56.1089;RPL=19.0;RPR=40.0;EPP=5.99147;EPPR=3.37904;DPRA=0.0;ODDS=43.5471;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983051;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.325;Dels=0.0;FS=9.7565;HaplotypeScore=1.966 [...]
+chr5 56180480 . A G 679.4555 REJECT NS=2;DP=231;DPB=260.0;AC=2;AN=4;AF=0.5;RO=217;AO=43;PRO=0.0;PAO=0.0;QR=8314;QA=1645;PQR=0.0;PQA=0.0;SRF=163;SRR=54;SAF=32;SAR=11;SRP=121.901;SAP=25.2805;AB=0.165385;ABP=255.87;RUN=1;RPP=25.2805;RPPR=37.8439;RPL=11.0;RPR=32.0;EPP=3.46479;EPPR=3.50063;DPRA=0.0;ODDS=36.347;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.976744;PAIREDR=0.995392;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6905;Dels=0.0;FS=0.0;HaplotypeScore=4 [...]
+chr5 58500382 . T C 5513.56 REJECT NS=2;DP=320;DPB=360.0;AC=2;AN=4;AF=0.5;RO=168;AO=192;PRO=0.0;PAO=0.0;QR=6427;QA=7314;PQR=0.0;PQA=0.0;SRF=101;SRR=67;SAF=116;SAR=76;SRP=17.9521;SAP=21.1059;AB=0.533333;ABP=6.48466;RUN=1;RPP=11.8771;RPPR=7.19814;RPL=82.0;RPR=110.0;EPP=7.5342;EPPR=3.0103;DPRA=0.0;ODDS=218.659;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9702;PAIRED=1.0;PAIREDR=0.994048;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.142;Dels=0.0;FS=1.4745;HaplotypeScore [...]
+chr5 58500417 . G A 1018.49 REJECT NS=2;DP=346;DPB=394.0;AC=2;AN=4;AF=0.5;RO=328;AO=66;PRO=0.0;PAO=0.0;QR=12493;QA=2385;PQR=0.0;PQA=0.0;SRF=175;SRR=153;SAF=36;SAR=30;SRP=6.21455;SAP=4.19474;AB=0.167513;ABP=381.331;RUN=1;RPP=9.45891;RPPR=11.5903;RPL=26.0;RPR=40.0;EPP=3.1419;EPPR=7.48565;DPRA=0.0;ODDS=9.39473;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9242;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993902;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0445;Dels=0.0;FS=1.3385;HaplotypeScor [...]
+chr5 66003113 . G C 1454.6100000000001 REJECT NS=2;DP=317;DPB=361.0;AC=2;AN=4;AF=0.5;RO=286;AO=75;PRO=0.0;PAO=0.0;QR=11016;QA=2877;PQR=0.0;PQA=0.0;SRF=132;SRR=154;SAF=33;SAR=42;SRP=6.6851;SAP=5.35549;AB=0.207756;ABP=270.811;RUN=1;RPP=21.1059;RPPR=3.28363;RPL=50.0;RPR=25.0;EPP=7.90335;EPPR=11.7873;DPRA=0.0;ODDS=101.936;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996503;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3045;Dels=0.0;FS=2.8035;Haplo [...]
+chr5 67522722 . C T 2477.825 REJECT NS=2;DP=380;DPB=439.0;AC=2;AN=4;AF=0.5;RO=321;AO=118;PRO=0.0;PAO=0.0;QR=12195;QA=4375;PQR=0.0;PQA=0.0;SRF=143;SRR=178;SAF=52;SAR=66;SRP=11.2971;SAP=6.61715;AB=0.268793;ABP=206.847;RUN=1;RPP=3.30474;RPPR=4.15354;RPL=61.0;RPR=57.0;EPP=3.0103;EPPR=4.53236;DPRA=0.0;ODDS=197.975;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8692;PAIRED=1.0;PAIREDR=0.996885;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.253;Dels=0.0;FS=2.533;HaplotypeSco [...]
+chr5 67522851 . A C 1658.365 REJECT NS=2;DP=200;DPB=239.0;AC=2;AN=4;AF=0.5;RO=168;AO=71;PRO=0.0;PAO=0.0;QR=6288;QA=2768;PQR=0.0;PQA=0.0;SRF=33;SRR=135;SAF=16;SAR=55;SRP=137.486;SAP=49.5287;AB=0.297071;ABP=88.4973;RUN=1;RPP=22.1254;RPPR=77.6676;RPL=48.0;RPR=23.0;EPP=3.28556;EPPR=14.6432;DPRA=0.0;ODDS=104.54;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985915;PAIREDR=0.982143;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.156;Dels=0.0;FS=1.3595;HaplotypeScor [...]
+chr5 67569746 . G A 5569.52 REJECT NS=2;DP=329;DPB=371.0;AC=2;AN=4;AF=0.5;RO=177;AO=194;PRO=0.0;PAO=0.0;QR=6803;QA=7414;PQR=0.0;PQA=0.0;SRF=104;SRR=73;SAF=118;SAR=76;SRP=14.8;SAP=22.755;AB=0.522911;ABP=4.70182;RUN=1;RPP=7.48756;RPPR=13.3279;RPL=87.0;RPR=107.0;EPP=3.18939;EPPR=6.55581;DPRA=0.0;ODDS=257.106;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989691;PAIREDR=0.99435;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.425;Dels=0.0;FS=0.944;HaplotypeScore=3 [...]
+chr5 79950508 . C T 3682.77 PASS DP=84;AC=2;AN=4;AF=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.83;SOR=1.911 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:0,83:83:99.0:3711,253,0:83:100:83:1:.:.:.:.:.:-0.000248759 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-27.9349
+chr5 79950508 . CGCCA TGCCG 2611.25 REJECT NS=1;DP=75;DPB=81.8;AC=2;AN=4;AF=1.0;RO=0;AO=75;PRO=0.0;PAO=11.0;QR=0;QA=2615;PQR=0.0;PQA=345.0;SRF=0;SRR=0;SAF=26;SAR=49;SRP=0.0;SAP=18.3264;AB=0.0;ABP=0.0;RUN=1;RPP=3.73412;RPPR=0.0;RPL=40.0;RPR=35.0;EPP=5.35549;EPPR=0.0;DPRA=0.0;ODDS=57.1821;GTI=0;TYPE=complex;CIGAR=1X3M1X;NUMALT=1;MEANALT=1.0;LEN=5;MQM=60.0;MQMR=0.0;PAIRED=0.986667;PAIREDR=0.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:Ca [...]
+chr5 79950512 . A G 3570.77 PASS DP=74;AC=2;AN=4;AF=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.99;SOR=1.641 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:0,74:74:99.0:3599,244,0:74:100:74:1:.:.:.:.:.:-0.000248759 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-27.9349
+chr5 79950781 . A G 854.871 REJECT NS=1;DP=63;DPB=63.0;AC=1;AN=4;AF=0.5;RO=31;AO=32;PRO=0.0;PAO=0.0;QR=1181;QA=1233;PQR=0.0;PQA=0.0;SRF=6;SRR=25;SAF=5;SAR=27;SRP=28.2974;SAP=35.8538;AB=0.507937;ABP=3.04477;RUN=1;RPP=7.35324;RPPR=11.486;RPL=20.0;RPR=12.0;EPP=3.28173;EPPR=6.44263;DPRA=0.0;ODDS=186.398;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.967742;technology.ILLUMINA=1.0;BaseQRankSum=-0.036;FS=1.255;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.9 [...]
+chr5 80149981 . A G 13052.3 REJECT NS=2;DP=348;DPB=401.0;AC=4;AN=4;AF=1.0;RO=0;AO=401;PRO=0.0;PAO=0.0;QR=0;QA=15201;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=244;SAR=157;SRP=0.0;SAP=43.9975;AB=0.0;ABP=0.0;RUN=1;RPP=4.22871;RPPR=0.0;RPL=193.0;RPR=208.0;EPP=8.21425;EPPR=0.0;DPRA=0.0;ODDS=69.7776;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992519;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.195;SOR=1.19 [...]
+chr5 80168937 . G A 13285.95 REJECT NS=2;DP=357;DPB=408.0;AC=4;AN=4;AF=1.0;RO=0;AO=407;PRO=0.0;PAO=0.0;QR=0;QA=15369;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=240;SAR=167;SRP=0.0;SAP=31.4422;AB=0.0;ABP=0.0;RUN=1;RPP=4.21075;RPPR=0.0;RPL=196.0;RPR=211.0;EPP=5.83268;EPPR=0.0;DPRA=0.0;ODDS=67.3085;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.8293;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.905;SOR=1.05 G [...]
+chr5 86629061 . C CT 250.642 REJECT NS=2;DP=240;DPB=308.95;AC=2;AN=2;AF=0.0;RO=168;AO=20;PRO=54.6667;PAO=41.6667;QR=6259;QA=712;PQR=1903.33;PQA=1429.33;SRF=118;SRR=50;SAF=15;SAR=5;SRP=62.7775;SAP=13.8677;AB=0.0833333;ABP=364.922;RUN=1;RPP=4.74748;RPPR=59.3135;RPL=8.0;RPR=12.0;EPP=6.91895;EPPR=3.47562;DPRA=0.0;ODDS=19.5849;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=2;MEANALT=11.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.95;PAIREDR=0.994048;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr5 86629061 . CT C 250.642 REJECT NS=2;DP=240;DPB=308.95;AC=2;AN=4;AF=0.5;RO=168;AO=27;PRO=54.6667;PAO=37.6667;QR=6259;QA=1017;PQR=1903.33;PQA=1285.33;SRF=118;SRR=50;SAF=21;SAR=6;SRP=62.7775;SAP=21.1059;AB=0.1125;ABP=316.028;RUN=1;RPP=12.7417;RPPR=59.3135;RPL=8.0;RPR=19.0;EPP=3.73412;EPPR=3.47562;DPRA=0.0;ODDS=19.5849;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=2;MEANALT=11.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994048;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr5 88416354 . C T 5898.59 REJECT NS=2;DP=363;DPB=410.0;AC=2;AN=4;AF=0.5;RO=200;AO=210;PRO=0.0;PAO=0.0;QR=7502;QA=7885;PQR=0.0;PQA=0.0;SRF=87;SRR=113;SAF=82;SAR=128;SRP=10.3499;SAP=24.8905;AB=0.512195;ABP=3.53993;RUN=1;RPP=3.38255;RPPR=5.78978;RPL=108.0;RPR=102.0;EPP=5.03701;EPPR=3.40116;DPRA=0.0;ODDS=242.894;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.1429;MQMR=60.0;PAIRED=0.97619;PAIREDR=0.975;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3085;Dels=0.0;FS=2.226;HaplotypeS [...]
+chr5 91540296 . G A 4417.655000000001 REJECT NS=2;DP=293;DPB=343.0;AC=2;AN=4;AF=0.5;RO=176;AO=165;PRO=0.0;PAO=0.0;QR=6668;QA=6325;PQR=0.0;PQA=0.0;SRF=63;SRR=113;SAF=60;SAR=105;SRP=33.8551;SAP=29.6602;AB=0.48105;ABP=4.08021;RUN=1;RPP=58.6132;RPPR=36.372;RPL=115.0;RPR=50.0;EPP=7.76122;EPPR=20.8262;DPRA=0.0;ODDS=303.171;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.981818;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9265;Dels=0.0;FS=0.0;Haplotype [...]
+chr5 98216994 . GTTC TTTT 56.6292 REJECT NS=2;DP=356;DPB=367.0;AC=1;AN=4;AF=0.25;RO=300;AO=27;PRO=23.0;PAO=0.0;QR=9693;QA=421;PQR=536.0;PQA=0.0;SRF=120;SRR=180;SAF=27;SAR=0;SRP=29.068;SAP=61.6401;AB=0.108696;ABP=125.368;RUN=1;RPP=9.52472;RPPR=197.69;RPL=18.0;RPR=9.0;EPP=9.52472;EPPR=14.5915;DPRA=0.0;ODDS=13.0394;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=1;MEANALT=5.5;LEN=4;MQM=57.5185;MQMR=59.2367;PAIRED=0.962963;PAIREDR=0.99;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr5 102000423 . A G 15334.15 REJECT NS=2;DP=404;DPB=450.0;AC=4;AN=4;AF=1.0;RO=2;AO=447;PRO=0.0;PAO=0.0;QR=32;QA=17145;PQR=0.0;PQA=0.0;SRF=2;SRR=0;SAF=212;SAR=235;SRP=7.35324;SAP=5.58012;AB=0.0;ABP=0.0;RUN=1;RPP=6.55169;RPPR=3.0103;RPL=210.0;RPR=237.0;EPP=7.67872;EPPR=3.0103;DPRA=0.0;ODDS=59.81;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997763;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.693;Dels=0.0;FS=0.0;HaplotypeScore=6.7883;MLEAC=2;MLE [...]
+chr5 103500206 . C T 9105.93 REJECT NS=2;DP=243;DPB=274.0;AC=4;AN=4;AF=1.0;RO=0;AO=274;PRO=0.0;PAO=0.0;QR=0;QA=10411;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=178;SAR=96;SRP=0.0;SAP=56.2985;AB=0.0;ABP=0.0;RUN=1;RPP=67.2035;RPPR=0.0;RPL=92.0;RPR=182.0;EPP=41.8432;EPPR=0.0;DPRA=0.0;ODDS=42.4263;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.989051;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.51;SOR=1.60 [...]
+chr5 103500223 . C T 11927.8 REJECT NS=2;DP=313;DPB=353.0;AC=4;AN=4;AF=1.0;RO=0;AO=353;PRO=0.0;PAO=0.0;QR=0;QA=13581;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=216;SAR=137;SRP=0.0;SAP=41.4017;AB=0.0;ABP=0.0;RUN=1;RPP=34.0199;RPPR=0.0;RPL=141.0;RPR=212.0;EPP=58.5274;EPPR=0.0;DPRA=0.0;ODDS=53.6118;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991501;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9304;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.05;SOR=1. [...]
+chr5 103500243 . G T 5157.03 REJECT NS=2;DP=325;DPB=366.0;AC=2;AN=4;AF=0.5;RO=181;AO=183;PRO=0.0;PAO=0.0;QR=6861;QA=6952;PQR=0.0;PQA=0.0;SRF=85;SRR=96;SAF=101;SAR=82;SRP=4.46195;SAP=7.29391;AB=0.5;ABP=3.0103;RUN=1;RPP=5.68014;RPPR=21.2579;RPL=84.0;RPR=99.0;EPP=47.1636;EPPR=3.98206;DPRA=0.0;ODDS=203.174;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.983425;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.563;Dels=0.0;FS=6.2745;HaplotypeScore=3.866;M [...]
+chr5 103500335 . A G 3172.2650000000003 REJECT NS=2;DP=221;DPB=252.0;AC=2;AN=4;AF=0.5;RO=132;AO=119;PRO=0.0;PAO=0.0;QR=5043;QA=4490;PQR=0.0;PQA=0.0;SRF=39;SRR=93;SAF=36;SAR=83;SRP=50.9801;SAP=43.3194;AB=0.472222;ABP=4.69922;RUN=1;RPP=30.765;RPPR=29.3312;RPL=79.0;RPR=40.0;EPP=6.09416;EPPR=4.65535;DPRA=0.0;ODDS=180.425;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983193;PAIREDR=0.992424;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.9645;Dels=0.0;FS=0.832;H [...]
+chr5 108016782 . C A 3785.38 REJECT NS=2;DP=301;DPB=341.0;AC=2;AN=4;AF=0.5;RO=193;AO=148;PRO=0.0;PAO=0.0;QR=7207;QA=5446;PQR=0.0;PQA=0.0;SRF=62;SRR=131;SAF=48;SAR=100;SRP=56.577;SAP=42.6837;AB=0.434018;ABP=15.9054;RUN=1;RPP=12.9286;RPPR=23.8137;RPL=87.0;RPR=61.0;EPP=19.9713;EPPR=21.9235;DPRA=0.0;ODDS=236.395;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993243;PAIREDR=0.989637;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.6855;Dels=0.0;FS=1.5235;Haplotype [...]
+chr5 111017980 . A C 3082.34 PASS SOMATIC;NS=2;DP=435;DPB=435.0;AC=1;AN=3;AF=0.25;RO=318;AO=117;PRO=0.0;PAO=0.0;QR=12262;QA=4475;PQR=0.0;PQA=0.0;SRF=144;SRR=174;SAF=57;SAR=60;SRP=9.15598;SAP=3.17734;AB=0.358896;ABP=59.3887;RUN=1;RPP=4.51363;RPPR=3.44733;RPL=54.0;RPR=63.0;EPP=8.37402;EPPR=3.0103;DPRA=2.99083;ODDS=68.9431;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991453;PAIREDR=0.990566;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.645;Dels=0.0;FS [...]
+chr5 112162854 . T C 1836.21 REJECT NS=2;DP=368;DPB=419.0;AC=2;AN=4;AF=0.5;RO=322;AO=97;PRO=0.0;PAO=0.0;QR=12424;QA=3743;PQR=0.0;PQA=0.0;SRF=176;SRR=146;SAF=58;SAR=39;SRP=9.07963;SAP=11.0918;AB=0.231504;ABP=265.375;RUN=1;RPP=4.10723;RPPR=3.4419;RPL=45.0;RPR=52.0;EPP=11.0918;EPPR=13.8002;DPRA=0.0;ODDS=202.854;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989691;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0655;Dels=0.0;FS=3.894;HaplotypeScore=2 [...]
+chr5 112164561 . G A 1819.34 REJECT NS=2;DP=307;DPB=363.0;AC=2;AN=4;AF=0.5;RO=275;AO=88;PRO=0.0;PAO=0.0;QR=10458;QA=3247;PQR=0.0;PQA=0.0;SRF=167;SRR=108;SAF=65;SAR=23;SRP=30.4972;SAP=46.5385;AB=0.242424;ABP=212.195;RUN=1;RPP=3.109;RPPR=23.5485;RPL=45.0;RPR=43.0;EPP=22.3561;EPPR=7.94546;DPRA=0.0;ODDS=44.4347;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.977273;PAIREDR=0.992727;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0295;Dels=0.0;FS=5.197;HaplotypeSco [...]
+chr5 112175770 . G A 1916.83 REJECT NS=2;DP=324;DPB=376.0;AC=2;AN=4;AF=0.5;RO=284;AO=92;PRO=0.0;PAO=0.0;QR=10914;QA=3492;PQR=0.0;PQA=0.0;SRF=160;SRR=124;SAF=34;SAR=58;SRP=12.9196;SAP=16.6056;AB=0.244681;ABP=215.907;RUN=1;RPP=4.52089;RPPR=6.71098;RPL=50.0;RPR=42.0;EPP=12.4515;EPPR=14.0512;DPRA=0.0;ODDS=124.677;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.98913;PAIREDR=0.996479;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5305;Dels=0.0;FS=11.86;HaplotypeSc [...]
+chr5 112176325 . G A 1463.1799999999998 REJECT NS=2;DP=361;DPB=399.0;AC=2;AN=4;AF=0.5;RO=321;AO=78;PRO=0.0;PAO=0.0;QR=12169;QA=2957;PQR=0.0;PQA=0.0;SRF=148;SRR=173;SAF=32;SAR=46;SRP=7.23824;SAP=8.46682;AB=0.195489;ABP=324.372;RUN=1;RPP=4.79202;RPPR=3.17942;RPL=35.0;RPR=43.0;EPP=3.45573;EPPR=3.55824;DPRA=0.0;ODDS=77.5074;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987179;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0325;Dels=0.0;FS=0.327;Hapl [...]
+chr5 112176559 . T G 2120.225 REJECT NS=2;DP=368;DPB=424.0;AC=2;AN=4;AF=0.5;RO=322;AO=102;PRO=0.0;PAO=0.0;QR=12419;QA=3834;PQR=0.0;PQA=0.0;SRF=172;SRR=150;SAF=48;SAR=54;SRP=6.27425;SAP=3.7767;AB=0.240566;ABP=250.886;RUN=1;RPP=3.0103;RPPR=3.0103;RPL=51.0;RPR=51.0;EPP=11.5259;EPPR=5.70778;DPRA=0.0;ODDS=138.827;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996894;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1205;Dels=0.0;FS=3.803;HaplotypeScore= [...]
+chr5 112176756 . T A 5530.335 REJECT NS=2;DP=353;DPB=406.0;AC=2;AN=4;AF=0.5;RO=205;AO=200;PRO=0.0;PAO=0.0;QR=7743;QA=7612;PQR=0.0;PQA=0.0;SRF=109;SRR=96;SAF=105;SAR=95;SRP=4.80044;SAP=4.09604;AB=0.492611;ABP=3.20284;RUN=1;RPP=4.09604;RPPR=3.8683;RPL=95.0;RPR=105.0;EPP=3.0103;EPPR=4.80044;DPRA=0.0;ODDS=334.211;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3975;Dels=0.0;FS=1.049;HaplotypeScore=11. [...]
+chr5 112177171 . G A 2084.005 REJECT NS=2;DP=354;DPB=411.0;AC=2;AN=4;AF=0.5;RO=311;AO=98;PRO=0.0;PAO=0.0;QR=11860;QA=3629;PQR=0.0;PQA=0.0;SRF=150;SRR=161;SAF=53;SAR=45;SRP=3.85515;SAP=4.4284;AB=0.238443;ABP=247.235;RUN=1;RPP=5.22609;RPPR=3.35243;RPL=54.0;RPR=44.0;EPP=4.4284;EPPR=8.10034;DPRA=0.0;ODDS=75.4325;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989796;PAIREDR=0.996785;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9815;Dels=0.0;FS=3.5755;HaplotypeS [...]
+chr5 112213678 . CTG C 1228.25 REJECT NS=2;DP=226;DPB=361.07;AC=2;AN=2;AF=0.0;RO=74;AO=26;PRO=66.6167;PAO=64.6167;QR=2767;QA=783;PQR=2423.58;PQA=2354.58;SRF=40;SRR=34;SAF=14;SAR=12;SRP=4.06669;SAP=3.34437;AB=0.115044;ABP=293.911;RUN=1;RPP=3.0103;RPPR=17.2129;RPL=13.0;RPR=13.0;EPP=4.34659;EPPR=12.5178;DPRA=0.0;ODDS=35.1193;GTI=0;TYPE=del;CIGAR=1M2D40M;NUMALT=5;MEANALT=14.0;LEN=2;MQM=59.9231;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr5 112213678 . CTGTG C 1228.25 REJECT NS=2;DP=226;DPB=361.07;AC=2;AN=3;AF=0.25;RO=74;AO=51;PRO=66.6167;PAO=54.6167;QR=2767;QA=1621;PQR=2423.58;PQA=1980.58;SRF=40;SRR=34;SAF=24;SAR=27;SRP=4.06669;SAP=3.3935;AB=0.225664;ABP=150.747;RUN=1;RPP=5.09662;RPPR=17.2129;RPL=22.0;RPR=29.0;EPP=3.05288;EPPR=12.5178;DPRA=0.0;ODDS=35.1193;GTI=0;TYPE=del;CIGAR=1M4D38M;NUMALT=5;MEANALT=14.0;LEN=4;MQM=60.1961;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0 [...]
+chr5 112213678 . CTGTGTG C 1228.25 REJECT NS=2;DP=226;DPB=361.07;AC=2;AN=2;AF=0.0;RO=74;AO=13;PRO=66.6167;PAO=49.95;QR=2767;QA=395;PQR=2423.58;PQA=1813.58;SRF=40;SRR=34;SAF=6;SAR=7;SRP=4.06669;SAP=3.17734;AB=0.0787879;ABP=257.283;RUN=1;RPP=3.17734;RPPR=17.2129;RPL=6.0;RPR=7.0;EPP=3.17734;EPPR=12.5178;DPRA=0.0;ODDS=35.1193;GTI=0;TYPE=del;CIGAR=1M6D36M;NUMALT=5;MEANALT=18.0;LEN=6;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr5 112213678 . CTGTGTGTGTG C 1228.25 REJECT NS=2;DP=226;DPB=361.07;AC=2;AN=3;AF=0.25;RO=74;AO=31;PRO=66.6167;PAO=42.2;QR=2767;QA=951;PQR=2423.58;PQA=1524.83;SRF=40;SRR=34;SAF=18;SAR=13;SRP=4.06669;SAP=4.76149;AB=0.137168;ABP=261.435;RUN=1;RPP=3.64073;RPPR=17.2129;RPL=17.0;RPR=14.0;EPP=8.68415;EPPR=12.5178;DPRA=0.0;ODDS=35.1193;GTI=0;TYPE=del;CIGAR=1M10D32M;NUMALT=5;MEANALT=14.0;LEN=10;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.628 [...]
+chr5 112213678 . CTGTGTGTGTGTG C 1228.25 REJECT NS=2;DP=226;DPB=361.07;AC=2;AN=2;AF=0.0;RO=74;AO=8;PRO=66.6167;PAO=40.0;QR=2767;QA=189;PQR=2423.58;PQA=1439.83;SRF=40;SRR=34;SAF=2;SAR=6;SRP=4.06669;SAP=7.35324;AB=0.0353982;ABP=426.736;RUN=1;RPP=7.35324;RPPR=17.2129;RPL=2.0;RPR=6.0;EPP=7.35324;EPPR=12.5178;DPRA=0.0;ODDS=35.1193;GTI=0;TYPE=del;CIGAR=1M12D30M;NUMALT=5;MEANALT=14.0;LEN=12;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr5 112213747 . GTAAC G 1084.01 REJECT NS=2;DP=332;DPB=394.111;AC=1;AN=4;AF=0.25;RO=256;AO=67;PRO=87.5;PAO=58.5;QR=9516;QA=2295;PQR=2935.0;PQA=1926.0;SRF=105;SRR=151;SAF=22;SAR=45;SRP=20.9589;SAP=20.1552;AB=0.483516;ABP=3.22506;RUN=1;RPP=5.63551;RPPR=7.11574;RPL=38.0;RPR=29.0;EPP=3.04271;EPPR=52.0041;DPRA=0.0;ODDS=10.4253;GTI=0;TYPE=del;CIGAR=1M4D13M;NUMALT=1;MEANALT=5.5;LEN=4;MQM=60.1493;MQMR=60.0391;PAIRED=1.0;PAIREDR=0.988281;technology.ILLUMINA=1.0;END=112213751;HOMLEN=13;HOMSEQ=TAA [...]
+chr5 112213805 . C G 1093.48 REJECT NS=2;DP=308;DPB=349.0;AC=2;AN=4;AF=0.5;RO=287;AO=62;PRO=0.0;PAO=0.0;QR=10971;QA=2384;PQR=0.0;PQA=0.0;SRF=128;SRR=159;SAF=18;SAR=44;SRP=10.2813;SAP=26.6864;AB=0.17765;ABP=317.998;RUN=1;RPP=8.05372;RPPR=36.9745;RPL=37.0;RPR=25.0;EPP=3.0103;EPPR=18.3317;DPRA=0.0;ODDS=78.3667;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.1613;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986063;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.255;Dels=0.0;FS=6.884;HaplotypeScore= [...]
+chr5 114014076 . G T 4286.35 REJECT NS=2;DP=278;DPB=318.0;AC=2;AN=4;AF=0.5;RO=163;AO=155;PRO=0.0;PAO=0.0;QR=6176;QA=5976;PQR=0.0;PQA=0.0;SRF=52;SRR=111;SAF=42;SAR=113;SRP=49.3839;SAP=73.6322;AB=0.487421;ABP=3.44733;RUN=1;RPP=36.6471;RPPR=19.3296;RPL=102.0;RPR=53.0;EPP=6.16244;EPPR=6.86033;DPRA=0.0;ODDS=241.135;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.98773;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.597;Dels=0.0;FS=1.634;HaplotypeScore=4 [...]
+chr5 115501700 . G A 4540.47 REJECT NS=2;DP=309;DPB=358.0;AC=2;AN=4;AF=0.5;RO=192;AO=166;PRO=0.0;PAO=0.0;QR=7316;QA=6386;PQR=0.0;PQA=0.0;SRF=118;SRR=74;SAF=103;SAR=63;SRP=24.906;SAP=23.9402;AB=0.463687;ABP=7.11062;RUN=1;RPP=33.1493;RPPR=35.9895;RPL=59.0;RPR=107.0;EPP=30.69;EPPR=26.9417;DPRA=0.0;ODDS=286.347;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984375;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.887;Dels=0.0;FS=3.445;HaplotypeScore=5.9 [...]
+chr5 115501792 . T C 4076.04 REJECT NS=2;DP=314;DPB=367.0;AC=2;AN=4;AF=0.5;RO=213;AO=154;PRO=0.0;PAO=0.0;QR=8240;QA=5940;PQR=0.0;PQA=0.0;SRF=76;SRR=137;SAF=60;SAR=94;SRP=40.9448;SAP=19.3104;AB=0.419619;ABP=23.6067;RUN=1;RPP=23.3714;RPPR=16.9669;RPL=96.0;RPR=58.0;EPP=5.77399;EPPR=3.10205;DPRA=0.0;ODDS=289.71;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987013;PAIREDR=0.99061;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9315;Dels=0.0;FS=1.1635;HaplotypeSco [...]
+chr5 118507216 . CT C 11893.95 REJECT NS=2;DP=335;DPB=337.143;AC=4;AN=4;AF=1.0;RO=0;AO=379;PRO=7.0;PAO=14.0;QR=0;QA=13927;PQR=260.5;PQA=468.5;SRF=0;SRR=0;SAF=130;SAR=249;SRP=0.0;SAP=84.1454;AB=0.0;ABP=0.0;RUN=1;RPP=92.5334;RPPR=0.0;RPL=252.0;RPR=127.0;EPP=15.6667;EPPR=0.0;DPRA=0.0;ODDS=70.3079;GTI=0;TYPE=del;CIGAR=1M1D5M;NUMALT=1;MEANALT=2.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994723;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=118507217;HOMLEN=2;HOMSEQ=TT;SVLEN=-1;SVTYPE=DEL;FS=0.0;MLEAC= [...]
+chr5 118507219 . TGTAGGGTGACAGACTTCTTATTGCAAGAGGATATTGTCTTAT GTAGGGTGACAGACTTCTTATTGCAAGAGGATATTGTCTTA . PASS SOMATIC;AC=1;AN=4;END=118507261;HOMLEN=0;SVLEN=-43;SVTYPE=RPL;NTLEN=41 GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:-0.000218184 0/1:119,56:56:32:175:.:.:.:1:.:.:-0.0141286
+chr5 121518309 . G A 14307.349999999999 REJECT NS=2;DP=375;DPB=434.0;AC=4;AN=4;AF=1.0;RO=0;AO=434;PRO=0.0;PAO=0.0;QR=0;QA=16751;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=165;SAR=269;SRP=0.0;SAP=57.127;AB=0.0;ABP=0.0;RUN=1;RPP=7.51335;RPPR=0.0;RPL=232.0;RPR=202.0;EPP=5.01166;EPPR=0.0;DPRA=0.0;ODDS=77.3134;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.990783;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.866;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29. [...]
+chr5 129025813 . CCA C 4536.88 REJECT NS=2;DP=343;DPB=315.75;AC=2;AN=4;AF=0.5;RO=219;AO=171;PRO=13.5;PAO=5.5;QR=8343;QA=6313;PQR=485.0;PQA=186.0;SRF=104;SRR=115;SAF=83;SAR=88;SRP=4.21006;SAP=3.32777;AB=0.43734;ABP=16.3446;RUN=1;RPP=4.54684;RPPR=5.24126;RPL=80.0;RPR=91.0;EPP=6.68022;EPPR=21.3439;DPRA=0.0;ODDS=309.63;GTI=0;TYPE=del;CIGAR=1M2D1M;NUMALT=1;MEANALT=1.5;LEN=2;MQM=60.1754;MQMR=60.0;PAIRED=0.994152;PAIREDR=0.986301;technology.ILLUMINA=1.0;MQ0=0;END=129025815;HOMLEN=1;HOMSEQ=C;SVL [...]
+chr5 131915213 . G A 5259.88 REJECT NS=2;DP=240;DPB=278.0;AC=2;AN=4;AF=0.5;RO=89;AO=189;PRO=0.0;PAO=0.0;QR=3282;QA=6908;PQR=0.0;PQA=0.0;SRF=33;SRR=56;SAF=60;SAR=129;SRP=15.9171;SAP=57.7107;AB=0.679856;ABP=81.1208;RUN=1;RPP=86.0203;RPPR=48.1232;RPL=137.0;RPR=52.0;EPP=4.95199;EPPR=3.0347;DPRA=0.0;ODDS=122.52;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989418;PAIREDR=0.977528;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.678;Dels=0.0;FS=3.656;HaplotypeScor [...]
+chr5 131925483 . G C 5927.44 REJECT NS=2;DP=342;DPB=391.0;AC=2;AN=4;AF=0.5;RO=186;AO=205;PRO=0.0;PAO=0.0;QR=7076;QA=7883;PQR=0.0;PQA=0.0;SRF=73;SRR=113;SAF=77;SAR=128;SRP=21.6896;SAP=30.5615;AB=0.524297;ABP=5.01516;RUN=1;RPP=9.63064;RPPR=4.69144;RPL=90.0;RPR=115.0;EPP=13.1897;EPPR=23.6043;DPRA=0.0;ODDS=293.99;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995122;PAIREDR=0.983871;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.167;Dels=0.0;FS=2.1295;Haplotype [...]
+chr5 131927550 . AT A 59.3753 REJECT NS=2;DP=223;DPB=245.812;AC=2;AN=3;AF=0.25;RO=195;AO=12;PRO=27.5;PAO=27.5;QR=7361;QA=431;PQR=919.833;PQA=919.833;SRF=147;SRR=48;SAF=11;SAR=1;SRP=112.152;SAP=21.1059;AB=0.127273;ABP=69.3784;RUN=1;RPP=9.52472;RPPR=59.1456;RPL=3.0;RPR=9.0;EPP=5.9056;EPPR=3.11052;DPRA=0.0;ODDS=13.6717;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=2;MEANALT=4.5;LEN=1;MQM=61.6667;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994872;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr5 131927563 . C T 59.3753 REJECT NS=2;DP=223;DPB=245.812;AC=2;AN=2;AF=0.0;RO=195;AO=3;PRO=27.5;PAO=2.0;QR=7361;QA=48;PQR=919.833;PQA=23.3333;SRF=147;SRR=48;SAF=3;SAR=0;SRP=112.152;SAP=9.52472;AB=0.0545455;ABP=97.8049;RUN=1;RPP=9.52472;RPPR=59.1456;RPL=3.0;RPR=0.0;EPP=9.52472;EPPR=3.11052;DPRA=0.327381;ODDS=13.6717;GTI=0;TYPE=snp;CIGAR=13M1X2M;NUMALT=2;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994872;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr5 138036255 . G T 916.9975 REJECT NS=2;DP=204;DPB=230.0;AC=2;AN=4;AF=0.5;RO=182;AO=48;PRO=0.0;PAO=0.0;QR=7051;QA=1824;PQR=0.0;PQA=0.0;SRF=118;SRR=64;SAF=34;SAR=14;SRP=37.8016;SAP=21.1059;AB=0.208696;ABP=172.536;RUN=1;RPP=29.068;RPPR=103.996;RPL=12.0;RPR=36.0;EPP=3.73412;EPPR=6.06468;DPRA=0.0;ODDS=55.7325;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.076;Dels=0.0;FS=2.9385;HaplotypeScore=0.9973 [...]
+chr5 138117938 . A G 5836.1 REJECT NS=2;DP=219;DPB=254.0;AC=2;AN=4;AF=0.5;RO=57;AO=197;PRO=0.0;PAO=0.0;QR=2157;QA=7440;PQR=0.0;PQA=0.0;SRF=37;SRR=20;SAF=123;SAR=74;SRP=14.02;SAP=29.4758;AB=0.775591;ABP=170.573;RUN=1;RPP=78.9457;RPPR=11.5819;RPL=57.0;RPR=140.0;EPP=8.84131;EPPR=3.35316;DPRA=0.0;ODDS=96.9595;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4685;Dels=0.0;FS=7.257;HaplotypeScore=0.9999;ML [...]
+chr5 138221989 . G C 1588.48 REJECT NS=2;DP=292;DPB=325.0;AC=2;AN=4;AF=0.5;RO=244;AO=81;PRO=0.0;PAO=0.0;QR=9252;QA=3094;PQR=0.0;PQA=0.0;SRF=88;SRR=156;SAF=19;SAR=62;SRP=44.1615;SAP=52.5788;AB=0.249231;ABP=180.53;RUN=1;RPP=7.5409;RPPR=18.709;RPL=47.0;RPR=34.0;EPP=3.68051;EPPR=46.6177;DPRA=0.0;ODDS=192.127;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987654;PAIREDR=0.991803;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0575;Dels=0.0;FS=5.929;HaplotypeScore= [...]
+chr5 138266546 . G A 2764.44 REJECT NS=2;DP=400;DPB=467.0;AC=2;AN=4;AF=0.5;RO=336;AO=131;PRO=0.0;PAO=0.0;QR=12774;QA=4992;PQR=0.0;PQA=0.0;SRF=193;SRR=143;SAF=73;SAR=58;SRP=19.1671;SAP=6.73993;AB=0.280514;ABP=198.42;RUN=1;RPP=4.35297;RPPR=3.0103;RPL=61.0;RPR=70.0;EPP=3.15949;EPPR=8.82674;DPRA=0.0;ODDS=236.671;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992366;PAIREDR=0.997024;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4375;Dels=0.0;FS=0.9075;Haplotype [...]
+chr5 147014141 . C T 2644.71 PASS SOMATIC;NS=2;DP=393;DPB=393.0;AC=1;AN=3;AF=0.25;RO=293;AO=100;PRO=0.0;PAO=0.0;QR=11309;QA=3883;PQR=0.0;PQA=0.0;SRF=137;SRR=156;SAF=56;SAR=44;SRP=5.68573;SAP=6.13722;AB=0.343643;ABP=64.804;RUN=1;RPP=3.79203;RPPR=22.2867;RPL=53.0;RPR=47.0;EPP=7.26639;EPPR=5.68573;DPRA=2.85294;ODDS=64.6152;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996587;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.583;Dels=0.0;FS=8.61 [...]
+chr5 149435608 . G C 4073.29 REJECT NS=2;DP=254;DPB=293.0;AC=2;AN=4;AF=0.5;RO=149;AO=144;PRO=0.0;PAO=0.0;QR=5656;QA=5541;PQR=0.0;PQA=0.0;SRF=95;SRR=54;SAF=91;SAR=53;SRP=27.5086;SAP=24.7853;AB=0.491468;ABP=3.19558;RUN=1;RPP=40.7095;RPPR=3.37464;RPL=47.0;RPR=97.0;EPP=3.25157;EPPR=15.2667;DPRA=0.0;ODDS=212.289;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.831;Dels=0.0;FS=4.024;HaplotypeScore=3.9325;M [...]
+chr5 149435759 . G A 5129.785 REJECT NS=2;DP=351;DPB=410.0;AC=2;AN=4;AF=0.5;RO=217;AO=193;PRO=0.0;PAO=0.0;QR=8264;QA=7092;PQR=0.0;PQA=0.0;SRF=124;SRR=93;SAF=103;SAR=90;SRP=12.6268;SAP=4.91174;AB=0.470732;ABP=6.06095;RUN=1;RPP=3.02155;RPPR=3.82085;RPL=97.0;RPR=96.0;EPP=3.11156;EPPR=8.30389;DPRA=0.0;ODDS=277.342;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994819;PAIREDR=0.986175;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.0045;Dels=0.0;FS=1.6285;Haploty [...]
+chr5 149449526 . C T 3265.17 PASS SOMATIC;NS=2;DP=403;DPB=403.0;AC=1;AN=3;AF=0.25;RO=283;AO=120;PRO=0.0;PAO=0.0;QR=10878;QA=4628;PQR=0.0;PQA=0.0;SRF=162;SRR=121;SAF=68;SAR=52;SRP=15.9087;SAP=7.64277;AB=0.38961;ABP=35.6106;RUN=1;RPP=4.16842;RPPR=3.07936;RPL=64.0;RPR=56.0;EPP=7.64277;EPPR=3.38628;DPRA=3.24211;ODDS=60.2985;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991667;PAIREDR=0.996466;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.712;Dels=0.0;FS [...]
+chr5 149456771 . CT AA 5309.165000000001 REJECT NS=2;DP=333;DPB=384.0;AC=2;AN=4;AF=0.5;RO=196;AO=182;PRO=2.0;PAO=6.0;QR=7387;QA=6900;PQR=0.0;PQA=201.0;SRF=116;SRR=80;SAF=113;SAR=69;SRP=17.3686;SAP=26.109;AB=0.478947;ABP=4.47319;RUN=1;RPP=9.88265;RPPR=3.40914;RPL=79.0;RPR=103.0;EPP=6.876;EPPR=4.11819;DPRA=0.0;ODDS=282.215;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=1;MEANALT=2.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989796;technology.ILLUMINA=1.0;MQ0=0;JOINED;BaseQRankSum=-0.7875;Dels=0.0;FS=7 [...]
+chr5 149457678 . G A 5506.845 REJECT NS=2;DP=372;DPB=425.0;AC=2;AN=4;AF=0.5;RO=223;AO=202;PRO=0.0;PAO=0.0;QR=8544;QA=7704;PQR=0.0;PQA=0.0;SRF=121;SRR=102;SAF=109;SAR=93;SRP=6.52555;SAP=5.76226;AB=0.475294;ABP=5.26352;RUN=1;RPP=20.2101;RPPR=5.82445;RPL=81.0;RPR=121.0;EPP=8.21323;EPPR=3.25374;DPRA=0.0;ODDS=327.583;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985149;PAIREDR=0.991031;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.123;Dels=0.0;FS=0.571;Haplotyp [...]
+chr5 149460553 . A G 5456.445 REJECT NS=2;DP=375;DPB=431.0;AC=2;AN=4;AF=0.5;RO=229;AO=202;PRO=0.0;PAO=0.0;QR=8740;QA=7711;PQR=0.0;PQA=0.0;SRF=82;SRR=147;SAF=89;SAR=113;SRP=43.0735;SAP=9.20222;AB=0.468677;ABP=6.68316;RUN=1;RPP=3.3973;RPPR=5.14384;RPL=104.0;RPR=98.0;EPP=11.4382;EPPR=10.985;DPRA=0.0;ODDS=362.295;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995633;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.3705;Dels=0.0;FS=7.517;HaplotypeScore= [...]
+chr5 149495395 . T C 2542.76 PASS SOMATIC;NS=2;DP=410;DPB=410.0;AC=1;AN=3;AF=0.25;RO=311;AO=99;PRO=0.0;PAO=0.0;QR=12037;QA=3848;PQR=0.0;PQA=0.0;SRF=220;SRR=91;SAF=60;SAR=39;SRP=119.202;SAP=12.6832;AB=0.315287;ABP=96.0655;RUN=1;RPP=9.34924;RPPR=6.08946;RPL=41.0;RPR=58.0;EPP=3.03223;EPPR=10.6139;DPRA=3.27083;ODDS=60.8716;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996785;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.648;Dels=0.0;FS=8.066 [...]
+chr5 149497177 . T C 1661.91 PASS SOMATIC;NS=2;DP=371;DPB=371.0;AC=1;AN=3;AF=0.25;RO=289;AO=80;PRO=0.0;PAO=0.0;QR=10321;QA=2776;PQR=0.0;PQA=0.0;SRF=212;SRR=77;SAF=46;SAR=34;SRP=139.948;SAP=6.91895;AB=0.284698;ABP=116.151;RUN=1;RPP=9.95901;RPPR=16.9032;RPL=32.0;RPR=48.0;EPP=24.2907;EPPR=49.9036;DPRA=3.12222;ODDS=56.374;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=59.8893;PAIRED=0.975;PAIREDR=0.986159;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.954;Dels=0.0;FS=1 [...]
+chr5 149499672 . T C 2051.09 PASS SOMATIC;NS=2;DP=368;DPB=368.0;AC=1;AN=3;AF=0.25;RO=283;AO=84;PRO=0.0;PAO=0.0;QR=10938;QA=3190;PQR=0.0;PQA=0.0;SRF=102;SRR=181;SAF=30;SAR=54;SRP=50.8978;SAP=17.9004;AB=0.307692;ABP=90.7044;RUN=1;RPP=8.07707;RPPR=6.39411;RPL=49.0;RPR=35.0;EPP=11.386;EPPR=8.60395;DPRA=2.87368;ODDS=59.6455;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.398;Dels=0.0;FS=1.036;Hap [...]
+chr5 149505489 . A G 11141.8 REJECT NS=2;DP=408;DPB=474.0;AC=2;AN=4;AF=0.5;RO=111;AO=362;PRO=0.0;PAO=0.0;QR=4264;QA=13901;PQR=0.0;PQA=0.0;SRF=53;SRR=58;SAF=191;SAR=171;SRP=3.49937;SAP=5.40972;AB=0.763713;ABP=289.333;RUN=1;RPP=14.6235;RPPR=3.96888;RPL=203.0;RPR=159.0;EPP=5.91359;EPPR=3.18637;DPRA=0.0;ODDS=142.015;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990991;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.984;Dels=0.0;FS=1.864;HaplotypeSco [...]
+chr5 149506703 . G A 1835.04 REJECT NS=2;DP=363;DPB=419.0;AC=2;AN=4;AF=0.5;RO=328;AO=89;PRO=0.0;PAO=0.0;QR=12617;QA=3366;PQR=0.0;PQA=0.0;SRF=164;SRR=164;SAF=46;SAR=43;SRP=3.0103;SAP=3.22989;AB=0.212411;ABP=304.016;RUN=1;RPP=11.8182;RPPR=12.5701;RPL=35.0;RPR=54.0;EPP=3.0347;EPPR=3.03678;DPRA=0.0;ODDS=60.9849;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984756;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6865;Dels=0.0;FS=1.189;HaplotypeScore=4. [...]
+chr5 149506836 . G T 2305.6949999999997 REJECT NS=2;DP=339;DPB=407.0;AC=2;AN=4;AF=0.5;RO=300;AO=107;PRO=0.0;PAO=0.0;QR=11392;QA=3916;PQR=0.0;PQA=0.0;SRF=165;SRR=135;SAF=49;SAR=58;SRP=9.52472;SAP=4.65412;AB=0.262899;ABP=201.745;RUN=1;RPP=3.51765;RPPR=8.68508;RPL=56.0;RPR=51.0;EPP=6.44001;EPPR=5.35549;DPRA=0.0;ODDS=97.9519;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.981308;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.2425;Dels=0.0;FS=4.9215;H [...]
+chr5 149507396 . T TAA 85.9136 REJECT NS=2;DP=22;DPB=110.8;AC=2;AN=4;AF=0.5;RO=3;AO=4;PRO=91.8333;PAO=89.3333;QR=113;QA=85;PQR=3144.5;PQA=3056.5;SRF=0;SRR=3;SAF=1;SAR=3;SRP=9.52472;SAP=5.18177;AB=0.181818;ABP=22.3561;RUN=1;RPP=11.6962;RPPR=3.73412;RPL=0.0;RPR=4.0;EPP=5.18177;EPPR=3.73412;DPRA=0.0;ODDS=1.66122;GTI=1;TYPE=ins;CIGAR=1M2I34M;NUMALT=2;MEANALT=7.5;LEN=2;MQM=51.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr5 149507423 . CTTTGG ACTTTGA 85.9136 REJECT NS=2;DP=22;DPB=110.8;AC=2;AN=2;AF=0.0;RO=3;AO=2;PRO=91.8333;PAO=24.8333;QR=113;QA=32;PQR=3144.5;PQA=801.0;SRF=0;SRR=3;SAF=2;SAR=0;SRP=9.52472;SAP=7.35324;AB=0.117647;ABP=24.5973;RUN=1;RPP=3.0103;RPPR=3.73412;RPL=1.0;RPR=1.0;EPP=3.0103;EPPR=3.73412;DPRA=0.0;ODDS=1.66122;GTI=1;TYPE=complex;CIGAR=1M1I31M1X2M;NUMALT=2;MEANALT=11.0;LEN=36;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr5 149508475 . C T 6514.525 REJECT NS=2;DP=399;DPB=461.0;AC=2;AN=4;AF=0.5;RO=224;AO=237;PRO=0.0;PAO=0.0;QR=8477;QA=9055;PQR=0.0;PQA=0.0;SRF=92;SRR=132;SAF=122;SAR=115;SRP=18.5208;SAP=3.45925;AB=0.5141;ABP=3.80635;RUN=1;RPP=3.23936;RPPR=3.04908;RPL=116.0;RPR=121.0;EPP=16.9462;EPPR=14.2166;DPRA=0.0;ODDS=357.623;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991561;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.054;Dels=0.0;FS=10.352;HaplotypeSco [...]
+chr5 149508544 . C G 6949.125 REJECT NS=2;DP=432;DPB=495.0;AC=2;AN=4;AF=0.5;RO=239;AO=255;PRO=0.0;PAO=0.0;QR=9099;QA=9610;PQR=0.0;PQA=0.0;SRF=130;SRR=109;SAF=134;SAR=121;SRP=7.01708;SAP=4.44943;AB=0.515152;ABP=3.99733;RUN=1;RPP=3.42756;RPPR=3.4555;RPL=131.0;RPR=124.0;EPP=5.4713;EPPR=3.23744;DPRA=0.0;ODDS=354.856;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995816;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.806;Dels=0.0;FS=1.645;HaplotypeScor [...]
+chr5 149509111 . C T 10238.885 REJECT NS=2;DP=442;DPB=509.0;AC=3;AN=4;AF=0.75;RO=144;AO=365;PRO=0.0;PAO=0.0;QR=5561;QA=14075;PQR=0.0;PQA=0.0;SRF=78;SRR=66;SAF=179;SAR=186;SRP=5.18177;SAP=3.30181;AB=0.618037;ABP=48.6343;RUN=1;RPP=14.0104;RPPR=3.25157;RPL=161.0;RPR=204.0;EPP=3.73016;EPPR=6.8707;DPRA=0.0;ODDS=83.3486;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99726;PAIREDR=0.993056;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.275;Dels=0.0;FS=3.47;Haplotyp [...]
+chr5 149509270 . A G 7757.865 REJECT NS=2;DP=338;DPB=392.0;AC=3;AN=4;AF=0.75;RO=108;AO=284;PRO=0.0;PAO=0.0;QR=4075;QA=10784;PQR=0.0;PQA=0.0;SRF=44;SRR=64;SAF=146;SAR=138;SRP=11.0528;SAP=3.49965;AB=0.622378;ABP=40.2138;RUN=1;RPP=6.06871;RPPR=3.09072;RPL=152.0;RPR=132.0;EPP=6.06871;EPPR=5.02092;DPRA=0.0;ODDS=67.0994;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996479;PAIREDR=0.981481;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.279;Dels=0.0;FS=5.318;Haplot [...]
+chr5 156002438 . G A 3137.19 PASS SOMATIC;NS=2;DP=413;DPB=413.0;AC=1;AN=3;AF=0.25;RO=295;AO=117;PRO=0.0;PAO=0.0;QR=11333;QA=4506;PQR=0.0;PQA=0.0;SRF=165;SRR=130;SAF=62;SAR=55;SRP=12.0274;SAP=3.91972;AB=0.375;ABP=45.354;RUN=1;RPP=14.61;RPPR=3.37099;RPL=46.0;RPR=71.0;EPP=11.1951;EPPR=3.37099;DPRA=3.08911;ODDS=63.993;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99661;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.103;Dels=0.0;FS=0.0;Haploty [...]
+chr5 158204425 . A G 6116.025 REJECT NS=2;DP=353;DPB=405.0;AC=2;AN=4;AF=0.5;RO=189;AO=216;PRO=0.0;PAO=0.0;QR=7346;QA=8225;PQR=0.0;PQA=0.0;SRF=109;SRR=80;SAF=142;SAR=74;SRP=12.6728;SAP=49.4959;AB=0.533333;ABP=6.91895;RUN=1;RPP=8.80089;RPPR=7.15793;RPL=96.0;RPR=120.0;EPP=26.1727;EPPR=26.2761;DPRA=0.0;ODDS=330.177;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994709;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.1985;Dels=0.0;FS=5.3895;HaplotypeSc [...]
+chr5 170820024 . G A 2217.65 PASS SOMATIC;NS=2;DP=344;DPB=344.0;AC=1;AN=3;AF=0.25;RO=256;AO=87;PRO=0.0;PAO=0.0;QR=9628;QA=3373;PQR=0.0;PQA=0.0;SRF=105;SRR=151;SAF=27;SAR=60;SRP=20.9589;SAP=30.1911;AB=0.360996;ABP=43.4574;RUN=1;RPP=84.1036;RPPR=109.412;RPL=72.0;RPR=15.0;EPP=4.23331;EPPR=7.11574;DPRA=2.33981;ODDS=65.1955;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988506;PAIREDR=0.984375;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.994;Dels=0.0;FS= [...]
+chr5 176516631 . G A 1799.6799999999998 REJECT NS=2;DP=351;DPB=398.0;AC=2;AN=4;AF=0.5;RO=305;AO=93;PRO=0.0;PAO=0.0;QR=11570;QA=3523;PQR=0.0;PQA=0.0;SRF=163;SRR=142;SAF=52;SAR=41;SRP=6.15004;SAP=5.83555;AB=0.233668;ABP=248.223;RUN=1;RPP=6.95631;RPPR=4.21351;RPL=40.0;RPR=53.0;EPP=6.95631;EPPR=34.9701;DPRA=0.0;ODDS=173.732;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996721;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.066;Dels=0.0;FS=3.415;Haplo [...]
+chr5 176516953 . A G 9860.735 REJECT NS=2;DP=266;DPB=307.0;AC=4;AN=4;AF=1.0;RO=1;AO=306;PRO=0.0;PAO=0.0;QR=2;QA=11578;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=97;SAR=209;SRP=5.18177;SAP=92.0265;AB=0.0;ABP=0.0;RUN=1;RPP=6.44492;RPPR=5.18177;RPL=164.0;RPR=142.0;EPP=32.0768;EPPR=5.18177;DPRA=0.0;ODDS=54.2128;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993464;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.7286;MLEAC=2;MLEAF=1.0;MQ=60.0;QD [...]
+chr5 176517461 . T G 7363.8150000000005 REJECT NS=2;DP=197;DPB=226.0;AC=4;AN=4;AF=1.0;RO=1;AO=225;PRO=0.0;PAO=0.0;QR=39;QA=8636;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=161;SAR=64;SRP=5.18177;SAP=93.8165;AB=0.0;ABP=0.0;RUN=1;RPP=17.6895;RPPR=5.18177;RPL=93.0;RPR=132.0;EPP=5.79944;EPPR=5.18177;DPRA=0.0;ODDS=39.879;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995556;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.015;Dels=0.0;FS=2.4775;HaplotypeScore=1.966 [...]
+chr5 176517797 . C T 15758.3 REJECT NS=2;DP=417;DPB=476.0;AC=4;AN=4;AF=1.0;RO=0;AO=476;PRO=0.0;PAO=0.0;QR=0;QA=18124;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=224;SAR=252;SRP=0.0;SAP=6.58684;AB=0.0;ABP=0.0;RUN=1;RPP=3.30226;RPPR=0.0;RPL=242.0;RPR=234.0;EPP=15.3457;EPPR=0.0;DPRA=0.0;ODDS=77.2787;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991597;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9243;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.335;SOR=0 [...]
+chr5 176518784 . C T 13170.45 REJECT NS=2;DP=352;DPB=408.0;AC=4;AN=4;AF=1.0;RO=0;AO=408;PRO=0.0;PAO=0.0;QR=0;QA=15441;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=157;SAR=251;SRP=0.0;SAP=50.0376;AB=0.0;ABP=0.0;RUN=1;RPP=8.46027;RPPR=0.0;RPL=220.0;RPR=188.0;EPP=3.54252;EPPR=0.0;DPRA=0.0;ODDS=73.5812;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997549;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9653;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.44;SOR=1 [...]
+chr5 176519287 . G A 4953.8 REJECT NS=2;DP=136;DPB=160.0;AC=4;AN=4;AF=1.0;RO=0;AO=160;PRO=0.0;PAO=0.0;QR=0;QA=6040;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=129;SAR=31;SRP=0.0;SAP=133.353;AB=0.0;ABP=0.0;RUN=1;RPP=85.5805;RPPR=0.0;RPL=41.0;RPR=119.0;EPP=24.725;EPPR=0.0;DPRA=0.0;ODDS=33.6741;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99375;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9638;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.02;SOR=2.971 GT [...]
+chr5 176520243 . G A 3493.7799999999997 REJECT NS=2;DP=246;DPB=285.0;AC=2;AN=4;AF=0.5;RO=151;AO=134;PRO=0.0;PAO=0.0;QR=5690;QA=5020;PQR=0.0;PQA=0.0;SRF=54;SRR=97;SAF=38;SAR=96;SRP=29.6001;SAP=57.524;AB=0.470175;ABP=5.21225;RUN=1;RPP=10.8535;RPPR=3.36982;RPL=78.0;RPR=56.0;EPP=3.59368;EPPR=3.36982;DPRA=0.0;ODDS=242.588;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985075;PAIREDR=0.993377;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.038;Dels=0.0;FS=3.6925;Ha [...]
+chr5 176522728 . C T 7940.265 REJECT NS=2;DP=212;DPB=248.0;AC=4;AN=4;AF=1.0;RO=0;AO=248;PRO=0.0;PAO=0.0;QR=0;QA=9433;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=73;SAR=175;SRP=0.0;SAP=94.1071;AB=0.0;ABP=0.0;RUN=1;RPP=6.51267;RPPR=0.0;RPL=134.0;RPR=114.0;EPP=18.4558;EPPR=0.0;DPRA=0.0;ODDS=48.6122;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.66;SOR=1.896 GT [...]
+chr5 176523597 . A G 14461.75 REJECT NS=2;DP=385;DPB=438.0;AC=4;AN=4;AF=1.0;RO=0;AO=438;PRO=0.0;PAO=0.0;QR=0;QA=16682;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=243;SAR=195;SRP=0.0;SAP=14.4328;AB=0.0;ABP=0.0;RUN=1;RPP=31.646;RPPR=0.0;RPL=181.0;RPR=257.0;EPP=3.98201;EPPR=0.0;DPRA=0.0;ODDS=69.8518;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993151;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8967;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.33;SOR=0. [...]
+chr5 176637192 . T C 2685.99 PASS SOMATIC;NS=2;DP=385;DPB=385.0;AC=1;AN=3;AF=0.25;RO=283;AO=102;PRO=0.0;PAO=0.0;QR=10916;QA=3935;PQR=0.0;PQA=0.0;SRF=137;SRR=146;SAF=44;SAR=58;SRP=3.63182;SAP=7.18293;AB=0.346939;ABP=62.8366;RUN=1;RPP=3.7767;RPPR=15.9087;RPL=54.0;RPR=48.0;EPP=3.09546;EPPR=6.39411;DPRA=3.23077;ODDS=57.7601;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989399;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.143;Dels=0.0;FS=2.68 [...]
+chr5 176639217 . T TA 191.802 REJECT NS=2;DP=140;DPB=165.667;AC=2;AN=3;AF=0.25;RO=94;AO=17;PRO=18.8333;PAO=11.8333;QR=3527;QA=527;PQR=682.333;PQA=411.333;SRF=22;SRR=72;SAF=4;SAR=13;SRP=60.7622;SAP=13.3567;AB=0.121429;ABP=177.286;RUN=1;RPP=6.20364;RPPR=60.7622;RPL=11.0;RPR=6.0;EPP=4.1599;EPPR=10.4949;DPRA=0.0;ODDS=13.1792;GTI=0;TYPE=ins;CIGAR=1M1I17M;NUMALT=3;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.696;FS=1.721; [...]
+chr5 176639217 . T TAA 191.802 REJECT NS=2;DP=140;DPB=165.667;AC=2;AN=2;AF=0.0;RO=94;AO=5;PRO=18.8333;PAO=9.83333;QR=3527;QA=166;PQR=682.333;PQA=356.333;SRF=22;SRR=72;SAF=0;SAR=5;SRP=60.7622;SAP=13.8677;AB=0.0357143;ABP=265.138;RUN=1;RPP=13.8677;RPPR=60.7622;RPL=5.0;RPR=0.0;EPP=13.8677;EPPR=10.4949;DPRA=0.0;ODDS=13.1792;GTI=0;TYPE=ins;CIGAR=1M2I17M;NUMALT=3;MEANALT=7.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr5 176639217 . TA T 191.802 REJECT NS=2;DP=140;DPB=165.667;AC=2;AN=3;AF=0.25;RO=94;AO=12;PRO=18.8333;PAO=13.5;QR=3527;QA=430;PQR=682.333;PQA=482.0;SRF=22;SRR=72;SAF=2;SAR=10;SRP=60.7622;SAP=14.5915;AB=0.0857143;ABP=211.72;RUN=1;RPP=14.5915;RPPR=60.7622;RPL=10.0;RPR=2.0;EPP=5.9056;EPPR=10.4949;DPRA=0.0;ODDS=13.1792;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=3;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr5 176721198 . T C 12158.5 REJECT NS=2;DP=319;DPB=371.0;AC=4;AN=4;AF=1.0;RO=0;AO=371;PRO=0.0;PAO=0.0;QR=0;QA=14309;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=173;SAR=198;SRP=0.0;SAP=6.66844;AB=0.0;ABP=0.0;RUN=1;RPP=5.12324;RPPR=0.0;RPL=176.0;RPR=195.0;EPP=6.66844;EPPR=0.0;DPRA=0.0;ODDS=69.2287;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994609;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9329;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.18;SOR=0. [...]
+chr5 176721272 . G C 8741.55 REJECT NS=2;DP=317;DPB=366.0;AC=2;AN=4;AF=0.5;RO=77;AO=289;PRO=0.0;PAO=0.0;QR=2959;QA=10912;PQR=0.0;PQA=0.0;SRF=50;SRR=27;SAF=160;SAR=129;SRP=17.9286;SAP=10.231;AB=0.789617;ABP=269.662;RUN=1;RPP=9.32936;RPPR=3.0385;RPL=130.0;RPR=159.0;EPP=10.231;EPPR=3.26411;DPRA=0.0;ODDS=31.4059;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99308;PAIREDR=0.974026;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5445;Dels=0.0;FS=9.3315;HaplotypeSc [...]
+chr5 176939735 . A G 10413.885 REJECT NS=2;DP=280;DPB=326.0;AC=4;AN=4;AF=1.0;RO=0;AO=326;PRO=0.0;PAO=0.0;QR=0;QA=12329;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=144;SAR=182;SRP=0.0;SAP=12.6287;AB=0.0;ABP=0.0;RUN=1;RPP=7.51311;RPPR=0.0;RPL=150.0;RPR=176.0;EPP=4.31585;EPPR=0.0;DPRA=0.0;ODDS=61.1396;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993865;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.965;SOR [...]
+chr5 176940384 . G A 5110.97 REJECT NS=2;DP=323;DPB=365.0;AC=2;AN=4;AF=0.5;RO=183;AO=181;PRO=0.0;PAO=0.0;QR=6901;QA=6988;PQR=0.0;PQA=0.0;SRF=101;SRR=82;SAF=94;SAR=87;SRP=7.29391;SAP=3.59816;AB=0.49589;ABP=3.06384;RUN=1;RPP=16.0751;RPPR=22.957;RPL=74.0;RPR=107.0;EPP=19.4343;EPPR=11.6606;DPRA=0.0;ODDS=252.896;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.1665;Dels=0.0;FS=2.176;HaplotypeScore=9.8327; [...]
+chr5 176940871 . G C 7588.195 REJECT NS=2;DP=199;DPB=226.0;AC=4;AN=4;AF=1.0;RO=0;AO=226;PRO=0.0;PAO=0.0;QR=0;QA=8744;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=59;SAR=167;SRP=0.0;SAP=115.081;AB=0.0;ABP=0.0;RUN=1;RPP=50.0909;RPPR=0.0;RPL=148.0;RPR=78.0;EPP=3.16403;EPPR=0.0;DPRA=0.0;ODDS=37.4428;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99115;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9662;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.565;SOR=2.06 [...]
+chr5 176942371 . CAG C 111.982 PASS SOMATIC;NS=2;DP=207;DPB=248.6;AC=2;AN=3;AF=0.25;RO=147;AO=22;PRO=37.3333;PAO=25.3333;QR=5041;QA=728;PQR=1304.33;PQA=889.333;SRF=32;SRR=115;SAF=3;SAR=19;SRP=104.774;SAP=28.2783;AB=0.12987;ABP=186.26;RUN=1;RPP=17.2236;RPPR=65.4217;RPL=17.0;RPR=5.0;EPP=6.56362;EPPR=7.27939;DPRA=0.0;ODDS=8.65789;GTI=0;TYPE=del;CIGAR=1M2D17M;NUMALT=2;MEANALT=14.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr5 176942371 . CAGAG C 111.982 REJECT NS=2;DP=207;DPB=248.6;AC=2;AN=2;AF=0.0;RO=147;AO=9;PRO=37.3333;PAO=20.3333;QR=5041;QA=260;PQR=1304.33;PQA=714.333;SRF=32;SRR=115;SAF=0;SAR=9;SRP=104.774;SAP=22.5536;AB=0.038961;ABP=287.332;RUN=1;RPP=9.04217;RPPR=65.4217;RPL=7.0;RPR=2.0;EPP=9.04217;EPPR=7.27939;DPRA=0.0;ODDS=8.65789;GTI=0;TYPE=del;CIGAR=1M4D15M;NUMALT=2;MEANALT=14.0;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr5 180030322 . C T 1653.57 REJECT NS=2;DP=382;DPB=427.0;AC=2;AN=4;AF=0.5;RO=337;AO=88;PRO=0.0;PAO=0.0;QR=12813;QA=3411;PQR=0.0;PQA=0.0;SRF=157;SRR=180;SAF=49;SAR=39;SRP=6.41893;SAP=5.47788;AB=0.206089;ABP=323.397;RUN=1;RPP=3.40511;RPPR=3.78997;RPL=46.0;RPR=42.0;EPP=7.84676;EPPR=22.502;DPRA=0.0;ODDS=135.643;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988636;PAIREDR=0.994065;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.204;Dels=0.0;FS=4.974;HaplotypeSco [...]
+chr5 180041208 . T C 7404.120000000001 REJECT NS=2;DP=206;DPB=236.0;AC=4;AN=4;AF=1.0;RO=0;AO=236;PRO=0.0;PAO=0.0;QR=0;QA=8701;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=84;SAR=152;SRP=0.0;SAP=45.5564;AB=0.0;ABP=0.0;RUN=1;RPP=204.552;RPPR=0.0;RPL=192.0;RPR=44.0;EPP=6.69076;EPPR=0.0;DPRA=0.0;ODDS=41.6734;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.7875;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.285;SOR [...]
+chr5 180045911 . G A 1839.66 REJECT NS=1;DP=117;DPB=117.0;AC=1;AN=4;AF=0.5;RO=52;AO=65;PRO=0.0;PAO=0.0;QR=1947;QA=2460;PQR=0.0;PQA=0.0;SRF=15;SRR=37;SAF=27;SAR=38;SRP=23.2217;SAP=7.05258;AB=0.555556;ABP=6.14687;RUN=1;RPP=4.64726;RPPR=3.17734;RPL=36.0;RPR=29.0;EPP=4.64726;EPPR=3.0103;DPRA=0.0;ODDS=314.531;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.2;FS=6.147;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.573; [...]
+chr5 180046426 . C CTGGCCGCTTAGCTAAGGCACAG 2294.045 REJECT NS=2;DP=181;DPB=657.6;AC=2;AN=4;AF=0.5;RO=82;AO=96;PRO=88.5;PAO=90.5;QR=3044;QA=2897;PQR=3209.5;PQA=3299.5;SRF=44;SRR=38;SAF=47;SAR=49;SRP=3.96363;SAP=3.10078;AB=0.530387;ABP=4.46195;RUN=1;RPP=3.8246;RPPR=5.65844;RPL=45.0;RPR=51.0;EPP=12.0581;EPPR=3.11623;DPRA=0.0;ODDS=61.1766;GTI=0;TYPE=ins;CIGAR=1M22I4M;NUMALT=1;MEANALT=2.5;LEN=22;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=180046426;HOMLEN=0;SVL [...]
+chr5 180046492 . CAG C 9862.83 PASS SOMATIC;NS=2;DP=393;DPB=278.5;AC=2;AN=3;AF=0.375;RO=84;AO=120;PRO=16.5;PAO=8.5;QR=3158;QA=4524;PQR=560.5;PQA=278.5;SRF=42;SRR=42;SAF=52;SAR=68;SRP=3.0103;SAP=7.64277;AB=0.377358;ABP=44.5551;RUN=1;RPP=8.87328;RPPR=3.42391;RPL=51.0;RPR=69.0;EPP=8.87328;EPPR=9.62812;DPRA=0.0;ODDS=394.638;GTI=0;TYPE=del;CIGAR=1M2D1M;NUMALT=2;MEANALT=3.0;LEN=2;MQM=60.6667;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;ALERT;END=180046494;HO [...]
+chr5 180046493 . AGA C 9862.83 REJECT NS=2;DP=443;DPB=278.5;AC=2;AN=3;AF=0.5;RO=84;AO=237;PRO=16.5;PAO=11.0;QR=3158;QA=8480;PQR=560.5;PQA=408.0;SRF=42;SRR=42;SAF=125;SAR=112;SRP=3.0103;SAP=4.55873;AB=0.534989;ABP=7.72088;RUN=1;RPP=14.2342;RPPR=3.42391;RPL=101.0;RPR=136.0;EPP=3.23936;EPPR=9.62812;DPRA=0.0;ODDS=394.638;GTI=0;TYPE=complex;CIGAR=1M2D1X;NUMALT=2;MEANALT=2.5;LEN=3;MQM=60.0422;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr5 180046495 . A C 4526.77 PASS DP=227;AC=2;AN=4;AF=0.5;MQ0=0;ALERT;BaseQRankSum=-0.188;Dels=0.0;FS=4.1775;HaplotypeScore=131.756;MLEAC=1;MLEAF=0.5;MQ=60.15;MQRankSum=-0.617;QD=20.24;ReadPosRankSum=1.0675;SOR=0.7555;ClippingRankSum=0.458 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:59,71:130:99.0:2786,0,2317:71:55:130:1:.:.:.:.:.:-0.000492842 0/1:148,174:323:99.0:6324,0,5458:174:54:322:.:1:.:.:.:.:-0.196235
+chr5 180046495 . AGG A . PASS AC=2;AN=4;END=180046497;HOMLEN=3;HOMSEQ=GGG;SVLEN=-2;SVTYPE=DEL GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:59,86:86:59:145:.:.:.:1:.:.:-0.000492842 0/1:115,259:259:69:374:.:.:.:1:.:.:-0.196235
+chr5 180047863 . C G 10637.2 REJECT NS=2;DP=288;DPB=332.0;AC=4;AN=4;AF=1.0;RO=0;AO=331;PRO=0.0;PAO=0.0;QR=0;QA=12537;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=192;SAR=139;SRP=0.0;SAP=21.4383;AB=0.0;ABP=0.0;RUN=1;RPP=105.516;RPPR=0.0;RPL=103.0;RPR=228.0;EPP=11.0467;EPPR=0.0;DPRA=0.0;ODDS=59.2181;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.9232;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.47;SOR=1.339 G [...]
+chr5 180048056 . C T 5667.59 REJECT NS=2;DP=408;DPB=479.0;AC=2;AN=4;AF=0.5;RO=264;AO=214;PRO=0.0;PAO=0.0;QR=9970;QA=8198;PQR=0.0;PQA=0.0;SRF=134;SRR=130;SAF=96;SAR=118;SRP=3.1419;SAP=7.92148;AB=0.446764;ABP=14.8015;RUN=1;RPP=3.37559;RPPR=5.67529;RPL=110.0;RPR=104.0;EPP=6.29795;EPPR=20.415;DPRA=0.0;ODDS=426.903;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995327;PAIREDR=0.992424;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.718;Dels=0.0;FS=3.535;HaplotypeS [...]
+chr5 180052946 . G A 4820.66 REJECT NS=2;DP=290;DPB=335.0;AC=2;AN=4;AF=0.5;RO=159;AO=176;PRO=0.0;PAO=0.0;QR=6050;QA=6682;PQR=0.0;PQA=0.0;SRF=96;SRR=63;SAF=110;SAR=66;SRP=17.8828;SAP=26.8965;AB=0.525373;ABP=4.8836;RUN=1;RPP=4.78696;RPPR=3.6795;RPL=82.0;RPR=94.0;EPP=6.16881;EPPR=33.1787;DPRA=0.0;ODDS=264.03;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988636;PAIREDR=0.993711;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5965;Dels=0.0;FS=1.547;HaplotypeScore [...]
+chr5 180055862 . T C 2903.81 REJECT NS=2;DP=193;DPB=220.667;AC=2;AN=3;AF=0.5;RO=72;AO=113;PRO=3.5;PAO=3.5;QR=2457;QA=3813;PQR=17.5;PQA=17.5;SRF=61;SRR=11;SAF=84;SAR=29;SRP=78.4086;SAP=61.1404;AB=0.520737;ABP=3.82085;RUN=1;RPP=19.1714;RPPR=15.074;RPL=42.0;RPR=71.0;EPP=3.18325;EPPR=6.02623;DPRA=0.0;ODDS=96.193;GTI=0;TYPE=snp;CIGAR=1X2M;NUMALT=2;MEANALT=3.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99115;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;ALERT;BaseQRankSum=1.898;Dels=0.0;F [...]
+chr5 180055862 . T G 1776.77 PASS DP=48;AC=1;AN=3;AF=0.5;SPLITMULTIALLELIC;ALERT;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;QD=27.42;SOR=2.208 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR ./1:0,16:48:99.0:1805,1175,1250:16:33:48:1:.:.:.:.:.:-0.000492842 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.196235
+chr5 180055862 . TGG GGA 3309.85 REJECT NS=2;DP=217;DPB=220.667;AC=2;AN=2;AF=0.25;RO=72;AO=29;PRO=3.5;PAO=2.0;QR=2457;QA=976;PQR=17.5;PQA=65.0;SRF=61;SRR=11;SAF=19;SAR=10;SRP=78.4086;SAP=9.07545;AB=0.133641;ABP=255.992;RUN=1;RPP=4.88226;RPPR=15.074;RPL=12.0;RPR=17.0;EPP=3.08518;EPPR=6.02623;DPRA=0.0;ODDS=96.193;GTI=0;TYPE=complex;CIGAR=1X1M1X;NUMALT=2;MEANALT=3.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr5 180055864 . G A 276.77 PASS DP=113;AC=2;AN=4;AF=0.5;MQ0=0;ALERT;BaseQRankSum=-0.6855;Dels=0.0;FS=3.9525;HaplotypeScore=47.2732;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.242;QD=4.845;ReadPosRankSum=-1.005;SOR=0.2485;ClippingRankSum=-0.073 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:34,16:50:99.0:485,0,1343:16:32:50:1:.:.:.:.:.:-0.000492842 0/1:159,17:176:99.0:125,0,5785:17:10:176:.:1:.:.:.:.:-0.196235
+chr5 180057231 . C A 4369.07 REJECT NS=2;DP=307;DPB=348.0;AC=2;AN=4;AF=0.5;RO=183;AO=165;PRO=0.0;PAO=0.0;QR=6864;QA=5988;PQR=0.0;PQA=0.0;SRF=98;SRR=85;SAF=99;SAR=66;SRP=5.01565;SAP=17.342;AB=0.474138;ABP=5.03202;RUN=1;RPP=4.60271;RPPR=10.4265;RPL=77.0;RPR=88.0;EPP=4.0763;EPPR=3.59173;DPRA=0.0;ODDS=150.519;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.5565;Dels=0.0;FS=5.415;HaplotypeScore=7.7728;M [...]
+chr5 180057356 . C G 3653.71 REJECT NS=2;DP=248;DPB=286.0;AC=2;AN=4;AF=0.5;RO=154;AO=132;PRO=0.0;PAO=0.0;QR=5777;QA=5026;PQR=0.0;PQA=0.0;SRF=71;SRR=83;SAF=61;SAR=71;SRP=5.04077;SAP=4.65535;AB=0.461538;ABP=6.6851;RUN=1;RPP=40.9124;RPPR=38.2615;RPL=90.0;RPR=42.0;EPP=3.0761;EPPR=6.62002;DPRA=0.0;ODDS=154.222;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992424;PAIREDR=0.993506;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.358;Dels=0.0;FS=8.0905;HaplotypeScore [...]
+chr6 397261 . G A 4439.6 REJECT NS=2;DP=282;DPB=328.0;AC=2;AN=4;AF=0.5;RO=163;AO=164;PRO=0.0;PAO=0.0;QR=6212;QA=6137;PQR=0.0;PQA=0.0;SRF=48;SRR=115;SAF=42;SAR=122;SRP=62.8124;SAP=87.7507;AB=0.5;ABP=3.0103;RUN=1;RPP=50.6768;RPPR=27.6425;RPL=112.0;RPR=52.0;EPP=3.8577;EPPR=12.722;DPRA=0.0;ODDS=234.959;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.2575;Dels=0.0;FS=2.0495;HaplotypeScore=8.6986;MLEAC=1 [...]
+chr6 397269 . T G 3822.915 REJECT NS=2;DP=244;DPB=285.0;AC=2;AN=4;AF=0.5;RO=143;AO=142;PRO=0.0;PAO=0.0;QR=5223;QA=5358;PQR=0.0;PQA=0.0;SRF=42;SRR=101;SAF=34;SAR=108;SRP=55.8697;SAP=86.7496;AB=0.498246;ABP=3.01792;RUN=1;RPP=73.7208;RPPR=36.5542;RPL=105.0;RPR=37.0;EPP=5.21236;EPPR=8.49213;DPRA=0.0;ODDS=217.074;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.8765;Dels=0.0;FS=2.8035;HaplotypeScore=9.676 [...]
+chr6 397290 . T C 2366.95 REJECT NS=2;DP=168;DPB=196.0;AC=2;AN=4;AF=0.5;RO=100;AO=94;PRO=0.0;PAO=0.0;QR=3688;QA=3526;PQR=0.0;PQA=0.0;SRF=30;SRR=70;SAF=18;SAR=76;SRP=37.7539;SAP=80.7213;AB=0.479592;ABP=3.71935;RUN=1;RPP=103.637;RPPR=128.435;RPL=80.0;RPR=14.0;EPP=36.3678;EPPR=20.0346;DPRA=0.0;ODDS=146.61;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4745;Dels=0.0;FS=5.458;HaplotypeScore=6.746;MLEAC= [...]
+chr6 407629 . C T 155.018 REJECT NS=2;DP=44;DPB=105.269;AC=2;AN=2;AF=0.0;RO=14;AO=3;PRO=41.0;PAO=0.0;QR=482;QA=42;PQR=1482.6;PQA=0.0;SRF=1;SRR=13;SAF=0;SAR=3;SRP=25.3454;SAP=9.52472;AB=0.0681818;ABP=74.2741;RUN=1;RPP=9.52472;RPPR=25.3454;RPL=3.0;RPR=0.0;EPP=9.52472;EPPR=18.5208;DPRA=0.0;ODDS=16.2903;GTI=0;TYPE=snp;CIGAR=1X25M;NUMALT=5;MEANALT=9.0;LEN=1;MQM=60.0;MQMR=59.5;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:C [...]
+chr6 407629 . C CT 155.018 REJECT NS=2;DP=44;DPB=105.269;AC=2;AN=2;AF=0.0;RO=14;AO=2;PRO=41.0;PAO=26.0;QR=482;QA=54;PQR=1482.6;PQA=942.6;SRF=1;SRR=13;SAF=1;SAR=1;SRP=25.3454;SAP=3.0103;AB=0.0571429;ABP=62.6327;RUN=1;RPP=7.35324;RPPR=25.3454;RPL=2.0;RPR=0.0;EPP=3.0103;EPPR=18.5208;DPRA=0.0;ODDS=16.2903;GTI=0;TYPE=ins;CIGAR=1M1I25M;NUMALT=5;MEANALT=14.0;LEN=1;MQM=60.0;MQMR=59.5;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:Cal [...]
+chr6 407629 . CT C 155.018 REJECT NS=2;DP=44;DPB=105.269;AC=2;AN=4;AF=0.5;RO=14;AO=9;PRO=41.0;PAO=22.5;QR=482;QA=261;PQR=1482.6;PQA=806.1;SRF=1;SRR=13;SAF=4;SAR=5;SRP=25.3454;SAP=3.25157;AB=0.204545;ABP=36.372;RUN=1;RPP=22.5536;RPPR=25.3454;RPL=9.0;RPR=0.0;EPP=3.25157;EPPR=18.5208;DPRA=0.0;ODDS=16.2903;GTI=0;TYPE=del;CIGAR=1M1D24M;NUMALT=5;MEANALT=9.0;LEN=1;MQM=59.6667;MQMR=59.5;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV: [...]
+chr6 407629 . CTT C 155.018 REJECT NS=2;DP=44;DPB=105.269;AC=2;AN=2;AF=0.0;RO=14;AO=3;PRO=41.0;PAO=15.5;QR=482;QA=44;PQR=1482.6;PQA=549.1;SRF=1;SRR=13;SAF=0;SAR=3;SRP=25.3454;SAP=9.52472;AB=0.0857143;ABP=55.1877;RUN=1;RPP=3.73412;RPPR=25.3454;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=18.5208;DPRA=0.0;ODDS=16.2903;GTI=0;TYPE=del;CIGAR=1M2D23M;NUMALT=5;MEANALT=14.0;LEN=2;MQM=60.0;MQMR=59.5;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV: [...]
+chr6 407629 . CTTTT C 155.018 REJECT NS=2;DP=44;DPB=105.269;AC=2;AN=2;AF=0.0;RO=14;AO=2;PRO=41.0;PAO=13.0;QR=482;QA=28;PQR=1482.6;PQA=460.6;SRF=1;SRR=13;SAF=0;SAR=2;SRP=25.3454;SAP=7.35324;AB=0.0571429;ABP=62.6327;RUN=1;RPP=3.0103;RPPR=25.3454;RPL=1.0;RPR=1.0;EPP=3.0103;EPPR=18.5208;DPRA=0.0;ODDS=16.2903;GTI=0;TYPE=del;CIGAR=1M4D21M;NUMALT=5;MEANALT=14.0;LEN=4;MQM=60.0;MQMR=59.5;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV: [...]
+chr6 1504122 . C T 1450.5149999999999 REJECT NS=2;DP=343;DPB=395.0;AC=2;AN=4;AF=0.5;RO=320;AO=75;PRO=0.0;PAO=0.0;QR=12253;QA=2878;PQR=0.0;PQA=0.0;SRF=165;SRR=155;SAF=40;SAR=35;SRP=3.68889;SAP=3.73412;AB=0.189873;ABP=332.992;RUN=1;RPP=4.429;RPPR=4.74748;RPL=34.0;RPR=41.0;EPP=13.4623;EPPR=79.2561;DPRA=0.0;ODDS=36.3312;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986667;PAIREDR=0.996875;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.44;Dels=0.0;FS=5.6995;Hapl [...]
+chr6 7504298 . G A 1543.55 REJECT NS=2;DP=226;DPB=263.0;AC=2;AN=4;AF=0.5;RO=193;AO=70;PRO=0.0;PAO=0.0;QR=7407;QA=2735;PQR=0.0;PQA=0.0;SRF=118;SRR=75;SAF=41;SAR=29;SRP=23.8137;SAP=7.47733;AB=0.26616;ABP=127.924;RUN=1;RPP=34.7758;RPPR=69.7184;RPL=19.0;RPR=51.0;EPP=4.12706;EPPR=7.97206;DPRA=0.0;ODDS=115.819;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994819;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.05;Dels=0.0;FS=2.4905;HaplotypeScore=4.8771 [...]
+chr6 13505827 . C T 13616.0 REJECT NS=2;DP=354;DPB=406.0;AC=4;AN=4;AF=1.0;RO=0;AO=406;PRO=0.0;PAO=0.0;QR=0;QA=15711;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=203;SAR=203;SRP=0.0;SAP=3.0103;AB=0.0;ABP=0.0;RUN=1;RPP=7.20349;RPPR=0.0;RPL=217.0;RPR=189.0;EPP=12.445;EPPR=0.0;DPRA=0.0;ODDS=67.3277;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.987685;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.966;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.49;SOR=0.713 [...]
+chr6 18006061 . G A 4734.05 REJECT NS=2;DP=339;DPB=387.0;AC=2;AN=4;AF=0.5;RO=209;AO=178;PRO=0.0;PAO=0.0;QR=7919;QA=6661;PQR=0.0;PQA=0.0;SRF=85;SRR=124;SAF=75;SAR=103;SRP=18.8132;SAP=12.5745;AB=0.459948;ABP=8.40251;RUN=1;RPP=4.23023;RPPR=17.234;RPL=94.0;RPR=84.0;EPP=4.767;EPPR=3.27005;DPRA=0.0;ODDS=299.818;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995215;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2665;Dels=0.0;FS=0.845;HaplotypeScore=7.73 [...]
+chr6 19526053 . T C 7439.27 REJECT NS=2;DP=329;DPB=379.0;AC=3;AN=4;AF=0.75;RO=109;AO=270;PRO=0.0;PAO=0.0;QR=4283;QA=10361;PQR=0.0;PQA=0.0;SRF=75;SRR=34;SAF=183;SAR=87;SRP=36.4988;SAP=77.1299;AB=0.6121;ABP=33.6814;RUN=1;RPP=11.2458;RPPR=3.50834;RPL=119.0;RPR=151.0;EPP=23.1165;EPPR=13.5489;DPRA=0.0;ODDS=62.1412;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.972477;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.95;Dels=0.0;FS=0.512;HaplotypeScore=2 [...]
+chr6 26031868 . G A 5194.6 REJECT NS=2;DP=223;DPB=258.0;AC=3;AN=4;AF=0.75;RO=65;AO=192;PRO=0.0;PAO=0.0;QR=2534;QA=7266;PQR=0.0;PQA=0.0;SRF=41;SRR=24;SAF=139;SAR=53;SRP=12.665;SAP=86.6572;AB=0.648936;ABP=39.2323;RUN=1;RPP=55.3066;RPPR=23.8898;RPL=62.0;RPR=130.0;EPP=5.22701;EPPR=7.05258;DPRA=0.0;ODDS=44.7055;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994792;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.668;Dels=0.0;FS=3.05;HaplotypeScore=6.756 [...]
+chr6 35423489 . A G 2434.965 REJECT NS=2;DP=152;DPB=176.0;AC=2;AN=4;AF=0.5;RO=83;AO=92;PRO=0.0;PAO=0.0;QR=3142;QA=3464;PQR=0.0;PQA=0.0;SRF=55;SRR=28;SAF=62;SAR=30;SRP=22.0826;SAP=27.1797;AB=0.522727;ABP=3.79993;RUN=1;RPP=66.8327;RPPR=71.0585;RPL=20.0;RPR=72.0;EPP=3.38795;EPPR=22.0826;DPRA=0.0;ODDS=115.792;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987952;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.481;Dels=0.0;FS=0.0;HaplotypeScore=1.9662; [...]
+chr6 35423662 . A C 5168.93 REJECT NS=2;DP=321;DPB=363.0;AC=2;AN=4;AF=0.5;RO=180;AO=183;PRO=0.0;PAO=0.0;QR=6911;QA=6987;PQR=0.0;PQA=0.0;SRF=101;SRR=79;SAF=87;SAR=96;SRP=8.84915;SAP=3.97144;AB=0.504132;ABP=3.06414;RUN=1;RPP=3.59173;RPPR=3.78238;RPL=88.0;RPR=95.0;EPP=3.30695;EPPR=5.37479;DPRA=0.0;ODDS=268.539;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994444;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3935;Dels=0.0;FS=6.692;HaplotypeScore=3. [...]
+chr6 35425416 . A G 1178.55 REJECT NS=1;DP=108;DPB=108.0;AC=1;AN=4;AF=0.5;RO=62;AO=45;PRO=0.0;PAO=0.0;QR=2388;QA=1696;PQR=0.0;PQA=0.0;SRF=30;SRR=32;SAF=17;SAR=28;SRP=3.15039;SAP=8.84915;AB=0.416667;ABP=9.52472;RUN=1;RPP=6.91895;RPPR=19.9618;RPL=27.0;RPR=18.0;EPP=3.44459;EPPR=4.27115;DPRA=0.0;ODDS=271.371;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.977778;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=1.093;FS=4.812;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum= [...]
+chr6 36009383 . G A 5213.515 REJECT NS=2;DP=390;DPB=454.0;AC=2;AN=4;AF=0.5;RO=256;AO=198;PRO=0.0;PAO=0.0;QR=9925;QA=7590;PQR=0.0;PQA=0.0;SRF=123;SRR=133;SAF=86;SAR=112;SRP=3.85853;SAP=10.424;AB=0.436123;ABP=19.1002;RUN=1;RPP=20.5576;RPPR=20.9589;RPL=119.0;RPR=79.0;EPP=28.2783;EPPR=25.9465;DPRA=0.0;ODDS=379.36;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989899;PAIREDR=0.996094;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.419;Dels=0.0;FS=4.4175;Haplotype [...]
+chr6 36547332 . C A 130.78 REJECT NS=2;DP=75;DPB=237.935;AC=2;AN=2;AF=0.0;RO=14;AO=9;PRO=65.5714;PAO=58.6881;QR=506;QA=146;PQR=2284.46;PQA=2048.91;SRF=9;SRR=5;SAF=0;SAR=9;SRP=5.49198;SAP=22.5536;AB=0.12;ABP=97.0785;RUN=1;RPP=9.04217;RPPR=25.3454;RPL=2.0;RPR=7.0;EPP=9.04217;EPPR=3.63072;DPRA=0.0;ODDS=5.5628;GTI=0;TYPE=snp;CIGAR=1X45M;NUMALT=6;MEANALT=21.0;LEN=1;MQM=60.0;MQMR=59.2857;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMIC [...]
+chr6 36547332 . C CA 130.78 REJECT NS=2;DP=75;DPB=237.935;AC=2;AN=3;AF=0.25;RO=14;AO=4;PRO=65.5714;PAO=63.9048;QR=506;QA=91;PQR=2284.46;PQA=2245.46;SRF=9;SRR=5;SAF=1;SAR=3;SRP=5.49198;SAP=5.18177;AB=0.0689655;ABP=96.6082;RUN=1;RPP=11.6962;RPPR=25.3454;RPL=0.0;RPR=4.0;EPP=5.18177;EPPR=3.63072;DPRA=0.0;ODDS=5.5628;GTI=0;TYPE=ins;CIGAR=1M1I45M;NUMALT=6;MEANALT=34.0;LEN=1;MQM=60.0;MQMR=59.2857;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr6 36547332 . CA C 130.78 REJECT NS=2;DP=75;DPB=237.935;AC=2;AN=3;AF=0.25;RO=14;AO=5;PRO=65.5714;PAO=61.6548;QR=506;QA=180;PQR=2284.46;PQA=2160.04;SRF=9;SRR=5;SAF=5;SAR=0;SRP=5.49198;SAP=13.8677;AB=0.0666667;ABP=125.337;RUN=1;RPP=6.91895;RPPR=25.3454;RPL=1.0;RPR=4.0;EPP=6.91895;EPPR=3.63072;DPRA=0.0;ODDS=5.5628;GTI=0;TYPE=del;CIGAR=1M1D44M;NUMALT=6;MEANALT=21.0;LEN=1;MQM=57.4;MQMR=59.2857;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr6 36547332 . CAAAA C 130.78 REJECT NS=2;DP=75;DPB=237.935;AC=2;AN=2;AF=0.0;RO=14;AO=3;PRO=65.5714;PAO=56.6048;QR=506;QA=88;PQR=2284.46;PQA=1979.74;SRF=9;SRR=5;SAF=2;SAR=1;SRP=5.49198;SAP=3.73412;AB=0.0517241;ABP=104.246;RUN=1;RPP=3.73412;RPPR=25.3454;RPL=1.0;RPR=2.0;EPP=9.52472;EPPR=3.63072;DPRA=0.0;ODDS=5.5628;GTI=0;TYPE=del;CIGAR=1M4D41M;NUMALT=6;MEANALT=34.0;LEN=4;MQM=56.3333;MQMR=59.2857;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr6 36547352 . G A 371.77 PASS SOMATIC;DP=215;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-6.903;Dels=0.03;FS=52.324;HaplotypeScore=51.7851;MLEAC=1;MLEAF=0.5;MQ=54.48;MQRankSum=-6.359;QD=1.73;ReadPosRankSum=4.355;SOR=7.081 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.000763682 0/1:146,60:208:99.0:400,0,3983:60:29:206:.:1:.:.:.:.:-0.0443037
+chr6 36547352 . GAAAAGAAAAAAAAAGT AAAAAAAAAAAAAAAGG 130.78 REJECT NS=2;DP=75;DPB=237.935;AC=2;AN=2;AF=0.0;RO=14;AO=3;PRO=65.5714;PAO=33.2881;QR=506;QA=42;PQR=2284.46;PQA=811.193;SRF=9;SRR=5;SAF=3;SAR=0;SRP=5.49198;SAP=9.52472;AB=0.0517241;ABP=104.246;RUN=1;RPP=3.73412;RPPR=25.3454;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=3.63072;DPRA=0.0;ODDS=5.5628;GTI=0;TYPE=complex;CIGAR=20M1X4M1X10M1X9M;NUMALT=6;MEANALT=34.0;LEN=46;MQM=46.6667;MQMR=59.2857;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLIT [...]
+chr6 36547352 . GAAAAGAAAAAAAAAGT AAAAAAAAAAAAAAAAGG 130.78 REJECT NS=2;DP=75;DPB=237.935;AC=2;AN=2;AF=0.0;RO=14;AO=4;PRO=65.5714;PAO=29.2881;QR=506;QA=56;PQR=2284.46;PQA=714.193;SRF=9;SRR=5;SAF=4;SAR=0;SRP=5.49198;SAP=11.6962;AB=0.0533333;ABP=132.98;RUN=1;RPP=3.0103;RPPR=25.3454;RPL=2.0;RPR=2.0;EPP=3.0103;EPPR=3.63072;DPRA=0.0;ODDS=5.5628;GTI=0;TYPE=complex;CIGAR=1M1I19M1X4M1X10M1X9M;NUMALT=6;MEANALT=21.0;LEN=47;MQM=50.0;MQMR=59.2857;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITM [...]
+chr6 36645588 . A C 5147.34 REJECT NS=2;DP=230;DPB=268.0;AC=3;AN=4;AF=0.75;RO=75;AO=193;PRO=0.0;PAO=0.0;QR=2851;QA=7317;PQR=0.0;PQA=0.0;SRF=42;SRR=33;SAF=112;SAR=81;SRP=5.35549;SAP=13.8227;AB=0.611399;ABP=23.8137;RUN=1;RPP=92.1307;RPPR=38.4777;RPL=52.0;RPR=141.0;EPP=12.4725;EPPR=9.52472;DPRA=0.0;ODDS=47.752;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994819;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.826;Dels=0.0;FS=0.5775;HaplotypeScore=2. [...]
+chr6 36645696 . A G 7674.43 REJECT NS=2;DP=305;DPB=348.0;AC=3;AN=4;AF=0.75;RO=82;AO=266;PRO=0.0;PAO=0.0;QR=3097;QA=10203;PQR=0.0;PQA=0.0;SRF=29;SRR=53;SAF=96;SAR=170;SRP=18.2636;SAP=47.7132;AB=0.688213;ABP=83.9327;RUN=1;RPP=47.7132;RPPR=4.70511;RPL=170.0;RPR=96.0;EPP=4.61033;EPPR=5.65844;DPRA=0.0;ODDS=54.0227;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992481;PAIREDR=0.97561;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.487;Dels=0.0;FS=0.0;HaplotypeScore [...]
+chr6 36652339 . C G 4494.505 REJECT NS=2;DP=199;DPB=230.0;AC=3;AN=4;AF=0.75;RO=66;AO=164;PRO=0.0;PAO=0.0;QR=2495;QA=6313;PQR=0.0;PQA=0.0;SRF=18;SRR=48;SAF=41;SAR=123;SRP=32.6213;SAP=92.0407;AB=0.609467;ABP=20.6005;RUN=1;RPP=41.6201;RPPR=11.433;RPL=109.0;RPR=55.0;EPP=10.6369;EPPR=7.74806;DPRA=0.0;ODDS=39.0703;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.028;Dels=0.0;FS=0.333;HaplotypeScore=2.9304; [...]
+chr6 36754019 . C G 1962.925 REJECT NS=2;DP=311;DPB=358.0;AC=2;AN=4;AF=0.5;RO=261;AO=97;PRO=0.0;PAO=0.0;QR=9814;QA=3591;PQR=0.0;PQA=0.0;SRF=164;SRR=97;SAF=62;SAR=35;SRP=40.358;SAP=19.3299;AB=0.27095;ABP=166.15;RUN=1;RPP=4.10723;RPPR=10.0073;RPL=45.0;RPR=52.0;EPP=11.0918;EPPR=30.0414;DPRA=0.0;ODDS=162.304;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989691;PAIREDR=0.984674;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.7215;Dels=0.0;FS=2.5225;HaplotypeScor [...]
+chr6 36754609 . C A 1494.505 REJECT NS=2;DP=323;DPB=361.0;AC=2;AN=4;AF=0.5;RO=284;AO=77;PRO=0.0;PAO=0.0;QR=10884;QA=2993;PQR=0.0;PQA=0.0;SRF=168;SRR=116;SAF=37;SAR=40;SRP=23.6852;SAP=3.26411;AB=0.213296;ABP=260.754;RUN=1;RPP=4.39215;RPPR=30.536;RPL=35.0;RPR=42.0;EPP=3.71532;EPPR=23.6852;DPRA=0.0;ODDS=125.084;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987013;PAIREDR=0.989437;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.57;Dels=0.0;FS=6.332;HaplotypeScor [...]
+chr6 36754662 . T C 1640.585 REJECT NS=2;DP=365;DPB=413.0;AC=2;AN=4;AF=0.5;RO=325;AO=88;PRO=0.0;PAO=0.0;QR=12486;QA=3354;PQR=0.0;PQA=0.0;SRF=148;SRR=177;SAF=39;SAR=49;SRP=8.6294;SAP=5.47788;AB=0.213075;ABP=298.336;RUN=1;RPP=6.56362;RPPR=4.51363;RPL=38.0;RPR=50.0;EPP=3.109;EPPR=4.94124;DPRA=0.0;ODDS=135.065;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.977273;PAIREDR=0.990769;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4765;Dels=0.0;FS=0.702;HaplotypeSco [...]
+chr6 41656640 . G A 15004.849999999999 REJECT NS=2;DP=403;DPB=465.0;AC=4;AN=4;AF=1.0;RO=1;AO=463;PRO=0.0;PAO=0.0;QR=40;QA=17503;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=221;SAR=242;SRP=5.18177;SAP=5.07859;AB=0.0;ABP=0.0;RUN=1;RPP=5.94155;RPPR=5.18177;RPL=244.0;RPR=219.0;EPP=3.24011;EPPR=5.18177;DPRA=0.0;ODDS=74.2064;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9806;MQMR=60.0;PAIRED=0.99568;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.673;Dels=0.0;FS=0.0;HaplotypeScore=7. [...]
+chr6 41656820 . C T 2076.26 REJECT NS=2;DP=426;DPB=482.0;AC=2;AN=4;AF=0.5;RO=375;AO=107;PRO=0.0;PAO=0.0;QR=14229;QA=4037;PQR=0.0;PQA=0.0;SRF=167;SRR=208;SAF=47;SAR=60;SRP=12.7443;SAP=6.44001;AB=0.221992;ABP=326.587;RUN=1;RPP=3.51765;RPPR=4.68378;RPL=56.0;RPR=51.0;EPP=5.46589;EPPR=6.07352;DPRA=0.0;ODDS=168.835;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997333;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5445;Dels=0.0;FS=1.875;HaplotypeScore= [...]
+chr6 41657873 . C CT 46.964 REJECT NS=2;DP=188;DPB=252.812;AC=2;AN=3;AF=0.25;RO=133;AO=20;PRO=41.5833;PAO=31.5833;QR=4793;QA=559;PQR=1417.83;PQA=1047.83;SRF=23;SRR=110;SAF=4;SAR=16;SRP=126.588;SAP=18.6449;AB=0.106383;ABP=256.01;RUN=1;RPP=13.8677;RPPR=23.0107;RPL=15.0;RPR=5.0;EPP=6.91895;EPPR=5.76954;DPRA=0.0;ODDS=6.94838;GTI=0;TYPE=ins;CIGAR=1M1I15M;NUMALT=3;MEANALT=7.5;LEN=1;MQM=59.0;MQMR=59.8195;PAIRED=1.0;PAIREDR=0.984962;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr6 41657873 . CT C 46.964 REJECT NS=2;DP=188;DPB=252.812;AC=2;AN=3;AF=0.25;RO=133;AO=18;PRO=41.5833;PAO=28.0833;QR=4793;QA=581;PQR=1417.83;PQA=951.833;SRF=23;SRR=110;SAF=0;SAR=18;SRP=126.588;SAP=42.0968;AB=0.0957447;ABP=269.87;RUN=1;RPP=3.49285;RPPR=23.0107;RPL=10.0;RPR=8.0;EPP=3.49285;EPPR=5.76954;DPRA=0.0;ODDS=6.94838;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=3;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=59.8195;PAIRED=1.0;PAIREDR=0.984962;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=1.409;F [...]
+chr6 41657873 . CTT C 46.964 REJECT NS=2;DP=188;DPB=252.812;AC=2;AN=2;AF=0.0;RO=133;AO=5;PRO=41.5833;PAO=25.75;QR=4793;QA=172;PQR=1417.83;PQA=868.5;SRF=23;SRR=110;SAF=2;SAR=3;SRP=126.588;SAP=3.44459;AB=0.0265957;ABP=368.973;RUN=1;RPP=6.91895;RPPR=23.0107;RPL=1.0;RPR=4.0;EPP=3.44459;EPPR=5.76954;DPRA=0.0;ODDS=6.94838;GTI=0;TYPE=del;CIGAR=1M2D13M;NUMALT=3;MEANALT=7.5;LEN=2;MQM=60.0;MQMR=59.8195;PAIRED=1.0;PAIREDR=0.984962;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr6 41691296 . A G 1031.01 REJECT NS=1;DP=92;DPB=92.0;AC=1;AN=4;AF=0.5;RO=52;AO=40;PRO=0.0;PAO=0.0;QR=2038;QA=1488;PQR=0.0;PQA=0.0;SRF=22;SRR=30;SAF=14;SAR=26;SRP=5.68288;SAP=10.8276;AB=0.434783;ABP=6.40913;RUN=1;RPP=3.87889;RPPR=5.68288;RPL=22.0;RPR=18.0;EPP=6.48466;EPPR=5.68288;DPRA=0.0;ODDS=237.399;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=0.942;FS=2.89;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.71;QD= [...]
+chr6 41814760 . A G 8928.61 REJECT NS=2;DP=349;DPB=400.0;AC=2;AN=4;AF=0.5;RO=107;AO=293;PRO=0.0;PAO=0.0;QR=4102;QA=11210;PQR=0.0;PQA=0.0;SRF=48;SRR=59;SAF=144;SAR=149;SRP=5.46589;SAP=3.19558;AB=0.7325;ABP=190.821;RUN=1;RPP=11.0811;RPPR=3.19295;RPL=163.0;RPR=130.0;EPP=3.90705;EPPR=4.00471;DPRA=0.0;ODDS=197.897;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993174;PAIREDR=0.962617;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.282;Dels=0.0;FS=6.2065;HaplotypeS [...]
+chr6 41903782 . A C 7983.87 REJECT NS=2;DP=318;DPB=365.0;AC=2;AN=4;AF=0.5;RO=99;AO=266;PRO=0.0;PAO=0.0;QR=3813;QA=10152;PQR=0.0;PQA=0.0;SRF=38;SRR=61;SAF=83;SAR=183;SRP=14.6134;SAP=84.6446;AB=0.728767;ABP=168.929;RUN=1;RPP=3.14091;RPPR=3.55865;RPL=135.0;RPR=131.0;EPP=17.4106;EPPR=7.94546;DPRA=0.0;ODDS=248.546;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.214;Dels=0.0;FS=4.4305;HaplotypeScore=3.93 [...]
+chr6 42110589 . A G 8309.0 REJECT NS=2;DP=358;DPB=408.0;AC=3;AN=4;AF=0.75;RO=113;AO=295;PRO=0.0;PAO=0.0;QR=4279;QA=11250;PQR=0.0;PQA=0.0;SRF=68;SRR=45;SAF=179;SAR=116;SRP=13.1759;SAP=32.2258;AB=0.636656;ABP=53.4569;RUN=1;RPP=4.2543;RPPR=23.9371;RPL=141.0;RPR=154.0;EPP=12.0274;EPPR=5.3355;DPRA=0.0;ODDS=61.5223;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989831;PAIREDR=0.99115;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.399;Dels=0.0;FS=0.221;HaplotypeSco [...]
+chr6 42111321 . G A 8905.735 REJECT NS=2;DP=393;DPB=455.0;AC=3;AN=4;AF=0.75;RO=132;AO=323;PRO=0.0;PAO=0.0;QR=5050;QA=12364;PQR=0.0;PQA=0.0;SRF=75;SRR=57;SAF=198;SAR=125;SRP=8.34028;SAP=38.8362;AB=0.60479;ABP=34.8672;RUN=1;RPP=8.6642;RPPR=8.34028;RPL=147.0;RPR=176.0;EPP=19.1518;EPPR=7.22164;DPRA=0.0;ODDS=76.4458;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996904;PAIREDR=0.969697;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.825;Dels=0.0;FS=1.234;Haplotyp [...]
+chr6 44216544 . GT G 5710.49 REJECT NS=2;DP=224;DPB=249.059;AC=4;AN=4;AF=0.875;RO=11;AO=199;PRO=25.0;PAO=45.0;QR=420;QA=7237;PQR=888.5;PQA=1656.5;SRF=3;SRR=8;SAF=77;SAR=122;SRP=7.94546;SAP=25.1069;AB=0.849057;ABP=59.0998;RUN=1;RPP=207.816;RPPR=19.0002;RPL=168.0;RPR=31.0;EPP=8.78271;EPPR=4.78696;DPRA=0.0;ODDS=7.0866;GTI=0;TYPE=del;CIGAR=1M1D15M;NUMALT=1;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.98995;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8065;FS=1.0475;MLEAC=2;MLEAF [...]
+chr6 44217374 . T G 2043.65 PASS SOMATIC;NS=2;DP=395;DPB=395.0;AC=1;AN=3;AF=0.25;RO=312;AO=83;PRO=0.0;PAO=0.0;QR=11965;QA=3192;PQR=0.0;PQA=0.0;SRF=144;SRR=168;SAF=38;SAR=45;SRP=7.01917;SAP=4.29225;AB=0.291228;ABP=110.906;RUN=1;RPP=6.17594;RPPR=3.45573;RPL=36.0;RPR=47.0;EPP=3.66436;EPPR=4.01252;DPRA=2.59091;ODDS=69.6033;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987952;PAIREDR=0.990385;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.059;Dels=0.0;FS= [...]
+chr6 44217910 . A G 1223.3400000000001 REJECT NS=2;DP=321;DPB=362.0;AC=2;AN=4;AF=0.5;RO=292;AO=70;PRO=0.0;PAO=0.0;QR=11204;QA=2628;PQR=0.0;PQA=0.0;SRF=141;SRR=151;SAF=34;SAR=36;SRP=3.75395;SAP=3.13438;AB=0.19337;ABP=298.642;RUN=1;RPP=30.9292;RPPR=110.097;RPL=50.0;RPR=20.0;EPP=3.13438;EPPR=3.27802;DPRA=0.0;ODDS=94.9443;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985714;PAIREDR=0.993151;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.505;Dels=0.0;FS=2.173;Ha [...]
+chr6 44218120 . A G 14959.8 REJECT NS=2;DP=405;DPB=464.0;AC=4;AN=4;AF=1.0;RO=1;AO=463;PRO=0.0;PAO=0.0;QR=27;QA=17454;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=236;SAR=227;SRP=5.18177;SAP=3.39019;AB=0.0;ABP=0.0;RUN=1;RPP=4.70339;RPPR=5.18177;RPL=222.0;RPR=241.0;EPP=4.06555;EPPR=5.18177;DPRA=0.0;ODDS=73.6766;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=55.8963;MQMR=60.0;PAIRED=0.993521;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=12.7201;MLEAC=2;MLEAF=1.0;MQ=56. [...]
+chr6 44228162 . G A 1244.275 REJECT NS=2;DP=234;DPB=271.0;AC=2;AN=4;AF=0.5;RO=202;AO=68;PRO=0.0;PAO=0.0;QR=7777;QA=2573;PQR=0.0;PQA=0.0;SRF=130;SRR=72;SAF=44;SAR=24;SRP=39.1728;SAP=15.7837;AB=0.250923;ABP=149.044;RUN=1;RPP=21.4039;RPPR=52.7177;RPL=22.0;RPR=46.0;EPP=3.52123;EPPR=4.55828;DPRA=0.0;ODDS=174.122;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99505;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.129;Dels=0.0;FS=5.555;HaplotypeScore=4.89 [...]
+chr6 55500196 . T C 10143.835 REJECT NS=2;DP=284;DPB=326.0;AC=4;AN=4;AF=1.0;RO=0;AO=326;PRO=0.0;PAO=0.0;QR=0;QA=11985;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=115;SAR=211;SRP=0.0;SAP=64.3977;AB=0.0;ABP=0.0;RUN=1;RPP=72.3109;RPPR=0.0;RPL=214.0;RPR=112.0;EPP=45.6404;EPPR=0.0;DPRA=0.0;ODDS=56.0266;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9969;MQMR=0.0;PAIRED=0.990798;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=25.1392;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.565; [...]
+chr6 81035908 . CAAAAT C 2733.2 REJECT NS=2;DP=244;DPB=254.667;AC=2;AN=4;AF=0.5;RO=161;AO=119;PRO=37.0;PAO=18.0;QR=6061;QA=4084;PQR=1130.5;PQA=452.5;SRF=103;SRR=58;SAF=84;SAR=35;SRP=30.3223;SAP=46.8229;AB=0.421986;ABP=17.918;RUN=1;RPP=30.765;RPPR=30.3223;RPL=40.0;RPR=79.0;EPP=5.21827;EPPR=10.1451;DPRA=0.0;ODDS=158.725;GTI=0;TYPE=del;CIGAR=1M5D6M;NUMALT=1;MEANALT=2.0;LEN=5;MQM=60.084;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993789;technology.ILLUMINA=1.0;MQ0=0;END=81035913;HOMLEN=4;HOMSEQ=AAAA;SVLE [...]
+chr6 90003708 . C A 2118.045 REJECT NS=2;DP=391;DPB=453.0;AC=2;AN=4;AF=0.5;RO=351;AO=102;PRO=0.0;PAO=0.0;QR=13439;QA=3883;PQR=0.0;PQA=0.0;SRF=158;SRR=193;SAF=50;SAR=52;SRP=10.5888;SAP=3.09546;AB=0.225166;ABP=300.214;RUN=1;RPP=8.46027;RPPR=41.6204;RPL=43.0;RPR=59.0;EPP=30.6008;EPPR=68.6432;DPRA=0.0;ODDS=113.872;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.980392;PAIREDR=0.994302;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.816;Dels=0.0;FS=3.087;HaplotypeS [...]
+chr6 91257746 . C G 3319.92 REJECT NS=2;DP=255;DPB=288.0;AC=2;AN=4;AF=0.5;RO=161;AO=127;PRO=0.0;PAO=0.0;QR=6188;QA=4746;PQR=0.0;PQA=0.0;SRF=114;SRR=47;SAF=84;SAR=43;SRP=63.5553;SAP=31.7524;AB=0.440972;ABP=11.7263;RUN=1;RPP=79.7642;RPPR=30.3223;RPL=30.0;RPR=97.0;EPP=6.8574;EPPR=11.4399;DPRA=0.0;ODDS=146.896;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.522;Dels=0.0;FS=2.0635;HaplotypeScore=1.9243; [...]
+chr6 91266349 . T TA 1931.75 REJECT NS=2;DP=192;DPB=238.593;AC=2;AN=4;AF=0.5;RO=105;AO=71;PRO=45.5;PAO=42.5;QR=3908;QA=2394;PQR=1656.5;PQA=1505.5;SRF=23;SRR=82;SAF=19;SAR=52;SRP=74.9998;SAP=36.3164;AB=0.369792;ABP=31.2847;RUN=1;RPP=25.3061;RPPR=18.0865;RPL=49.0;RPR=22.0;EPP=3.04088;EPPR=3.03098;DPRA=0.0;ODDS=157.167;GTI=0;TYPE=ins;CIGAR=1M1I26M;NUMALT=1;MEANALT=6.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.014;FS=5.0765;MLEAC=1;MLEAF=0. [...]
+chr6 91506655 . A G 13952.7 REJECT NS=2;DP=374;DPB=425.0;AC=4;AN=4;AF=1.0;RO=0;AO=425;PRO=0.0;PAO=0.0;QR=0;QA=16085;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=231;SAR=194;SRP=0.0;SAP=10.005;AB=0.0;ABP=0.0;RUN=1;RPP=10.7816;RPPR=0.0;RPL=193.0;RPR=232.0;EPP=82.8438;EPPR=0.0;DPRA=0.0;ODDS=67.3079;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.7705;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.34;SOR=0.911 GT: [...]
+chr6 93005341 . C T 5559.48 REJECT NS=2;DP=358;DPB=424.0;AC=2;AN=4;AF=0.5;RO=215;AO=206;PRO=0.0;PAO=0.0;QR=8194;QA=7907;PQR=0.0;PQA=0.0;SRF=114;SRR=101;SAF=99;SAR=107;SRP=4.71718;SAP=3.68493;AB=0.485849;ABP=3.74778;RUN=1;RPP=12.4973;RPPR=21.685;RPL=118.0;RPR=88.0;EPP=3.68493;EPPR=16.837;DPRA=0.0;ODDS=427.251;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990291;PAIREDR=0.995349;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.917;Dels=0.0;FS=6.611;HaplotypeSco [...]
+chr6 93967249 . T TA 124.782 PASS SOMATIC;NS=2;DP=245;DPB=287.875;AC=2;AN=2;AF=0.0;RO=191;AO=16;PRO=37.1667;PAO=21.1667;QR=7220;QA=591;PQR=1377.67;PQA=783.667;SRF=40;SRR=151;SAF=3;SAR=13;SRP=143.087;SAP=16.582;AB=0.0653061;ABP=405.123;RUN=1;RPP=11.6962;RPPR=16.9373;RPL=12.0;RPR=4.0;EPP=3.55317;EPPR=15.3911;DPRA=0.0;ODDS=17.0959;GTI=0;TYPE=ins;CIGAR=1M1I15M;NUMALT=2;MEANALT=8.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989529;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO [...]
+chr6 93967249 . TA T 124.782 REJECT NS=2;DP=245;DPB=287.875;AC=2;AN=4;AF=0.5;RO=191;AO=24;PRO=37.1667;PAO=20.6667;QR=7220;QA=872;PQR=1377.67;PQA=764.667;SRF=40;SRR=151;SAF=4;SAR=20;SRP=143.087;SAP=26.1727;AB=0.0979592;ABP=346.98;RUN=1;RPP=3.37221;RPPR=16.9373;RPL=13.0;RPR=11.0;EPP=6.26751;EPPR=15.3911;DPRA=0.0;ODDS=17.0959;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=2;MEANALT=8.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989529;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr6 93982124 . A G 12434.95 REJECT NS=2;DP=330;DPB=378.0;AC=4;AN=4;AF=1.0;RO=0;AO=378;PRO=0.0;PAO=0.0;QR=0;QA=14422;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=157;SAR=221;SRP=0.0;SAP=26.5403;AB=0.0;ABP=0.0;RUN=1;RPP=58.1818;RPPR=0.0;RPL=238.0;RPR=140.0;EPP=23.691;EPPR=0.0;DPRA=0.0;ODDS=64.2391;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997354;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.9229;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.79;SOR=1.1 [...]
+chr6 94067981 . C T 2719.36 PASS SOMATIC;NS=2;DP=373;DPB=373.0;AC=1;AN=3;AF=0.25;RO=271;AO=102;PRO=0.0;PAO=0.0;QR=10379;QA=3955;PQR=0.0;PQA=0.0;SRF=188;SRR=83;SAF=62;SAR=40;SRP=91.3516;SAP=13.3141;AB=0.364286;ABP=47.8047;RUN=1;RPP=15.2727;RPPR=58.2106;RPL=39.0;RPR=63.0;EPP=8.46027;EPPR=3.01831;DPRA=3.01075;ODDS=58.9426;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.98893;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.519;Dels=0.0;FS=5.304; [...]
+chr6 94120192 . G A 1523.72 PASS SOMATIC;NS=2;DP=265;DPB=265.0;AC=1;AN=3;AF=0.25;RO=202;AO=63;PRO=0.0;PAO=0.0;QR=7576;QA=2423;PQR=0.0;PQA=0.0;SRF=140;SRR=62;SAF=43;SAR=20;SRP=68.4125;SAP=21.2438;AB=0.304348;ABP=71.8365;RUN=1;RPP=28.1373;RPPR=68.4125;RPL=18.0;RPR=45.0;EPP=5.80219;EPPR=3.3973;DPRA=3.56897;ODDS=37.1989;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.980198;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.754;Dels=0.0;FS=2.152;Ha [...]
+chr6 96000122 . C T 4405.530000000001 REJECT NS=2;DP=309;DPB=354.0;AC=2;AN=4;AF=0.5;RO=190;AO=164;PRO=0.0;PAO=0.0;QR=7263;QA=6291;PQR=0.0;PQA=0.0;SRF=59;SRR=131;SAF=58;SAR=106;SRP=62.2572;SAP=33.5168;AB=0.463277;ABP=7.15695;RUN=1;RPP=64.2352;RPPR=33.9138;RPL=116.0;RPR=48.0;EPP=4.91696;EPPR=3.42174;DPRA=0.0;ODDS=278.173;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8171;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994737;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9605;Dels=0.0;FS=2.867;Ha [...]
+chr6 99283172 . A ACAG 320.43 REJECT NS=2;DP=112;DPB=140.75;AC=2;AN=4;AF=0.5;RO=88;AO=18;PRO=27.0;PAO=28.0;QR=3374;QA=692;PQR=915.0;PQA=951.0;SRF=54;SRR=34;SAF=9;SAR=9;SRP=12.8806;SAP=3.0103;AB=0.160714;ABP=114.996;RUN=1;RPP=3.49285;RPPR=3.89863;RPL=8.0;RPR=10.0;EPP=3.0103;EPPR=3.109;DPRA=0.0;ODDS=17.9466;GTI=0;TYPE=ins;CIGAR=1M3I19M;NUMALT=1;MEANALT=2.5;LEN=3;MQM=60.5556;MQMR=60.0;PAIRED=1.0;PAIREDR=0.965909;technology.ILLUMINA=1.0;BaseQRankSum=0.495;FS=1.86;MLEAC=1;MLEAF=0.5;MQ=60.69;M [...]
+chr6 99283376 . T G 7810.375 REJECT NS=2;DP=210;DPB=243.0;AC=4;AN=4;AF=1.0;RO=0;AO=243;PRO=0.0;PAO=0.0;QR=0;QA=9117;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=156;SAR=87;SRP=0.0;SAP=45.5551;AB=0.0;ABP=0.0;RUN=1;RPP=4.5205;RPPR=0.0;RPL=115.0;RPR=128.0;EPP=3.44817;EPPR=0.0;DPRA=0.0;ODDS=44.7984;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.987654;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.9635;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.435;SOR=1.56 [...]
+chr6 106534484 . A AT 67.5798 REJECT NS=2;DP=290;DPB=336.7;AC=2;AN=4;AF=0.5;RO=231;AO=28;PRO=44.5;PAO=26.5;QR=8695;QA=942;PQR=1636.67;PQA=973.667;SRF=61;SRR=170;SAF=4;SAR=24;SRP=114.695;SAP=34.0313;AB=0.0965517;ABP=413.014;RUN=1;RPP=4.25114;RPPR=70.9276;RPL=16.0;RPR=12.0;EPP=4.25114;EPPR=13.2472;DPRA=0.0;ODDS=5.90075;GTI=1;TYPE=ins;CIGAR=1M1I19M;NUMALT=2;MEANALT=7.0;LEN=1;MQM=60.0;MQMR=59.9134;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr6 106534484 . AT A 67.5798 REJECT NS=2;DP=290;DPB=336.7;AC=2;AN=2;AF=0.0;RO=231;AO=16;PRO=44.5;PAO=25.0;QR=8695;QA=552;PQR=1636.67;PQA=916.667;SRF=61;SRR=170;SAF=3;SAR=13;SRP=114.695;SAP=16.582;AB=0.0551724;ABP=501.431;RUN=1;RPP=11.6962;RPPR=70.9276;RPL=12.0;RPR=4.0;EPP=3.55317;EPPR=13.2472;DPRA=0.0;ODDS=5.90075;GTI=1;TYPE=del;CIGAR=1M1D18M;NUMALT=2;MEANALT=7.0;LEN=1;MQM=60.0;MQMR=59.9134;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr6 106555025 . G A 3456.1 PASS SOMATIC;NS=2;DP=416;DPB=416.0;AC=1;AN=3;AF=0.25;RO=285;AO=131;PRO=0.0;PAO=0.0;QR=10829;QA=4848;PQR=0.0;PQA=0.0;SRF=154;SRR=131;SAF=55;SAR=76;SRP=7.04086;SAP=10.3204;AB=0.421222;ABP=19.7746;RUN=1;RPP=3.15949;RPPR=7.04086;RPL=67.0;RPR=64.0;EPP=5.01601;EPPR=9.41805;DPRA=2.9619;ODDS=66.4962;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984733;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.317;Dels=0.0;FS=17.2 [...]
+chr6 112382313 . G T 2057.145 REJECT NS=2;DP=383;DPB=438.0;AC=2;AN=4;AF=0.5;RO=329;AO=107;PRO=0.0;PAO=0.0;QR=12587;QA=3993;PQR=0.0;PQA=0.0;SRF=169;SRR=160;SAF=54;SAR=53;SRP=3.54492;SAP=3.03059;AB=0.244292;ABP=251.768;RUN=1;RPP=4.00471;RPPR=4.91776;RPL=50.0;RPR=57.0;EPP=4.00471;EPPR=3.54492;DPRA=0.0;ODDS=223.072;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99696;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.7615;Dels=0.0;FS=2.0905;HaplotypeSco [...]
+chr6 117631463 . T TTAA 2053.05 REJECT NS=2;DP=169;DPB=204.8;AC=2;AN=4;AF=0.5;RO=83;AO=81;PRO=34.5;PAO=34.5;QR=3161;QA=2910;PQR=1228.5;PQA=1228.5;SRF=9;SRR=74;SAF=18;SAR=63;SRP=113.546;SAP=57.2971;AB=0.47929;ABP=3.6399;RUN=1;RPP=7.5409;RPPR=5.12945;RPL=47.0;RPR=34.0;EPP=9.04217;EPPR=5.12945;DPRA=0.0;ODDS=81.9133;GTI=0;TYPE=ins;CIGAR=1M3I19M;NUMALT=1;MEANALT=3.0;LEN=3;MQM=60.7407;MQMR=60.0;PAIRED=0.987654;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.582;FS=5.7575;MLEAC=1;MLEAF [...]
+chr6 117642992 . A AT 1894.72 REJECT NS=2;DP=147;DPB=257.231;AC=2;AN=2;AF=0.0;RO=48;AO=26;PRO=36.4405;PAO=34.1071;QR=1716;QA=772;PQR=1274.88;PQA=1158.71;SRF=13;SRR=35;SAF=14;SAR=12;SRP=24.906;SAP=3.34437;AB=0.176871;ABP=136.327;RUN=1;RPP=4.34659;RPPR=11.8771;RPL=15.0;RPR=11.0;EPP=3.0103;EPPR=14.5915;DPRA=0.0;ODDS=32.8453;GTI=0;TYPE=ins;CIGAR=1M1I25M;NUMALT=7;MEANALT=23.0;LEN=1;MQM=59.7692;MQMR=58.3958;PAIRED=0.961538;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSu [...]
+chr6 117642992 . A ATT 1894.72 REJECT NS=2;DP=147;DPB=257.231;AC=2;AN=2;AF=0.0;RO=48;AO=10;PRO=36.4405;PAO=32.1071;QR=1716;QA=297;PQR=1274.88;PQA=1117.71;SRF=13;SRR=35;SAF=5;SAR=5;SRP=24.906;SAP=3.0103;AB=0.0680272;ABP=241.267;RUN=1;RPP=3.87889;RPPR=11.8771;RPL=6.0;RPR=4.0;EPP=6.48466;EPPR=14.5915;DPRA=0.0;ODDS=32.8453;GTI=0;TYPE=ins;CIGAR=1M2I25M;NUMALT=7;MEANALT=23.0;LEN=2;MQM=60.0;MQMR=58.3958;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr6 117642992 . AT A 1894.72 REJECT NS=2;DP=147;DPB=257.231;AC=2;AN=2;AF=0.0;RO=48;AO=7;PRO=36.4405;PAO=22.6071;QR=1716;QA=172;PQR=1274.88;PQA=773.046;SRF=13;SRR=35;SAF=2;SAR=5;SRP=24.906;SAP=5.80219;AB=0.047619;ABP=264.311;RUN=1;RPP=5.80219;RPPR=11.8771;RPL=2.0;RPR=5.0;EPP=5.80219;EPPR=14.5915;DPRA=0.0;ODDS=32.8453;GTI=0;TYPE=del;CIGAR=1M1D24M;NUMALT=7;MEANALT=23.0;LEN=1;MQM=59.4286;MQMR=58.3958;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr6 117642992 . ATT A 1894.72 REJECT NS=2;DP=147;DPB=257.231;AC=2;AN=2;AF=0.0;RO=48;AO=5;PRO=36.4405;PAO=21.2143;QR=1716;QA=136;PQR=1274.88;PQA=722.082;SRF=13;SRR=35;SAF=1;SAR=4;SRP=24.906;SAP=6.91895;AB=0.0340136;ABP=280.264;RUN=1;RPP=3.44459;RPPR=11.8771;RPL=3.0;RPR=2.0;EPP=6.91895;EPPR=14.5915;DPRA=0.0;ODDS=32.8453;GTI=0;TYPE=del;CIGAR=1M2D23M;NUMALT=7;MEANALT=23.0;LEN=2;MQM=60.0;MQMR=58.3958;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr6 117643012 . TG T 1894.72 REJECT NS=2;DP=147;DPB=257.231;AC=2;AN=2;AF=0.0;RO=48;AO=2;PRO=36.4405;PAO=18.8571;QR=1716;QA=28;PQR=1274.88;PQA=664.363;SRF=13;SRR=35;SAF=2;SAR=0;SRP=24.906;SAP=7.35324;AB=0.05;ABP=73.366;RUN=1;RPP=3.0103;RPPR=11.8771;RPL=1.0;RPR=1.0;EPP=3.0103;EPPR=14.5915;DPRA=0.0;ODDS=32.8453;GTI=0;TYPE=del;CIGAR=21M1D4M;NUMALT=7;MEANALT=16.0;LEN=1;MQM=60.0;MQMR=58.3958;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr6 117643013 . G TT 1894.72 REJECT NS=2;DP=147;DPB=257.231;AC=2;AN=2;AF=0.0;RO=48;AO=4;PRO=36.4405;PAO=19.5238;QR=1716;QA=56;PQR=1274.88;PQA=686.696;SRF=13;SRR=35;SAF=4;SAR=0;SRP=24.906;SAP=11.6962;AB=0.0272109;ABP=288.419;RUN=1;RPP=5.18177;RPPR=11.8771;RPL=3.0;RPR=1.0;EPP=5.18177;EPPR=14.5915;DPRA=0.0;ODDS=32.8453;GTI=0;TYPE=complex;CIGAR=1M1I20M1X4M;NUMALT=7;MEANALT=23.0;LEN=27;MQM=60.0;MQMR=58.3958;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr6 117643017 . A G 1894.72 REJECT NS=2;DP=147;DPB=257.231;AC=2;AN=4;AF=0.5;RO=48;AO=4;PRO=36.4405;PAO=23.1429;QR=1716;QA=50;PQR=1274.88;PQA=841.506;SRF=13;SRR=35;SAF=4;SAR=0;SRP=24.906;SAP=11.6962;AB=0.0272109;ABP=288.419;RUN=1;RPP=3.0103;RPPR=11.8771;RPL=2.0;RPR=2.0;EPP=3.0103;EPPR=14.5915;DPRA=0.0;ODDS=32.8453;GTI=0;TYPE=snp;CIGAR=25M1X;NUMALT=7;MEANALT=23.0;LEN=1;MQM=60.0;MQMR=58.3958;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr6 117647254 . TTA T 1725.24 REJECT SOMATIC;NS=2;DP=202;DPB=292.974;AC=1;AN=3;AF=0.0;RO=28;AO=14;PRO=61.0333;PAO=55.0333;QR=1062;QA=448;PQR=2225.6;PQA=2010.6;SRF=10;SRR=18;SAF=4;SAR=10;SRP=7.97367;SAP=8.59409;AB=0.0693069;ABP=328.473;RUN=1;RPP=3.63072;RPPR=10.7656;RPL=6.0;RPR=8.0;EPP=3.63072;EPPR=5.80219;DPRA=0.0;ODDS=21.6582;GTI=0;TYPE=del;CIGAR=1M2D35M;NUMALT=4;MEANALT=9.5;LEN=2;MQM=60.0;MQMR=58.8214;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:Q [...]
+chr6 117647254 . TTATA T 1725.24 REJECT NS=2;DP=202;DPB=292.974;AC=2;AN=2;AF=0.25;RO=28;AO=31;PRO=61.0333;PAO=53.5333;QR=1062;QA=846;PQR=2225.6;PQA=1954.1;SRF=10;SRR=18;SAF=9;SAR=22;SRP=7.97367;SAP=14.8483;AB=0.153465;ABP=213.708;RUN=1;RPP=6.44263;RPPR=10.7656;RPL=19.0;RPR=12.0;EPP=3.08035;EPPR=5.80219;DPRA=0.0;ODDS=21.6582;GTI=0;TYPE=del;CIGAR=1M4D33M;NUMALT=4;MEANALT=9.5;LEN=4;MQM=59.3548;MQMR=58.8214;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr6 117647254 . TTATATA T 1725.24 REJECT NS=2;DP=202;DPB=292.974;AC=2;AN=3;AF=0.5;RO=28;AO=75;PRO=61.0333;PAO=48.2;QR=1062;QA=2316;PQR=2225.6;PQA=1756.1;SRF=10;SRR=18;SAF=34;SAR=41;SRP=7.97367;SAP=4.429;AB=0.371287;ABP=32.0779;RUN=1;RPP=9.52472;RPPR=10.7656;RPL=45.0;RPR=30.0;EPP=6.51361;EPPR=5.80219;DPRA=0.0;ODDS=21.6582;GTI=0;TYPE=del;CIGAR=1M6D31M;NUMALT=4;MEANALT=9.5;LEN=6;MQM=60.2667;MQMR=58.8214;PAIRED=0.986667;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSu [...]
+chr6 117647254 . TTATATATA T 1725.24 REJECT SOMATIC;NS=2;DP=202;DPB=292.974;AC=1;AN=3;AF=0.0;RO=28;AO=30;PRO=61.0333;PAO=41.2;QR=1062;QA=998;PQR=2225.6;PQA=1489.6;SRF=10;SRR=18;SAF=21;SAR=9;SRP=7.97367;SAP=13.4334;AB=0.148515;ABP=219.771;RUN=1;RPP=3.0103;RPPR=10.7656;RPL=15.0;RPR=15.0;EPP=3.29983;EPPR=5.80219;DPRA=0.0;ODDS=21.6582;GTI=0;TYPE=del;CIGAR=1M8D29M;NUMALT=4;MEANALT=9.5;LEN=8;MQM=59.9;MQMR=58.8214;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:A [...]
+chr6 117657490 . C T 236.356 REJECT NS=2;DP=86;DPB=86.0;AC=1;AN=4;AF=0.25;RO=71;AO=15;PRO=0.0;PAO=0.0;QR=2594;QA=538;PQR=0.0;PQA=0.0;SRF=6;SRR=65;SAF=2;SAR=13;SRP=109.474;SAP=20.5268;AB=0.578947;ABP=4.03889;RUN=1;RPP=10.1038;RPPR=9.89173;RPL=11.0;RPR=4.0;EPP=10.1038;EPPR=25.3061;DPRA=0.0;ODDS=13.5133;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.933333;PAIREDR=0.971831;technology.ILLUMINA=1.0;BaseQRankSum=-0.241;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum= [...]
+chr6 117657902 . T G 1701.5549999999998 REJECT NS=2;DP=310;DPB=361.0;AC=2;AN=4;AF=0.5;RO=271;AO=90;PRO=0.0;PAO=0.0;QR=10400;QA=3475;PQR=0.0;PQA=0.0;SRF=183;SRR=88;SAF=66;SAR=24;SRP=75.3259;SAP=45.5712;AB=0.249307;ABP=200.073;RUN=1;RPP=4.55446;RPPR=7.24908;RPL=41.0;RPR=49.0;EPP=6.48466;EPPR=5.326;DPRA=0.0;ODDS=188.789;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.1556;MQMR=60.0;PAIRED=0.988889;PAIREDR=0.99631;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2765;Dels=0.0;FS=4.5375 [...]
+chr6 117659702 . C CA 370.48 REJECT NS=2;DP=409;DPB=473.667;AC=2;AN=2;AF=0.0;RO=299;AO=32;PRO=52.5;PAO=44.5;QR=11066;QA=989;PQR=1829.83;PQA=1552.83;SRF=121;SRR=178;SAF=16;SAR=16;SRP=26.606;SAP=3.0103;AB=0.0782396;ABP=634.941;RUN=1;RPP=5.45321;RPPR=3.36616;RPL=19.0;RPR=13.0;EPP=3.28173;EPPR=3.01756;DPRA=0.0;ODDS=26.5407;GTI=0;TYPE=ins;CIGAR=1M1I14M;NUMALT=2;MEANALT=12.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993311;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr6 117659702 . CA C 370.48 REJECT NS=2;DP=409;DPB=473.667;AC=2;AN=4;AF=0.5;RO=299;AO=47;PRO=52.5;PAO=41.0;QR=11066;QA=1592;PQR=1829.83;PQA=1422.33;SRF=121;SRR=178;SAF=22;SAR=25;SRP=26.606;SAP=3.42611;AB=0.114914;ABP=529.818;RUN=1;RPP=3.0565;RPPR=3.36616;RPL=23.0;RPR=24.0;EPP=16.3625;EPPR=3.01756;DPRA=0.0;ODDS=26.5407;GTI=0;TYPE=del;CIGAR=1M1D13M;NUMALT=2;MEANALT=12.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993311;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.352;FS=8. [...]
+chr6 117661264 . T C 17890.25 REJECT NS=2;DP=473;DPB=554.0;AC=4;AN=4;AF=1.0;RO=0;AO=554;PRO=0.0;PAO=0.0;QR=0;QA=21122;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=282;SAR=272;SRP=0.0;SAP=3.40226;AB=0.0;ABP=0.0;RUN=1;RPP=4.57815;RPPR=0.0;RPL=267.0;RPR=287.0;EPP=3.07301;EPPR=0.0;DPRA=0.0;ODDS=103.405;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99278;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9625;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.12;SOR=0. [...]
+chr6 117678083 . A G 11092.55 REJECT NS=2;DP=302;DPB=347.0;AC=4;AN=4;AF=1.0;RO=0;AO=347;PRO=0.0;PAO=0.0;QR=0;QA=12983;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=113;SAR=234;SRP=0.0;SAP=94.6314;AB=0.0;ABP=0.0;RUN=1;RPP=44.068;RPPR=0.0;RPL=214.0;RPR=133.0;EPP=4.81882;EPPR=0.0;DPRA=0.0;ODDS=59.823;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994236;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.866;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.145;SOR=1.6 [...]
+chr6 117708971 . C T 5179.67 REJECT NS=2;DP=338;DPB=381.0;AC=2;AN=4;AF=0.5;RO=198;AO=183;PRO=0.0;PAO=0.0;QR=7521;QA=6982;PQR=0.0;PQA=0.0;SRF=99;SRR=99;SAF=97;SAR=86;SRP=3.0103;SAP=4.44608;AB=0.480315;ABP=4.29267;RUN=1;RPP=11.6606;RPPR=9.32731;RPL=78.0;RPR=105.0;EPP=3.11709;EPPR=3.40511;DPRA=0.0;ODDS=244.52;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994536;PAIREDR=0.994949;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.725;Dels=0.0;FS=4.787;HaplotypeScore [...]
+chr6 117724462 . C A 4777.84 REJECT NS=2;DP=234;DPB=265.0;AC=3;AN=4;AF=0.75;RO=84;AO=180;PRO=0.0;PAO=0.0;QR=3172;QA=6747;PQR=0.0;PQA=0.0;SRF=21;SRR=63;SAF=49;SAR=131;SRP=48.6112;SAP=84.1269;AB=0.583333;ABP=15.3153;RUN=1;RPP=123.648;RPPR=23.2774;RPL=140.0;RPR=40.0;EPP=5.37479;EPPR=8.07707;DPRA=0.0;ODDS=39.0198;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.431;Dels=0.0;FS=0.996;HaplotypeScore=6.8235 [...]
+chr6 117725448 . T G 1646.065 REJECT NS=2;DP=306;DPB=364.0;AC=2;AN=4;AF=0.5;RO=274;AO=90;PRO=0.0;PAO=0.0;QR=10352;QA=3320;PQR=0.0;PQA=0.0;SRF=165;SRR=109;SAF=39;SAR=51;SRP=27.8634;SAP=6.48466;AB=0.247253;ABP=204.981;RUN=1;RPP=9.18693;RPPR=8.36766;RPL=37.0;RPR=53.0;EPP=7.73928;EPPR=13.2812;DPRA=0.0;ODDS=167.771;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0365;PAIRED=0.988889;PAIREDR=0.99635;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.384;Dels=0.0;FS=10.689;Haplot [...]
+chr6 117725578 . T A 7692.47 REJECT NS=2;DP=328;DPB=378.0;AC=3;AN=4;AF=0.75;RO=100;AO=277;PRO=0.0;PAO=0.0;QR=3880;QA=10546;PQR=0.0;PQA=0.0;SRF=49;SRR=51;SAF=130;SAR=147;SRP=3.09716;SAP=5.27584;AB=0.637993;ABP=49.156;RUN=1;RPP=36.1311;RPPR=3.79203;RPL=171.0;RPR=106.0;EPP=5.27584;EPPR=3.35774;DPRA=0.0;ODDS=62.7417;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.54;Dels=0.0;FS=1.0475;HaplotypeScore=5.9 [...]
+chr6 117730819 . G A 4853.895 REJECT NS=2;DP=309;DPB=359.0;AC=2;AN=4;AF=0.5;RO=178;AO=181;PRO=0.0;PAO=0.0;QR=6763;QA=6908;PQR=0.0;PQA=0.0;SRF=37;SRR=141;SAF=44;SAR=137;SRP=134.958;SAP=106.773;AB=0.504178;ABP=3.06474;RUN=1;RPP=4.46195;RPPR=3.0103;RPL=96.0;RPR=85.0;EPP=23.1774;EPPR=24.5298;DPRA=0.0;ODDS=287.011;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.15;Dels=0.0;FS=2.6085;HaplotypeScore=3.9993 [...]
+chr6 117735716 . G GA 1467.96 REJECT NS=2;DP=272;DPB=312.312;AC=2;AN=2;AF=0.0;RO=167;AO=13;PRO=40.5;PAO=35.5;QR=6276;QA=381;PQR=1451.83;PQA=1249.83;SRF=37;SRR=130;SAF=2;SAR=11;SRP=115.472;SAP=16.5402;AB=0.0477941;ABP=486.131;RUN=1;RPP=11.1951;RPPR=42.3439;RPL=10.0;RPR=3.0;EPP=4.51363;EPPR=5.93594;DPRA=0.0;ODDS=98.2562;GTI=0;TYPE=ins;CIGAR=1M1I15M;NUMALT=2;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=59.8802;PAIRED=1.0;PAIREDR=0.994012;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr6 117735716 . GA G 1467.96 REJECT NS=2;DP=272;DPB=312.312;AC=2;AN=4;AF=0.5;RO=167;AO=75;PRO=40.5;PAO=31.0;QR=6276;QA=2526;PQR=1451.83;PQA=1106.33;SRF=37;SRR=130;SAF=18;SAR=57;SRP=115.472;SAP=47.0478;AB=0.275735;ABP=121.835;RUN=1;RPP=5.35549;RPPR=42.3439;RPL=42.0;RPR=33.0;EPP=18.3264;EPPR=5.93594;DPRA=0.0;ODDS=98.2562;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=2;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=59.8802;PAIRED=1.0;PAIREDR=0.994012;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=1.178;FS= [...]
+chr6 117737390 . G A 4012.64 REJECT NS=2;DP=248;DPB=286.0;AC=2;AN=4;AF=0.5;RO=143;AO=142;PRO=0.0;PAO=0.0;QR=5568;QA=5489;PQR=0.0;PQA=0.0;SRF=89;SRR=54;SAF=97;SAR=45;SRP=21.6121;SAP=44.36;AB=0.496503;ABP=3.04067;RUN=1;RPP=54.4528;RPPR=23.7987;RPL=42.0;RPR=100.0;EPP=3.98899;EPPR=11.0432;DPRA=0.0;ODDS=214.61;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993007;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.367;Dels=0.0;FS=2.648;HaplotypeScore=0.957 [...]
+chr6 120016758 . T C 9669.01 REJECT NS=2;DP=384;DPB=445.0;AC=2;AN=4;AF=0.5;RO=121;AO=324;PRO=0.0;PAO=0.0;QR=4477;QA=12206;PQR=0.0;PQA=0.0;SRF=51;SRR=70;SAF=134;SAR=190;SRP=9.48883;SAP=24.028;AB=0.72809;ABP=204.098;RUN=1;RPP=13.7336;RPPR=3.02825;RPL=142.0;RPR=182.0;EPP=13.7336;EPPR=20.2565;DPRA=0.0;ODDS=258.649;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996914;PAIREDR=0.975207;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.938;Dels=0.0;FS=0.0;HaplotypeSco [...]
+chr6 127443092 . T C 14599.55 REJECT NS=2;DP=382;DPB=441.0;AC=4;AN=4;AF=1.0;RO=0;AO=441;PRO=0.0;PAO=0.0;QR=0;QA=17025;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=196;SAR=245;SRP=0.0;SAP=14.8328;AB=0.0;ABP=0.0;RUN=1;RPP=14.8328;RPPR=0.0;RPL=245.0;RPR=196.0;EPP=3.84245;EPPR=0.0;DPRA=0.0;ODDS=76.0875;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0454;MQMR=0.0;PAIRED=0.988662;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.8628;MLEAC=2;MLEAF=1.0;MQ=60.035;QD=28.0;S [...]
+chr6 127443135 . C CTG 12400.2 REJECT NS=2;DP=329;DPB=508.0;AC=4;AN=4;AF=1.0;RO=0;AO=364;PRO=26.0;PAO=29.0;QR=0;QA=13733;PQR=894.5;PQA=996.5;SRF=0;SRR=0;SAF=172;SAR=192;SRP=0.0;SAP=5.39653;AB=0.0;ABP=0.0;RUN=1;RPP=4.53749;RPPR=0.0;RPL=190.0;RPR=174.0;EPP=3.86934;EPPR=0.0;DPRA=0.0;ODDS=63.5575;GTI=0;TYPE=ins;CIGAR=1M2I5M;NUMALT=1;MEANALT=1.0;LEN=2;MQM=60.0;MQMR=0.0;PAIRED=0.994505;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=127443135;HOMLEN=1;HOMSEQ=T;SVLEN=2;SVTYPE=INS;FS=0.0;MLEAC=2;M [...]
+chr6 127445707 . G GT 5602.01 REJECT NS=2;DP=256;DPB=303.526;AC=2;AN=2;AF=0.0;RO=48;AO=9;PRO=32.9167;PAO=28.9167;QR=1743;QA=315;PQR=1157.92;PQA=1015.92;SRF=25;SRR=23;SAF=4;SAR=5;SRP=3.19126;SAP=3.25157;AB=0.0351562;ABP=483.482;RUN=1;RPP=9.04217;RPPR=3.0103;RPL=7.0;RPR=2.0;EPP=3.25157;EPPR=7.5342;DPRA=0.0;ODDS=84.3565;GTI=0;TYPE=ins;CIGAR=1M1I18M;NUMALT=3;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr6 127445707 . GT G 4793.87 REJECT NS=2;DP=242;DPB=303.526;AC=2;AN=4;AF=0.5;RO=48;AO=183;PRO=32.9167;PAO=36.4167;QR=1743;QA=6677;PQR=1157.92;PQA=1282.42;SRF=25;SRR=23;SAF=101;SAR=82;SRP=3.19126;SAP=7.29391;AB=0.714844;ABP=105.646;RUN=1;RPP=3.02217;RPPR=3.0103;RPL=91.0;RPR=92.0;EPP=6.43957;EPPR=7.5342;DPRA=0.0;ODDS=84.3565;GTI=0;TYPE=del;CIGAR=1M1D17M;NUMALT=3;MEANALT=5.0;LEN=1;MQM=60.2732;MQMR=60.0;PAIRED=0.989071;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum [...]
+chr6 127445707 . GTT G 5602.01 PASS SOMATIC;NS=2;DP=256;DPB=303.526;AC=2;AN=2;AF=0.0;RO=48;AO=11;PRO=32.9167;PAO=23.75;QR=1743;QA=373;PQR=1157.92;PQA=788.75;SRF=25;SRR=23;SAF=5;SAR=6;SRP=3.19126;SAP=3.20771;AB=0.0429688;ABP=467.468;RUN=1;RPP=3.20771;RPPR=3.0103;RPL=6.0;RPR=5.0;EPP=4.78696;EPPR=7.5342;DPRA=0.0;ODDS=84.3565;GTI=0;TYPE=del;CIGAR=1M2D16M;NUMALT=3;MEANALT=5.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr6 127446610 . G C 14005.15 REJECT NS=2;DP=364;DPB=412.0;AC=4;AN=4;AF=1.0;RO=0;AO=412;PRO=0.0;PAO=0.0;QR=0;QA=15943;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=207;SAR=205;SRP=0.0;SAP=3.03138;AB=0.0;ABP=0.0;RUN=1;RPP=6.5732;RPPR=0.0;RPL=193.0;RPR=219.0;EPP=11.4432;EPPR=0.0;DPRA=0.0;ODDS=63.6327;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995146;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.866;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=24.29;SOR=0.7 [...]
+chr6 127446790 . T C 13871.5 REJECT NS=2;DP=371;DPB=419.0;AC=4;AN=4;AF=1.0;RO=1;AO=418;PRO=0.0;PAO=0.0;QR=16;QA=15784;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=191;SAR=227;SRP=5.18177;SAP=9.7429;AB=0.0;ABP=0.0;RUN=1;RPP=3.34277;RPPR=5.18177;RPL=205.0;RPR=213.0;EPP=3.52979;EPPR=5.18177;DPRA=0.0;ODDS=63.5638;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995215;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.657;Dels=0.0;FS=0.0;HaplotypeScore=4.8906;MLEAC=2;M [...]
+chr6 127448249 . C G 13572.599999999999 REJECT NS=2;DP=363;DPB=421.0;AC=4;AN=4;AF=1.0;RO=0;AO=421;PRO=0.0;PAO=0.0;QR=0;QA=15979;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=209;SAR=212;SRP=0.0;SAP=3.05672;AB=0.0;ABP=0.0;RUN=1;RPP=4.8723;RPPR=0.0;RPL=201.0;RPR=220.0;EPP=4.50093;EPPR=0.0;DPRA=0.0;ODDS=76.0402;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.990499;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31. [...]
+chr6 127449246 . A G 14434.349999999999 REJECT NS=2;DP=386;DPB=441.0;AC=4;AN=4;AF=1.0;RO=0;AO=440;PRO=0.0;PAO=0.0;QR=0;QA=16669;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=218;SAR=222;SRP=0.0;SAP=3.08926;AB=0.0;ABP=0.0;RUN=1;RPP=3.72096;RPPR=0.0;RPL=226.0;RPR=214.0;EPP=3.72096;EPPR=0.0;DPRA=0.0;ODDS=72.2994;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9045;MQMR=0.0;PAIRED=0.997727;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.7817;MLEAC=2;MLEAF=1.0;MQ=59.96; [...]
+chr6 127449447 . A G 15571.25 REJECT NS=2;DP=410;DPB=468.0;AC=4;AN=4;AF=1.0;RO=0;AO=467;PRO=0.0;PAO=0.0;QR=0;QA=17926;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=234;SAR=233;SRP=0.0;SAP=3.01495;AB=0.0;ABP=0.0;RUN=1;RPP=10.0827;RPPR=0.0;RPL=214.0;RPR=253.0;EPP=11.6078;EPPR=0.0;DPRA=0.0;ODDS=75.8059;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.9574;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.615;SOR=0.737 [...]
+chr6 127450254 . C T 15771.5 REJECT NS=2;DP=415;DPB=465.0;AC=4;AN=4;AF=1.0;RO=1;AO=464;PRO=0.0;PAO=0.0;QR=16;QA=17788;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=226;SAR=238;SRP=5.18177;SAP=3.68421;AB=0.0;ABP=0.0;RUN=1;RPP=9.07545;RPPR=5.18177;RPL=214.0;RPR=250.0;EPP=15.6647;EPPR=5.18177;DPRA=0.0;ODDS=66.0511;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=55.0;PAIRED=0.997845;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.704;Dels=0.0;FS=0.0;HaplotypeScore=6.7656;MLEAC=2; [...]
+chr6 127451665 . C T 13188.3 REJECT NS=2;DP=348;DPB=401.0;AC=4;AN=4;AF=1.0;RO=1;AO=400;PRO=0.0;PAO=0.0;QR=15;QA=15323;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=192;SAR=208;SRP=5.18177;SAP=4.40004;AB=0.0;ABP=0.0;RUN=1;RPP=3.55317;RPPR=5.18177;RPL=195.0;RPR=205.0;EPP=4.76919;EPPR=5.18177;DPRA=0.0;ODDS=68.7845;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.9975;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.697;Dels=0.0;FS=0.0;HaplotypeScore=0.9987;MLEAC=2;ML [...]
+chr6 127452116 . C T 13598.2 REJECT NS=2;DP=356;DPB=416.0;AC=4;AN=4;AF=1.0;RO=0;AO=416;PRO=0.0;PAO=0.0;QR=0;QA=16101;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=177;SAR=239;SRP=0.0;SAP=23.0755;AB=0.0;ABP=0.0;RUN=1;RPP=6.01695;RPPR=0.0;RPL=220.0;RPR=196.0;EPP=28.5877;EPPR=0.0;DPRA=0.0;ODDS=79.2073;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.9568;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.955;SOR=1.0035 [...]
+chr6 127452426 . C G 14280.65 REJECT NS=2;DP=381;DPB=436.0;AC=4;AN=4;AF=1.0;RO=0;AO=435;PRO=0.0;PAO=0.0;QR=0;QA=16559;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=221;SAR=214;SRP=0.0;SAP=3.2549;AB=0.0;ABP=0.0;RUN=1;RPP=3.05523;RPPR=0.0;RPL=219.0;RPR=216.0;EPP=3.61432;EPPR=0.0;DPRA=0.0;ODDS=72.9676;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9724;MQMR=0.0;PAIRED=0.995402;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.7813;MLEAC=2;MLEAF=1.0;MQ=59.985;QD=26.005; [...]
+chr6 127452581 . T C 14059.75 REJECT NS=2;DP=368;DPB=431.0;AC=4;AN=4;AF=1.0;RO=0;AO=430;PRO=0.0;PAO=0.0;QR=0;QA=16548;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=225;SAR=205;SRP=0.0;SAP=5.03027;AB=0.0;ABP=0.0;RUN=1;RPP=4.30308;RPPR=0.0;RPL=207.0;RPR=223.0;EPP=17.7359;EPPR=0.0;DPRA=0.0;ODDS=81.6042;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9581;MQMR=0.0;PAIRED=0.988372;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.8799;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.805;S [...]
+chr6 127452639 . C G 13839.099999999999 REJECT NS=2;DP=364;DPB=422.0;AC=4;AN=4;AF=1.0;RO=0;AO=421;PRO=0.0;PAO=0.0;QR=0;QA=16192;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=211;SAR=210;SRP=0.0;SAP=3.01546;AB=0.0;ABP=0.0;RUN=1;RPP=6.7704;RPPR=0.0;RPL=224.0;RPR=197.0;EPP=11.6807;EPPR=0.0;DPRA=0.0;ODDS=75.4595;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.988124;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.8995;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27 [...]
+chr6 127452935 . C T 12984.0 REJECT NS=2;DP=336;DPB=386.0;AC=4;AN=4;AF=1.0;RO=0;AO=386;PRO=0.0;PAO=0.0;QR=0;QA=15004;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=197;SAR=189;SRP=0.0;SAP=3.37034;AB=0.0;ABP=0.0;RUN=1;RPP=3.82038;RPPR=0.0;RPL=199.0;RPR=187.0;EPP=4.11291;EPPR=0.0;DPRA=0.0;ODDS=65.5045;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994819;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8982;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.55;SOR=0. [...]
+chr6 127454247 . C T 13040.599999999999 REJECT NS=2;DP=344;DPB=386.0;AC=4;AN=4;AF=1.0;RO=0;AO=384;PRO=0.0;PAO=0.0;QR=0;QA=14657;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=186;SAR=198;SRP=0.0;SAP=3.8246;AB=0.0;ABP=0.0;RUN=1;RPP=4.11866;RPPR=0.0;RPL=199.0;RPR=185.0;EPP=5.74726;EPPR=0.0;DPRA=0.0;ODDS=53.6086;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994792;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.8909;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30 [...]
+chr6 127454893 . G A 2332.63 REJECT NS=2;DP=348;DPB=403.0;AC=2;AN=4;AF=0.5;RO=296;AO=106;PRO=0.0;PAO=0.0;QR=11065;QA=4011;PQR=0.0;PQA=0.0;SRF=158;SRR=138;SAF=50;SAR=56;SRP=5.94472;SAP=3.74778;AB=0.263027;ABP=199.58;RUN=1;RPP=3.0103;RPPR=3.74391;RPL=53.0;RPR=53.0;EPP=5.96022;EPPR=3.03964;DPRA=0.0;ODDS=137.681;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996622;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.907;Dels=0.0;FS=3.24;HaplotypeScore=10. [...]
+chr6 127455029 . A G 13861.55 REJECT NS=2;DP=367;DPB=413.0;AC=4;AN=4;AF=1.0;RO=0;AO=413;PRO=0.0;PAO=0.0;QR=0;QA=15662;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=215;SAR=198;SRP=0.0;SAP=4.5298;AB=0.0;ABP=0.0;RUN=1;RPP=11.8487;RPPR=0.0;RPL=227.0;RPR=186.0;EPP=3.01556;EPPR=0.0;DPRA=0.0;ODDS=61.0891;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.987893;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8567;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.705;SOR=0 [...]
+chr6 127455138 . C T 15269.349999999999 REJECT NS=2;DP=403;DPB=456.0;AC=4;AN=4;AF=1.0;RO=0;AO=456;PRO=0.0;PAO=0.0;QR=0;QA=17426;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=252;SAR=204;SRP=0.0;SAP=13.982;AB=0.0;ABP=0.0;RUN=1;RPP=4.55319;RPPR=0.0;RPL=237.0;RPR=219.0;EPP=3.02935;EPPR=0.0;DPRA=0.0;ODDS=67.9513;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.989035;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30 [...]
+chr6 127455821 . A C 13485.8 REJECT NS=2;DP=366;DPB=419.0;AC=4;AN=4;AF=1.0;RO=2;AO=417;PRO=0.0;PAO=0.0;QR=32;QA=15651;PQR=0.0;PQA=0.0;SRF=2;SRR=0;SAF=214;SAR=203;SRP=7.35324;SAP=3.64039;AB=0.0;ABP=0.0;RUN=1;RPP=15.5132;RPPR=7.35324;RPL=233.0;RPR=184.0;EPP=5.765;EPPR=7.35324;DPRA=0.0;ODDS=69.7874;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990408;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.387;Dels=0.0;FS=0.0;HaplotypeScore=5.799;MLEAC=2;MLE [...]
+chr6 127456122 . A G 13715.05 REJECT NS=2;DP=364;DPB=423.0;AC=4;AN=4;AF=1.0;RO=0;AO=423;PRO=0.0;PAO=0.0;QR=0;QA=16156;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=194;SAR=229;SRP=0.0;SAP=9.29884;AB=0.0;ABP=0.0;RUN=1;RPP=3.42611;RPPR=0.0;RPL=216.0;RPR=207.0;EPP=5.27418;EPPR=0.0;DPRA=0.0;ODDS=77.3109;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.990544;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=10.6316;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=25.78;SOR= [...]
+chr6 127456561 . TA T 223.466 REJECT NS=2;DP=61;DPB=171.744;AC=2;AN=2;AF=0.25;RO=2;AO=4;PRO=64.7167;PAO=57.7167;QR=74;QA=93;PQR=2280.92;PQA=2021.92;SRF=1;SRR=1;SAF=2;SAR=2;SRP=3.0103;SAP=3.0103;AB=0.0655738;ABP=103.005;RUN=1;RPP=5.18177;RPPR=3.0103;RPL=1.0;RPR=3.0;EPP=5.18177;EPPR=7.35324;DPRA=0.0;ODDS=0.907768;GTI=0;TYPE=del;CIGAR=1M1D37M;NUMALT=5;MEANALT=20.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr6 127456561 . TAA T 223.466 REJECT NS=2;DP=61;DPB=171.744;AC=2;AN=3;AF=0.5;RO=2;AO=7;PRO=64.7167;PAO=53.05;QR=74;QA=234;PQR=2280.92;PQA=1861.42;SRF=1;SRR=1;SAF=6;SAR=1;SRP=3.0103;SAP=10.7656;AB=0.114754;ABP=81.6461;RUN=1;RPP=10.7656;RPPR=3.0103;RPL=1.0;RPR=6.0;EPP=5.80219;EPPR=7.35324;DPRA=0.0;ODDS=0.907768;GTI=0;TYPE=del;CIGAR=1M2D36M;NUMALT=5;MEANALT=20.0;LEN=2;MQM=62.8571;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.679;FS=0.0;MLEA [...]
+chr6 127456561 . TAAA T 223.466 REJECT SOMATIC;NS=2;DP=61;DPB=171.744;AC=1;AN=3;AF=0.0;RO=2;AO=7;PRO=64.7167;PAO=46.65;QR=74;QA=232;PQR=2280.92;PQA=1629.88;SRF=1;SRR=1;SAF=6;SAR=1;SRP=3.0103;SAP=10.7656;AB=0.114754;ABP=81.6461;RUN=1;RPP=3.32051;RPPR=3.0103;RPL=3.0;RPR=4.0;EPP=5.80219;EPPR=7.35324;DPRA=0.0;ODDS=0.907768;GTI=0;TYPE=del;CIGAR=1M3D35M;NUMALT=5;MEANALT=20.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr6 127456585 . AATTTAC TTTAA 223.466 REJECT SOMATIC;NS=2;DP=61;DPB=171.744;AC=1;AN=3;AF=0.0;RO=2;AO=4;PRO=64.7167;PAO=20.6333;QR=74;QA=64;PQR=2280.92;PQA=667.833;SRF=1;SRR=1;SAF=4;SAR=0;SRP=3.0103;SAP=11.6962;AB=0.0655738;ABP=103.005;RUN=1;RPP=11.6962;RPPR=3.0103;RPL=4.0;RPR=0.0;EPP=11.6962;EPPR=7.35324;DPRA=0.0;ODDS=0.907768;GTI=0;TYPE=complex;CIGAR=1M2D27M1X8M;NUMALT=5;MEANALT=20.0;LEN=37;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO: [...]
+chr6 127456585 . AATTTACAAC TTTAAAAA 223.466 REJECT SOMATIC;NS=2;DP=61;DPB=171.744;AC=1;AN=3;AF=0.0;RO=2;AO=4;PRO=64.7167;PAO=15.2333;QR=74;QA=73;PQR=2280.92;PQA=497.033;SRF=1;SRR=1;SAF=4;SAR=0;SRP=3.0103;SAP=11.6962;AB=0.0784314;ABP=81.7368;RUN=1;RPP=11.6962;RPPR=3.0103;RPL=4.0;RPR=0.0;EPP=11.6962;EPPR=7.35324;DPRA=0.0;ODDS=0.907768;GTI=0;TYPE=complex;CIGAR=1M2D27M1X2M1X5M;NUMALT=5;MEANALT=33.0;LEN=37;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT [...]
+chr6 127457001 . T G 3276.73 REJECT NS=2;DP=93;DPB=108.0;AC=4;AN=4;AF=1.0;RO=0;AO=108;PRO=0.0;PAO=0.0;QR=0;QA=3908;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=82;SAR=26;SRP=0.0;SAP=66.0634;AB=0.0;ABP=0.0;RUN=1;RPP=3.332;RPPR=0.0;RPL=52.0;RPR=56.0;EPP=3.332;EPPR=0.0;DPRA=0.0;ODDS=22.4684;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.981481;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.935;SOR=2.665 GT:GQ [...]
+chr6 127457071 . CA C 391.136 REJECT NS=2;DP=81;DPB=179.84;AC=2;AN=4;AF=0.5;RO=8;AO=28;PRO=92.3333;PAO=43.3333;QR=272;QA=786;PQR=3220.58;PQA=1481.58;SRF=7;SRR=1;SAF=17;SAR=11;SRP=12.7819;SAP=5.80219;AB=0.345679;ABP=19.7655;RUN=1;RPP=18.2106;RPPR=20.3821;RPL=7.0;RPR=21.0;EPP=22.8638;EPPR=12.7819;DPRA=0.0;ODDS=11.2004;GTI=0;TYPE=del;CIGAR=1M1D23M;NUMALT=3;MEANALT=15.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.964286;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-1.136;FS [...]
+chr6 127457071 . CAA C 391.136 REJECT NS=2;DP=81;DPB=179.84;AC=2;AN=2;AF=0.0;RO=8;AO=12;PRO=92.3333;PAO=34.3333;QR=272;QA=307;PQR=3220.58;PQA=1158.58;SRF=7;SRR=1;SAF=4;SAR=8;SRP=12.7819;SAP=5.9056;AB=0.148148;ABP=90.1105;RUN=1;RPP=5.9056;RPPR=20.3821;RPL=4.0;RPR=8.0;EPP=5.9056;EPPR=12.7819;DPRA=0.0;ODDS=11.2004;GTI=0;TYPE=del;CIGAR=1M2D22M;NUMALT=3;MEANALT=15.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr6 127457071 . CAAA C 391.136 REJECT NS=2;DP=81;DPB=179.84;AC=2;AN=2;AF=0.0;RO=8;AO=5;PRO=92.3333;PAO=31.0;QR=272;QA=141;PQR=3220.58;PQA=976.25;SRF=7;SRR=1;SAF=3;SAR=2;SRP=12.7819;SAP=3.44459;AB=0.078125;ABP=101.948;RUN=1;RPP=6.91895;RPPR=20.3821;RPL=1.0;RPR=4.0;EPP=6.91895;EPPR=12.7819;DPRA=0.0;ODDS=11.2004;GTI=0;TYPE=del;CIGAR=1M3D21M;NUMALT=3;MEANALT=18.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr6 127457260 . A G 13858.95 REJECT NS=2;DP=367;DPB=420.0;AC=4;AN=4;AF=1.0;RO=1;AO=419;PRO=0.0;PAO=0.0;QR=40;QA=16063;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=227;SAR=192;SRP=5.18177;SAP=9.35888;AB=0.0;ABP=0.0;RUN=1;RPP=14.4585;RPPR=5.18177;RPL=186.0;RPR=233.0;EPP=3.13986;EPPR=5.18177;DPRA=0.0;ODDS=70.4671;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995227;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.644;Dels=0.0;FS=1.673;HaplotypeScore=2.9329;MLEA [...]
+chr6 127458308 . G A 5534.72 REJECT NS=2;DP=150;DPB=168.0;AC=4;AN=4;AF=1.0;RO=0;AO=168;PRO=0.0;PAO=0.0;QR=0;QA=6445;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=21;SAR=147;SRP=0.0;SAP=208.214;AB=0.0;ABP=0.0;RUN=1;RPP=4.30284;RPPR=0.0;RPL=79.0;RPR=89.0;EPP=3.83753;EPPR=0.0;DPRA=0.0;ODDS=26.8399;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994048;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.965;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.755;SOR=3.808 [...]
+chr6 127458826 . G C 6718.55 REJECT NS=2;DP=409;DPB=475.0;AC=2;AN=4;AF=0.5;RO=238;AO=237;PRO=0.0;PAO=0.0;QR=9175;QA=9091;PQR=0.0;PQA=0.0;SRF=115;SRR=123;SAF=127;SAR=110;SRP=3.59423;SAP=5.65821;AB=0.498947;ABP=3.01487;RUN=1;RPP=3.09276;RPPR=7.42624;RPL=120.0;RPR=117.0;EPP=18.4122;EPPR=4.32413;DPRA=0.0;ODDS=377.305;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9496;PAIRED=0.991561;PAIREDR=0.995798;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.548;Dels=0.0;FS=3.266;Hap [...]
+chr6 127459004 . G T 11115.849999999999 REJECT NS=2;DP=299;DPB=348.0;AC=4;AN=4;AF=1.0;RO=1;AO=347;PRO=0.0;PAO=0.0;QR=40;QA=13155;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=148;SAR=199;SRP=5.18177;SAP=19.287;AB=0.0;ABP=0.0;RUN=1;RPP=3.51719;RPPR=5.18177;RPL=178.0;RPR=169.0;EPP=18.0354;EPPR=5.18177;DPRA=0.0;ODDS=58.0269;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.976945;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9973;MLEAC=2;MLEAF=1.0 [...]
+chr6 127459552 . G C 13008.8 REJECT NS=2;DP=347;DPB=405.0;AC=4;AN=4;AF=1.0;RO=0;AO=404;PRO=0.0;PAO=0.0;QR=0;QA=15364;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=201;SAR=203;SRP=0.0;SAP=3.0318;AB=0.0;ABP=0.0;RUN=1;RPP=15.3941;RPPR=0.0;RPL=178.0;RPR=226.0;EPP=3.0318;EPPR=0.0;DPRA=0.0;ODDS=76.6189;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992574;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8299;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.13;SOR=0.98 [...]
+chr6 127460349 . G A 14822.2 REJECT NS=2;DP=389;DPB=456.0;AC=4;AN=4;AF=1.0;RO=0;AO=456;PRO=0.0;PAO=0.0;QR=0;QA=17531;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=249;SAR=207;SRP=0.0;SAP=11.4105;AB=0.0;ABP=0.0;RUN=1;RPP=3.02935;RPPR=0.0;RPL=229.0;RPR=227.0;EPP=20.1535;EPPR=0.0;DPRA=0.0;ODDS=84.7529;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.986842;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.8371;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.885;SOR=0 [...]
+chr6 127460690 . C CT 7044.99 REJECT NS=2;DP=269;DPB=351.083;AC=4;AN=4;AF=1.0;RO=6;AO=259;PRO=40.5;PAO=46.5;QR=221;QA=9161;PQR=1362.0;PQA=1575.0;SRF=4;SRR=2;SAF=127;SAR=132;SRP=4.45795;SAP=3.2199;AB=0.0;ABP=0.0;RUN=1;RPP=3.42112;RPPR=3.0103;RPL=133.0;RPR=126.0;EPP=5.43329;EPPR=8.80089;DPRA=0.0;ODDS=50.9116;GTI=0;TYPE=ins;CIGAR=1M1I11M;NUMALT=1;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.338;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQR [...]
+chr6 127461152 . T C 14589.9 REJECT NS=2;DP=390;DPB=448.0;AC=4;AN=4;AF=1.0;RO=0;AO=448;PRO=0.0;PAO=0.0;QR=0;QA=16964;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=225;SAR=223;SRP=0.0;SAP=3.02969;AB=0.0;ABP=0.0;RUN=1;RPP=3.08785;RPPR=0.0;RPL=226.0;RPR=222.0;EPP=10.0094;EPPR=0.0;DPRA=0.0;ODDS=76.0382;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0223;MQMR=0.0;PAIRED=0.995536;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9662;MLEAC=2;MLEAF=1.0;MQ=60.05;QD=29.255;S [...]
+chr6 127461682 . A C 13811.8 REJECT NS=2;DP=370;DPB=428.0;AC=4;AN=4;AF=1.0;RO=2;AO=426;PRO=0.0;PAO=0.0;QR=49;QA=16135;PQR=0.0;PQA=0.0;SRF=1;SRR=1;SAF=188;SAR=238;SRP=3.0103;SAP=15.7537;AB=0.0;ABP=0.0;RUN=1;RPP=4.31522;RPPR=7.35324;RPL=221.0;RPR=205.0;EPP=4.31522;EPPR=3.0103;DPRA=0.0;ODDS=68.606;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99061;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.932;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF [...]
+chr6 127462149 . T C 13330.5 REJECT NS=2;DP=352;DPB=395.0;AC=4;AN=4;AF=1.0;RO=1;AO=394;PRO=0.0;PAO=0.0;QR=15;QA=15039;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=203;SAR=191;SRP=5.18177;SAP=3.80393;AB=0.0;ABP=0.0;RUN=1;RPP=3.36303;RPPR=5.18177;RPL=201.0;RPR=193.0;EPP=3.20871;EPPR=5.18177;DPRA=0.0;ODDS=55.0284;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992386;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.8294;MLEAC=2;MLEAF=1.0;MQ=60.0;Q [...]
+chr6 127463376 . C A 14297.3 REJECT NS=2;DP=374;DPB=418.0;AC=4;AN=4;AF=1.0;RO=0;AO=418;PRO=0.0;PAO=0.0;QR=0;QA=16080;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=240;SAR=178;SRP=0.0;SAP=22.9795;AB=0.0;ABP=0.0;RUN=1;RPP=12.1741;RPPR=0.0;RPL=188.0;RPR=230.0;EPP=14.0027;EPPR=0.0;DPRA=0.0;ODDS=59.2237;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995215;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.26;SOR=1.0 [...]
+chr6 127463645 . G A 14863.9 REJECT NS=2;DP=388;DPB=439.0;AC=4;AN=4;AF=1.0;RO=1;AO=438;PRO=0.0;PAO=0.0;QR=15;QA=16946;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=234;SAR=204;SRP=5.18177;SAP=7.47223;AB=0.0;ABP=0.0;RUN=1;RPP=5.86593;RPPR=5.18177;RPL=231.0;RPR=207.0;EPP=3.32759;EPPR=5.18177;DPRA=0.0;ODDS=67.9569;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997717;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.722;Dels=0.0;FS=0.0;HaplotypeScore=1.9243;MLEAC=2; [...]
+chr6 127464127 . AT A 747.6310000000001 REJECT NS=2;DP=44;DPB=57.9167;AC=3;AN=3;AF=0.75;RO=4;AO=30;PRO=12.6667;PAO=14.6667;QR=150;QA=1080;PQR=397.833;PQA=473.833;SRF=1;SRR=3;SAF=21;SAR=9;SRP=5.18177;SAP=13.4334;AB=0.666667;ABP=13.8677;RUN=1;RPP=5.61607;RPPR=11.6962;RPL=12.0;RPR=18.0;EPP=13.4334;EPPR=5.18177;DPRA=0.0;ODDS=1.22909;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=2;MEANALT=4.5;LEN=1;MQM=60.5333;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum [...]
+chr6 127464127 . ATT A 936.532 REJECT NS=2;DP=45;DPB=57.9167;AC=2;AN=2;AF=0.25;RO=4;AO=6;PRO=12.6667;PAO=9.66667;QR=150;QA=216;PQR=397.833;PQA=284.333;SRF=1;SRR=3;SAF=4;SAR=2;SRP=5.18177;SAP=4.45795;AB=0.133333;ABP=55.5599;RUN=1;RPP=4.45795;RPPR=11.6962;RPL=2.0;RPR=4.0;EPP=16.0391;EPPR=5.18177;DPRA=0.0;ODDS=1.22909;GTI=0;TYPE=del;CIGAR=1M2D21M;NUMALT=2;MEANALT=4.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr6 127464754 . C T 14485.599999999999 REJECT NS=2;DP=383;DPB=436.0;AC=4;AN=4;AF=1.0;RO=0;AO=436;PRO=0.0;PAO=0.0;QR=0;QA=16711;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=243;SAR=193;SRP=0.0;SAP=15.4614;AB=0.0;ABP=0.0;RUN=1;RPP=4.28529;RPPR=0.0;RPL=226.0;RPR=210.0;EPP=24.7051;EPPR=0.0;DPRA=0.0;ODDS=70.4752;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997706;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=12.5783;MLEAC=2;MLEAF=1.0;MQ=60.0;QD= [...]
+chr6 127465044 . T C 14152.5 REJECT NS=2;DP=375;DPB=430.0;AC=4;AN=4;AF=1.0;RO=0;AO=430;PRO=0.0;PAO=0.0;QR=0;QA=16375;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=204;SAR=226;SRP=0.0;SAP=5.45447;AB=0.0;ABP=0.0;RUN=1;RPP=3.1921;RPPR=0.0;RPL=212.0;RPR=218.0;EPP=7.55524;EPPR=0.0;DPRA=0.0;ODDS=71.6913;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.988372;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.205;SOR=0.795 [...]
+chr6 127465788 . G GTTTTTTTGTTTTTT 3183.57 REJECT SOMATIC;NS=2;DP=9;DPB=90.6111;AC=1;AN=3;AF=0.25;RO=0;AO=2;PRO=28.0;PAO=57.0;QR=0;QA=55;PQR=949.667;PQA=1680.67;SRF=0;SRR=0;SAF=2;SAR=0;SRP=0.0;SAP=7.35324;AB=0.4;ABP=3.44459;RUN=1;RPP=3.0103;RPPR=0.0;RPL=1.0;RPR=1.0;EPP=3.0103;EPPR=0.0;DPRA=1.25;ODDS=1.60669;GTI=0;TYPE=ins;CIGAR=1M14I17M;NUMALT=2;MEANALT=3.0;LEN=14;MQM=50.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMIC [...]
+chr6 127465788 . G GTTTTTTTGTTTTTTT 3183.57 REJECT NS=2;DP=20;DPB=90.6111;AC=3;AN=3;AF=0.875;RO=0;AO=3;PRO=28.0;PAO=57.0;QR=0;QA=104;PQR=949.667;PQA=1680.67;SRF=0;SRR=0;SAF=3;SAR=0;SRP=0.0;SAP=9.52472;AB=0.4;ABP=3.44459;RUN=1;RPP=9.52472;RPPR=0.0;RPL=3.0;RPR=0.0;EPP=9.52472;EPPR=0.0;DPRA=0.0;ODDS=1.60669;GTI=0;TYPE=ins;CIGAR=1M15I17M;NUMALT=2;MEANALT=3.5;LEN=15;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;FS=0.0;MLEAC=1;MLEAF=0.75;MQ=65.905;QD= [...]
+chr6 127467444 . GA G 8264.885 REJECT NS=2;DP=273;DPB=346.167;AC=4;AN=4;AF=1.0;RO=7;AO=250;PRO=63.5;PAO=106.5;QR=264;QA=9208;PQR=2259.0;PQA=3903.0;SRF=5;SRR=2;SAF=118;SAR=132;SRP=5.80219;SAP=4.71273;AB=0.0;ABP=0.0;RUN=1;RPP=4.26107;RPPR=3.32051;RPL=119.0;RPR=131.0;EPP=6.48466;EPPR=5.80219;DPRA=0.0;ODDS=38.7958;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=1;MEANALT=5.5;LEN=1;MQM=60.08;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.059;FS=1.382;MLEAC=2;MLEAF=1.0;MQ=60 [...]
+chr6 127468188 . G A 12215.3 REJECT NS=2;DP=352;DPB=409.0;AC=4;AN=4;AF=1.0;RO=1;AO=404;PRO=0.0;PAO=0.0;QR=34;QA=14478;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=188;SAR=216;SRP=5.18177;SAP=7.22425;AB=0.0;ABP=0.0;RUN=1;RPP=3.0963;RPPR=5.18177;RPL=200.0;RPR=204.0;EPP=3.0963;EPPR=5.18177;DPRA=0.0;ODDS=74.6254;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.089;Dels=0.0;FS=0.0;HaplotypeScore=7.8365;MLEAC=2;MLEAF=1 [...]
+chr6 127468274 . A C 13086.7 REJECT NS=2;DP=346;DPB=409.0;AC=4;AN=4;AF=1.0;RO=0;AO=409;PRO=0.0;PAO=0.0;QR=0;QA=15649;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=225;SAR=184;SRP=0.0;SAP=11.9351;AB=0.0;ABP=0.0;RUN=1;RPP=3.14303;RPPR=0.0;RPL=207.0;RPR=202.0;EPP=5.81888;EPPR=0.0;DPRA=0.0;ODDS=80.7977;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992665;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9662;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.155;SOR=0 [...]
+chr6 127476516 . G A 15219.0 REJECT NS=2;DP=403;DPB=456.0;AC=4;AN=4;AF=1.0;RO=0;AO=456;PRO=0.0;PAO=0.0;QR=0;QA=17345;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=228;SAR=228;SRP=0.0;SAP=3.0103;AB=0.0;ABP=0.0;RUN=1;RPP=3.0103;RPPR=0.0;RPL=228.0;RPR=228.0;EPP=10.6295;EPPR=0.0;DPRA=0.0;ODDS=70.414;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993421;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8325;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.88;SOR=0.720 [...]
+chr6 128297950 . G GA 253.169 REJECT NS=2;DP=200;DPB=229.444;AC=2;AN=4;AF=0.5;RO=149;AO=26;PRO=33.3333;PAO=22.3333;QR=5591;QA=860;PQR=1178.17;PQA=754.167;SRF=43;SRR=106;SAF=16;SAR=10;SRP=60.8531;SAP=6.01695;AB=0.13;ABP=240.83;RUN=1;RPP=36.4176;RPPR=93.9644;RPL=23.0;RPR=3.0;EPP=4.34659;EPPR=38.0016;DPRA=0.0;ODDS=1.38899;GTI=1;TYPE=ins;CIGAR=1M1I17M;NUMALT=2;MEANALT=7.0;LEN=1;MQM=60.3846;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986577;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr6 128297950 . GA G 253.169 REJECT NS=2;DP=200;DPB=229.444;AC=2;AN=2;AF=0.0;RO=149;AO=13;PRO=33.3333;PAO=18.3333;QR=5591;QA=427;PQR=1178.17;PQA=627.667;SRF=43;SRR=106;SAF=4;SAR=9;SRP=60.8531;SAP=7.18621;AB=0.065;ABP=331.728;RUN=1;RPP=23.2217;RPPR=93.9644;RPL=12.0;RPR=1.0;EPP=11.1951;EPPR=38.0016;DPRA=0.0;ODDS=1.38899;GTI=1;TYPE=del;CIGAR=1M1D16M;NUMALT=2;MEANALT=7.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986577;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr6 128330249 . T C 4941.995000000001 REJECT NS=2;DP=224;DPB=254.0;AC=3;AN=4;AF=0.75;RO=77;AO=177;PRO=0.0;PAO=0.0;QR=2977;QA=6868;PQR=0.0;PQA=0.0;SRF=54;SRR=23;SAF=132;SAR=45;SRP=30.1114;SAP=95.8683;AB=0.603093;ABP=20.9194;RUN=1;RPP=83.502;RPPR=41.6174;RPL=48.0;RPR=129.0;EPP=4.49475;EPPR=3.0385;DPRA=0.0;ODDS=38.4505;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988701;PAIREDR=0.987013;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.596;Dels=0.0;FS=0.2975;Ha [...]
+chr6 128330423 . T TA 193.091 REJECT NS=2;DP=206;DPB=227.562;AC=2;AN=2;AF=0.0;RO=152;AO=14;PRO=21.6667;PAO=14.6667;QR=5650;QA=459;PQR=789.0;PQA=513.0;SRF=24;SRR=128;SAF=3;SAR=11;SRP=157.528;SAP=12.937;AB=0.0679612;ABP=336.995;RUN=1;RPP=8.59409;RPPR=54.4399;RPL=10.0;RPR=4.0;EPP=3.0103;EPPR=8.7247;DPRA=0.0;ODDS=19.838;GTI=0;TYPE=ins;CIGAR=1M1I15M;NUMALT=2;MEANALT=6.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr6 128330423 . TA T 193.091 REJECT NS=2;DP=206;DPB=227.562;AC=2;AN=4;AF=0.5;RO=152;AO=22;PRO=21.6667;PAO=14.6667;QR=5650;QA=792;PQR=789.0;PQA=533.0;SRF=24;SRR=128;SAF=3;SAR=19;SRP=157.528;SAP=28.2783;AB=0.106796;ABP=279.652;RUN=1;RPP=4.58955;RPPR=54.4399;RPL=13.0;RPR=9.0;EPP=6.56362;EPPR=8.7247;DPRA=0.0;ODDS=19.838;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=2;MEANALT=6.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr6 128385956 . GA G 1496.16 PASS SOMATIC;NS=2;DP=230;DPB=272.312;AC=1;AN=4;AF=0.25;RO=154;AO=61;PRO=52.0;PAO=42.0;QR=5800;QA=2234;PQR=1907.0;PQA=1556.0;SRF=40;SRR=114;SAF=12;SAR=49;SRP=80.2245;SAP=51.7438;AB=0.345238;ABP=37.9607;RUN=1;RPP=15.8611;RPPR=41.138;RPL=40.0;RPR=21.0;EPP=3.90025;EPPR=8.65049;DPRA=0.0;ODDS=10.4632;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=1;MEANALT=5.0;LEN=1;MQM=60.1639;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.876;FS=4.401;MLEAC=1 [...]
+chr6 128388799 . G T 2121.35 REJECT NS=2;DP=356;DPB=408.0;AC=2;AN=4;AF=0.5;RO=307;AO=100;PRO=0.0;PAO=0.0;QR=11429;QA=3638;PQR=0.0;PQA=0.0;SRF=165;SRR=142;SAF=53;SAR=47;SRP=6.75202;SAP=3.79203;AB=0.245098;ABP=233.272;RUN=1;RPP=3.35774;RPPR=3.18713;RPL=48.0;RPR=52.0;EPP=5.18177;EPPR=3.07396;DPRA=0.0;ODDS=79.0965;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=59.9544;PAIRED=0.99;PAIREDR=0.983713;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.3335;Dels=0.0;FS=1.153;Haplotype [...]
+chr6 128403745 . A G 1489.275 REJECT NS=2;DP=320;DPB=362.0;AC=2;AN=4;AF=0.5;RO=277;AO=85;PRO=0.0;PAO=0.0;QR=10591;QA=3168;PQR=0.0;PQA=0.0;SRF=81;SRR=196;SAF=23;SAR=62;SRP=106.684;SAP=41.8669;AB=0.234807;ABP=224.141;RUN=1;RPP=34.305;RPPR=6.46741;RPL=60.0;RPR=25.0;EPP=5.07959;EPPR=11.5472;DPRA=0.0;ODDS=185.696;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988235;PAIREDR=0.99278;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.112;Dels=0.0;FS=0.4595;HaplotypeSco [...]
+chr6 128505804 . A C 1310.435 REJECT NS=2;DP=346;DPB=389.0;AC=2;AN=4;AF=0.5;RO=318;AO=71;PRO=0.0;PAO=0.0;QR=12261;QA=2749;PQR=0.0;PQA=0.0;SRF=140;SRR=178;SAF=33;SAR=38;SRP=12.8707;SAP=3.7749;AB=0.182519;ABP=343.574;RUN=1;RPP=3.28556;RPPR=4.7584;RPL=37.0;RPR=34.0;EPP=3.04088;EPPR=3.44733;DPRA=0.0;ODDS=82.1836;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985915;PAIREDR=0.990566;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6135;Dels=0.0;FS=1.2475;HaplotypeS [...]
+chr6 129004492 . A G 1271.47 REJECT NS=2;DP=240;DPB=277.0;AC=2;AN=4;AF=0.5;RO=214;AO=63;PRO=0.0;PAO=0.0;QR=8285;QA=2376;PQR=0.0;PQA=0.0;SRF=157;SRR=57;SAF=49;SAR=14;SRP=104.481;SAP=45.2334;AB=0.227437;ABP=181.753;RUN=1;RPP=21.2438;RPPR=67.9515;RPL=20.0;RPR=43.0;EPP=4.69922;EPPR=3.37559;DPRA=0.0;ODDS=41.1182;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984127;PAIREDR=0.985981;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.049;Dels=0.0;FS=7.4975;HaplotypeSc [...]
+chr6 132017457 . C T 1932.41 REJECT NS=2;DP=362;DPB=422.0;AC=2;AN=4;AF=0.5;RO=324;AO=97;PRO=0.0;PAO=0.0;QR=12321;QA=3647;PQR=0.0;PQA=0.0;SRF=182;SRR=142;SAF=50;SAR=47;SRP=13.7336;SAP=3.21178;AB=0.229858;ABP=270.503;RUN=1;RPP=3.03269;RPPR=15.9855;RPL=49.0;RPR=48.0;EPP=19.3299;EPPR=11.6962;DPRA=0.0;ODDS=120.647;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989691;PAIREDR=0.996914;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.431;Dels=0.0;FS=3.813;HaplotypeS [...]
+chr6 135522348 . AT A 6620.105 REJECT NS=2;DP=298;DPB=352.933;AC=2;AN=4;AF=0.5;RO=68;AO=242;PRO=50.0;PAO=52.0;QR=2533;QA=8998;PQR=1734.5;PQA=1819.5;SRF=43;SRR=25;SAF=127;SAR=115;SRP=13.3567;SAP=4.30242;AB=0.751553;ABP=179.992;RUN=1;RPP=15.9674;RPPR=13.3567;RPL=102.0;RPR=140.0;EPP=10.0452;EPPR=5.05404;DPRA=0.0;ODDS=126.461;GTI=0;TYPE=del;CIGAR=1M1D13M;NUMALT=1;MEANALT=5.0;LEN=1;MQM=60.124;MQMR=60.0;PAIRED=0.991736;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.658;FS=10.455;MLEA [...]
+chr6 135522682 . A G 12140.4 REJECT NS=2;DP=441;DPB=512.0;AC=2;AN=4;AF=0.5;RO=118;AO=394;PRO=0.0;PAO=0.0;QR=4505;QA=15114;PQR=0.0;PQA=0.0;SRF=56;SRR=62;SAF=204;SAR=190;SRP=3.67278;SAP=4.09052;AB=0.769531;ABP=326.085;RUN=1;RPP=3.80393;RPPR=4.18805;RPL=203.0;RPR=191.0;EPP=3.80393;EPPR=3.0103;DPRA=0.0;ODDS=202.876;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9898;MQMR=60.0;PAIRED=0.992386;PAIREDR=0.991525;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7205;Dels=0.0;FS=3.278;Haplo [...]
+chr6 135522939 . T C 11588.5 REJECT NS=2;DP=418;DPB=485.0;AC=2;AN=4;AF=0.5;RO=112;AO=373;PRO=0.0;PAO=0.0;QR=4355;QA=14434;PQR=0.0;PQA=0.0;SRF=60;SRR=52;SAF=170;SAR=203;SRP=4.25114;SAP=9.35007;AB=0.769072;ABP=308.006;RUN=1;RPP=3.15584;RPPR=16.1167;RPL=184.0;RPR=189.0;EPP=12.7965;EPPR=3.08785;DPRA=0.0;ODDS=194.55;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997319;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.979;Dels=0.0;FS=4.0975;HaplotypeScor [...]
+chr6 135523583 . T C 3968.72 REJECT NS=2;DP=151;DPB=175.0;AC=2;AN=4;AF=0.5;RO=40;AO=135;PRO=0.0;PAO=0.0;QR=1550;QA=5133;PQR=0.0;PQA=0.0;SRF=8;SRR=32;SAF=26;SAR=109;SRP=34.2795;SAP=113.82;AB=0.771429;ABP=114.996;RUN=1;RPP=4.31318;RPPR=3.22745;RPL=72.0;RPR=63.0;EPP=3.02638;EPPR=3.22745;DPRA=0.0;ODDS=52.1958;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9481;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.506;Dels=0.0;FS=0.0;HaplotypeScore=2.9637;M [...]
+chr6 135523774 . A G 4885.01 REJECT NS=2;DP=183;DPB=216.0;AC=2;AN=4;AF=0.5;RO=49;AO=167;PRO=0.0;PAO=0.0;QR=1874;QA=6347;PQR=0.0;PQA=0.0;SRF=39;SRR=10;SAF=136;SAR=31;SRP=40.2799;SAP=146.366;AB=0.773148;ABP=142.99;RUN=1;RPP=20.8112;RPPR=8.37251;RPL=65.0;RPR=102.0;EPP=4.58364;EPPR=5.18177;DPRA=0.0;ODDS=53.0167;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.8922;MQMR=59.7551;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.657;Dels=0.0;FS=1.9345;HaplotypeScore=3 [...]
+chr6 135524516 . A G 10392.4 REJECT NS=2;DP=390;DPB=449.0;AC=2;AN=4;AF=0.5;RO=100;AO=349;PRO=0.0;PAO=0.0;QR=3796;QA=12995;PQR=0.0;PQA=0.0;SRF=47;SRR=53;SAF=199;SAR=150;SRP=3.79203;SAP=17.9493;AB=0.777283;ABP=302.862;RUN=1;RPP=5.75419;RPPR=4.40004;RPL=185.0;RPR=164.0;EPP=3.16585;EPPR=3.79203;DPRA=0.0;ODDS=150.574;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.2579;MQMR=60.0;PAIRED=0.994269;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.9085;Dels=0.0;FS=6.3875;Haploty [...]
+chr6 135524520 . T TTGG 5926.12 REJECT NS=2;DP=321;DPB=453.28;AC=2;AN=4;AF=0.5;RO=82;AO=222;PRO=89.0;PAO=101.0;QR=3044;QA=7197;PQR=3094.0;PQA=3528.0;SRF=38;SRR=44;SAF=128;SAR=94;SRP=3.96363;SAP=14.3176;AB=0.685185;ABP=99.5202;RUN=1;RPP=14.3176;RPPR=15.8273;RPL=128.0;RPR=94.0;EPP=3.98844;EPPR=3.11623;DPRA=0.0;ODDS=185.647;GTI=0;TYPE=ins;CIGAR=1M3I24M;NUMALT=1;MEANALT=10.5;LEN=3;MQM=60.0;MQMR=59.8659;PAIRED=0.995495;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.5485;FS=7.0835;M [...]
+chr6 135524553 . C T 10902.3 REJECT NS=2;DP=416;DPB=481.0;AC=2;AN=4;AF=0.5;RO=102;AO=376;PRO=0.0;PAO=0.0;QR=3846;QA=13668;PQR=0.0;PQA=0.0;SRF=47;SRR=55;SAF=176;SAR=200;SRP=4.37279;SAP=6.33681;AB=0.781705;ABP=334.559;RUN=1;RPP=4.48875;RPPR=7.18293;RPL=196.0;RPR=180.0;EPP=32.9489;EPPR=6.07591;DPRA=0.0;ODDS=118.228;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=59.9973;MQMR=60.0;PAIRED=0.992021;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.5825;Dels=0.0;FS=3.5415;Haploty [...]
+chr6 135525396 . G T 10411.1 REJECT NS=2;DP=395;DPB=451.0;AC=2;AN=4;AF=0.5;RO=112;AO=338;PRO=0.0;PAO=0.0;QR=4213;QA=13033;PQR=0.0;PQA=0.0;SRF=42;SRR=70;SAF=138;SAR=200;SRP=18.2106;SAP=27.706;AB=0.749446;ABP=246.759;RUN=1;RPP=4.65497;RPPR=3.32051;RPL=177.0;RPR=161.0;EPP=3.0103;EPPR=5.80219;DPRA=0.0;ODDS=215.366;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.8728;MQMR=60.0;PAIRED=0.982249;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6045;Dels=0.0;FS=1.5185;HaplotypeS [...]
+chr6 135525737 . A G 5774.4 REJECT NS=2;DP=220;DPB=262.0;AC=2;AN=4;AF=0.5;RO=67;AO=195;PRO=0.0;PAO=0.0;QR=2539;QA=7373;PQR=0.0;PQA=0.0;SRF=51;SRR=16;SAF=133;SAR=62;SRP=42.7126;SAP=59.1456;AB=0.744275;ABP=138.802;RUN=1;RPP=34.2906;RPPR=3.04271;RPL=71.0;RPR=124.0;EPP=4.35773;EPPR=12.3768;DPRA=0.0;ODDS=85.7879;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989744;PAIREDR=0.985075;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.1115;Dels=0.0;FS=3.325;HaplotypeSc [...]
+chr6 135525927 . T C 7489.06 REJECT NS=2;DP=299;DPB=347.0;AC=2;AN=4;AF=0.5;RO=94;AO=253;PRO=0.0;PAO=0.0;QR=3584;QA=9480;PQR=0.0;PQA=0.0;SRF=30;SRR=64;SAF=100;SAR=153;SRP=29.7148;SAP=27.1197;AB=0.729107;ABP=161.215;RUN=1;RPP=14.7603;RPPR=7.53805;RPL=145.0;RPR=108.0;EPP=4.94145;EPPR=3.1027;DPRA=0.0;ODDS=192.14;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.7447;PAIRED=0.992095;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.542;Dels=0.0;FS=13.6715;HaplotypeSc [...]
+chr6 135526239 . G A 8313.37 REJECT NS=2;DP=323;DPB=369.0;AC=2;AN=4;AF=0.5;RO=91;AO=278;PRO=0.0;PAO=0.0;QR=3502;QA=10621;PQR=0.0;PQA=0.0;SRF=66;SRR=25;SAF=195;SAR=83;SRP=43.1229;SAP=100.992;AB=0.753388;ABP=208.794;RUN=1;RPP=78.0276;RPPR=17.9243;RPL=90.0;RPR=188.0;EPP=5.00993;EPPR=5.89764;DPRA=0.0;ODDS=118.256;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992806;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.207;Dels=0.0;FS=2.8015;HaplotypeScore= [...]
+chr6 135526367 . C T 563.577 REJECT NS=2;DP=273;DPB=396.0;AC=2;AN=2;AF=0.0;RO=123;AO=14;PRO=71.4167;PAO=25.9333;QR=4383;QA=205;PQR=2510.08;PQA=855.817;SRF=53;SRR=70;SAF=0;SAR=14;SRP=8.11238;SAP=33.4109;AB=0.0512821;ABP=480.456;RUN=1;RPP=3.0103;RPPR=3.16919;RPL=7.0;RPR=7.0;EPP=3.0103;EPPR=8.11238;DPRA=0.0;ODDS=22.0627;GTI=0;TYPE=snp;CIGAR=1X26M;NUMALT=5;MEANALT=19.0;LEN=1;MQM=58.7143;MQMR=60.0;PAIRED=0.928571;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr6 135526367 . C CT 563.577 REJECT NS=2;DP=273;DPB=396.0;AC=2;AN=2;AF=0.0;RO=123;AO=21;PRO=71.4167;PAO=48.9167;QR=4383;QA=534;PQR=2510.08;PQA=1615.58;SRF=53;SRR=70;SAF=8;SAR=13;SRP=8.11238;SAP=5.59539;AB=0.0769231;ABP=427.45;RUN=1;RPP=3.94093;RPPR=3.16919;RPL=12.0;RPR=9.0;EPP=8.07707;EPPR=8.11238;DPRA=0.0;ODDS=22.0627;GTI=0;TYPE=ins;CIGAR=1M1I26M;NUMALT=5;MEANALT=19.0;LEN=1;MQM=59.9048;MQMR=60.0;PAIRED=0.952381;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr6 135526367 . CT C 563.577 REJECT NS=2;DP=273;DPB=396.0;AC=2;AN=4;AF=0.5;RO=123;AO=43;PRO=71.4167;PAO=52.5833;QR=4383;QA=1141;PQR=2510.08;PQA=1753.58;SRF=53;SRR=70;SAF=18;SAR=25;SRP=8.11238;SAP=5.48477;AB=0.157509;ABP=281.158;RUN=1;RPP=3.46479;RPPR=3.16919;RPL=23.0;RPR=20.0;EPP=3.46479;EPPR=8.11238;DPRA=0.0;ODDS=22.0627;GTI=0;TYPE=del;CIGAR=1M1D25M;NUMALT=5;MEANALT=19.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr6 135526367 . CTT C 563.577 REJECT NS=2;DP=273;DPB=396.0;AC=2;AN=2;AF=0.0;RO=123;AO=15;PRO=71.4167;PAO=38.8333;QR=4383;QA=414;PQR=2510.08;PQA=1329.33;SRF=53;SRR=70;SAF=8;SAR=7;SRP=8.11238;SAP=3.15506;AB=0.0549451;ABP=472.693;RUN=1;RPP=10.1038;RPPR=3.16919;RPL=11.0;RPR=4.0;EPP=4.31318;EPPR=8.11238;DPRA=0.0;ODDS=22.0627;GTI=0;TYPE=del;CIGAR=1M2D24M;NUMALT=5;MEANALT=19.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr6 135526388 . A T 563.577 REJECT NS=2;DP=273;DPB=396.0;AC=2;AN=2;AF=0.0;RO=123;AO=17;PRO=71.4167;PAO=36.3167;QR=4383;QA=272;PQR=2510.08;PQA=1243.6;SRF=53;SRR=70;SAF=17;SAR=0;SRP=8.11238;SAP=39.9253;AB=0.0622711;ABP=457.357;RUN=1;RPP=6.20364;RPPR=3.16919;RPL=11.0;RPR=6.0;EPP=6.20364;EPPR=8.11238;DPRA=0.0;ODDS=22.0627;GTI=0;TYPE=snp;CIGAR=21M1X5M;NUMALT=5;MEANALT=19.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr6 135526768 . C T 11562.7 REJECT NS=2;DP=439;DPB=496.0;AC=2;AN=4;AF=0.5;RO=122;AO=374;PRO=0.0;PAO=0.0;QR=4650;QA=14444;PQR=0.0;PQA=0.0;SRF=57;SRR=65;SAF=176;SAR=198;SRP=4.14943;SAP=5.82044;AB=0.754032;ABP=281.029;RUN=1;RPP=19.9408;RPPR=5.57335;RPL=214.0;RPR=160.0;EPP=4.14829;EPPR=3.0815;DPRA=0.0;ODDS=193.143;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994652;PAIREDR=0.991803;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.548;Dels=0.0;FS=1.807;Haplotype [...]
+chr6 135527314 . G A 13.72 LowQual SOMATIC;DP=2;AC=2;AN=4;AF=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=41.5;QD=6.86;SOR=1.609 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-2.60133 1/1:1,1:2:3.0:40,3,0:1:50:2:.:1:.:.:.:.:-2.79535
+chr6 135528722 . A G 9918.85 REJECT NS=2;DP=365;DPB=417.0;AC=2;AN=4;AF=0.5;RO=93;AO=324;PRO=0.0;PAO=0.0;QR=3632;QA=12359;PQR=0.0;PQA=0.0;SRF=43;SRR=50;SAF=150;SAR=174;SRP=4.15441;SAP=6.8707;AB=0.776978;ABP=280.881;RUN=1;RPP=3.9754;RPPR=4.15441;RPL=168.0;RPR=156.0;EPP=3.9754;EPPR=3.22044;DPRA=0.0;ODDS=175.024;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989247;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.9605;Dels=0.0;FS=1.102;HaplotypeScore= [...]
+chr6 135528875 . C T 647.016 REJECT NS=2;DP=120;DPB=166.955;AC=2;AN=2;AF=0.0;RO=29;AO=16;PRO=24.5667;PAO=2.73333;QR=1035;QA=240;PQR=871.4;PQA=89.9;SRF=6;SRR=23;SAF=0;SAR=16;SRP=24.6501;SAP=37.7539;AB=0.133333;ABP=143.143;RUN=1;RPP=7.89611;RPPR=12.0706;RPL=11.0;RPR=5.0;EPP=7.89611;EPPR=3.08518;DPRA=0.0;ODDS=38.2594;GTI=0;TYPE=snp;CIGAR=1X21M;NUMALT=5;MEANALT=13.0;LEN=1;MQM=58.75;MQMR=59.4483;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;ALERT;BaseQRankSum=0.653;De [...]
+chr6 135528875 . C CT 647.016 REJECT NS=2;DP=120;DPB=166.955;AC=2;AN=4;AF=0.5;RO=29;AO=33;PRO=24.5667;PAO=24.0667;QR=1035;QA=814;PQR=871.4;PQA=840.4;SRF=6;SRR=23;SAF=9;SAR=24;SRP=24.6501;SAP=17.8158;AB=0.275;ABP=55.7771;RUN=1;RPP=6.23461;RPPR=12.0706;RPL=20.0;RPR=13.0;EPP=3.60252;EPPR=3.08518;DPRA=0.0;ODDS=38.2594;GTI=0;TYPE=ins;CIGAR=1M1I21M;NUMALT=5;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=59.4483;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;ALERT;BaseQRankSum=0.5845; [...]
+chr6 135528875 . C TT 647.016 REJECT NS=2;DP=120;DPB=166.955;AC=2;AN=2;AF=0.0;RO=29;AO=3;PRO=24.5667;PAO=2.73333;QR=1035;QA=30;PQR=871.4;PQA=89.9;SRF=6;SRR=23;SAF=0;SAR=3;SRP=24.6501;SAP=9.52472;AB=0.09375;ABP=48.8827;RUN=1;RPP=3.73412;RPPR=12.0706;RPL=1.0;RPR=2.0;EPP=3.73412;EPPR=3.08518;DPRA=0.0;ODDS=38.2594;GTI=0;TYPE=complex;CIGAR=1X1I21M;NUMALT=5;MEANALT=12.0;LEN=23;MQM=62.6667;MQMR=59.4483;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr6 135528875 . C CTT 647.016 REJECT NS=2;DP=120;DPB=166.955;AC=2;AN=2;AF=0.0;RO=29;AO=11;PRO=24.5667;PAO=21.0667;QR=1035;QA=220;PQR=871.4;PQA=748.4;SRF=6;SRR=23;SAF=1;SAR=10;SRP=24.6501;SAP=19.0002;AB=0.0916667;ABP=176.8;RUN=1;RPP=12.6832;RPPR=12.0706;RPL=9.0;RPR=2.0;EPP=7.94546;EPPR=3.08518;DPRA=0.0;ODDS=38.2594;GTI=0;TYPE=ins;CIGAR=1M2I21M;NUMALT=5;MEANALT=13.0;LEN=2;MQM=59.9091;MQMR=59.4483;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr6 135528875 . CT C 647.016 REJECT NS=2;DP=120;DPB=166.955;AC=2;AN=2;AF=0.0;RO=29;AO=8;PRO=24.5667;PAO=14.8333;QR=1035;QA=243;PQR=871.4;PQA=517.0;SRF=6;SRR=23;SAF=2;SAR=6;SRP=24.6501;SAP=7.35324;AB=0.0666667;ABP=198.732;RUN=1;RPP=12.7819;RPPR=12.0706;RPL=7.0;RPR=1.0;EPP=4.09604;EPPR=3.08518;DPRA=0.0;ODDS=38.2594;GTI=0;TYPE=del;CIGAR=1M1D20M;NUMALT=5;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=59.4483;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr6 135529116 . C T 467.613 REJECT NS=2;DP=18;DPB=21.0;AC=3;AN=4;AF=0.75;RO=3;AO=18;PRO=0.0;PAO=0.0;QR=83;QA=639;PQR=0.0;PQA=0.0;SRF=0;SRR=3;SAF=0;SAR=18;SRP=9.52472;SAP=42.0968;AB=0.6;ABP=3.44459;RUN=1;RPP=4.9405;RPPR=3.73412;RPL=7.0;RPR=11.0;EPP=4.9405;EPPR=3.73412;DPRA=0.0;ODDS=4.33518;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.3333;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.123;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=1;MLEAF=0.75;MQ [...]
+chr6 135529211 . T A 49.2151 REJECT NS=2;DP=9;DPB=9.0;AC=2;AN=4;AF=0.5;RO=4;AO=5;PRO=0.0;PAO=0.0;QR=134;QA=154;PQR=0.0;PQA=0.0;SRF=0;SRR=4;SAF=0;SAR=5;SRP=11.6962;SAP=13.8677;AB=0.555556;ABP=3.25157;RUN=1;RPP=13.8677;RPPR=5.18177;RPL=5.0;RPR=0.0;EPP=13.8677;EPPR=5.18177;DPRA=0.0;ODDS=3.92914;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=47.0;PAIRED=1.0;PAIREDR=0.5;technology.ILLUMINA=1.0;MQ0=1;BaseQRankSum=-0.55;Dels=0.0;FS=0.0;HaplotypeScore=3.9951;MLEAC=1;MLEAF=0.5;M [...]
+chr6 135529561 . C T 659.653 REJECT NS=2;DP=26;DPB=30.0;AC=2;AN=4;AF=0.5;RO=4;AO=26;PRO=0.0;PAO=0.0;QR=147;QA=987;PQR=0.0;PQA=0.0;SRF=4;SRR=0;SAF=26;SAR=0;SRP=11.6962;SAP=59.4686;AB=0.866667;ABP=38.0434;RUN=1;RPP=24.391;RPPR=5.18177;RPL=5.0;RPR=21.0;EPP=24.391;EPPR=5.18177;DPRA=0.0;ODDS=1.93868;GTI=1;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.775;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=1;MLEAF=0.5;M [...]
+chr6 135529684 . G GT 266.301 REJECT NS=2;DP=36;DPB=56.16;AC=2;AN=3;AF=0.25;RO=6;AO=10;PRO=15.0833;PAO=16.0833;QR=207;QA=377;PQR=488.083;PQA=528.083;SRF=6;SRR=0;SAF=10;SAR=0;SRP=16.0391;SAP=24.725;AB=0.277778;ABP=18.4519;RUN=1;RPP=3.87889;RPPR=3.0103;RPL=6.0;RPR=4.0;EPP=3.87889;EPPR=3.0103;DPRA=0.0;ODDS=0.211229;GTI=0;TYPE=ins;CIGAR=1M1I24M;NUMALT=3;MEANALT=10.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.9;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.778;FS=0.0;MLEAC [...]
+chr6 135529684 . G GTT 266.301 REJECT NS=2;DP=36;DPB=56.16;AC=2;AN=3;AF=0.25;RO=6;AO=3;PRO=15.0833;PAO=15.0833;QR=207;QA=109;PQR=488.083;PQA=488.083;SRF=6;SRR=0;SAF=3;SAR=0;SRP=16.0391;SAP=9.52472;AB=0.0833333;ABP=57.2971;RUN=1;RPP=3.73412;RPPR=3.0103;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=3.0103;DPRA=0.0;ODDS=0.211229;GTI=0;TYPE=ins;CIGAR=1M2I24M;NUMALT=3;MEANALT=10.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr6 135529702 . A TT 266.301 REJECT NS=2;DP=36;DPB=56.16;AC=2;AN=2;AF=0.0;RO=6;AO=3;PRO=15.0833;PAO=8.75;QR=207;QA=55;PQR=488.083;PQA=274.75;SRF=6;SRR=0;SAF=3;SAR=0;SRP=16.0391;SAP=9.52472;AB=0.0833333;ABP=57.2971;RUN=1;RPP=3.73412;RPPR=3.0103;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=3.0103;DPRA=0.0;ODDS=0.211229;GTI=0;TYPE=complex;CIGAR=1M1I17M1X6M;NUMALT=3;MEANALT=10.0;LEN=26;MQM=55.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr6 135531451 . C G 12596.8 REJECT NS=2;DP=450;DPB=513.0;AC=2;AN=4;AF=0.5;RO=107;AO=406;PRO=0.0;PAO=0.0;QR=4154;QA=15659;PQR=0.0;PQA=0.0;SRF=57;SRR=50;SAF=229;SAR=177;SRP=4.00471;SAP=17.4725;AB=0.791423;ABP=381.435;RUN=1;RPP=9.19311;RPPR=3.51765;RPL=220.0;RPR=186.0;EPP=15.3331;EPPR=3.51765;DPRA=0.0;ODDS=94.4542;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997537;PAIREDR=0.990654;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.2145;Dels=0.0;FS=1.358;Haploty [...]
+chr6 135531639 . G T 13671.9 REJECT NS=2;DP=499;DPB=569.0;AC=2;AN=4;AF=0.5;RO=123;AO=445;PRO=0.0;PAO=0.0;QR=4648;QA=17012;PQR=0.0;PQA=0.0;SRF=58;SRR=65;SAF=196;SAR=249;SRP=3.87536;SAP=16.7174;AB=0.782074;ABP=396.245;RUN=1;RPP=13.7896;RPPR=3.45166;RPL=246.0;RPR=199.0;EPP=4.10824;EPPR=8.11238;DPRA=0.0;ODDS=119.758;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9865;MQMR=60.0;PAIRED=0.993258;PAIREDR=0.98374;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4485;Dels=0.0;FS=4.666;Haplo [...]
+chr6 135531800 . T C 10358.7 REJECT NS=2;DP=384;DPB=446.0;AC=2;AN=4;AF=0.5;RO=101;AO=343;PRO=0.0;PAO=0.0;QR=3882;QA=12948;PQR=0.0;PQA=0.0;SRF=46;SRR=55;SAF=190;SAR=153;SRP=4.75178;SAP=11.6772;AB=0.769058;ABP=283.452;RUN=1;RPP=15.8302;RPPR=3.54779;RPL=194.0;RPR=149.0;EPP=3.32051;EPPR=4.06379;DPRA=0.0;ODDS=86.0357;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997085;PAIREDR=0.980198;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.5895;Dels=0.0;FS=6.8475;Haplot [...]
+chr6 135533284 . T G 8296.39 REJECT NS=2;DP=304;DPB=353.0;AC=2;AN=4;AF=0.5;RO=78;AO=275;PRO=0.0;PAO=0.0;QR=3013;QA=10462;PQR=0.0;PQA=0.0;SRF=27;SRR=51;SAF=94;SAR=181;SRP=19.0458;SAP=62.7771;AB=0.779037;ABP=241.743;RUN=1;RPP=9.65106;RPPR=4.01252;RPL=123.0;RPR=152.0;EPP=32.3923;EPPR=7.01917;DPRA=0.0;ODDS=141.707;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.956364;PAIREDR=0.884615;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.342;Dels=0.0;FS=2.935;HaplotypeS [...]
+chr6 135534823 . T C 5182.32 REJECT NS=2;DP=143;DPB=167.0;AC=4;AN=4;AF=1.0;RO=0;AO=167;PRO=0.0;PAO=0.0;QR=0;QA=6248;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=37;SAR=130;SRP=0.0;SAP=115.472;AB=0.0;ABP=0.0;RUN=1;RPP=13.9457;RPPR=0.0;RPL=98.0;RPR=69.0;EPP=27.0525;EPPR=0.0;DPRA=0.0;ODDS=33.0507;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8802;MQMR=0.0;PAIRED=0.994012;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=59.93;QD=29.375;SOR=2. [...]
+chr6 135535018 . G A 7692.53 REJECT NS=2;DP=277;DPB=314.0;AC=2;AN=4;AF=0.5;RO=58;AO=256;PRO=0.0;PAO=0.0;QR=2214;QA=9692;PQR=0.0;PQA=0.0;SRF=39;SRR=19;SAF=163;SAR=93;SRP=17.986;SAP=44.5736;AB=0.815287;ABP=274.126;RUN=1;RPP=65.7455;RPPR=6.75422;RPL=85.0;RPR=171.0;EPP=11.6962;EPPR=12.5947;DPRA=0.0;ODDS=4.7613;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992188;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.964;Dels=0.0;FS=0.4645;HaplotypeScore=2.8 [...]
+chr6 135535240 . C T 3880.62 REJECT NS=2;DP=159;DPB=185.0;AC=2;AN=4;AF=0.5;RO=43;AO=141;PRO=0.0;PAO=0.0;QR=1583;QA=5259;PQR=0.0;PQA=0.0;SRF=5;SRR=38;SAF=17;SAR=124;SRP=58.0041;SAP=179.331;AB=0.762162;ABP=113.45;RUN=1;RPP=43.067;RPPR=4.27278;RPL=96.0;RPR=45.0;EPP=60.3156;EPPR=5.48477;DPRA=0.0;ODDS=58.511;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.978723;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1095;Dels=0.0;FS=0.727;HaplotypeScore=1.9947 [...]
+chr6 135535447 . T C 6004.35 REJECT NS=2;DP=235;DPB=266.0;AC=2;AN=4;AF=0.5;RO=59;AO=207;PRO=0.0;PAO=0.0;QR=2138;QA=7909;PQR=0.0;PQA=0.0;SRF=43;SRR=16;SAF=177;SAR=30;SRP=29.8409;SAP=229.693;AB=0.778195;ABP=181.822;RUN=1;RPP=55.8914;RPPR=9.23028;RPL=68.0;RPR=139.0;EPP=30.2953;EPPR=5.99147;DPRA=0.0;ODDS=34.3347;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0966;MQMR=60.0;PAIRED=0.995169;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.443;Dels=0.0;FS=4.942;HaplotypeScore [...]
+chr6 135535469 . G GA 177.405 REJECT NS=2;DP=308;DPB=355.688;AC=2;AN=4;AF=0.5;RO=239;AO=31;PRO=32.0;PAO=29.0;QR=8946;QA=1094;PQR=1163.83;PQA=1052.83;SRF=185;SRR=54;SAF=22;SAR=9;SRP=158.929;SAP=14.8483;AB=0.100649;ABP=429.662;RUN=1;RPP=3.64073;RPPR=6.29022;RPL=14.0;RPR=17.0;EPP=11.486;EPPR=10.6513;DPRA=0.0;ODDS=0.729642;GTI=0;TYPE=ins;CIGAR=1M1I15M;NUMALT=2;MEANALT=8.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.967742;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr6 135535469 . GA G 177.405 REJECT NS=2;DP=308;DPB=355.688;AC=2;AN=2;AF=0.0;RO=239;AO=22;PRO=32.0;PAO=29.0;QR=8946;QA=805;PQR=1163.83;PQA=1054.33;SRF=185;SRR=54;SAF=17;SAR=5;SRP=158.929;SAP=17.2236;AB=0.0714286;ABP=494.383;RUN=1;RPP=6.56362;RPPR=6.29022;RPL=8.0;RPR=14.0;EPP=4.58955;EPPR=10.6513;DPRA=0.0;ODDS=0.729642;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=2;MEANALT=8.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr6 135536496 . T C 11781.3 REJECT NS=2;DP=445;DPB=499.0;AC=2;AN=4;AF=0.5;RO=115;AO=384;PRO=0.0;PAO=0.0;QR=4311;QA=14678;PQR=0.0;PQA=0.0;SRF=51;SRR=64;SAF=181;SAR=203;SRP=6.20142;SAP=5.74726;AB=0.769539;ABP=317.9;RUN=1;RPP=5.27225;RPPR=7.25883;RPL=182.0;RPR=202.0;EPP=3.03292;EPPR=4.53977;DPRA=0.0;ODDS=140.563;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997396;PAIREDR=0.991304;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.727;Dels=0.0;FS=1.902;HaplotypeS [...]
+chr6 135536586 . A G 11412.5 REJECT NS=2;DP=427;DPB=486.0;AC=2;AN=4;AF=0.5;RO=111;AO=374;PRO=0.0;PAO=0.0;QR=4209;QA=14257;PQR=0.0;PQA=0.0;SRF=59;SRR=52;SAF=201;SAR=173;SRP=3.96888;SAP=7.56226;AB=0.769547;ABP=309.715;RUN=1;RPP=31.4601;RPPR=21.8102;RPL=222.0;RPR=152.0;EPP=3.38189;EPPR=3.18637;DPRA=0.0;ODDS=201.747;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994652;PAIREDR=0.981982;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0095;Dels=0.0;FS=1.773;Haploty [...]
+chr6 135537890 . C G 12114.2 REJECT NS=2;DP=441;DPB=503.0;AC=2;AN=4;AF=0.5;RO=110;AO=393;PRO=0.0;PAO=0.0;QR=4215;QA=15067;PQR=0.0;PQA=0.0;SRF=50;SRR=60;SAF=215;SAR=178;SRP=4.98437;SAP=10.5745;AB=0.781312;ABP=348.758;RUN=1;RPP=4.60713;RPPR=4.2737;RPL=205.0;RPR=188.0;EPP=4.60713;EPPR=4.2737;DPRA=0.0;ODDS=145.823;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994911;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4395;Dels=0.0;FS=6.8875;HaplotypeScor [...]
+chr6 135537897 . A G 11688.1 REJECT NS=2;DP=438;DPB=500.0;AC=2;AN=4;AF=0.5;RO=110;AO=390;PRO=0.0;PAO=0.0;QR=4127;QA=14586;PQR=0.0;PQA=0.0;SRF=53;SRR=57;SAF=218;SAR=172;SRP=3.32615;SAP=14.7919;AB=0.78;ABP=343.497;RUN=1;RPP=4.1016;RPPR=3.08926;RPL=202.0;RPR=188.0;EPP=3.56709;EPPR=4.2737;DPRA=0.0;ODDS=134.333;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994872;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.276;Dels=0.0;FS=6.8925;HaplotypeScore=4.8 [...]
+chr6 135538507 . C CA 2357.8900000000003 REJECT NS=2;DP=125;DPB=195.462;AC=3;AN=4;AF=0.5;RO=13;AO=94;PRO=39.6667;PAO=46.6667;QR=492;QA=3113;PQR=1335.33;PQA=1559.83;SRF=9;SRR=4;SAF=69;SAR=25;SRP=7.18621;SAP=47.7334;AB=0.712121;ABP=54.5992;RUN=1;RPP=26.6655;RPPR=16.5402;RPL=31.0;RPR=63.0;EPP=3.1027;EPPR=16.5402;DPRA=0.0;ODDS=6.59421;GTI=0;TYPE=ins;CIGAR=1M1I25M;NUMALT=2;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989362;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRan [...]
+chr6 135538507 . C CAA 2690.05 REJECT NS=2;DP=132;DPB=195.462;AC=2;AN=2;AF=0.0;RO=13;AO=8;PRO=39.6667;PAO=38.6667;QR=492;QA=235;PQR=1335.33;PQA=1286.83;SRF=9;SRR=4;SAF=6;SAR=2;SRP=7.18621;SAP=7.35324;AB=0.0606061;ABP=224.369;RUN=1;RPP=4.09604;RPPR=16.5402;RPL=5.0;RPR=3.0;EPP=12.7819;EPPR=16.5402;DPRA=0.0;ODDS=6.59421;GTI=0;TYPE=ins;CIGAR=1M2I25M;NUMALT=2;MEANALT=9.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr6 135538592 . G A 12043.0 REJECT NS=2;DP=331;DPB=384.0;AC=4;AN=4;AF=1.0;RO=0;AO=384;PRO=0.0;PAO=0.0;QR=0;QA=14258;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=290;SAR=94;SRP=0.0;SAP=220.248;AB=0.0;ABP=0.0;RUN=1;RPP=3.10078;RPPR=0.0;RPL=194.0;RPR=190.0;EPP=18.3011;EPPR=0.0;DPRA=0.0;ODDS=69.0972;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.026;MQMR=0.0;PAIRED=0.994792;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8212;MLEAC=2;MLEAF=1.0;MQ=60.02;QD=30.595;SOR [...]
+chr6 135538639 . A G 12048.8 REJECT NS=2;DP=325;DPB=373.0;AC=4;AN=4;AF=1.0;RO=0;AO=373;PRO=0.0;PAO=0.0;QR=0;QA=14037;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=231;SAR=142;SRP=0.0;SAP=49.1235;AB=0.0;ABP=0.0;RUN=1;RPP=3.15584;RPPR=0.0;RPL=184.0;RPR=189.0;EPP=23.2754;EPPR=0.0;DPRA=0.0;ODDS=63.5599;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994638;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9329;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.32;SOR=1. [...]
+chr6 136943947 . GTACTACAGAACAGCTTTTAGTAGCTACAAT G . PASS AC=2;AN=4;END=136943977;HOMLEN=4;HOMSEQ=TACT;SVLEN=-30;SVTYPE=DEL GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:23,51:51:69:74:.:.:.:1:.:.:-0.00135401 0/1:119,41:41:26:160:.:.:.:1:.:.:-0.00154183
+chr6 136977568 . T C 1951.28 PASS SOMATIC;NS=2;DP=280;DPB=280.0;AC=1;AN=3;AF=0.25;RO=199;AO=78;PRO=0.0;PAO=0.0;QR=7598;QA=2957;PQR=0.0;PQA=0.0;SRF=56;SRR=143;SAF=12;SAR=66;SRP=85.6026;SAP=84.19;AB=0.366197;ABP=36.1329;RUN=1;RPP=3.45573;RPPR=17.9487;RPL=41.0;RPR=37.0;EPP=4.79202;EPPR=3.2831;DPRA=3.1791;ODDS=42.8346;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994975;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.087;Dels=0.0;FS=15.235;Hap [...]
+chr6 137113137 . G A 7985.79 REJECT NS=2;DP=229;DPB=265.0;AC=4;AN=4;AF=1.0;RO=0;AO=263;PRO=0.0;PAO=0.0;QR=0;QA=9450;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=94;SAR=169;SRP=0.0;SAP=49.4534;AB=0.0;ABP=0.0;RUN=1;RPP=10.9448;RPPR=0.0;RPL=147.0;RPR=116.0;EPP=7.37801;EPPR=0.0;DPRA=0.0;ODDS=48.6104;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.8713;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.39;SOR=1.533 GT: [...]
+chr6 138195961 . TCTC T 732.317 REJECT NS=2;DP=210;DPB=211.818;AC=2;AN=4;AF=0.5;RO=165;AO=44;PRO=19.5;PAO=10.5;QR=6240;QA=1592;PQR=674.5;PQA=353.5;SRF=140;SRR=25;SAF=38;SAR=6;SRP=177.057;SAP=53.5464;AB=0.209524;ABP=156.916;RUN=1;RPP=7.94546;RPPR=23.0273;RPL=17.0;RPR=27.0;EPP=3.20771;EPPR=6.81367;DPRA=0.0;ODDS=47.9549;GTI=0;TYPE=del;CIGAR=1M3D7M;NUMALT=1;MEANALT=1.5;LEN=3;MQM=60.6818;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;END=138195964;HOMLEN=5;HOMSEQ=CTCCT;SVLEN=-3;SVTY [...]
+chr6 145522157 . C T 1542.49 REJECT NS=2;DP=173;DPB=228.857;AC=2;AN=2;AF=0.0;RO=30;AO=8;PRO=27.8;PAO=5.15;QR=1076;QA=120;PQR=1003.42;PQA=180.4;SRF=11;SRR=19;SAF=0;SAR=8;SRP=7.64277;SAP=20.3821;AB=0.0462428;ABP=312.401;RUN=1;RPP=7.35324;RPPR=38.0434;RPL=2.0;RPR=6.0;EPP=7.35324;EPPR=3.0103;DPRA=0.0;ODDS=6.88813;GTI=0;TYPE=snp;CIGAR=1X20M;NUMALT=5;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMIC [...]
+chr6 145522157 . C CT 1542.49 REJECT NS=2;DP=173;DPB=228.857;AC=2;AN=2;AF=0.0;RO=30;AO=7;PRO=27.8;PAO=22.8;QR=1076;QA=186;PQR=1003.42;PQA=802.417;SRF=11;SRR=19;SAF=3;SAR=4;SRP=7.64277;SAP=3.32051;AB=0.0510949;ABP=242.807;RUN=1;RPP=18.2106;RPPR=38.0434;RPL=7.0;RPR=0.0;EPP=3.32051;EPPR=3.0103;DPRA=0.0;ODDS=6.88813;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=5;MEANALT=17.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr6 145522157 . CT C 1542.49 REJECT NS=2;DP=173;DPB=228.857;AC=2;AN=4;AF=0.5;RO=30;AO=81;PRO=27.8;PAO=28.3;QR=1076;QA=2008;PQR=1003.42;PQA=985.25;SRF=11;SRR=19;SAF=20;SAR=61;SRP=7.64277;SAP=48.0751;AB=0.468208;ABP=4.52908;RUN=1;RPP=43.7857;RPPR=38.0434;RPL=60.0;RPR=21.0;EPP=3.25157;EPPR=3.0103;DPRA=0.0;ODDS=6.88813;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=5;MEANALT=11.5;LEN=1;MQM=60.1235;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-2.05;FS=9.513;ML [...]
+chr6 145522157 . CTT C 1542.49 REJECT NS=2;DP=173;DPB=228.857;AC=2;AN=2;AF=0.0;RO=30;AO=22;PRO=27.8;PAO=17.55;QR=1076;QA=534;PQR=1003.42;PQA=629.083;SRF=11;SRR=19;SAF=1;SAR=21;SRP=7.64277;SAP=42.4916;AB=0.127168;ABP=211.886;RUN=1;RPP=22.3561;RPPR=38.0434;RPL=18.0;RPR=4.0;EPP=17.2236;EPPR=3.0103;DPRA=0.0;ODDS=6.88813;GTI=0;TYPE=del;CIGAR=1M2D18M;NUMALT=5;MEANALT=11.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.168;FS=2.907 [...]
+chr6 145522157 . CTTT C 1542.49 REJECT NS=2;DP=173;DPB=228.857;AC=2;AN=2;AF=0.0;RO=30;AO=10;PRO=27.8;PAO=14.4;QR=1076;QA=309;PQR=1003.42;PQA=517.433;SRF=11;SRR=19;SAF=5;SAR=5;SRP=7.64277;SAP=3.0103;AB=0.0578035;ABP=296.837;RUN=1;RPP=10.8276;RPPR=38.0434;RPL=8.0;RPR=2.0;EPP=6.48466;EPPR=3.0103;DPRA=0.0;ODDS=6.88813;GTI=0;TYPE=del;CIGAR=1M3D17M;NUMALT=5;MEANALT=11.5;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr6 152129077 . T C 11889.6 REJECT NS=2;DP=433;DPB=497.0;AC=2;AN=4;AF=0.5;RO=112;AO=385;PRO=0.0;PAO=0.0;QR=4186;QA=14831;PQR=0.0;PQA=0.0;SRF=63;SRR=49;SAF=208;SAR=177;SRP=6.81038;SAP=8.43052;AB=0.774648;ABP=328.639;RUN=1;RPP=18.8536;RPPR=3.32051;RPL=166.0;RPR=219.0;EPP=21.3353;EPPR=6.81038;DPRA=0.0;ODDS=129.514;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997403;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.549;Dels=0.0;FS=1.7025;HaplotypeSco [...]
+chr6 152201875 . T C 8889.720000000001 REJECT NS=2;DP=363;DPB=413.0;AC=3;AN=4;AF=0.75;RO=107;AO=306;PRO=0.0;PAO=0.0;QR=4181;QA=11876;PQR=0.0;PQA=0.0;SRF=56;SRR=51;SAF=162;SAR=144;SRP=3.51765;SAP=5.30951;AB=0.659236;ABP=72.1655;RUN=1;RPP=4.82696;RPPR=4.00471;RPL=161.0;RPR=145.0;EPP=5.84883;EPPR=3.19295;DPRA=0.0;ODDS=62.7742;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990654;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.18;Dels=0.0;FS=0.217;Ha [...]
+chr6 152265282 . A AT 2722.09 REJECT NS=2;DP=175;DPB=236.0;AC=3;AN=4;AF=0.75;RO=64;AO=126;PRO=19.0;PAO=19.5;QR=2410;QA=4474;PQR=616.333;PQA=633.833;SRF=46;SRR=18;SAF=96;SAR=30;SRP=29.6108;SAP=78.0812;AB=0.546667;ABP=5.84769;RUN=1;RPP=42.7172;RPPR=29.6108;RPL=39.0;RPR=87.0;EPP=3.28604;EPPR=3.0103;DPRA=0.0;ODDS=9.17384;GTI=0;TYPE=ins;CIGAR=1M1I12M;NUMALT=2;MEANALT=4.5;LEN=1;MQM=60.4762;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.7035;FS= [...]
+chr6 152265282 . A ATT 3451.45 REJECT SOMATIC;NS=2;DP=200;DPB=236.0;AC=1;AN=3;AF=0.0;RO=64;AO=4;PRO=19.0;PAO=19.5;QR=2410;QA=150;PQR=616.333;PQA=633.833;SRF=46;SRR=18;SAF=3;SAR=1;SRP=29.6108;SAP=5.18177;AB=0.00666667;ABP=320.103;RUN=1;RPP=11.6962;RPPR=29.6108;RPL=0.0;RPR=4.0;EPP=5.18177;EPPR=3.0103;DPRA=0.0;ODDS=9.17384;GTI=0;TYPE=ins;CIGAR=1M2I12M;NUMALT=2;MEANALT=4.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr6 152265522 . G C 7969.6900000000005 REJECT NS=2;DP=348;DPB=398.0;AC=3;AN=4;AF=0.75;RO=111;AO=285;PRO=0.0;PAO=0.0;QR=4273;QA=10913;PQR=0.0;PQA=0.0;SRF=53;SRR=58;SAF=153;SAR=132;SRP=3.49937;SAP=6.37037;AB=0.622074;ABP=41.7119;RUN=1;RPP=12.3438;RPPR=6.31642;RPL=160.0;RPR=125.0;EPP=3.20078;EPPR=3.18637;DPRA=0.0;ODDS=62.7589;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989474;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.419;Dels=0.0;FS=4.646; [...]
+chr6 152420095 . G A 4046.8100000000004 REJECT NS=2;DP=272;DPB=311.0;AC=2;AN=4;AF=0.5;RO=159;AO=149;PRO=0.0;PAO=0.0;QR=6098;QA=5715;PQR=0.0;PQA=0.0;SRF=44;SRR=115;SAF=34;SAR=115;SRP=71.8555;SAP=98.628;AB=0.4791;ABP=4.1903;RUN=1;RPP=15.2667;RPPR=9.03306;RPL=89.0;RPR=60.0;EPP=3.72441;EPPR=10.2349;DPRA=0.0;ODDS=244.885;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=59.8742;PAIRED=0.993289;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.478;Dels=0.0;FS=2.8565;Haplo [...]
+chr6 152443744 . G T 5471.01 REJECT NS=2;DP=353;DPB=405.0;AC=2;AN=4;AF=0.5;RO=209;AO=196;PRO=0.0;PAO=0.0;QR=7904;QA=7445;PQR=0.0;PQA=0.0;SRF=69;SRR=140;SAF=66;SAR=130;SRP=55.3854;SAP=48.3896;AB=0.483951;ABP=3.91642;RUN=1;RPP=5.84651;RPPR=17.234;RPL=106.0;RPR=90.0;EPP=3.71935;EPPR=3.5194;DPRA=0.0;ODDS=297.41;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989796;PAIREDR=0.990431;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.2665;Dels=0.0;FS=10.792;HaplotypeS [...]
+chr6 152453291 . G A 1666.79 REJECT NS=2;DP=394;DPB=444.0;AC=2;AN=4;AF=0.5;RO=357;AO=86;PRO=0.0;PAO=0.0;QR=13551;QA=3252;PQR=0.0;PQA=0.0;SRF=167;SRR=190;SAF=43;SAR=43;SRP=6.22797;SAP=3.0103;AB=0.193694;ABP=364.844;RUN=1;RPP=3.41429;RPPR=10.4614;RPL=41.0;RPR=45.0;EPP=7.95924;EPPR=46.9568;DPRA=0.0;ODDS=74.2674;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988796;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.187;Dels=0.0;FS=2.8545;HaplotypeScore=1 [...]
+chr6 152464839 . A G 5825.0650000000005 REJECT NS=2;DP=369;DPB=418.0;AC=2;AN=4;AF=0.5;RO=213;AO=205;PRO=0.0;PAO=0.0;QR=8074;QA=7877;PQR=0.0;PQA=0.0;SRF=109;SRR=104;SAF=100;SAR=105;SRP=3.26517;SAP=3.27511;AB=0.490431;ABP=3.34277;RUN=1;RPP=7.68161;RPPR=4.73321;RPL=92.0;RPR=113.0;EPP=11.9186;EPPR=5.30411;DPRA=0.0;ODDS=310.787;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990244;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.728;Dels=0.0;FS=1.3565;H [...]
+chr6 152489294 . T C 13772.75 REJECT NS=2;DP=368;DPB=420.0;AC=4;AN=4;AF=1.0;RO=0;AO=420;PRO=0.0;PAO=0.0;QR=0;QA=15894;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=202;SAR=218;SRP=0.0;SAP=4.33386;AB=0.0;ABP=0.0;RUN=1;RPP=29.8125;RPPR=0.0;RPL=246.0;RPR=174.0;EPP=32.8732;EPPR=0.0;DPRA=0.0;ODDS=69.152;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9857;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=9.8564;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.765;SOR=0.7 [...]
+chr6 152529260 . G A 1965.57 REJECT NS=2;DP=337;DPB=392.0;AC=2;AN=4;AF=0.5;RO=299;AO=93;PRO=0.0;PAO=0.0;QR=10937;QA=3451;PQR=0.0;PQA=0.0;SRF=119;SRR=180;SAF=41;SAR=52;SRP=30.0339;SAP=5.83555;AB=0.237245;ABP=238.083;RUN=1;RPP=6.95631;RPPR=3.36616;RPL=40.0;RPR=53.0;EPP=20.0318;EPPR=16.4386;DPRA=0.0;ODDS=89.1369;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989247;PAIREDR=0.993311;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.442;Dels=0.0;FS=1.132;HaplotypeSc [...]
+chr6 152540278 . A C 13595.9 REJECT NS=2;DP=362;DPB=407.0;AC=4;AN=4;AF=1.0;RO=1;AO=406;PRO=0.0;PAO=0.0;QR=36;QA=15519;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=196;SAR=210;SRP=5.18177;SAP=4.0586;AB=0.0;ABP=0.0;RUN=1;RPP=5.14968;RPPR=5.18177;RPL=213.0;RPR=193.0;EPP=24.9176;EPPR=5.18177;DPRA=0.0;ODDS=59.8722;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995074;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.273;Dels=0.0;FS=1.5395;HaplotypeScore=11.6473;MLEAC [...]
+chr6 152542548 . A G 7620.73 REJECT NS=2;DP=289;DPB=332.0;AC=2;AN=4;AF=0.5;RO=74;AO=257;PRO=0.0;PAO=0.0;QR=2850;QA=9699;PQR=0.0;PQA=0.0;SRF=54;SRR=20;SAF=168;SAR=89;SRP=36.9322;SAP=55.7424;AB=0.774096;ABP=219.66;RUN=1;RPP=82.5098;RPPR=4.06669;RPL=80.0;RPR=177.0;EPP=14.5774;EPPR=12.5178;DPRA=0.0;ODDS=56.9279;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992218;PAIREDR=0.986486;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0005;Dels=0.0;FS=3.026;HaplotypeSco [...]
+chr6 152555112 . C T 1773.69 REJECT NS=2;DP=322;DPB=375.0;AC=2;AN=4;AF=0.5;RO=287;AO=86;PRO=0.0;PAO=0.0;QR=10907;QA=3328;PQR=0.0;PQA=0.0;SRF=90;SRR=197;SAF=28;SAR=58;SRP=89.6346;SAP=25.735;AB=0.229333;ABP=241.635;RUN=1;RPP=25.735;RPPR=74.1998;RPL=58.0;RPR=28.0;EPP=3.1113;EPPR=3.01787;DPRA=0.0;ODDS=127.436;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996516;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6145;Dels=0.0;FS=1.16;HaplotypeScore=3.857 [...]
+chr6 152558111 . T TA 541.507 REJECT NS=2;DP=160;DPB=176.417;AC=2;AN=4;AF=0.5;RO=124;AO=33;PRO=14.5;PAO=11.5;QR=4646;QA=1227;PQR=503.0;PQA=351.0;SRF=9;SRR=115;SAF=1;SAR=32;SRP=199.774;SAP=66.2462;AB=0.20625;ABP=122.93;RUN=1;RPP=17.8158;RPPR=104.159;RPL=24.0;RPR=9.0;EPP=22.0271;EPPR=70.3259;DPRA=0.0;ODDS=3.17695;GTI=1;TYPE=ins;CIGAR=1M1I11M;NUMALT=1;MEANALT=2.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991935;technology.ILLUMINA=1.0;BaseQRankSum=-1.102;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.2 [...]
+chr6 152570415 . G A 8126.665 REJECT NS=2;DP=217;DPB=247.0;AC=4;AN=4;AF=1.0;RO=0;AO=247;PRO=0.0;PAO=0.0;QR=0;QA=9458;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=51;SAR=196;SRP=0.0;SAP=187.849;AB=0.0;ABP=0.0;RUN=1;RPP=60.6906;RPPR=0.0;RPL=164.0;RPR=83.0;EPP=3.08942;EPPR=0.0;DPRA=0.0;ODDS=41.127;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991903;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8895;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.36;SOR=2.379 [...]
+chr6 152615200 . G A 2935.9 PASS SOMATIC;NS=2;DP=389;DPB=389.0;AC=1;AN=3;AF=0.25;RO=277;AO=111;PRO=0.0;PAO=0.0;QR=10577;QA=4267;PQR=0.0;PQA=0.0;SRF=105;SRR=172;SAF=32;SAR=79;SRP=38.2007;SAP=46.2246;AB=0.372483;ABP=45.099;RUN=1;RPP=3.96888;RPPR=14.9338;RPL=59.0;RPR=52.0;EPP=4.59489;EPPR=12.6134;DPRA=3.27473;ODDS=57.1099;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99639;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.23;Dels=0.0;FS=8.819;H [...]
+chr6 152629617 . C T 2015.47 PASS SOMATIC;NS=2;DP=338;DPB=338.0;AC=1;AN=3;AF=0.25;RO=256;AO=82;PRO=0.0;PAO=0.0;QR=9303;QA=3126;PQR=0.0;PQA=0.0;SRF=179;SRR=77;SAF=58;SAR=24;SRP=91.2603;SAP=33.6228;AB=0.327935;ABP=66.5281;RUN=1;RPP=9.78953;RPPR=35.6163;RPL=33.0;RPR=49.0;EPP=9.78953;EPPR=3.55317;DPRA=0.0;ODDS=50.015;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996094;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.478;Dels=0.0;FS=0.542;Haplo [...]
+chr6 152629772 . G A 560.371 REJECT NS=2;DP=134;DPB=176.0;AC=2;AN=2;AF=0.0;RO=56;AO=7;PRO=40.6667;PAO=1.0;QR=2028;QA=98;PQR=1420.83;PQA=14.0;SRF=7;SRR=49;SAF=0;SAR=7;SRP=71.4117;SAP=18.2106;AB=0.0522388;ABP=236.363;RUN=1;RPP=3.32051;RPPR=12.937;RPL=3.0;RPR=4.0;EPP=3.32051;EPPR=3.16541;DPRA=0.0;ODDS=4.49007;GTI=0;TYPE=snp;CIGAR=1X27M;NUMALT=4;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV: [...]
+chr6 152629772 . G GA 560.371 REJECT NS=2;DP=134;DPB=176.0;AC=2;AN=3;AF=0.25;RO=56;AO=13;PRO=40.6667;PAO=21.6667;QR=2028;QA=336;PQR=1420.83;PQA=700.833;SRF=7;SRR=49;SAF=1;SAR=12;SRP=71.4117;SAP=23.2217;AB=0.0970149;ABP=192.026;RUN=1;RPP=3.17734;RPPR=12.937;RPL=7.0;RPR=6.0;EPP=3.17734;EPPR=3.16541;DPRA=0.0;ODDS=4.49007;GTI=0;TYPE=ins;CIGAR=1M1I27M;NUMALT=4;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr6 152629772 . GA G 560.371 REJECT NS=2;DP=134;DPB=176.0;AC=2;AN=3;AF=0.375;RO=56;AO=36;PRO=40.6667;PAO=21.1667;QR=2028;QA=935;PQR=1420.83;PQA=654.833;SRF=7;SRR=49;SAF=4;SAR=32;SRP=71.4117;SAP=50.3001;AB=0.268657;ABP=65.3024;RUN=1;RPP=3.0103;RPPR=12.937;RPL=18.0;RPR=18.0;EPP=3.9754;EPPR=3.16541;DPRA=0.0;ODDS=4.49007;GTI=0;TYPE=del;CIGAR=1M1D26M;NUMALT=4;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.1765;FS=0 [...]
+chr6 152629772 . GAA G 560.371 REJECT NS=2;DP=134;DPB=176.0;AC=2;AN=2;AF=0.0;RO=56;AO=6;PRO=40.6667;PAO=13.5;QR=2028;QA=131;PQR=1420.83;PQA=465.5;SRF=7;SRR=49;SAF=0;SAR=6;SRP=71.4117;SAP=16.0391;AB=0.0447761;ABP=244.206;RUN=1;RPP=3.0103;RPPR=12.937;RPL=3.0;RPR=3.0;EPP=3.0103;EPPR=3.16541;DPRA=0.0;ODDS=4.49007;GTI=0;TYPE=del;CIGAR=1M2D25M;NUMALT=4;MEANALT=11.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr6 152647681 . A T 4959.610000000001 REJECT NS=2;DP=325;DPB=375.0;AC=2;AN=4;AF=0.5;RO=193;AO=181;PRO=0.0;PAO=0.0;QR=7364;QA=6848;PQR=0.0;PQA=0.0;SRF=92;SRR=101;SAF=76;SAR=105;SRP=3.92164;SAP=13.0998;AB=0.482667;ABP=3.98891;RUN=1;RPP=4.46195;RPPR=3.11156;RPL=96.0;RPR=85.0;EPP=5.03781;EPPR=3.92164;DPRA=0.0;ODDS=303.634;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994475;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.563;Dels=0.0;FS=3.2595;Haplo [...]
+chr6 152652034 . A T 6351.135 REJECT NS=2;DP=361;DPB=423.0;AC=2;AN=4;AF=0.5;RO=198;AO=225;PRO=0.0;PAO=0.0;QR=7507;QA=8735;PQR=0.0;PQA=0.0;SRF=80;SRR=118;SAF=111;SAR=114;SRP=18.8467;SAP=3.09716;AB=0.531915;ABP=6.75262;RUN=1;RPP=7.26639;RPPR=3.18577;RPL=102.0;RPR=123.0;EPP=3.4832;EPPR=11.6085;DPRA=0.0;ODDS=375.924;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995556;PAIREDR=0.994949;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.354;Dels=0.0;FS=6.2015;Haploty [...]
+chr6 152653037 . T C 2976.6099999999997 REJECT NS=2;DP=200;DPB=227.0;AC=2;AN=4;AF=0.5;RO=118;AO=109;PRO=0.0;PAO=0.0;QR=4488;QA=4180;PQR=0.0;PQA=0.0;SRF=28;SRR=90;SAF=30;SAR=79;SRP=73.7488;SAP=50.8425;AB=0.480176;ABP=3.78514;RUN=1;RPP=47.0175;RPPR=11.917;RPL=78.0;RPR=31.0;EPP=3.98647;EPPR=4.85053;DPRA=0.0;ODDS=150.407;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990826;PAIREDR=0.991525;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.925;Dels=0.0;FS=2.025;Hap [...]
+chr6 152658142 . T C 4502.33 REJECT NS=2;DP=278;DPB=321.0;AC=2;AN=4;AF=0.5;RO=155;AO=166;PRO=0.0;PAO=0.0;QR=5996;QA=6346;PQR=0.0;PQA=0.0;SRF=45;SRR=110;SAF=56;SAR=110;SRP=62.2004;SAP=41.155;AB=0.517134;ABP=3.82883;RUN=1;RPP=18.1321;RPPR=7.05905;RPL=100.0;RPR=66.0;EPP=9.34158;EPPR=3.36054;DPRA=0.0;ODDS=244.626;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.5395;Dels=0.0;FS=2.0765;HaplotypeScore=0.9 [...]
+chr6 152665261 . C A 14630.55 REJECT NS=2;DP=393;DPB=449.0;AC=4;AN=4;AF=1.0;RO=0;AO=449;PRO=0.0;PAO=0.0;QR=0;QA=16939;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=256;SAR=193;SRP=0.0;SAP=22.2053;AB=0.0;ABP=0.0;RUN=1;RPP=3.40204;RPPR=0.0;RPL=229.0;RPR=220.0;EPP=15.5894;EPPR=0.0;DPRA=0.0;ODDS=73.5902;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997773;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8634;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.63;SOR=1 [...]
+chr6 152671475 . A C 10377.5 REJECT NS=2;DP=276;DPB=318.0;AC=4;AN=4;AF=1.0;RO=0;AO=317;PRO=0.0;PAO=0.0;QR=0;QA=12077;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=112;SAR=205;SRP=0.0;SAP=62.2566;AB=0.0;ABP=0.0;RUN=1;RPP=18.1421;RPPR=0.0;RPL=182.0;RPR=135.0;EPP=14.5253;EPPR=0.0;DPRA=0.0;ODDS=56.0487;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996845;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.745;SOR=1.28 [...]
+chr6 152671919 . G GA 4652.485 REJECT NS=2;DP=204;DPB=247.533;AC=4;AN=4;AF=1.0;RO=5;AO=178;PRO=20.0;PAO=23.5;QR=184;QA=6152;PQR=732.0;PQA=819.5;SRF=3;SRR=2;SAF=24;SAR=154;SRP=3.44459;SAP=209.178;AB=0.0;ABP=0.0;RUN=1;RPP=69.8136;RPPR=13.8677;RPL=126.0;RPR=52.0;EPP=13.9897;EPPR=3.44459;DPRA=0.0;ODDS=13.6494;GTI=0;TYPE=ins;CIGAR=1M1I14M;NUMALT=2;MEANALT=4.5;LEN=1;MQM=59.9494;MQMR=60.0;PAIRED=0.994382;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.357;FS=7.3885;M [...]
+chr6 152671919 . G GAA 5182.24 REJECT NS=2;DP=206;DPB=247.533;AC=0;AN=4;AF=0.0;RO=5;AO=16;PRO=20.0;PAO=18.5;QR=184;QA=468;PQR=732.0;PQA=679.5;SRF=3;SRR=2;SAF=1;SAR=15;SRP=3.44459;SAP=29.6108;AB=0.0;ABP=0.0;RUN=1;RPP=3.55317;RPPR=13.8677;RPL=7.0;RPR=9.0;EPP=3.0103;EPPR=3.44459;DPRA=0.0;ODDS=13.6494;GTI=0;TYPE=ins;CIGAR=1M2I14M;NUMALT=2;MEANALT=4.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:C [...]
+chr6 152673147 . G A 7600.950000000001 REJECT NS=2;DP=205;DPB=233.0;AC=4;AN=4;AF=1.0;RO=0;AO=233;PRO=0.0;PAO=0.0;QR=0;QA=8824;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=151;SAR=82;SRP=0.0;SAP=47.381;AB=0.0;ABP=0.0;RUN=1;RPP=67.2132;RPPR=0.0;RPL=75.0;RPR=158.0;EPP=14.4268;EPPR=0.0;DPRA=0.0;ODDS=38.0419;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995708;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9987;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.945 [...]
+chr6 152673519 . A C 6863.445 REJECT NS=2;DP=204;DPB=235.0;AC=4;AN=4;AF=1.0;RO=1;AO=231;PRO=0.0;PAO=0.0;QR=16;QA=8379;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=48;SAR=183;SRP=5.18177;SAP=174.331;AB=0.0;ABP=0.0;RUN=1;RPP=252.767;RPPR=5.18177;RPL=197.0;RPR=34.0;EPP=74.1613;EPPR=5.18177;DPRA=0.0;ODDS=41.1025;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=59.9913;MQMR=70.0;PAIRED=0.995671;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.562;Dels=0.01;FS=0.0;HaplotypeScore=20.4057;MLEAC [...]
+chr6 152675854 . A G 15495.7 REJECT NS=2;DP=418;DPB=475.0;AC=4;AN=4;AF=1.0;RO=0;AO=474;PRO=0.0;PAO=0.0;QR=0;QA=17824;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=225;SAR=249;SRP=0.0;SAP=5.64905;AB=0.0;ABP=0.0;RUN=1;RPP=3.02862;RPPR=0.0;RPL=236.0;RPR=238.0;EPP=3.30349;EPPR=0.0;DPRA=0.0;ODDS=74.7436;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991561;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8771;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.445;SOR=0 [...]
+chr6 152683413 . G T 14552.2 REJECT NS=2;DP=396;DPB=450.0;AC=4;AN=4;AF=1.0;RO=0;AO=450;PRO=0.0;PAO=0.0;QR=0;QA=16757;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=214;SAR=236;SRP=0.0;SAP=5.34584;AB=0.0;ABP=0.0;RUN=1;RPP=3.31913;RPPR=0.0;RPL=221.0;RPR=229.0;EPP=9.26414;EPPR=0.0;DPRA=0.0;ODDS=70.4014;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995556;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8659;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.305;SOR=0 [...]
+chr6 152694184 . T C 11662.75 REJECT NS=2;DP=310;DPB=356.0;AC=4;AN=4;AF=1.0;RO=0;AO=356;PRO=0.0;PAO=0.0;QR=0;QA=13549;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=231;SAR=125;SRP=0.0;SAP=71.5459;AB=0.0;ABP=0.0;RUN=1;RPP=23.5295;RPPR=0.0;RPL=149.0;RPR=207.0;EPP=3.0103;EPPR=0.0;DPRA=0.0;ODDS=61.0938;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.988764;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.975;SOR=1. [...]
+chr6 152712440 . G T 3395.26 PASS SOMATIC;NS=2;DP=476;DPB=476.0;AC=1;AN=3;AF=0.25;RO=347;AO=129;PRO=0.0;PAO=0.0;QR=13352;QA=4917;PQR=0.0;PQA=0.0;SRF=200;SRR=147;SAF=66;SAR=63;SRP=20.5886;SAP=3.1618;AB=0.359331;ABP=64.7128;RUN=1;RPP=3.02713;RPPR=5.26938;RPL=64.0;RPR=65.0;EPP=4.37378;EPPR=3.16675;DPRA=3.06838;ODDS=74.0176;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992248;PAIREDR=0.997118;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.625;Dels=0.0;F [...]
+chr6 152765726 . G GA 94.1347 REJECT NS=2;DP=184;DPB=205.824;AC=2;AN=2;AF=0.0;RO=138;AO=16;PRO=24.1667;PAO=12.1667;QR=5115;QA=511;PQR=862.667;PQA=421.667;SRF=11;SRR=127;SAF=1;SAR=15;SRP=214.745;SAP=29.6108;AB=0.0882353;ABP=203.297;RUN=1;RPP=3.55317;RPPR=48.8945;RPL=7.0;RPR=9.0;EPP=5.18177;EPPR=23.4033;DPRA=0.0;ODDS=6.10582;GTI=0;TYPE=ins;CIGAR=1M1I16M;NUMALT=2;MEANALT=6.0;LEN=1;MQM=58.75;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992754;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr6 152765726 . GA G 94.1347 REJECT NS=2;DP=184;DPB=205.824;AC=2;AN=3;AF=0.25;RO=138;AO=19;PRO=24.1667;PAO=11.6667;QR=5115;QA=681;PQR=862.667;PQA=403.667;SRF=11;SRR=127;SAF=4;SAR=15;SRP=214.745;SAP=16.8392;AB=0.117647;ABP=175.706;RUN=1;RPP=22.325;RPPR=48.8945;RPL=16.0;RPR=3.0;EPP=5.8675;EPPR=23.4033;DPRA=0.0;ODDS=6.10582;GTI=0;TYPE=del;CIGAR=1M1D15M;NUMALT=2;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992754;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr6 152772264 . A G 2032.025 REJECT NS=2;DP=376;DPB=430.0;AC=2;AN=4;AF=0.5;RO=331;AO=99;PRO=0.0;PAO=0.0;QR=12742;QA=3705;PQR=0.0;PQA=0.0;SRF=146;SRR=185;SAF=42;SAR=57;SRP=12.9886;SAP=7.94546;AB=0.230233;ABP=274.818;RUN=1;RPP=16.7191;RPPR=17.5021;RPL=62.0;RPR=37.0;EPP=3.20771;EPPR=8.52755;DPRA=0.0;ODDS=115.16;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989899;PAIREDR=0.990937;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.31;Dels=0.0;FS=2.7905;HaplotypeSc [...]
+chr6 152777819 . G A 1734.4650000000001 REJECT NS=2;DP=342;DPB=391.0;AC=2;AN=4;AF=0.5;RO=300;AO=91;PRO=0.0;PAO=0.0;QR=11475;QA=3389;PQR=0.0;PQA=0.0;SRF=163;SRR=137;SAF=50;SAR=41;SRP=7.90335;SAP=4.94315;AB=0.232737;ABP=245.599;RUN=1;RPP=5.89764;RPPR=54.0833;RPL=40.0;RPR=51.0;EPP=8.37933;EPPR=42.6469;DPRA=0.0;ODDS=153.861;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996667;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.627;Dels=0.0;FS=3.9345;Hap [...]
+chr6 152784621 . T C 1563.12 REJECT NS=2;DP=302;DPB=350.0;AC=2;AN=4;AF=0.5;RO=270;AO=80;PRO=0.0;PAO=0.0;QR=10252;QA=2951;PQR=0.0;PQA=0.0;SRF=80;SRR=190;SAF=23;SAR=57;SRP=100.324;SAP=34.3881;AB=0.228571;ABP=226.982;RUN=1;RPP=18.6449;RPPR=28.2315;RPL=52.0;RPR=28.0;EPP=3.11887;EPPR=3.52502;DPRA=0.0;ODDS=77.5156;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.9875;PAIREDR=0.992593;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.465;Dels=0.0;FS=0.904;HaplotypeScor [...]
+chr6 152793412 . C A 5015.46 REJECT NS=2;DP=227;DPB=266.0;AC=3;AN=4;AF=0.75;RO=77;AO=189;PRO=0.0;PAO=0.0;QR=2883;QA=7285;PQR=0.0;PQA=0.0;SRF=57;SRR=20;SAF=154;SAR=35;SRP=41.6174;SAP=165.71;AB=0.590426;ABP=16.3625;RUN=1;RPP=30.596;RPPR=20.6359;RPL=70.0;RPR=119.0;EPP=3.02179;EPPR=3.26411;DPRA=0.0;ODDS=49.6754;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0529;MQMR=60.0;PAIRED=0.994709;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.766;Dels=0.0;FS=4.286;HaplotypeScore= [...]
+chr6 152809527 . A T 1297.435 REJECT NS=2;DP=298;DPB=337.0;AC=2;AN=4;AF=0.5;RO=267;AO=70;PRO=0.0;PAO=0.0;QR=10188;QA=2722;PQR=0.0;PQA=0.0;SRF=169;SRR=98;SAF=42;SAR=28;SRP=44.008;SAP=9.09042;AB=0.207715;ABP=253.078;RUN=1;RPP=38.8706;RPPR=46.3503;RPL=18.0;RPR=52.0;EPP=4.12706;EPPR=10.826;DPRA=0.0;ODDS=111.971;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988764;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.03;Dels=0.0;FS=2.4935;HaplotypeScore=3.9 [...]
+chr6 153344531 . T A 10683.5 REJECT NS=2;DP=393;DPB=450.0;AC=2;AN=4;AF=0.5;RO=103;AO=347;PRO=0.0;PAO=0.0;QR=4023;QA=13367;PQR=0.0;PQA=0.0;SRF=52;SRR=51;SAF=149;SAR=198;SRP=3.03138;SAP=18.0354;AB=0.771111;ABP=290.301;RUN=1;RPP=11.5773;RPPR=4.04333;RPL=192.0;RPR=155.0;EPP=36.3584;EPPR=20.7405;DPRA=0.0;ODDS=163.102;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997118;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.029;Dels=0.0;FS=8.9715;HaplotypeSco [...]
+chr6 157099165 . GTCC G 66.73 PASS DP=63;AC=1;AN=4;AF=0.5;BaseQRankSum=-1.362;FS=9.37;MLEAC=1;MLEAF=0.5;MQ=60.17;MQRankSum=0.702;QD=1.06;ReadPosRankSum=-0.072;SOR=0.061;ClippingRankSum=0.069 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:48,6:54:99.0:104,0,2005:6:11:54:1:.:.:.:.:.:-0.00471738 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-27.8757
+chr6 157405930 . G A 8945.48 REJECT NS=2;DP=348;DPB=389.0;AC=2;AN=4;AF=0.5;RO=89;AO=300;PRO=0.0;PAO=0.0;QR=3431;QA=11192;PQR=0.0;PQA=0.0;SRF=47;SRR=42;SAF=147;SAR=153;SRP=3.62026;SAP=3.27088;AB=0.771208;ABP=251.535;RUN=1;RPP=3.27088;RPPR=8.49998;RPL=147.0;RPR=153.0;EPP=8.68508;EPPR=7.13366;DPRA=0.0;ODDS=190.111;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988764;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.1635;Dels=0.0;FS=0.62;HaplotypeScor [...]
+chr6 157507504 . C T 1526.1 REJECT NS=2;DP=251;DPB=289.0;AC=2;AN=4;AF=0.5;RO=217;AO=72;PRO=0.0;PAO=0.0;QR=8433;QA=2762;PQR=0.0;PQA=0.0;SRF=182;SRR=35;SAF=58;SAR=14;SRP=219.247;SAP=61.3988;AB=0.249135;ABP=160.987;RUN=1;RPP=10.7311;RPPR=5.90226;RPL=28.0;RPR=44.0;EPP=15.074;EPPR=3.50063;DPRA=0.0;ODDS=101.379;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.197;Dels=0.0;FS=2.03;HaplotypeScore=3.9545;MLEA [...]
+chr6 157507698 . G C 2208.5299999999997 REJECT NS=2;DP=490;DPB=568.0;AC=2;AN=4;AF=0.5;RO=451;AO=117;PRO=0.0;PAO=0.0;QR=17303;QA=4400;PQR=0.0;PQA=0.0;SRF=180;SRR=271;SAF=32;SAR=85;SRP=42.8816;SAP=55.1442;AB=0.205986;ABP=429.491;RUN=1;RPP=6.14687;RPPR=3.4003;RPL=65.0;RPR=52.0;EPP=3.17734;EPPR=6.52029;DPRA=0.0;ODDS=131.788;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991453;PAIREDR=0.995565;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3635;Dels=0.0;FS=6.74 [...]
+chr6 160453561 . T G 1279.24 REJECT NS=2;DP=224;DPB=260.0;AC=2;AN=4;AF=0.5;RO=194;AO=66;PRO=0.0;PAO=0.0;QR=7417;QA=2568;PQR=0.0;PQA=0.0;SRF=144;SRR=50;SAF=47;SAR=19;SRP=101.913;SAP=28.8048;AB=0.253846;ABP=139.846;RUN=1;RPP=41.044;RPPR=119.464;RPL=16.0;RPR=50.0;EPP=3.53672;EPPR=6.63688;DPRA=0.0;ODDS=141.218;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7195;Dels=0.0;FS=1.6225;HaplotypeScore=6.8321; [...]
+chr6 160453978 . A G 2173.355 REJECT NS=2;DP=332;DPB=383.0;AC=2;AN=4;AF=0.5;RO=279;AO=103;PRO=0.0;PAO=0.0;QR=10831;QA=3926;PQR=0.0;PQA=0.0;SRF=156;SRR=123;SAF=58;SAR=45;SRP=11.486;SAP=6.5732;AB=0.26893;ABP=180.634;RUN=1;RPP=4.71796;RPPR=8.68415;RPL=47.0;RPR=56.0;EPP=3.53736;EPPR=3.01808;DPRA=0.0;ODDS=190.473;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989247;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.309;Dels=0.0;FS=1.9865;HaplotypeScore= [...]
+chr6 160464289 . G A 1616.73 REJECT NS=2;DP=344;DPB=391.0;AC=2;AN=4;AF=0.5;RO=307;AO=84;PRO=0.0;PAO=0.0;QR=11624;QA=3109;PQR=0.0;PQA=0.0;SRF=151;SRR=156;SAF=43;SAR=41;SRP=3.18713;SAP=3.1137;AB=0.214834;ABP=279.187;RUN=1;RPP=3.1137;RPPR=3.58323;RPL=41.0;RPR=43.0;EPP=4.66476;EPPR=3.86616;DPRA=0.0;ODDS=96.7407;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988095;PAIREDR=0.996743;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3015;Dels=0.0;FS=0.392;HaplotypeSco [...]
+chr6 160468278 . A G 13672.0 REJECT NS=2;DP=372;DPB=425.0;AC=4;AN=4;AF=1.0;RO=2;AO=422;PRO=0.0;PAO=0.0;QR=78;QA=15850;PQR=0.0;PQA=0.0;SRF=1;SRR=1;SAF=233;SAR=189;SRP=3.0103;SAP=12.9723;AB=0.0;ABP=0.0;RUN=1;RPP=5.97421;RPPR=3.0103;RPL=223.0;RPR=199.0;EPP=7.6414;EPPR=7.35324;DPRA=0.0;ODDS=68.5748;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995261;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.617;Dels=0.0;FS=0.0;HaplotypeScore=6.8008;MLEAC=2;MLE [...]
+chr6 160468383 . T C 9374.220000000001 REJECT NS=2;DP=249;DPB=293.0;AC=4;AN=4;AF=1.0;RO=0;AO=293;PRO=0.0;PAO=0.0;QR=0;QA=11197;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=116;SAR=177;SRP=0.0;SAP=30.5873;AB=0.0;ABP=0.0;RUN=1;RPP=97.6435;RPPR=0.0;RPL=203.0;RPR=90.0;EPP=5.15213;EPPR=0.0;DPRA=0.0;ODDS=57.3183;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.989761;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.93; [...]
+chr6 160494409 . A G 13352.599999999999 REJECT NS=2;DP=355;DPB=412.0;AC=4;AN=4;AF=1.0;RO=0;AO=412;PRO=0.0;PAO=0.0;QR=0;QA=15640;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=158;SAR=254;SRP=0.0;SAP=51.5838;AB=0.0;ABP=0.0;RUN=1;RPP=4.71796;RPPR=0.0;RPL=197.0;RPR=215.0;EPP=12.3076;EPPR=0.0;DPRA=0.0;ODDS=74.1248;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995146;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8461;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=2 [...]
+chr6 160505199 . C G 11116.45 REJECT NS=2;DP=295;DPB=342.0;AC=4;AN=4;AF=1.0;RO=0;AO=342;PRO=0.0;PAO=0.0;QR=0;QA=13083;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=127;SAR=215;SRP=0.0;SAP=52.1795;AB=0.0;ABP=0.0;RUN=1;RPP=12.1787;RPPR=0.0;RPL=190.0;RPR=152.0;EPP=13.1692;EPPR=0.0;DPRA=0.0;ODDS=62.9896;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.9062;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.105;SOR=1.330 [...]
+chr6 160505207 . A G 1322.8 REJECT NS=2;DP=294;DPB=342.0;AC=2;AN=4;AF=0.5;RO=270;AO=71;PRO=0.0;PAO=0.0;QR=10065;QA=2710;PQR=0.0;PQA=0.0;SRF=86;SRR=184;SAF=30;SAR=41;SRP=80.2504;SAP=6.71098;AB=0.207602;ABP=256.984;RUN=1;RPP=5.48761;RPPR=9.31561;RPL=40.0;RPR=31.0;EPP=3.28556;EPPR=18.5806;DPRA=0.0;ODDS=112.534;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.7545;Dels=0.0;FS=6.1625;HaplotypeScore=3.8464 [...]
+chr6 160514246 . A G 8465.93 REJECT NS=2;DP=412;DPB=472.0;AC=3;AN=4;AF=0.75;RO=161;AO=311;PRO=0.0;PAO=0.0;QR=6193;QA=11926;PQR=0.0;PQA=0.0;SRF=91;SRR=70;SAF=153;SAR=158;SRP=8.95825;SAP=3.18486;AB=0.543909;ABP=8.92187;RUN=1;RPP=3.18486;RPPR=6.04497;RPL=153.0;RPR=158.0;EPP=6.7039;EPPR=3.34749;DPRA=0.0;ODDS=75.1323;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993569;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.464;Dels=0.0;FS=2.7355;HaplotypeSco [...]
+chr6 160517481 . C T 1357.165 REJECT NS=2;DP=326;DPB=370.0;AC=2;AN=4;AF=0.5;RO=293;AO=75;PRO=0.0;PAO=0.0;QR=11347;QA=2863;PQR=0.0;PQA=0.0;SRF=191;SRR=102;SAF=49;SAR=26;SRP=61.7142;SAP=18.3264;AB=0.202703;ABP=287.062;RUN=1;RPP=3.27088;RPPR=4.26279;RPL=36.0;RPR=39.0;EPP=7.90335;EPPR=14.2827;DPRA=0.0;ODDS=135.238;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996587;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6665;Dels=0.0;FS=0.4485;HaplotypeScor [...]
+chr6 160524773 . T A 4590.4 REJECT NS=2;DP=333;DPB=378.0;AC=2;AN=4;AF=0.5;RO=210;AO=168;PRO=0.0;PAO=0.0;QR=7901;QA=6332;PQR=0.0;PQA=0.0;SRF=107;SRR=103;SAF=92;SAR=76;SRP=3.17575;SAP=6.31921;AB=0.444444;ABP=13.1438;RUN=1;RPP=10.4553;RPPR=40.2355;RPL=72.0;RPR=96.0;EPP=3.21711;EPPR=8.01503;DPRA=0.0;ODDS=245.324;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994048;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.598;Dels=0.0;FS=2.3785;HaplotypeScore= [...]
+chr6 160670282 . A C 13484.7 REJECT NS=2;DP=362;DPB=416.0;AC=4;AN=4;AF=1.0;RO=1;AO=415;PRO=0.0;PAO=0.0;QR=16;QA=15716;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=233;SAR=182;SRP=5.18177;SAP=16.6199;AB=0.0;ABP=0.0;RUN=1;RPP=39.0567;RPPR=5.18177;RPL=249.0;RPR=166.0;EPP=42.6148;EPPR=5.18177;DPRA=0.0;ODDS=69.8213;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992771;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.62;Dels=0.0;FS=0.0;HaplotypeScore=11.6222;MLEAC=2; [...]
+chr6 161807855 . C G 10026.2 REJECT NS=2;DP=392;DPB=452.0;AC=2;AN=4;AF=0.5;RO=125;AO=327;PRO=0.0;PAO=0.0;QR=4812;QA=12594;PQR=0.0;PQA=0.0;SRF=61;SRR=64;SAF=154;SAR=173;SRP=3.16665;SAP=5.40755;AB=0.723451;ABP=199.039;RUN=1;RPP=6.52317;RPPR=5.11229;RPL=152.0;RPR=175.0;EPP=11.145;EPPR=9.28151;DPRA=0.0;ODDS=322.146;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990826;PAIREDR=0.992;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.747;Dels=0.0;FS=0.7355;HaplotypeSc [...]
+chr6 161990483 . C T 9546.505000000001 REJECT NS=2;DP=257;DPB=295.0;AC=4;AN=4;AF=1.0;RO=0;AO=295;PRO=0.0;PAO=0.0;QR=0;QA=11201;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=97;SAR=198;SRP=0.0;SAP=78.0991;AB=0.0;ABP=0.0;RUN=1;RPP=149.353;RPPR=0.0;RPL=218.0;RPR=77.0;EPP=3.60653;EPPR=0.0;DPRA=0.0;ODDS=51.0656;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8239;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.285;SO [...]
+chr6 162622304 . A G 4123.185 REJECT NS=2;DP=243;DPB=283.0;AC=2;AN=4;AF=0.5;RO=134;AO=149;PRO=0.0;PAO=0.0;QR=5168;QA=5640;PQR=0.0;PQA=0.0;SRF=35;SRR=99;SAF=44;SAR=105;SRP=69.3861;SAP=57.2388;AB=0.526502;ABP=4.73674;RUN=1;RPP=40.9163;RPPR=24.012;RPL=100.0;RPR=49.0;EPP=3.02487;EPPR=6.18648;DPRA=0.0;ODDS=236.017;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.977612;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.845;Dels=0.0;FS=1.837;HaplotypeScore=2 [...]
+chr6 162683814 . T A 85.0023 REJECT NS=2;DP=64;DPB=108.516;AC=2;AN=2;AF=0.0;RO=14;AO=11;PRO=46.0;PAO=0.0;QR=520;QA=167;PQR=1598.17;PQA=0.0;SRF=0;SRR=14;SAF=0;SAR=11;SRP=33.4109;SAP=26.8965;AB=0.171875;ABP=62.8615;RUN=1;RPP=7.94546;RPPR=3.0103;RPL=8.0;RPR=3.0;EPP=7.94546;EPPR=3.0103;DPRA=0.0;ODDS=1.94989;GTI=0;TYPE=snp;CIGAR=1X30M;NUMALT=4;MEANALT=8.5;LEN=1;MQM=58.0909;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:C [...]
+chr6 162683814 . TA T 85.0023 REJECT NS=2;DP=64;DPB=108.516;AC=2;AN=4;AF=0.5;RO=14;AO=13;PRO=46.0;PAO=33.0;QR=520;QA=260;PQR=1598.17;PQA=1004.17;SRF=0;SRR=14;SAF=0;SAR=13;SRP=33.4109;SAP=31.2394;AB=0.203125;ABP=52.0041;RUN=1;RPP=16.5402;RPPR=3.0103;RPL=11.0;RPR=2.0;EPP=16.5402;EPPR=3.0103;DPRA=0.0;ODDS=1.94989;GTI=0;TYPE=del;CIGAR=1M1D29M;NUMALT=4;MEANALT=8.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr6 162683814 . TAA T 85.0023 REJECT NS=2;DP=64;DPB=108.516;AC=2;AN=2;AF=0.0;RO=14;AO=7;PRO=46.0;PAO=26.0;QR=520;QA=112;PQR=1598.17;PQA=873.667;SRF=0;SRR=14;SAF=0;SAR=7;SRP=33.4109;SAP=18.2106;AB=0.109375;ABP=87.8334;RUN=1;RPP=18.2106;RPPR=3.0103;RPL=7.0;RPR=0.0;EPP=18.2106;EPPR=3.0103;DPRA=0.0;ODDS=1.94989;GTI=0;TYPE=del;CIGAR=1M2D28M;NUMALT=4;MEANALT=8.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMIC [...]
+chr6 162683814 . TAAA T 85.0023 REJECT NS=2;DP=64;DPB=108.516;AC=2;AN=2;AF=0.0;RO=14;AO=8;PRO=46.0;PAO=25.0;QR=520;QA=175;PQR=1598.17;PQA=856.0;SRF=0;SRR=14;SAF=1;SAR=7;SRP=33.4109;SAP=12.7819;AB=0.125;ABP=81.1833;RUN=1;RPP=12.7819;RPPR=3.0103;RPL=7.0;RPR=1.0;EPP=7.35324;EPPR=3.0103;DPRA=0.0;ODDS=1.94989;GTI=0;TYPE=del;CIGAR=1M3D27M;NUMALT=4;MEANALT=8.5;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:C [...]
+chr6 162864317 . A G 3645.72 REJECT NS=2;DP=206;DPB=236.0;AC=2;AN=4;AF=0.5;RO=108;AO=128;PRO=0.0;PAO=0.0;QR=4226;QA=4962;PQR=0.0;PQA=0.0;SRF=71;SRR=37;SAF=92;SAR=36;SRP=26.2531;SAP=56.2114;AB=0.542373;ABP=6.69076;RUN=1;RPP=68.2223;RPPR=57.3775;RPL=33.0;RPR=95.0;EPP=3.62103;EPPR=6.95112;DPRA=0.0;ODDS=169.06;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.976562;PAIREDR=0.972222;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4395;Dels=0.0;FS=3.357;HaplotypeSco [...]
+chr6 163092529 . C A 28.9587 REJECT NS=1;DP=47;DPB=99.4138;AC=1;AN=3;AF=0.0;RO=12;AO=3;PRO=44.9833;PAO=14.2333;QR=425;QA=43;PQR=1579.8;PQA=479.55;SRF=6;SRR=6;SAF=0;SAR=3;SRP=3.0103;SAP=9.52472;AB=0.0638298;ABP=80.6751;RUN=1;RPP=9.52472;RPPR=21.1059;RPL=0.0;RPR=3.0;EPP=9.52472;EPPR=3.73412;DPRA=0.0;ODDS=6.66672;GTI=0;TYPE=snp;CIGAR=1X28M;NUMALT=4;MEANALT=20.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr6 163092529 . CA C 28.9587 REJECT NS=1;DP=47;DPB=99.4138;AC=1;AN=4;AF=0.5;RO=12;AO=9;PRO=44.9833;PAO=17.4833;QR=425;QA=224;PQR=1579.8;PQA=600.8;SRF=6;SRR=6;SAF=4;SAR=5;SRP=3.0103;SAP=3.25157;AB=0.191489;ABP=41.8658;RUN=1;RPP=3.25157;RPPR=21.1059;RPL=4.0;RPR=5.0;EPP=3.25157;EPPR=3.73412;DPRA=0.0;ODDS=6.66672;GTI=0;TYPE=del;CIGAR=1M1D27M;NUMALT=4;MEANALT=20.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.888889;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.032;FS=5.198;MLEAC= [...]
+chr6 163092529 . CAA C 28.9587 REJECT NS=1;DP=47;DPB=99.4138;AC=1;AN=3;AF=0.0;RO=12;AO=3;PRO=44.9833;PAO=16.15;QR=425;QA=89;PQR=1579.8;PQA=550.8;SRF=6;SRR=6;SAF=2;SAR=1;SRP=3.0103;SAP=3.73412;AB=0.0638298;ABP=80.6751;RUN=1;RPP=9.52472;RPPR=21.1059;RPL=0.0;RPR=3.0;EPP=3.73412;EPPR=3.73412;DPRA=0.0;ODDS=6.66672;GTI=0;TYPE=del;CIGAR=1M2D26M;NUMALT=4;MEANALT=20.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr6 163092547 . AGAGT GAGA 28.9587 REJECT NS=1;DP=47;DPB=99.4138;AC=1;AN=3;AF=0.0;RO=12;AO=3;PRO=44.9833;PAO=8.15;QR=425;QA=48;PQR=1579.8;PQA=216.05;SRF=6;SRR=6;SAF=3;SAR=0;SRP=3.0103;SAP=9.52472;AB=0.0638298;ABP=80.6751;RUN=1;RPP=3.73412;RPPR=21.1059;RPL=1.0;RPR=2.0;EPP=3.73412;EPPR=3.73412;DPRA=0.0;ODDS=6.66672;GTI=0;TYPE=complex;CIGAR=1M1D20M1X6M;NUMALT=4;MEANALT=20.0;LEN=28;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr6 168043333 . G A 3488.26 PASS SOMATIC;NS=2;DP=431;DPB=431.0;AC=1;AN=3;AF=0.25;RO=302;AO=129;PRO=0.0;PAO=0.0;QR=11443;QA=4910;PQR=0.0;PQA=0.0;SRF=127;SRR=175;SAF=62;SAR=67;SRP=19.5768;SAP=3.43113;AB=0.401869;ABP=29.8594;RUN=1;RPP=3.02713;RPPR=5.33996;RPL=65.0;RPR=64.0;EPP=11.915;EPPR=4.0457;DPRA=2.91818;ODDS=69.5239;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984496;PAIREDR=0.980132;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.882;Dels=0.0;FS= [...]
+chr6 169540853 . A G 7888.27 REJECT NS=2;DP=287;DPB=335.0;AC=2;AN=4;AF=0.5;RO=78;AO=257;PRO=0.0;PAO=0.0;QR=2902;QA=9951;PQR=0.0;PQA=0.0;SRF=47;SRR=31;SAF=167;SAR=90;SRP=10.1372;SAP=53.1063;AB=0.767164;ABP=210.7;RUN=1;RPP=38.7086;RPPR=8.46682;RPL=96.0;RPR=161.0;EPP=11.1301;EPPR=14.1461;DPRA=0.0;ODDS=113.448;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996109;PAIREDR=0.987179;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.086;Dels=0.0;FS=3.5025;HaplotypeScor [...]
+chr7 2962753 . G A 2117.27 REJECT NS=1;DP=64;DPB=64.0;AC=2;AN=4;AF=1.0;RO=0;AO=64;PRO=0.0;PAO=0.0;QR=0;QA=2442;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=49;SAR=15;SRP=0.0;SAP=42.2325;AB=0.0;ABP=0.0;RUN=1;RPP=14.0034;RPPR=0.0;RPL=23.0;RPR=41.0;EPP=3.55317;EPPR=0.0;DPRA=0.0;ODDS=44.5653;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.984375;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=34.3;SOR=2.303 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV [...]
+chr7 2966445 . T G 1769.745 REJECT NS=2;DP=339;DPB=385.0;AC=2;AN=4;AF=0.5;RO=290;AO=90;PRO=0.0;PAO=0.0;QR=10160;QA=3355;PQR=0.0;PQA=0.0;SRF=93;SRR=197;SAF=34;SAR=56;SRP=83.9987;SAP=14.688;AB=0.233766;ABP=240.039;RUN=1;RPP=5.42305;RPPR=4.92719;RPL=50.0;RPR=40.0;EPP=5.42305;EPPR=5.43636;DPRA=0.0;ODDS=137.54;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988889;PAIREDR=0.996552;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.5365;Dels=0.0;FS=0.3405;HaplotypeScor [...]
+chr7 2969680 . G A 1688.3600000000001 REJECT NS=2;DP=379;DPB=433.0;AC=2;AN=4;AF=0.5;RO=341;AO=90;PRO=0.0;PAO=0.0;QR=13130;QA=3413;PQR=0.0;PQA=0.0;SRF=163;SRR=178;SAF=39;SAR=51;SRP=4.44309;SAP=6.48466;AB=0.207852;ABP=324.012;RUN=1;RPP=5.42305;RPPR=5.81857;RPL=40.0;RPR=50.0;EPP=6.48466;EPPR=8.36575;DPRA=0.0;ODDS=126.275;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997067;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.393;Dels=0.0;FS=1.4175;Haplo [...]
+chr7 2976767 . G A 2159.5 REJECT NS=2;DP=387;DPB=451.0;AC=2;AN=4;AF=0.5;RO=344;AO=106;PRO=0.0;PAO=0.0;QR=13237;QA=4092;PQR=0.0;PQA=0.0;SRF=173;SRR=171;SAF=48;SAR=58;SRP=3.03555;SAP=5.05886;AB=0.235033;ABP=278.036;RUN=1;RPP=3.0103;RPPR=27.2752;RPL=53.0;RPR=53.0;EPP=5.96022;EPPR=3.1113;DPRA=0.0;ODDS=186.554;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994186;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0795;Dels=0.0;FS=6.799;HaplotypeScore=2.99 [...]
+chr7 6013049 . C G 1190.62 REJECT NS=1;DP=99;DPB=99.0;AC=1;AN=4;AF=0.5;RO=39;AO=60;PRO=0.0;PAO=0.0;QR=1505;QA=2307;PQR=0.0;PQA=0.0;SRF=0;SRR=39;SAF=0;SAR=60;SRP=87.6977;SAP=133.299;AB=0.606061;ABP=12.6832;RUN=1;RPP=4.31318;RPPR=4.40227;RPL=27.0;RPR=33.0;EPP=4.31318;EPPR=4.40227;DPRA=0.0;ODDS=166.193;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=33.5;MQMR=35.3077;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.614;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=37.2;MQRankSum=1.275;QD [...]
+chr7 6026775 . T C 11761.5 REJECT NS=2;DP=330;DPB=372.0;AC=4;AN=4;AF=1.0;RO=0;AO=372;PRO=0.0;PAO=0.0;QR=0;QA=14216;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=162;SAR=210;SRP=0.0;SAP=16.4594;AB=0.0;ABP=0.0;RUN=1;RPP=3.1037;RPPR=0.0;RPL=184.0;RPR=188.0;EPP=8.98769;EPPR=0.0;DPRA=0.0;ODDS=57.2874;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=47.5376;MQMR=0.0;PAIRED=0.997312;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=4;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=49.345;QD=27.335;SOR= [...]
+chr7 6036980 . G C 12167.3 REJECT NS=2;DP=333;DPB=382.0;AC=4;AN=4;AF=1.0;RO=0;AO=382;PRO=0.0;PAO=0.0;QR=0;QA=14156;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=222;SAR=160;SRP=0.0;SAP=24.8615;AB=0.0;ABP=0.0;RUN=1;RPP=19.5863;RPPR=0.0;RPL=164.0;RPR=218.0;EPP=24.8615;EPPR=0.0;DPRA=0.0;ODDS=64.7352;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0393;MQMR=0.0;PAIRED=0.997382;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.8211;MLEAC=2;MLEAF=1.0;MQ=60.065;QD=32.24;SOR [...]
+chr7 6037057 . G A 1016.24 REJECT NS=2;DP=184;DPB=233.44;AC=2;AN=2;AF=0.0;RO=59;AO=9;PRO=31.7667;PAO=0.0;QR=2171;QA=129;PQR=1144.02;PQA=0.0;SRF=11;SRR=48;SAF=0;SAR=9;SRP=53.3958;SAP=22.5536;AB=0.048913;ABP=328.212;RUN=1;RPP=3.25157;RPPR=7.46366;RPL=4.0;RPR=5.0;EPP=3.25157;EPPR=3.34154;DPRA=0.0;ODDS=74.2522;GTI=0;TYPE=snp;CIGAR=1X24M;NUMALT=5;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV: [...]
+chr7 6037057 . G GA 755.985 REJECT NS=2;DP=184;DPB=233.44;AC=2;AN=4;AF=0.5;RO=59;AO=52;PRO=31.7667;PAO=23.2667;QR=2171;QA=1467;PQR=1144.02;PQA=826.017;SRF=11;SRR=48;SAF=6;SAR=46;SRP=53.3958;SAP=69.8248;AB=0.282609;ABP=78.5398;RUN=1;RPP=9.02361;RPPR=7.46366;RPL=32.0;RPR=20.0;EPP=3.0103;EPPR=3.34154;DPRA=0.0;ODDS=74.2522;GTI=0;TYPE=ins;CIGAR=1M1I24M;NUMALT=5;MEANALT=11.5;LEN=1;MQM=59.9808;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.6095;F [...]
+chr7 6037057 . G GAA 1016.24 REJECT NS=2;DP=184;DPB=233.44;AC=2;AN=2;AF=0.0;RO=59;AO=13;PRO=31.7667;PAO=20.2667;QR=2171;QA=345;PQR=1144.02;PQA=703.017;SRF=11;SRR=48;SAF=0;SAR=13;SRP=53.3958;SAP=31.2394;AB=0.0706522;ABP=297.622;RUN=1;RPP=3.17734;RPPR=7.46366;RPL=6.0;RPR=7.0;EPP=3.17734;EPPR=3.34154;DPRA=0.0;ODDS=74.2522;GTI=0;TYPE=ins;CIGAR=1M2I24M;NUMALT=5;MEANALT=11.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=0.923077;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr7 6037057 . GA G 1016.24 REJECT NS=2;DP=184;DPB=233.44;AC=2;AN=2;AF=0.0;RO=59;AO=32;PRO=31.7667;PAO=15.1;QR=2171;QA=880;PQR=1144.02;PQA=529.35;SRF=11;SRR=48;SAF=7;SAR=25;SRP=53.3958;SAP=24.9965;AB=0.173913;ABP=172.952;RUN=1;RPP=4.09604;RPPR=7.46366;RPL=18.0;RPR=14.0;EPP=9.79615;EPPR=3.34154;DPRA=0.0;ODDS=74.2522;GTI=0;TYPE=del;CIGAR=1M1D23M;NUMALT=5;MEANALT=11.5;LEN=1;MQM=59.375;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr7 6037057 . GAA G 1016.24 REJECT NS=2;DP=184;DPB=233.44;AC=2;AN=2;AF=0.0;RO=59;AO=4;PRO=31.7667;PAO=14.6;QR=2171;QA=117;PQR=1144.02;PQA=500.6;SRF=11;SRR=48;SAF=0;SAR=4;SRP=53.3958;SAP=11.6962;AB=0.0217391;ABP=368.573;RUN=1;RPP=5.18177;RPPR=7.46366;RPL=3.0;RPR=1.0;EPP=5.18177;EPPR=3.34154;DPRA=0.0;ODDS=74.2522;GTI=0;TYPE=del;CIGAR=1M2D22M;NUMALT=5;MEANALT=11.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr7 6048556 . G A 737.233 REJECT NS=1;DP=61;DPB=61.0;AC=1;AN=4;AF=0.5;RO=31;AO=30;PRO=0.0;PAO=0.0;QR=1140;QA=1083;PQR=0.0;PQA=0.0;SRF=19;SRR=12;SAF=16;SAR=14;SRP=6.44263;SAP=3.29983;AB=0.491803;ABP=3.0459;RUN=1;RPP=31.9633;RPPR=23.254;RPL=5.0;RPR=25.0;EPP=4.16842;EPPR=3.08035;DPRA=0.0;ODDS=169.754;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-1.811;FS=2.212;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.747;QD= [...]
+chr7 6426941 . C T 1410.81 REJECT NS=2;DP=278;DPB=326.0;AC=2;AN=4;AF=0.5;RO=257;AO=69;PRO=0.0;PAO=0.0;QR=9931;QA=2643;PQR=0.0;PQA=0.0;SRF=103;SRR=154;SAF=20;SAR=49;SRP=24.987;SAP=29.4771;AB=0.211656;ABP=238.435;RUN=1;RPP=4.55236;RPPR=15.8617;RPL=38.0;RPR=31.0;EPP=5.55942;EPPR=3.42432;DPRA=0.0;ODDS=54.6466;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985507;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.411;Dels=0.0;FS=6.9625;HaplotypeScore=2.96 [...]
+chr7 6426953 . C T 1192.98 REJECT NS=2;DP=233;DPB=274.0;AC=2;AN=4;AF=0.5;RO=215;AO=59;PRO=0.0;PAO=0.0;QR=8178;QA=2253;PQR=0.0;PQA=0.0;SRF=86;SRR=129;SAF=18;SAR=41;SRP=21.685;SAP=22.4799;AB=0.215328;ABP=195.875;RUN=1;RPP=22.4799;RPPR=51.0958;RPL=41.0;RPR=18.0;EPP=3.93042;EPPR=3.2628;DPRA=0.0;ODDS=56.5215;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.767;Dels=0.0;FS=3.2195;HaplotypeScore=1.9997;MLEA [...]
+chr7 6431690 . C T 1423.93 REJECT NS=1;DP=101;DPB=101.0;AC=1;AN=4;AF=0.5;RO=50;AO=51;PRO=0.0;PAO=0.0;QR=1940;QA=1969;PQR=0.0;PQA=0.0;SRF=15;SRR=35;SAF=23;SAR=28;SRP=20.3821;SAP=4.07475;AB=0.50495;ABP=3.0318;RUN=1;RPP=5.09662;RPPR=20.3821;RPL=29.0;RPR=22.0;EPP=25.534;EPPR=4.57376;DPRA=0.0;ODDS=319.456;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.960784;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.22;FS=6.758;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.3 [...]
+chr7 6441670 . T C 2209.37 REJECT NS=2;DP=370;DPB=428.0;AC=2;AN=4;AF=0.5;RO=325;AO=103;PRO=0.0;PAO=0.0;QR=12513;QA=3997;PQR=0.0;PQA=0.0;SRF=141;SRR=184;SAF=43;SAR=60;SRP=15.3643;SAP=9.10307;AB=0.240654;ABP=253.054;RUN=1;RPP=23.2703;RPPR=63.3104;RPL=67.0;RPR=36.0;EPP=3.53736;EPPR=3.33769;DPRA=0.0;ODDS=149.224;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8954;PAIRED=1.0;PAIREDR=0.993846;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.4425;Dels=0.0;FS=1.0055;HaplotypeSco [...]
+chr7 9002588 . A G 3598.425 REJECT NS=2;DP=236;DPB=268.0;AC=2;AN=4;AF=0.5;RO=136;AO=132;PRO=0.0;PAO=0.0;QR=5208;QA=5089;PQR=0.0;PQA=0.0;SRF=97;SRR=39;SAF=89;SAR=43;SRP=56.7223;SAP=37.8197;AB=0.492537;ABP=3.13994;RUN=1;RPP=79.0776;RPPR=76.8404;RPL=32.0;RPR=100.0;EPP=3.0761;EPPR=8.18351;DPRA=0.0;ODDS=165.533;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992424;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.3735;Dels=0.0;FS=0.6045;HaplotypeScore=2. [...]
+chr7 13504782 . A G 2896.22 PASS SOMATIC;NS=2;DP=390;DPB=390.0;AC=1;AN=3;AF=0.25;RO=279;AO=111;PRO=0.0;PAO=0.0;QR=10686;QA=4197;PQR=0.0;PQA=0.0;SRF=163;SRR=116;SAF=68;SAR=43;SRP=20.2031;SAP=15.2371;AB=0.375;ABP=43.1825;RUN=1;RPP=15.2371;RPPR=37.9484;RPL=43.0;RPR=68.0;EPP=3.49937;EPPR=5.81998;DPRA=3.14894;ODDS=59.5869;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.955;MQMR=60.0;PAIRED=0.972973;PAIREDR=0.996416;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.092;Dels=0.0;FS= [...]
+chr7 18668959 . G T 709.678 REJECT NS=2;DP=235;DPB=242.0;AC=2;AN=2;AF=0.0;RO=199;AO=15;PRO=7.5;PAO=7.5;QR=6260;QA=205;PQR=104.5;PQA=104.5;SRF=129;SRR=70;SAF=15;SAR=0;SRP=40.9947;SAP=35.5824;AB=0.0638298;ABP=391.334;RUN=1;RPP=3.15506;RPPR=105.681;RPL=7.0;RPR=8.0;EPP=3.15506;EPPR=5.46548;DPRA=0.0;ODDS=8.31989;GTI=0;TYPE=snp;CIGAR=1X2M;NUMALT=2;MEANALT=3.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984925;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr7 18668959 . GTC TTT 709.678 REJECT NS=2;DP=235;DPB=242.0;AC=2;AN=4;AF=0.5;RO=199;AO=12;PRO=7.5;PAO=0.0;QR=6260;QA=165;PQR=104.5;PQA=0.0;SRF=129;SRR=70;SAF=12;SAR=0;SRP=40.9947;SAP=29.068;AB=0.0510638;ABP=414.398;RUN=1;RPP=9.52472;RPPR=105.681;RPL=9.0;RPR=3.0;EPP=9.52472;EPPR=5.46548;DPRA=0.0;ODDS=8.31989;GTI=0;TYPE=complex;CIGAR=1X1M1X;NUMALT=2;MEANALT=3.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984925;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr7 18767343 . A G 3330.66 PASS SOMATIC;NS=2;DP=478;DPB=478.0;AC=1;AN=3;AF=0.25;RO=350;AO=128;PRO=0.0;PAO=0.0;QR=12984;QA=4845;PQR=0.0;PQA=0.0;SRF=153;SRR=197;SAF=53;SAR=75;SRP=15.0216;SAP=11.2212;AB=0.360563;ABP=62.9613;RUN=1;RPP=3.07816;RPPR=3.23365;RPL=65.0;RPR=63.0;EPP=7.35324;EPPR=15.0216;DPRA=2.88618;ODDS=77.4416;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997143;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.352;Dels=0.0;FS=2.97 [...]
+chr7 18993870 . C T 7420.365 REJECT NS=2;DP=314;DPB=354.0;AC=3;AN=4;AF=0.75;RO=91;AO=263;PRO=0.0;PAO=0.0;QR=3386;QA=9938;PQR=0.0;PQA=0.0;SRF=26;SRR=65;SAF=81;SAR=182;SRP=39.3049;SAP=87.2354;AB=0.667883;ABP=70.0882;RUN=1;RPP=24.4856;RPPR=7.04303;RPL=157.0;RPR=106.0;EPP=15.5685;EPPR=3.03416;DPRA=0.0;ODDS=50.9177;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992395;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.821;Dels=0.0;FS=0.0;HaplotypeScore=3. [...]
+chr7 22501599 . G A 7830.225 REJECT NS=2;DP=361;DPB=406.0;AC=3;AN=4;AF=0.75;RO=125;AO=281;PRO=0.0;PAO=0.0;QR=4781;QA=10594;PQR=0.0;PQA=0.0;SRF=58;SRR=67;SAF=148;SAR=133;SRP=4.41741;SAP=4.74902;AB=0.60443;ABP=32.9436;RUN=1;RPP=3.07985;RPPR=3.02767;RPL=139.0;RPR=142.0;EPP=3.38896;EPPR=8.03074;DPRA=0.0;ODDS=57.0619;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992883;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.957;Dels=0.0;FS=1.254;HaplotypeScor [...]
+chr7 27880888 . A C 11278.6 REJECT NS=2;DP=426;DPB=488.0;AC=2;AN=4;AF=0.5;RO=118;AO=370;PRO=0.0;PAO=0.0;QR=4339;QA=14082;PQR=0.0;PQA=0.0;SRF=64;SRR=54;SAF=176;SAR=194;SRP=4.85053;SAP=4.91181;AB=0.758197;ABP=285.586;RUN=1;RPP=3.03378;RPPR=4.18805;RPL=186.0;RPR=184.0;EPP=3.22158;EPPR=4.18805;DPRA=0.0;ODDS=173.742;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991892;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.5695;Dels=0.0;FS=5.4185;HaplotypeSco [...]
+chr7 27881889 . C T 5982.29 REJECT NS=2;DP=381;DPB=431.0;AC=2;AN=4;AF=0.5;RO=221;AO=209;PRO=0.0;PAO=0.0;QR=8442;QA=8024;PQR=0.0;PQA=0.0;SRF=127;SRR=94;SAF=110;SAR=99;SRP=13.7105;SAP=4.26747;AB=0.484919;ABP=3.86176;RUN=1;RPP=7.59221;RPPR=4.67084;RPL=94.0;RPR=115.0;EPP=7.59221;EPPR=4.67084;DPRA=0.0;ODDS=282.282;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.977376;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0435;Dels=0.0;FS=4.0835;HaplotypeScore [...]
+chr7 27882220 . G T 4244.1 PASS SOMATIC;NS=2;DP=569;DPB=569.0;AC=1;AN=3;AF=0.25;RO=407;AO=162;PRO=0.0;PAO=0.0;QR=15419;QA=6061;PQR=0.0;PQA=0.0;SRF=205;SRR=202;SAF=80;SAR=82;SRP=3.05832;SAP=3.06392;AB=0.381176;ABP=55.1307;RUN=1;RPP=4.9405;RPPR=4.21075;RPL=75.0;RPR=87.0;EPP=3.86817;EPPR=5.83268;DPRA=2.95139;ODDS=90.8002;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987654;PAIREDR=0.992629;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-2.243;Dels=0.0;FS= [...]
+chr7 27882260 . T C 12462.2 REJECT NS=2;DP=465;DPB=534.0;AC=2;AN=4;AF=0.5;RO=128;AO=406;PRO=0.0;PAO=0.0;QR=4969;QA=15543;PQR=0.0;PQA=0.0;SRF=57;SRR=71;SAF=190;SAR=216;SRP=6.33537;SAP=6.62586;AB=0.7603;ABP=317.28;RUN=1;RPP=3.20284;RPPR=7.35324;RPL=200.0;RPR=206.0;EPP=5.59895;EPPR=3.07816;DPRA=0.0;ODDS=201.834;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992611;PAIREDR=0.984375;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.2585;Dels=0.0;FS=1.6365;Haplotype [...]
+chr7 27882511 . G T 5874.63 REJECT NS=2;DP=385;DPB=454.0;AC=2;AN=4;AF=0.5;RO=226;AO=228;PRO=0.0;PAO=0.0;QR=8548;QA=8632;PQR=0.0;PQA=0.0;SRF=118;SRR=108;SAF=110;SAR=118;SRP=3.97113;SAP=3.61984;AB=0.502203;ABP=3.02943;RUN=1;RPP=3.16268;RPPR=3.0103;RPL=112.0;RPR=116.0;EPP=3.61984;EPPR=10.5432;DPRA=0.0;ODDS=366.599;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991228;PAIREDR=0.995575;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0215;Dels=0.0;FS=1.8885;Haplot [...]
+chr7 27882550 . A G 3093.98 PASS SOMATIC;NS=2;DP=430;DPB=430.0;AC=1;AN=3;AF=0.25;RO=309;AO=121;PRO=0.0;PAO=0.0;QR=11863;QA=4439;PQR=0.0;PQA=0.0;SRF=151;SRR=158;SAF=63;SAR=58;SRP=3.35464;SAP=3.45895;AB=0.391586;ABP=34.5564;RUN=1;RPP=9.48883;RPPR=3.86062;RPL=70.0;RPR=51.0;EPP=5.18177;EPPR=3.07355;DPRA=2.55372;ODDS=75.5958;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991736;PAIREDR=0.996764;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-2.551;Dels=0.0;F [...]
+chr7 27882908 . C G 4420.93 PASS SOMATIC;NS=2;DP=558;DPB=558.0;AC=1;AN=3;AF=0.25;RO=394;AO=164;PRO=0.0;PAO=0.0;QR=15180;QA=6266;PQR=0.0;PQA=0.0;SRF=198;SRR=196;SAF=82;SAR=82;SRP=3.03235;SAP=3.0103;AB=0.383178;ABP=53.7456;RUN=1;RPP=3.22215;RPPR=4.09052;RPL=80.0;RPR=84.0;EPP=3.22215;EPPR=4.09052;DPRA=3.29231;ODDS=82.101;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993902;PAIREDR=0.997462;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.991;Dels=0.0;FS= [...]
+chr7 27883018 . A G 3159.27 PASS SOMATIC;NS=2;DP=466;DPB=466.0;AC=1;AN=3;AF=0.25;RO=344;AO=122;PRO=0.0;PAO=0.0;QR=13010;QA=4607;PQR=0.0;PQA=0.0;SRF=177;SRR=167;SAF=59;SAR=63;SRP=3.64154;SAP=3.29508;AB=0.355685;ABP=65.0587;RUN=1;RPP=3.0815;RPPR=7.2775;RPL=60.0;RPR=62.0;EPP=5.57335;EPPR=3.0103;DPRA=2.78862;ODDS=77.7176;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991803;PAIREDR=0.994186;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.381;Dels=0.0;FS=0. [...]
+chr7 27885315 . CA C 30.7891 REJECT NS=2;DP=26;DPB=110.259;AC=2;AN=4;AF=0.5;RO=4;AO=2;PRO=98.5;PAO=96.5;QR=144;QA=62;PQR=3498.0;PQA=3409.0;SRF=4;SRR=0;SAF=2;SAR=0;SRP=11.6962;SAP=7.35324;AB=0.133333;ABP=20.5268;RUN=1;RPP=7.35324;RPPR=11.6962;RPL=0.0;RPR=2.0;EPP=7.35324;EPPR=11.6962;DPRA=0.0;ODDS=0.573411;GTI=1;TYPE=del;CIGAR=1M1D56M;NUMALT=1;MEANALT=12.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:Call [...]
+chr7 27885931 . T C 1263.52 PASS SOMATIC;NS=2;DP=212;DPB=212.0;AC=1;AN=3;AF=0.25;RO=160;AO=51;PRO=0.0;PAO=0.0;QR=5980;QA=1919;PQR=0.0;PQA=0.0;SRF=74;SRR=86;SAF=21;SAR=30;SRP=4.96463;SAP=6.45911;AB=0.335526;ABP=38.7253;RUN=1;RPP=3.3935;RPPR=12.1848;RPL=27.0;RPR=24.0;EPP=6.45911;EPPR=31.728;DPRA=2.53333;ODDS=38.3548;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.5882;MQMR=60.5625;PAIRED=1.0;PAIREDR=0.99375;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.018;Dels=0.0;FS=0.65 [...]
+chr7 27886011 . C CATATACGTATACGTGTAT 3724.39 REJECT NS=2;DP=178;DPB=1022.67;AC=2;AN=4;AF=0.5;RO=49;AO=135;PRO=5.5;PAO=12.5;QR=1859;QA=4669;PQR=129.0;PQA=369.0;SRF=40;SRR=9;SAF=108;SAR=27;SRP=45.5977;SAP=108.544;AB=0.725806;ABP=85.3862;RUN=1;RPP=11.5193;RPPR=4.11819;RPL=79.0;RPR=56.0;EPP=3.15506;EPPR=5.18177;DPRA=0.0;ODDS=107.149;GTI=0;TYPE=ins;CIGAR=1M18I2M;NUMALT=1;MEANALT=2.0;LEN=18;MQM=65.4074;MQMR=59.5918;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=27886011;HOMLEN=17;HO [...]
+chr7 27886171 . A G 14789.7 REJECT NS=2;DP=395;DPB=447.0;AC=4;AN=4;AF=1.0;RO=0;AO=447;PRO=0.0;PAO=0.0;QR=0;QA=16916;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=211;SAR=236;SRP=0.0;SAP=6.04648;AB=0.0;ABP=0.0;RUN=1;RPP=4.41423;RPPR=0.0;RPL=232.0;RPR=215.0;EPP=5.58012;EPPR=0.0;DPRA=0.0;ODDS=68.5771;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995526;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9108;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.13;SOR=0.7 [...]
+chr7 27886417 . GTTAT G 1712.26 PASS SOMATIC;NS=2;DP=218;DPB=200.375;AC=1;AN=4;AF=0.25;RO=147;AO=68;PRO=25.5;PAO=8.5;QR=5611;QA=2510;PQR=886.5;PQA=293.5;SRF=57;SRR=90;SAF=26;SAR=42;SRP=19.0969;SAP=11.1853;AB=0.402367;ABP=17.0028;RUN=1;RPP=4.1599;RPPR=13.779;RPL=37.0;RPR=31.0;EPP=3.13803;EPPR=8.34296;DPRA=3.44898;ODDS=33.4707;GTI=0;TYPE=del;CIGAR=1M4D3M;NUMALT=1;MEANALT=2.0;LEN=4;MQM=61.0294;MQMR=59.8776;PAIRED=1.0;PAIREDR=0.979592;technology.ILLUMINA=1.0;MQ0=0;END=27886421;HOMLEN=2;HOMSE [...]
+chr7 27886586 . G GT 1579.915 REJECT NS=2;DP=37;DPB=59.4167;AC=3;AN=4;AF=0.75;RO=4;AO=33;PRO=12.5;PAO=30.5;QR=148;QA=1245;PQR=449.0;PQA=1142.0;SRF=1;SRR=3;SAF=9;SAR=24;SRP=5.18177;SAP=17.8158;AB=0.7;ABP=6.48466;RUN=1;RPP=3.60252;RPPR=5.18177;RPL=15.0;RPR=18.0;EPP=6.23461;EPPR=3.0103;DPRA=0.0;ODDS=14.2891;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.7665;FS=0.0;MLEAC=1;MLEAF=0.75;MQ=60.0;MQR [...]
+chr7 27886761 . GC G 933.845 REJECT NS=2;DP=50;DPB=44.3333;AC=2;AN=3;AF=0.5;RO=11;AO=38;PRO=0.0;PAO=1.0;QR=421;QA=1201;PQR=0.0;PQA=31.0;SRF=10;SRR=1;SAF=34;SAR=4;SRP=19.0002;SAP=54.4399;AB=0.690909;ABP=20.4216;RUN=1;RPP=5.06748;RPPR=3.20771;RPL=16.0;RPR=22.0;EPP=14.2105;EPPR=3.20771;DPRA=0.0;ODDS=1.14568;GTI=0;TYPE=del;CIGAR=1M1D1M;NUMALT=2;MEANALT=2.0;LEN=1;MQM=55.7368;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.6635;FS=0.0;MLEAC=1;ML [...]
+chr7 27886761 . GCTTTT G . PASS SOMATIC;AC=1;AN=4;END=27886766;HOMLEN=0;SVLEN=-5;SVTYPE=DEL GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:-2.67715 0/1:13,25:25:66:38:.:.:.:1:.:.:-0.0261709
+chr7 27886762 . C T 933.845 REJECT NS=2;DP=55;DPB=44.3333;AC=2;AN=2;AF=0.25;RO=11;AO=5;PRO=0.0;PAO=1.0;QR=421;QA=187;PQR=0.0;PQA=31.0;SRF=10;SRR=1;SAF=3;SAR=2;SRP=19.0002;SAP=3.44459;AB=0.113636;ABP=60.0608;RUN=1;RPP=13.8677;RPPR=3.20771;RPL=5.0;RPR=0.0;EPP=3.44459;EPPR=3.20771;DPRA=0.0;ODDS=1.14568;GTI=0;TYPE=snp;CIGAR=1M1X1M;NUMALT=2;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC: [...]
+chr7 27886770 . CTTTT C 411.739 REJECT NS=2;DP=40;DPB=49.4615;AC=2;AN=3;AF=0.5;RO=4;AO=16;PRO=16.0;PAO=14.0;QR=134;QA=566;PQR=544.167;PQA=475.167;SRF=4;SRR=0;SAF=14;SAR=2;SRP=11.6962;SAP=22.5536;AB=0.4;ABP=6.48466;RUN=1;RPP=5.18177;RPPR=5.18177;RPL=6.0;RPR=10.0;EPP=11.6962;EPPR=5.18177;DPRA=0.0;ODDS=2.94883;GTI=0;TYPE=del;CIGAR=1M4D21M;NUMALT=2;MEANALT=9.0;LEN=4;MQM=55.5;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.0245;FS=0.0;MLEAC=1;M [...]
+chr7 27886770 . CTTTTT C 411.739 REJECT NS=2;DP=40;DPB=49.4615;AC=2;AN=2;AF=0.25;RO=4;AO=5;PRO=16.0;PAO=12.0;QR=134;QA=181;PQR=544.167;PQA=399.667;SRF=4;SRR=0;SAF=5;SAR=0;SRP=11.6962;SAP=13.8677;AB=0.16129;ABP=33.9012;RUN=1;RPP=3.44459;RPPR=5.18177;RPL=2.0;RPR=3.0;EPP=3.44459;EPPR=5.18177;DPRA=0.0;ODDS=2.94883;GTI=0;TYPE=del;CIGAR=1M5D20M;NUMALT=2;MEANALT=11.0;LEN=5;MQM=57.6;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr7 27887164 . C T 8870.28 REJECT NS=2;DP=336;DPB=386.0;AC=2;AN=4;AF=0.5;RO=90;AO=296;PRO=0.0;PAO=0.0;QR=3426;QA=11129;PQR=0.0;PQA=0.0;SRF=35;SRR=55;SAF=132;SAR=164;SRP=12.6613;SAP=10.5224;AB=0.766839;ABP=241.737;RUN=1;RPP=27.6888;RPPR=5.42305;RPL=177.0;RPR=119.0;EPP=3.74391;EPPR=12.6613;DPRA=0.0;ODDS=135.19;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9778;PAIRED=0.993243;PAIREDR=0.966667;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.2915;Dels=0.0;FS=6.1895;Haplo [...]
+chr7 27887303 . C T 3802.62 REJECT NS=2;DP=146;DPB=172.0;AC=2;AN=4;AF=0.5;RO=40;AO=132;PRO=0.0;PAO=0.0;QR=1491;QA=5051;PQR=0.0;PQA=0.0;SRF=6;SRR=34;SAF=17;SAR=115;SRP=45.5712;SAP=161.001;AB=0.767442;ABP=109.867;RUN=1;RPP=12.4858;RPPR=3.87889;RPL=78.0;RPR=54.0;EPP=37.8197;EPPR=3.87889;DPRA=0.0;ODDS=12.3857;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992424;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.544;Dels=0.0;FS=4.018;HaplotypeScore=1.966 [...]
+chr7 27887689 . A T 10781.9 REJECT NS=2;DP=396;DPB=459.0;AC=2;AN=4;AF=0.5;RO=100;AO=358;PRO=0.0;PAO=0.0;QR=3845;QA=13459;PQR=0.0;PQA=0.0;SRF=56;SRR=44;SAF=205;SAR=153;SRP=6.13722;SAP=19.4116;AB=0.779956;ABP=315.48;RUN=1;RPP=3.61686;RPPR=3.09716;RPL=174.0;RPR=184.0;EPP=6.50407;EPPR=5.18177;DPRA=0.0;ODDS=140.394;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994413;PAIREDR=0.99;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.3155;Dels=0.0;FS=1.357;HaplotypeSco [...]
+chr7 27887806 . C G 9710.6 REJECT NS=2;DP=376;DPB=431.0;AC=2;AN=4;AF=0.5;RO=112;AO=318;PRO=0.0;PAO=0.0;QR=4362;QA=12221;PQR=0.0;PQA=0.0;SRF=46;SRR=66;SAF=127;SAR=191;SRP=10.7656;SAP=30.98;AB=0.737819;ABP=214.741;RUN=1;RPP=25.9815;RPPR=7.97367;RPL=188.0;RPR=130.0;EPP=5.74171;EPPR=4.25114;DPRA=0.0;ODDS=244.115;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993711;PAIREDR=0.982143;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.8255;Dels=0.0;FS=0.5875;HaplotypeS [...]
+chr7 27887967 . G A 8733.52 REJECT NS=2;DP=323;DPB=370.0;AC=2;AN=4;AF=0.5;RO=77;AO=293;PRO=0.0;PAO=0.0;QR=2875;QA=10898;PQR=0.0;PQA=0.0;SRF=38;SRR=39;SAF=157;SAR=136;SRP=3.0385;SAP=6.27863;AB=0.791892;ABP=276.827;RUN=1;RPP=4.67781;RPPR=3.71532;RPL=154.0;RPR=139.0;EPP=4.26279;EPPR=5.29458;DPRA=0.0;ODDS=152.823;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8831;PAIRED=1.0;PAIREDR=0.974026;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.65;Dels=0.0;FS=1.4705;HaplotypeSco [...]
+chr7 27888014 . C T 10787.2 REJECT NS=2;DP=383;DPB=445.0;AC=2;AN=4;AF=0.5;RO=95;AO=350;PRO=0.0;PAO=0.0;QR=3570;QA=13470;PQR=0.0;PQA=0.0;SRF=52;SRR=43;SAF=205;SAR=145;SRP=4.86177;SAP=25.3454;AB=0.786517;ABP=320.314;RUN=1;RPP=35.1729;RPPR=8.15326;RPL=139.0;RPR=211.0;EPP=8.59409;EPPR=9.61615;DPRA=0.0;ODDS=139.518;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989474;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.568;Dels=0.0;FS=1.4815;HaplotypeScore [...]
+chr7 27888968 . G A 14126.65 REJECT NS=2;DP=380;DPB=436.0;AC=4;AN=4;AF=1.0;RO=0;AO=434;PRO=0.0;PAO=0.0;QR=0;QA=16392;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=182;SAR=252;SRP=0.0;SAP=27.5269;AB=0.0;ABP=0.0;RUN=1;RPP=3.09035;RPPR=0.0;RPL=219.0;RPR=215.0;EPP=3.73079;EPPR=0.0;DPRA=0.0;ODDS=73.5675;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993088;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8992;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.895;SOR=1 [...]
+chr7 27889187 . G A 5734.49 REJECT NS=2;DP=359;DPB=413.0;AC=2;AN=4;AF=0.5;RO=207;AO=206;PRO=0.0;PAO=0.0;QR=7754;QA=7808;PQR=0.0;PQA=0.0;SRF=92;SRR=115;SAF=97;SAR=109;SRP=8.55962;SAP=4.52822;AB=0.498789;ABP=3.01556;RUN=1;RPP=3.05246;RPPR=3.86001;RPL=102.0;RPR=104.0;EPP=4.52822;EPPR=14.4341;DPRA=0.0;ODDS=308.566;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.970874;PAIREDR=0.990338;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1965;Dels=0.0;FS=0.208;Haplotyp [...]
+chr7 27889371 . G GACACAGACACACACACACACACA 13260.7 PASS SOMATIC;DP=214;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-2.731;FS=3.813;MLEAC=1;MLEAF=0.5;MQ=56.91;MQRankSum=-0.29;QD=8.08;ReadPosRankSum=0.238;SOR=0.432 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.182923 0/1:57,114:199:99.0:13298,0,6164:114:67:171:.:1:.:.:.:.:-0.0261709
+chr7 27889371 . G GACACAGACACACACACACACACACAC . PASS SOMATIC;AC=1;AN=4;END=27889371;HOMLEN=5;HOMSEQ=ACACA;SVLEN=26;SVTYPE=INS GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:-0.182923 0/1:67,23:23:26:90:.:.:.:1:.:.:-0.0261709
+chr7 27889375 . C CAG 493.73 PASS DP=80;AC=1;AN=4;AF=0.5;BaseQRankSum=-1.053;FS=5.761;MLEAC=1;MLEAF=0.5;MQ=57.42;MQRankSum=-2.441;QD=6.17;ReadPosRankSum=-0.754;SOR=1.458;ClippingRankSum=0.052 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:46,18:64:99.0:531,0,2773:18:28:64:1:.:.:.:.:.:-0.182923 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0261709
+chr7 27889377 . C G 406.808 REJECT NS=2;DP=287;DPB=287.0;AC=1;AN=4;AF=0.25;RO=259;AO=28;PRO=0.0;PAO=0.0;QR=9650;QA=924;PQR=0.0;PQA=0.0;SRF=132;SRR=127;SAF=9;SAR=19;SRP=3.2199;SAP=10.7656;AB=0.321839;ABP=26.9963;RUN=1;RPP=63.8115;RPPR=28.3721;RPL=28.0;RPR=0.0;EPP=10.7656;EPPR=3.42112;DPRA=0.435;ODDS=93.6711;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=47.8571;MQMR=57.0734;PAIRED=0.964286;PAIREDR=0.992278;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC [...]
+chr7 27889391 . C T 1601.0 REJECT NS=2;DP=297;DPB=297.0;AC=2;AN=4;AF=0.5;RO=203;AO=94;PRO=0.0;PAO=0.0;QR=7510;QA=3135;PQR=0.0;PQA=0.0;SRF=97;SRR=106;SAF=49;SAR=45;SRP=3.87675;SAP=3.37991;AB=0.316498;ABP=89.8765;RUN=1;RPP=207.129;RPPR=4.30463;RPL=0.0;RPR=94.0;EPP=3.37991;EPPR=3.87675;DPRA=0.0;ODDS=52.8439;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.4787;MQMR=55.3941;PAIRED=1.0;PAIREDR=0.990148;technology.ILLUMINA=1.0;MQ0=6;BaseQRankSum=-3.976;Dels=0.0;FS=0.0;HaplotypeScore=1 [...]
+chr7 27890064 . T C 7673.26 REJECT NS=2;DP=477;DPB=552.0;AC=2;AN=4;AF=0.5;RO=277;AO=275;PRO=0.0;PAO=0.0;QR=10632;QA=10528;PQR=0.0;PQA=0.0;SRF=128;SRR=149;SAF=141;SAR=134;SRP=6.46741;SAP=3.39722;AB=0.498188;ABP=3.02604;RUN=1;RPP=3.0182;RPPR=3.95885;RPL=137.0;RPR=138.0;EPP=3.20771;EPPR=3.95885;DPRA=0.0;ODDS=484.32;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992727;PAIREDR=0.99639;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1625;Dels=0.0;FS=2.6185;Haplot [...]
+chr7 27890366 . G A 6156.91 REJECT NS=2;DP=424;DPB=490.0;AC=2;AN=4;AF=0.5;RO=254;AO=236;PRO=0.0;PAO=0.0;QR=9502;QA=8697;PQR=0.0;PQA=0.0;SRF=139;SRR=115;SAF=114;SAR=122;SRP=7.93458;SAP=3.59917;AB=0.481633;ABP=4.44613;RUN=1;RPP=3.15752;RPPR=5.78021;RPL=116.0;RPR=120.0;EPP=8.31016;EPPR=7.93458;DPRA=0.0;ODDS=421.588;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9685;PAIRED=0.987288;PAIREDR=0.992126;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3365;Dels=0.0;FS=10.5985;H [...]
+chr7 27890432 . A T 1187.2 REJECT NS=2;DP=260;DPB=344.792;AC=2;AN=2;AF=0.0;RO=65;AO=20;PRO=56.7;PAO=16.3667;QR=2369;QA=281;PQR=2024.28;PQA=551.45;SRF=30;SRR=35;SAF=0;SAR=20;SRP=3.84548;SAP=46.4397;AB=0.0769231;ABP=407.238;RUN=1;RPP=6.91895;RPPR=3.04371;RPL=7.0;RPR=13.0;EPP=6.91895;EPPR=3.04371;DPRA=0.0;ODDS=17.8994;GTI=0;TYPE=snp;CIGAR=1X23M;NUMALT=4;MEANALT=22.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984615;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr7 27890432 . A AT 1187.2 REJECT NS=2;DP=260;DPB=344.792;AC=2;AN=2;AF=0.0;RO=65;AO=33;PRO=56.7;PAO=50.7;QR=2369;QA=878;PQR=2024.28;PQA=1771.28;SRF=30;SRR=35;SAF=14;SAR=19;SRP=3.84548;SAP=4.65535;AB=0.126923;ABP=317.339;RUN=1;RPP=3.0761;RPPR=3.04371;RPL=17.0;RPR=16.0;EPP=4.65535;EPPR=3.04371;DPRA=0.0;ODDS=17.8994;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=4;MEANALT=22.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.969697;PAIREDR=0.984615;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.549 [...]
+chr7 27890432 . AT A 1187.2 REJECT NS=2;DP=260;DPB=344.792;AC=2;AN=4;AF=0.5;RO=65;AO=61;PRO=56.7;PAO=40.0333;QR=2369;QA=1856;PQR=2024.28;PQA=1421.78;SRF=30;SRR=35;SAF=25;SAR=36;SRP=3.84548;SAP=7.31765;AB=0.234615;ABP=162.062;RUN=1;RPP=18.709;RPPR=3.04371;RPL=41.0;RPR=20.0;EPP=4.7546;EPPR=3.04371;DPRA=0.0;ODDS=17.8994;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=4;MEANALT=22.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984615;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr7 27890432 . ATT A 1187.2 REJECT NS=2;DP=260;DPB=344.792;AC=2;AN=2;AF=0.0;RO=65;AO=17;PRO=56.7;PAO=33.2;QR=2369;QA=447;PQR=2024.28;PQA=1165.2;SRF=30;SRR=35;SAF=6;SAR=11;SRP=3.84548;SAP=6.20364;AB=0.0653846;ABP=429.588;RUN=1;RPP=4.1599;RPPR=3.04371;RPL=7.0;RPR=10.0;EPP=3.13803;EPPR=3.04371;DPRA=0.0;ODDS=17.8994;GTI=0;TYPE=del;CIGAR=1M2D21M;NUMALT=4;MEANALT=22.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984615;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr7 27890568 . A AT 37.0847 REJECT NS=2;DP=152;DPB=192.467;AC=2;AN=2;AF=0.0;RO=126;AO=8;PRO=28.5833;PAO=21.5833;QR=4725;QA=239;PQR=1012.58;PQA=757.583;SRF=17;SRR=109;SAF=4;SAR=4;SRP=148.878;SAP=3.0103;AB=0.0465116;ABP=79.8198;RUN=1;RPP=12.7819;RPPR=14.6604;RPL=7.0;RPR=1.0;EPP=4.09604;EPPR=12.937;DPRA=0.0;ODDS=8.53888;GTI=0;TYPE=ins;CIGAR=1M1I14M;NUMALT=3;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992063;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr7 27890568 . AT A 37.0847 REJECT NS=2;DP=152;DPB=192.467;AC=2;AN=3;AF=0.25;RO=126;AO=11;PRO=28.5833;PAO=20.25;QR=4725;QA=327;PQR=1012.58;PQA=709.583;SRF=17;SRR=109;SAF=5;SAR=6;SRP=148.878;SAP=3.20771;AB=0.162791;ABP=45.4803;RUN=1;RPP=7.94546;RPPR=14.6604;RPL=8.0;RPR=3.0;EPP=3.20771;EPPR=12.937;DPRA=0.0;ODDS=8.53888;GTI=0;TYPE=del;CIGAR=1M1D13M;NUMALT=3;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992063;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr7 27890579 . G T 37.0847 REJECT NS=2;DP=152;DPB=192.467;AC=2;AN=2;AF=0.0;RO=126;AO=2;PRO=28.5833;PAO=14.5833;QR=4725;QA=30;PQR=1012.58;PQA=503.25;SRF=17;SRR=109;SAF=1;SAR=1;SRP=148.878;SAP=3.0103;AB=0.0465116;ABP=79.8198;RUN=1;RPP=7.35324;RPPR=14.6604;RPL=2.0;RPR=0.0;EPP=3.0103;EPPR=12.937;DPRA=0.394495;ODDS=8.53888;GTI=0;TYPE=snp;CIGAR=11M1X3M;NUMALT=3;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992063;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr7 27890678 . A C 2333.82 REJECT NS=2;DP=91;DPB=105.0;AC=2;AN=4;AF=0.5;RO=25;AO=80;PRO=0.0;PAO=0.0;QR=937;QA=2994;PQR=0.0;PQA=0.0;SRF=5;SRR=20;SAF=32;SAR=48;SRP=22.5536;SAP=9.95901;AB=0.761905;ABP=65.5694;RUN=1;RPP=11.8048;RPPR=3.09716;RPL=49.0;RPR=31.0;EPP=8.33041;EPPR=10.0459;DPRA=0.0;ODDS=52.0946;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.9;MQMR=59.76;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1365;Dels=0.0;FS=3.586;HaplotypeScore=0.9998;MLEAC [...]
+chr7 27890750 . C T 1446.35 REJECT NS=2;DP=89;DPB=103.0;AC=2;AN=4;AF=0.5;RO=47;AO=56;PRO=0.0;PAO=0.0;QR=1740;QA=2080;PQR=0.0;PQA=0.0;SRF=36;SRR=11;SAF=46;SAR=10;SRP=31.8863;SAP=53.2644;AB=0.543689;ABP=4.71796;RUN=1;RPP=18.5208;RPPR=6.75262;RPL=18.0;RPR=38.0;EPP=12.937;EPPR=13.4056;DPRA=0.0;ODDS=55.8872;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.875;MQMR=59.4681;PAIRED=1.0;PAIREDR=0.957447;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.363;Dels=0.0;FS=2.853;HaplotypeScore=6.9 [...]
+chr7 27891062 . G A 1252.07 PASS SOMATIC;NS=2;DP=189;DPB=189.0;AC=1;AN=3;AF=0.25;RO=138;AO=51;PRO=0.0;PAO=0.0;QR=5221;QA=1971;PQR=0.0;PQA=0.0;SRF=27;SRR=111;SAF=5;SAR=46;SRP=114.039;SAP=74.5837;AB=0.354167;ABP=29.6108;RUN=1;RPP=6.45911;RPPR=3.0103;RPL=21.0;RPR=30.0;EPP=3.3935;EPPR=17.1721;DPRA=3.2;ODDS=29.0917;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992754;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.366;Dels=0.0;FS=8.024;Haplotyp [...]
+chr7 27891521 . G C 4496.77 PASS SOMATIC;DP=361;AC=1;AN=3;AF=0.5;MQ0=1;VT=SNP;BaseQRankSum=3.001;Dels=0.0;FS=1.305;HaplotypeScore=10.7143;MLEAC=1;MLEAF=0.5;MQ=56.53;MQRankSum=-0.394;QD=12.46;ReadPosRankSum=-0.628;SOR=0.744 GT:AD:BQ:DP:FA:SS:GMIMUT:GMIMAF:GMICOV:GQ:PL:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0:112,1:.:112:0.00885:0:1:1:113:.:.:.:.:.:.:.:0:-0.182923 0/1:215,126:38.0:341:0.362:2:126:37:341:99.0:4525,0,8014:.:1:.:.:.:1:-0.0261709
+chr7 27891521 . GTTAT CTTAC 3597.15 PASS SOMATIC;NS=2;DP=461;DPB=479.4;AC=1;AN=4;AF=0.25;RO=328;AO=129;PRO=30.0;PAO=10.0;QR=12159;QA=4841;PQR=856.0;PQA=381.0;SRF=163;SRR=165;SAF=64;SAR=65;SRP=3.03678;SAP=3.02713;AB=0.371758;ABP=52.5787;RUN=1;RPP=9.08706;RPPR=3.96363;RPL=55.0;RPR=74.0;EPP=5.04711;EPPR=3.03678;DPRA=3.04386;ODDS=25.6822;GTI=0;TYPE=complex;CIGAR=1X3M1X;NUMALT=1;MEANALT=1.0;LEN=5;MQM=55.0465;MQMR=54.9421;PAIRED=0.992248;PAIREDR=0.987805;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR: [...]
+chr7 27891525 . T C 4412.77 PASS SOMATIC;DP=357;AC=1;AN=3;AF=0.5;MQ0=1;VT=SNP;BaseQRankSum=2.085;Dels=0.0;FS=0.0;HaplotypeScore=17.4881;MLEAC=1;MLEAF=0.5;MQ=56.22;MQRankSum=0.185;QD=12.36;ReadPosRankSum=0.079;SOR=0.672 GT:AD:BQ:DP:FA:SS:GMIMUT:GMIMAF:GMICOV:GQ:PL:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0:115,0:.:112:0.0:0:0:0:115:.:.:.:.:.:.:.:0:-0.182923 0/1:215,125:38.0:340:0.361:2:125:36:340:99.0:4441,0,7896:.:1:.:.:.:1:-0.0261709
+chr7 27891749 . C CT 796.655 REJECT NS=2;DP=181;DPB=266.75;AC=2;AN=4;AF=0.5;RO=72;AO=35;PRO=70.5;PAO=59.5;QR=2648;QA=1006;PQR=2474.17;PQA=1996.17;SRF=18;SRR=54;SAF=14;SAR=21;SRP=42.0968;SAP=6.05036;AB=0.19337;ABP=150.826;RUN=1;RPP=20.9405;RPPR=12.7819;RPL=26.0;RPR=9.0;EPP=3.07234;EPPR=8.92153;DPRA=0.0;ODDS=1.14338;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=2;MEANALT=18.0;LEN=1;MQM=59.0;MQMR=58.625;PAIRED=1.0;PAIREDR=0.986111;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=2.285;FS= [...]
+chr7 27891749 . CT C 796.655 REJECT NS=2;DP=181;DPB=266.75;AC=2;AN=2;AF=0.0;RO=72;AO=20;PRO=70.5;PAO=38.0;QR=2648;QA=550;PQR=2474.17;PQA=1337.67;SRF=18;SRR=54;SAF=5;SAR=15;SRP=42.0968;SAP=13.8677;AB=0.110497;ABP=241.524;RUN=1;RPP=9.95901;RPPR=12.7819;RPL=14.0;RPR=6.0;EPP=3.44459;EPPR=8.92153;DPRA=0.0;ODDS=1.14338;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=2;MEANALT=18.0;LEN=1;MQM=59.25;MQMR=58.625;PAIRED=1.0;PAIREDR=0.986111;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr7 27891896 . G A 707.007 PASS SOMATIC;NS=2;DP=140;DPB=140.0;AC=1;AN=3;AF=0.25;RO=109;AO=31;PRO=0.0;PAO=0.0;QR=4056;QA=1144;PQR=0.0;PQA=0.0;SRF=42;SRR=67;SAF=11;SAR=20;SRP=15.4614;SAP=8.68415;AB=0.326316;ABP=27.9022;RUN=1;RPP=3.08035;RPPR=17.5333;RPL=16.0;RPR=15.0;EPP=18.771;EPPR=47.0175;DPRA=2.11111;ODDS=29.1105;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990826;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.806;Dels=0.0;FS=0.0;Haplo [...]
+chr7 27891913 . G A 783.827 PASS SOMATIC;NS=2;DP=146;DPB=146.0;AC=1;AN=3;AF=0.25;RO=112;AO=34;PRO=0.0;PAO=0.0;QR=4197;QA=1242;PQR=0.0;PQA=0.0;SRF=57;SRR=55;SAF=14;SAR=20;SRP=3.08785;SAP=5.30951;AB=0.354167;ABP=20.744;RUN=1;RPP=4.03217;RPPR=16.1167;RPL=19.0;RPR=15.0;EPP=28.557;EPPR=40.5458;DPRA=1.92;ODDS=32.2311;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991071;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-3.091;Dels=0.0;FS=2.787;Haplot [...]
+chr7 27892700 . C T 3671.7 PASS SOMATIC;NS=2;DP=496;DPB=496.0;AC=1;AN=3;AF=0.25;RO=360;AO=136;PRO=0.0;PAO=0.0;QR=13755;QA=5300;PQR=0.0;PQA=0.0;SRF=180;SRR=180;SAF=64;SAR=72;SRP=3.0103;SAP=4.03217;AB=0.355091;ABP=72.8659;RUN=1;RPP=3.07417;RPPR=5.92972;RPL=67.0;RPR=69.0;EPP=6.13977;EPPR=3.03443;DPRA=3.38938;ODDS=71.4175;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9972;PAIRED=0.985294;PAIREDR=0.997222;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.865;Dels=0.0;F [...]
+chr7 27892836 . C T 14145.6 REJECT NS=2;DP=506;DPB=587.0;AC=2;AN=4;AF=0.5;RO=127;AO=459;PRO=0.0;PAO=0.0;QR=4810;QA=17582;PQR=0.0;PQA=0.0;SRF=61;SRR=66;SAF=212;SAR=247;SRP=3.43776;SAP=8.80562;AB=0.781942;ABP=408.306;RUN=1;RPP=8.80562;RPPR=3.16418;RPL=212.0;RPR=247.0;EPP=6.98897;EPPR=3.43776;DPRA=0.0;ODDS=176.809;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995643;PAIREDR=0.992126;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.326;Dels=0.0;FS=1.4785;Haplotyp [...]
+chr7 27893086 . G A 2133.98 PASS SOMATIC;NS=2;DP=361;DPB=361.0;AC=1;AN=3;AF=0.25;RO=277;AO=84;PRO=0.0;PAO=0.0;QR=10597;QA=3209;PQR=0.0;PQA=0.0;SRF=130;SRR=147;SAF=34;SAR=50;SRP=5.27584;SAP=9.62812;AB=0.329412;ABP=67.4647;RUN=1;RPP=3.1137;RPPR=5.27584;RPL=41.0;RPR=43.0;EPP=8.07707;EPPR=4.77413;DPRA=2.40566;ODDS=67.1543;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99639;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.592;Dels=0.0;FS=6.391;H [...]
+chr7 27893603 . A G 218.046 REJECT NS=2;DP=22;DPB=22.0;AC=2;AN=4;AF=0.5;RO=12;AO=10;PRO=0.0;PAO=0.0;QR=419;QA=364;PQR=0.0;PQA=0.0;SRF=8;SRR=4;SAF=8;SAR=2;SRP=5.9056;SAP=10.8276;AB=0.454545;ABP=3.40511;RUN=1;RPP=6.48466;RPPR=3.73412;RPL=3.0;RPR=7.0;EPP=3.0103;EPPR=3.73412;DPRA=0.0;ODDS=4.35975;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.916667;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.048;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=1;MLEAF=0. [...]
+chr7 27893667 . A G 758.621 REJECT NS=2;DP=28;DPB=33.0;AC=3;AN=4;AF=0.75;RO=6;AO=27;PRO=0.0;PAO=0.0;QR=238;QA=1002;PQR=0.0;PQA=0.0;SRF=5;SRR=1;SAF=24;SAR=3;SRP=8.80089;SAP=38.4777;AB=0.444444;ABP=3.25157;RUN=1;RPP=6.95112;RPPR=4.45795;RPL=10.0;RPR=17.0;EPP=5.02092;EPPR=8.80089;DPRA=0.0;ODDS=8.97168;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.1111;MQMR=60.0;PAIRED=0.925926;PAIREDR=0.833333;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.469;Dels=0.0;FS=0.0;HaplotypeScore=0.0;M [...]
+chr7 27894157 . T C 18.59 LowQual SOMATIC;DP=1;AC=2;AN=4;AF=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-4.33512 1/1:0,1:1:3.0:45,3,0:1:100:1:.:1:.:.:.:.:-0.0261709
+chr7 27896074 . G C 167.214 REJECT NS=2;DP=7;DPB=9.0;AC=2;AN=4;AF=0.5;RO=2;AO=7;PRO=0.0;PAO=0.0;QR=75;QA=271;PQR=0.0;PQA=0.0;SRF=0;SRR=2;SAF=0;SAR=7;SRP=7.35324;SAP=18.2106;AB=0.777778;ABP=9.04217;RUN=1;RPP=5.80219;RPPR=7.35324;RPL=5.0;RPR=2.0;EPP=5.80219;EPPR=7.35324;DPRA=0.0;ODDS=0.743033;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0 [...]
+chr7 27896295 . T C 11.12 LowQual SOMATIC;DP=2;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.804;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=1;MLEAF=0.5;MQ=53.03;MQRankSum=0.804;QD=5.56;ReadPosRankSum=0.804;SOR=0.693 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-26.715 0/1:1,1:2:39.0:39,0,39:1:50:2:.:1:.:.:.:.:-6.40611
+chr7 27900596 . C A 11647.1 REJECT NS=2;DP=437;DPB=501.0;AC=2;AN=4;AF=0.5;RO=114;AO=386;PRO=0.0;PAO=0.0;QR=4444;QA=14541;PQR=0.0;PQA=0.0;SRF=58;SRR=56;SAF=193;SAR=193;SRP=3.08649;SAP=3.0103;AB=0.770459;ABP=321.324;RUN=1;RPP=9.51347;RPPR=5.75321;RPL=176.0;RPR=210.0;EPP=10.301;EPPR=10.6295;DPRA=0.0;ODDS=209.284;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997409;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.223;Dels=0.0;FS=0.565;HaplotypeScore= [...]
+chr7 27900640 . C G 3740.54 PASS SOMATIC;NS=2;DP=521;DPB=521.0;AC=1;AN=3;AF=0.25;RO=378;AO=143;PRO=0.0;PAO=0.0;QR=14376;QA=5444;PQR=0.0;PQA=0.0;SRF=176;SRR=202;SAF=74;SAR=69;SRP=6.89367;SAP=3.38993;AB=0.3575;ABP=73.5614;RUN=1;RPP=4.8477;RPPR=4.48093;RPL=66.0;RPR=77.0;EPP=19.5469;EPPR=3.0103;DPRA=3.30579;ODDS=76.3446;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994709;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.571;Dels=0.0;FS=4.665;Ha [...]
+chr7 27901051 . A AT 1904.17 REJECT NS=2;DP=339;DPB=447.077;AC=2;AN=2;AF=0.0;RO=233;AO=19;PRO=100.667;PAO=68.6667;QR=8799;QA=679;PQR=3613.83;PQA=2439.83;SRF=116;SRR=117;SAF=12;SAR=7;SRP=3.01962;SAP=5.8675;AB=0.0560472;ABP=583.357;RUN=1;RPP=4.03889;RPPR=5.70367;RPL=8.0;RPR=11.0;EPP=3.12459;EPPR=4.13797;DPRA=0.0;ODDS=162.649;GTI=0;TYPE=ins;CIGAR=1M1I25M;NUMALT=2;MEANALT=8.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr7 27901051 . AT A 1904.17 REJECT NS=2;DP=339;DPB=447.077;AC=2;AN=4;AF=0.5;RO=233;AO=73;PRO=100.667;PAO=78.6667;QR=8799;QA=2765;PQR=3613.83;PQA=2753.33;SRF=116;SRR=117;SAF=35;SAR=38;SRP=3.01962;SAP=3.27802;AB=0.215339;ABP=241.61;RUN=1;RPP=3.04005;RPPR=5.70367;RPL=36.0;RPR=37.0;EPP=3.04005;EPPR=4.13797;DPRA=0.0;ODDS=162.649;GTI=0;TYPE=del;CIGAR=1M1D24M;NUMALT=2;MEANALT=8.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986301;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.696;F [...]
+chr7 27901170 . CT C 7299.995 REJECT NS=2;DP=358;DPB=427.2;AC=2;AN=4;AF=0.5;RO=89;AO=276;PRO=77.5;PAO=73.5;QR=3338;QA=10286;PQR=2717.5;PQA=2544.5;SRF=42;SRR=47;SAF=143;SAR=133;SRP=3.62026;SAP=3.79707;AB=0.726316;ABP=172.065;RUN=1;RPP=6.15736;RPPR=7.13366;RPL=128.0;RPR=148.0;EPP=6.81824;EPPR=3.0347;DPRA=0.0;ODDS=207.608;GTI=0;TYPE=del;CIGAR=1M1D13M;NUMALT=1;MEANALT=5.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992754;PAIREDR=0.988764;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.9945;FS=5.6695;MLE [...]
+chr7 27901180 . TCATGCACAAAGCTTTCTTCTCTCTGTAAGGAGAAGGTTG CATGCACAAAGCTTTCTTCTCTCTGTAAGGAGCAGGTTGTTGT . PASS SOMATIC;AC=1;AN=4;END=27901219;HOMLEN=0;SVLEN=-40;SVTYPE=RPL;NTLEN=43 GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:0.00182088 0/1:158,251:251:61:409:.:.:.:1:.:.:-0.0111333
+chr7 27901180 . TCATGCACAAAGCTTTCTTCTCTCTGTAAGGAGAAGGTTG CATGCACAAAGCTTTCTTCTCTCTGTAAGGAGAAGGTTGTTGT . PASS AC=1;AN=4;END=27901219;HOMLEN=0;SVLEN=-40;SVTYPE=RPL;NTLEN=43 GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:70,39:39:36:109:.:.:.:1:.:.:0.00182088 0/0:.:.:.:.:.:.:.:.:.:.:-0.0111333
+chr7 27901219 . G GTTGT 9024.18 REJECT NS=2;DP=396;DPB=574.867;AC=2;AN=4;AF=0.5;RO=98;AO=306;PRO=60.5;PAO=70.5;QR=3741;QA=10757;PQR=2114.5;PQA=2471.5;SRF=50;SRR=48;SAF=164;SAR=142;SRP=3.09893;SAP=6.44492;AB=0.721698;ABP=184.021;RUN=1;RPP=3.46446;RPPR=3.36483;RPL=157.0;RPR=149.0;EPP=4.82696;EPPR=6.20103;DPRA=0.0;ODDS=141.301;GTI=0;TYPE=ins;CIGAR=1M4I14M;NUMALT=1;MEANALT=6.0;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=0.996732;PAIREDR=0.989796;technology.ILLUMINA=1.0;MQ0=0;END=27901219;HOMLEN=6;HOMSEQ [...]
+chr7 27902935 . G A 3715.59 PASS SOMATIC;NS=2;DP=496;DPB=496.0;AC=1;AN=3;AF=0.25;RO=352;AO=143;PRO=0.0;PAO=0.0;QR=13187;QA=5328;PQR=0.0;PQA=0.0;SRF=166;SRR=186;SAF=65;SAR=78;SRP=5.47788;SAP=5.57659;AB=0.381333;ABP=48.8776;RUN=1;RPP=6.42695;RPPR=3.89863;RPL=79.0;RPR=64.0;EPP=7.3988;EPPR=4.58955;DPRA=3.09917;ODDS=76.4015;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993007;PAIREDR=0.997159;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.459;Dels=0.0;FS [...]
+chr7 27903096 . C T 3505.48 PASS SOMATIC;NS=2;DP=497;DPB=497.0;AC=1;AN=3;AF=0.25;RO=365;AO=132;PRO=0.0;PAO=0.0;QR=13797;QA=5075;PQR=0.0;PQA=0.0;SRF=181;SRR=184;SAF=68;SAR=64;SRP=3.06384;SAP=3.27351;AB=0.356757;ABP=68.9526;RUN=1;RPP=3.0761;RPPR=3.49219;RPL=67.0;RPR=65.0;EPP=6.23461;EPPR=3.15903;DPRA=2.91339;ODDS=80.1781;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994521;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.917;Dels=0.0;FS=2.305 [...]
+chr7 27903215 . A C 11931.8 REJECT NS=2;DP=446;DPB=516.0;AC=2;AN=4;AF=0.5;RO=120;AO=396;PRO=0.0;PAO=0.0;QR=4546;QA=14905;PQR=0.0;PQA=0.0;SRF=56;SRR=64;SAF=189;SAR=207;SRP=4.16842;SAP=4.78696;AB=0.767442;ABP=323.58;RUN=1;RPP=12.6832;RPPR=4.81986;RPL=177.0;RPR=219.0;EPP=4.41408;EPPR=3.66174;DPRA=0.0;ODDS=145.322;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992424;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.2455;Dels=0.0;FS=2.0155;HaplotypeScor [...]
+chr7 27903830 . C A 6204.290000000001 REJECT NS=2;DP=404;DPB=462.0;AC=2;AN=4;AF=0.5;RO=237;AO=224;PRO=0.0;PAO=0.0;QR=8964;QA=8570;PQR=0.0;PQA=0.0;SRF=130;SRR=107;SAF=119;SAR=105;SRP=7.85717;SAP=4.91034;AB=0.484848;ABP=3.93153;RUN=1;RPP=7.70223;RPPR=6.3179;RPL=101.0;RPR=123.0;EPP=3.16541;EPPR=4.11894;DPRA=0.0;ODDS=347.973;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995536;PAIREDR=0.983122;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9575;Dels=0.0;FS=3.17 [...]
+chr7 27904259 . C T 6705.09 REJECT NS=2;DP=440;DPB=505.0;AC=2;AN=4;AF=0.5;RO=263;AO=242;PRO=0.0;PAO=0.0;QR=9931;QA=9205;PQR=0.0;PQA=0.0;SRF=114;SRR=149;SAF=118;SAR=124;SRP=13.1246;SAP=3.33333;AB=0.479208;ABP=4.90658;RUN=1;RPP=4.76901;RPPR=9.95406;RPL=128.0;RPR=114.0;EPP=15.9674;EPPR=5.39644;DPRA=0.0;ODDS=397.852;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995868;PAIREDR=0.996198;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.52;Dels=0.0;FS=3.8945;Haplotyp [...]
+chr7 27904674 . T G 9046.11 REJECT NS=2;DP=346;DPB=399.0;AC=2;AN=4;AF=0.5;RO=99;AO=299;PRO=0.0;PAO=0.0;QR=3755;QA=11426;PQR=0.0;PQA=0.0;SRF=32;SRR=67;SAF=114;SAR=185;SRP=29.8795;SAP=39.6203;AB=0.749373;ABP=218.53;RUN=1;RPP=53.0413;RPPR=5.66432;RPL=191.0;RPR=108.0;EPP=3.07566;EPPR=5.66432;DPRA=0.0;ODDS=128.626;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9097;MQMR=60.0;PAIRED=0.986622;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.301;Dels=0.0;FS=9.592;HaplotypeScor [...]
+chr7 27905732 . A G 2624.08 PASS SOMATIC;NS=2;DP=429;DPB=429.0;AC=1;AN=3;AF=0.25;RO=324;AO=105;PRO=0.0;PAO=0.0;QR=12309;QA=3920;PQR=0.0;PQA=0.0;SRF=161;SRR=163;SAF=55;SAR=50;SRP=3.03711;SAP=3.52732;AB=0.339806;ABP=71.886;RUN=1;RPP=4.68544;RPPR=4.32391;RPL=48.0;RPR=57.0;EPP=13.9504;EPPR=4.72603;DPRA=2.575;ODDS=75.8241;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.737;Dels=0.0;FS=2.037;Haplo [...]
+chr7 27905918 . G A 11890.8 REJECT NS=2;DP=429;DPB=490.0;AC=2;AN=4;AF=0.5;RO=106;AO=384;PRO=0.0;PAO=0.0;QR=4015;QA=14780;PQR=0.0;PQA=0.0;SRF=66;SRR=40;SAF=213;SAR=171;SRP=16.8586;SAP=12.9855;AB=0.783673;ABP=345.5;RUN=1;RPP=3.37221;RPPR=4.32138;RPL=188.0;RPR=196.0;EPP=4.11866;EPPR=8.25461;DPRA=0.0;ODDS=126.053;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994792;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.266;Dels=0.0;FS=3.253;HaplotypeScore=4 [...]
+chr7 27906384 . C T 12702.2 REJECT NS=2;DP=466;DPB=533.0;AC=2;AN=4;AF=0.5;RO=117;AO=416;PRO=0.0;PAO=0.0;QR=4416;QA=15808;PQR=0.0;PQA=0.0;SRF=56;SRR=61;SAF=190;SAR=226;SRP=3.47429;SAP=9.77527;AB=0.780488;ABP=367.235;RUN=1;RPP=3.19822;RPPR=3.02886;RPL=211.0;RPR=205.0;EPP=4.0334;EPPR=6.14687;DPRA=0.0;ODDS=103.496;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995192;PAIREDR=0.991453;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9155;Dels=0.0;FS=4.4605;Haplotyp [...]
+chr7 27906711 . T C 3354.32 PASS SOMATIC;NS=2;DP=435;DPB=435.0;AC=1;AN=3;AF=0.25;RO=310;AO=125;PRO=0.0;PAO=0.0;QR=11806;QA=4807;PQR=0.0;PQA=0.0;SRF=158;SRR=152;SAF=65;SAR=60;SRP=3.26247;SAP=3.44459;AB=0.37092;ABP=51.7814;RUN=1;RPP=5.94613;RPPR=7.74551;RPL=56.0;RPR=69.0;EPP=3.02767;EPPR=45.6272;DPRA=3.43878;ODDS=62.0801;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9516;PAIRED=1.0;PAIREDR=0.990323;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.754;Dels=0.0;FS=0. [...]
+chr7 27906927 . A C 10312.3 REJECT NS=2;DP=380;DPB=429.0;AC=2;AN=4;AF=0.5;RO=94;AO=335;PRO=0.0;PAO=0.0;QR=3618;QA=12846;PQR=0.0;PQA=0.0;SRF=49;SRR=45;SAF=155;SAR=180;SRP=3.37991;SAP=7.06155;AB=0.780886;ABP=296.999;RUN=1;RPP=14.9955;RPPR=3.1027;RPL=189.0;RPR=146.0;EPP=4.10576;EPPR=4.48875;DPRA=0.0;ODDS=146.368;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989362;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.9185;Dels=0.0;FS=4.469;HaplotypeScore [...]
+chr7 27907066 . G T 16143.85 REJECT NS=2;DP=427;DPB=485.0;AC=4;AN=4;AF=1.0;RO=0;AO=484;PRO=0.0;PAO=0.0;QR=0;QA=18467;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=249;SAR=235;SRP=0.0;SAP=3.88966;AB=0.0;ABP=0.0;RUN=1;RPP=3.45895;RPPR=0.0;RPL=237.0;RPR=247.0;EPP=4.15885;EPPR=0.0;DPRA=0.0;ODDS=76.6596;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995868;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.8457;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=35.18;SOR=0. [...]
+chr7 27907572 . G A 11009.3 REJECT NS=2;DP=405;DPB=451.0;AC=2;AN=4;AF=0.5;RO=92;AO=357;PRO=0.0;PAO=0.0;QR=3508;QA=13674;PQR=0.0;PQA=0.0;SRF=50;SRR=42;SAF=190;SAR=167;SRP=4.52089;SAP=6.22797;AB=0.791574;ABP=336.045;RUN=1;RPP=9.6342;RPPR=3.38795;RPL=162.0;RPR=195.0;EPP=3.50299;EPPR=3.38795;DPRA=0.0;ODDS=151.607;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.552;Dels=0.0;FS=0.8695;HaplotypeScore=1.997 [...]
+chr7 27907593 . C T 11540.5 REJECT NS=2;DP=416;DPB=461.0;AC=2;AN=4;AF=0.5;RO=89;AO=372;PRO=0.0;PAO=0.0;QR=3472;QA=14302;PQR=0.0;PQA=0.0;SRF=45;SRR=44;SAF=181;SAR=191;SRP=3.0347;SAP=3.59403;AB=0.806941;ABP=380.258;RUN=1;RPP=6.95631;RPPR=3.22989;RPL=173.0;RPR=199.0;EPP=8.98769;EPPR=10.0615;DPRA=0.0;ODDS=153.147;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.2385;Dels=0.0;FS=0.408;HaplotypeScore=3.964 [...]
+chr7 27908326 . T C 11616.6 REJECT NS=2;DP=425;DPB=489.0;AC=2;AN=4;AF=0.5;RO=113;AO=376;PRO=0.0;PAO=0.0;QR=4335;QA=14470;PQR=0.0;PQA=0.0;SRF=54;SRR=59;SAF=199;SAR=177;SRP=3.49071;SAP=5.80549;AB=0.768916;ABP=310.165;RUN=1;RPP=4.14224;RPPR=4.56684;RPL=195.0;RPR=181.0;EPP=8.9241;EPPR=5.3355;DPRA=0.0;ODDS=146.42;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9973;MQMR=60.0;PAIRED=0.99734;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.599;Dels=0.0;FS=2.8505;HaplotypeScor [...]
+chr7 27908541 . T C 13196.3 REJECT NS=2;DP=488;DPB=553.0;AC=2;AN=4;AF=0.5;RO=123;AO=430;PRO=0.0;PAO=0.0;QR=4675;QA=16416;PQR=0.0;PQA=0.0;SRF=66;SRR=57;SAF=223;SAR=207;SRP=4.44029;SAP=4.30308;AB=0.777577;ABP=373.099;RUN=1;RPP=5.91906;RPPR=3.45166;RPL=227.0;RPR=203.0;EPP=4.64648;EPPR=5.14646;DPRA=0.0;ODDS=185.535;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995349;PAIREDR=0.99187;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.687;Dels=0.0;FS=3.7385;Haplotype [...]
+chr7 27909578 . A G 1181.4 PASS SOMATIC;NS=2;DP=150;DPB=150.0;AC=1;AN=3;AF=0.25;RO=102;AO=48;PRO=0.0;PAO=0.0;QR=3845;QA=1787;PQR=0.0;PQA=0.0;SRF=15;SRR=87;SAF=4;SAR=44;SRP=113.372;SAP=75.3927;AB=0.436364;ABP=6.87947;RUN=1;RPP=3.73412;RPPR=3.35092;RPL=26.0;RPR=22.0;EPP=5.9056;EPPR=3.7767;DPRA=2.75;ODDS=25.9286;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.7353;PAIRED=0.979167;PAIREDR=0.990196;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.955;Dels=0.0;FS=1.237; [...]
+chr7 27909694 . A ATTTTTTTTT 115.06 PASS DP=22;AC=1;AN=4;AF=0.5;BaseQRankSum=0.731;FS=3.979;MLEAC=1;MLEAF=0.5;MQ=54.02;MQRankSum=-0.731;QD=5.23;ReadPosRankSum=0.727;SOR=1.447;ClippingRankSum=0.731 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:3,4:7:86.0:141,0,86:4:57:7:1:.:.:.:.:.:0.00182088 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0111333
+chr7 27909694 . ATT A 30.9459 REJECT NS=2;DP=36;DPB=97.1;AC=2;AN=4;AF=0.5;RO=6;AO=7;PRO=50.3333;PAO=41.3333;QR=207;QA=134;PQR=1801.33;PQA=1415.33;SRF=0;SRR=6;SAF=1;SAR=6;SRP=16.0391;SAP=10.7656;AB=0.194444;ABP=32.2045;RUN=1;RPP=3.32051;RPPR=16.0391;RPL=3.0;RPR=4.0;EPP=3.32051;EPPR=16.0391;DPRA=0.0;ODDS=6.31416;GTI=0;TYPE=del;CIGAR=1M2D37M;NUMALT=3;MEANALT=11.0;LEN=2;MQM=48.5714;MQMR=49.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.33;FS=1.752;MLE [...]
+chr7 27909694 . ATTT A 30.9459 REJECT NS=2;DP=36;DPB=97.1;AC=2;AN=2;AF=0.0;RO=6;AO=4;PRO=50.3333;PAO=35.0;QR=207;QA=152;PQR=1801.33;PQA=1239.33;SRF=0;SRR=6;SAF=3;SAR=1;SRP=16.0391;SAP=5.18177;AB=0.111111;ABP=50.3001;RUN=1;RPP=5.18177;RPPR=16.0391;RPL=1.0;RPR=3.0;EPP=11.6962;EPPR=16.0391;DPRA=0.0;ODDS=6.31416;GTI=0;TYPE=del;CIGAR=1M3D36M;NUMALT=3;MEANALT=11.0;LEN=3;MQM=60.0;MQMR=49.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr7 27909716 . TTG T 30.9459 REJECT NS=2;DP=36;DPB=97.1;AC=2;AN=2;AF=0.0;RO=6;AO=2;PRO=50.3333;PAO=35.3333;QR=207;QA=28;PQR=1801.33;PQA=1239.0;SRF=0;SRR=6;SAF=2;SAR=0;SRP=16.0391;SAP=7.35324;AB=0.0909091;ABP=34.9902;RUN=1;RPP=7.35324;RPPR=16.0391;RPL=2.0;RPR=0.0;EPP=7.35324;EPPR=16.0391;DPRA=0.0;ODDS=6.31416;GTI=0;TYPE=del;CIGAR=23M2D15M;NUMALT=3;MEANALT=13.0;LEN=2;MQM=60.0;MQMR=49.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr7 27909851 . G C 1595.85 PASS SOMATIC;NS=2;DP=249;DPB=249.0;AC=1;AN=3;AF=0.25;RO=182;AO=66;PRO=0.0;PAO=0.0;QR=6905;QA=2446;PQR=0.0;PQA=0.0;SRF=125;SRR=57;SAF=40;SAR=26;SRP=58.18;SAP=9.45891;AB=0.340206;ABP=46.0368;RUN=1;RPP=18.9344;RPPR=13.7484;RPL=22.0;RPR=44.0;EPP=13.6703;EPPR=12.3643;DPRA=3.52727;ODDS=35.3274;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.969697;PAIREDR=0.994505;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.498;Dels=0.0;FS=4.82 [...]
+chr7 27910566 . T C 3061.42 PASS SOMATIC;NS=2;DP=491;DPB=491.0;AC=1;AN=3;AF=0.25;RO=369;AO=121;PRO=0.0;PAO=0.0;QR=14003;QA=4612;PQR=0.0;PQA=0.0;SRF=190;SRR=179;SAF=66;SAR=55;SRP=3.72235;SAP=5.18177;AB=0.320955;ABP=107.984;RUN=1;RPP=5.18177;RPPR=5.13469;RPL=55.0;RPR=66.0;EPP=14.2266;EPPR=7.30028;DPRA=3.30702;ODDS=72.0439;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99729;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.946;Dels=0.0;FS=0.401 [...]
+chr7 27911353 . G A 3241.05 PASS SOMATIC;NS=2;DP=506;DPB=506.0;AC=1;AN=3;AF=0.25;RO=381;AO=125;PRO=0.0;PAO=0.0;QR=14498;QA=4779;PQR=0.0;PQA=0.0;SRF=194;SRR=187;SAF=56;SAR=69;SRP=3.28957;SAP=5.94613;AB=0.338753;ABP=86.3442;RUN=1;RPP=3.16665;RPPR=27.0903;RPL=64.0;RPR=61.0;EPP=5.11229;EPPR=13.5485;DPRA=2.69343;ODDS=86.4026;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992;PAIREDR=0.997375;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.69;Dels=0.0;FS=5.7 [...]
+chr7 27912080 . C T 12540.5 REJECT NS=2;DP=446;DPB=508.0;AC=2;AN=4;AF=0.5;RO=104;AO=404;PRO=0.0;PAO=0.0;QR=4033;QA=15604;PQR=0.0;PQA=0.0;SRF=64;SRR=40;SAF=224;SAR=180;SRP=15.0369;SAP=13.4162;AB=0.795276;ABP=387.72;RUN=1;RPP=15.3941;RPPR=4.34659;RPL=226.0;RPR=178.0;EPP=34.0559;EPPR=4.34659;DPRA=0.0;ODDS=173.402;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992574;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3195;Dels=0.0;FS=4.432;HaplotypeScor [...]
+chr7 27914334 . C CTCG 10278.715 PASS DP=182;AC=4;AN=4;AF=1.0;MQ0=0;ALERT;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.125;SOR=0.879 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:0,96:96:99.0:4590,307,0:96:100:96:1:.:.:.:.:.:0.00182088 1/1:0,262:268:99.0:16042,789,0:262:100:262:.:1:.:.:.:.:-0.0111333
+chr7 27914335 . GAGATC TCGGAATGA . PASS AC=4;AN=4;END=27914340;HOMLEN=0;SVLEN=-6;SVTYPE=RPL;NTLEN=9 GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:0,134:134:100:134:.:.:.:1:.:.:0.00182088 1/1:7,419:419:98:426:.:.:.:1:.:.:-0.0111333
+chr7 27914336 . A AAT 6727.73 PASS DP=133;AC=4;AN=4;AF=1.0;MQ0=0;ALERT;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.285;SOR=0.8495 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:0,100:100:99.0:4770,319,0:100:100:100:1:.:.:.:.:.:0.00182088 1/1:0,166:164:99.0:8760,500,0:166:100:166:.:1:.:.:.:.:-0.0111333
+chr7 27914338 . ATC A 7066.88 REJECT NS=2;DP=190;DPB=114.25;AC=4;AN=4;AF=1.0;RO=0;AO=214;PRO=4.0;PAO=11.0;QR=0;QA=7650;PQR=0.0;PQA=252.0;SRF=0;SRR=0;SAF=114;SAR=100;SRP=0.0;SAP=4.99913;AB=0.0;ABP=0.0;RUN=1;RPP=3.65971;RPPR=0.0;RPL=103.0;RPR=111.0;EPP=7.06913;EPPR=0.0;DPRA=0.0;ODDS=35.4717;GTI=0;TYPE=del;CIGAR=1M2D1M;NUMALT=1;MEANALT=1.5;LEN=2;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;ALERT;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.045;SOR=0.938 GT:GQ:DP:RO:QR:AO [...]
+chr7 27914584 . GA G 9795.24 REJECT NS=2;DP=413;DPB=415.2;AC=2;AN=4;AF=0.5;RO=131;AO=335;PRO=11.5;PAO=16.5;QR=4909;QA=12141;PQR=385.0;PQA=548.0;SRF=61;SRR=70;SAF=177;SAR=158;SRP=4.35297;SAP=5.3503;AB=0.715812;ABP=192.337;RUN=1;RPP=3.17235;RPPR=11.7791;RPL=165.0;RPR=170.0;EPP=3.32792;EPPR=16.9508;DPRA=0.0;ODDS=269.567;GTI=0;TYPE=del;CIGAR=1M1D3M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.3582;MQMR=60.0;PAIRED=0.99403;PAIREDR=0.984733;technology.ILLUMINA=1.0;MQ0=0;END=27914585;HOMLEN=1;HOMSEQ=A;SVL [...]
+chr7 27914839 . C A 10974.6 REJECT NS=2;DP=419;DPB=476.0;AC=2;AN=4;AF=0.5;RO=112;AO=363;PRO=0.0;PAO=0.0;QR=4325;QA=13713;PQR=0.0;PQA=0.0;SRF=54;SRR=58;SAF=163;SAR=200;SRP=3.32051;SAP=11.1997;AB=0.762605;ABP=288.13;RUN=1;RPP=4.7391;RPPR=4.94911;RPL=173.0;RPR=190.0;EPP=3.15985;EPPR=3.08785;DPRA=0.0;ODDS=208.138;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991736;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.93;Dels=0.0;FS=1.2825;HaplotypeScore= [...]
+chr7 27916042 . A G 16660.8 REJECT NS=2;DP=443;DPB=502.0;AC=4;AN=4;AF=1.0;RO=1;AO=501;PRO=0.0;PAO=0.0;QR=39;QA=18991;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=249;SAR=252;SRP=5.18177;SAP=3.04931;AB=0.0;ABP=0.0;RUN=1;RPP=4.57497;RPPR=5.18177;RPL=241.0;RPR=260.0;EPP=8.94392;EPPR=5.18177;DPRA=0.0;ODDS=77.1942;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996008;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.085;Dels=0.0;FS=1.5165;HaplotypeScore=6.9003;MLEAC= [...]
+chr7 27916893 . T C 11876.6 REJECT NS=2;DP=427;DPB=495.0;AC=2;AN=4;AF=0.5;RO=105;AO=390;PRO=0.0;PAO=0.0;QR=3914;QA=14766;PQR=0.0;PQA=0.0;SRF=50;SRR=55;SAF=185;SAR=205;SRP=3.52732;SAP=5.23745;AB=0.787879;ABP=359.329;RUN=1;RPP=3.81207;RPPR=3.19643;RPL=201.0;RPR=189.0;EPP=4.1016;EPPR=7.66346;DPRA=0.0;ODDS=73.0398;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.555;Dels=0.0;FS=0.3205;HaplotypeScore=6.84 [...]
+chr7 27917884 . T C 11283.8 REJECT NS=2;DP=434;DPB=490.0;AC=2;AN=4;AF=0.5;RO=115;AO=375;PRO=0.0;PAO=0.0;QR=4361;QA=14107;PQR=0.0;PQA=0.0;SRF=58;SRR=57;SAF=173;SAR=202;SRP=3.02918;SAP=7.88019;AB=0.765306;ABP=302.585;RUN=1;RPP=11.8178;RPPR=3.02918;RPL=168.0;RPR=207.0;EPP=3.98891;EPPR=26.1412;DPRA=0.0;ODDS=266.445;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4705;Dels=0.0;FS=1.2005;HaplotypeScore [...]
+chr7 27918415 . T C 12472.1 REJECT NS=2;DP=455;DPB=519.0;AC=2;AN=4;AF=0.5;RO=113;AO=405;PRO=0.0;PAO=0.0;QR=4384;QA=15499;PQR=0.0;PQA=0.0;SRF=55;SRR=58;SAF=206;SAR=199;SRP=3.18325;SAP=3.27302;AB=0.780347;ABP=357.312;RUN=1;RPP=3.44459;RPPR=4.56684;RPL=198.0;RPR=207.0;EPP=3.14434;EPPR=11.4848;DPRA=0.0;ODDS=240.966;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995062;PAIREDR=0.99115;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.0205;Dels=0.0;FS=0.8785;Haploty [...]
+chr7 27919474 . G A 3558.42 PASS SOMATIC;NS=2;DP=512;DPB=512.0;AC=1;AN=3;AF=0.25;RO=377;AO=134;PRO=0.0;PAO=0.0;QR=14245;QA=5181;PQR=0.0;PQA=0.0;SRF=186;SRR=191;SAF=73;SAR=61;SRP=3.1543;SAP=5.34382;AB=0.34715;ABP=81.3408;RUN=1;RPP=3.26958;RPPR=5.08961;RPL=69.0;RPR=65.0;EPP=3.59368;EPPR=7.85435;DPRA=3.06349;ODDS=78.9449;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992042;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.163;Dels=0.0;FS=5.434; [...]
+chr7 27919667 . G A 7956.965 REJECT NS=2;DP=473;DPB=545.0;AC=2;AN=4;AF=0.5;RO=265;AO=280;PRO=0.0;PAO=0.0;QR=10039;QA=10676;PQR=0.0;PQA=0.0;SRF=145;SRR=120;SAF=137;SAR=143;SRP=8.1317;SAP=3.28949;AB=0.513761;ABP=3.90678;RUN=1;RPP=4.12706;RPPR=3.01849;RPL=146.0;RPR=134.0;EPP=3.04132;EPPR=3.21516;DPRA=0.0;ODDS=434.62;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992857;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9175;Dels=0.0;FS=4.3845;HaplotypeS [...]
+chr7 27921286 . C T 12558.1 REJECT NS=2;DP=464;DPB=526.0;AC=2;AN=4;AF=0.5;RO=117;AO=409;PRO=0.0;PAO=0.0;QR=4376;QA=15624;PQR=0.0;PQA=0.0;SRF=53;SRR=64;SAF=199;SAR=210;SRP=5.25601;SAP=3.65272;AB=0.777567;ABP=355.004;RUN=1;RPP=8.11246;RPPR=3.91972;RPL=220.0;RPR=189.0;EPP=3.05808;EPPR=3.47429;DPRA=0.0;ODDS=163.055;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997555;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.168;Dels=0.0;FS=0.345;HaplotypeScore [...]
+chr7 27921926 . G T 287.721 REJECT NS=2;DP=388;DPB=456.588;AC=2;AN=2;AF=0.0;RO=265;AO=23;PRO=53.6667;PAO=18.6667;QR=9820;QA=343;PQR=1868.0;PQA=622.667;SRF=128;SRR=137;SAF=0;SAR=23;SRP=3.67403;SAP=52.9542;AB=0.0592784;ABP=657.608;RUN=1;RPP=10.6577;RPPR=19.6036;RPL=7.0;RPR=16.0;EPP=10.6577;EPPR=14.2282;DPRA=0.0;ODDS=13.0711;GTI=0;TYPE=snp;CIGAR=1X16M;NUMALT=3;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996226;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr7 27921926 . G GT 287.721 REJECT NS=2;DP=388;DPB=456.588;AC=2;AN=4;AF=0.5;RO=265;AO=43;PRO=53.6667;PAO=49.1667;QR=9820;QA=1195;PQR=1868.0;PQA=1718.0;SRF=128;SRR=137;SAF=20;SAR=23;SRP=3.67403;SAP=3.46479;AB=0.110825;ABP=513.441;RUN=1;RPP=7.10075;RPPR=19.6036;RPL=26.0;RPR=17.0;EPP=17.6046;EPPR=14.2282;DPRA=0.0;ODDS=13.0711;GTI=0;TYPE=ins;CIGAR=1M1I16M;NUMALT=3;MEANALT=12.5;LEN=1;MQM=59.5349;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996226;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO [...]
+chr7 27921926 . GT G 287.721 REJECT NS=2;DP=388;DPB=456.588;AC=2;AN=2;AF=0.0;RO=265;AO=29;PRO=53.6667;PAO=44.5;QR=9820;QA=980;PQR=1868.0;PQA=1548.33;SRF=128;SRR=137;SAF=15;SAR=14;SRP=3.67403;SAP=3.08518;AB=0.0747423;ABP=612.478;RUN=1;RPP=4.88226;RPPR=19.6036;RPL=17.0;RPR=12.0;EPP=9.07545;EPPR=14.2282;DPRA=0.0;ODDS=13.0711;GTI=0;TYPE=del;CIGAR=1M1D15M;NUMALT=3;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996226;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr7 27922001 . C G 6530.625 REJECT NS=2;DP=393;DPB=461.0;AC=2;AN=4;AF=0.5;RO=218;AO=243;PRO=0.0;PAO=0.0;QR=8057;QA=8984;PQR=0.0;PQA=0.0;SRF=125;SRR=93;SAF=137;SAR=106;SRP=13.2102;SAP=11.5979;AB=0.527115;ABP=5.95427;RUN=1;RPP=5.59283;RPPR=3.0103;RPL=113.0;RPR=130.0;EPP=12.7417;EPPR=6.23763;DPRA=0.0;ODDS=406.754;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0412;MQMR=60.0459;PAIRED=1.0;PAIREDR=0.995413;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.573;Dels=0.0;FS=3.3375;Haploty [...]
+chr7 27922780 . A G 12872.6 REJECT NS=2;DP=486;DPB=543.0;AC=2;AN=4;AF=0.5;RO=125;AO=416;PRO=0.0;PAO=0.0;QR=4782;QA=16027;PQR=0.0;PQA=0.0;SRF=47;SRR=78;SAF=184;SAR=232;SRP=19.7046;SAP=15.0369;AB=0.766114;ABP=337.013;RUN=1;RPP=3.09382;RPPR=3.44459;RPL=206.0;RPR=210.0;EPP=3.34437;EPPR=3.44459;DPRA=0.0;ODDS=269.498;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.024;MQMR=60.0;PAIRED=0.997596;PAIREDR=0.992;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.5;Dels=0.0;FS=1.1765;HaplotypeS [...]
+chr7 27922880 . A G 4637.82 PASS SOMATIC;NS=2;DP=548;DPB=548.0;AC=1;AN=3;AF=0.25;RO=380;AO=167;PRO=0.0;PAO=0.0;QR=14441;QA=6472;PQR=0.0;PQA=0.0;SRF=216;SRR=164;SAF=85;SAR=82;SRP=18.462;SAP=3.12733;AB=0.40048;ABP=38.8839;RUN=1;RPP=4.58364;RPPR=3.03316;RPL=78.0;RPR=89.0;EPP=3.0233;EPPR=3.58174;DPRA=3.18321;ODDS=82.6976;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994012;PAIREDR=0.994737;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.223;Dels=0.0;FS=2. [...]
+chr7 27923950 . T C 1878.15 PASS SOMATIC;NS=2;DP=224;DPB=224.0;AC=1;AN=3;AF=0.25;RO=154;AO=70;PRO=0.0;PAO=0.0;QR=5913;QA=2715;PQR=0.0;PQA=0.0;SRF=116;SRR=38;SAF=55;SAR=15;SRP=88.7976;SAP=52.644;AB=0.416667;ABP=13.1438;RUN=1;RPP=9.09042;RPPR=17.4492;RPL=28.0;RPR=42.0;EPP=4.99565;EPPR=30.3088;DPRA=3.0;ODDS=35.9546;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993506;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.549;Dels=0.0;FS=3.255;Haplot [...]
+chr7 27925158 . C T 14371.3 REJECT NS=2;DP=527;DPB=600.0;AC=2;AN=4;AF=0.5;RO=135;AO=465;PRO=0.0;PAO=0.0;QR=5067;QA=17865;PQR=0.0;PQA=0.0;SRF=63;SRR=72;SAF=223;SAR=242;SRP=4.31318;SAP=4.69611;AB=0.775;ABP=397.133;RUN=1;RPP=4.35988;RPPR=4.95658;RPL=241.0;RPR=224.0;EPP=5.92895;EPPR=3.41242;DPRA=0.0;ODDS=137.965;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993548;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.469;Dels=0.0;FS=2.913;HaplotypeScore=8. [...]
+chr7 27925318 . C T 3443.15 PASS SOMATIC;NS=2;DP=533;DPB=533.0;AC=1;AN=3;AF=0.25;RO=396;AO=137;PRO=0.0;PAO=0.0;QR=14679;QA=5206;PQR=0.0;PQA=0.0;SRF=183;SRR=213;SAF=57;SAR=80;SRP=7.94546;SAP=11.395;AB=0.317865;ABP=127.197;RUN=1;RPP=7.591;RPPR=13.6264;RPL=60.0;RPR=77.0;EPP=12.9167;EPPR=3.55865;DPRA=4.22549;ODDS=63.6981;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992701;PAIREDR=0.994949;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.357;Dels=0.0;FS=1. [...]
+chr7 27925645 . C G 4602.07 PASS SOMATIC;NS=2;DP=558;DPB=558.0;AC=1;AN=3;AF=0.25;RO=389;AO=169;PRO=0.0;PAO=0.0;QR=14833;QA=6483;PQR=0.0;PQA=0.0;SRF=197;SRR=192;SAF=92;SAR=77;SRP=3.14985;SAP=5.90131;AB=0.393023;ABP=45.753;RUN=1;RPP=6.72365;RPPR=9.84848;RPL=76.0;RPR=93.0;EPP=5.18177;EPPR=25.166;DPRA=3.35938;ODDS=80.772;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994083;PAIREDR=0.997429;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.469;Dels=0.0;FS=1. [...]
+chr7 27926199 . G A 3723.5 PASS SOMATIC;NS=2;DP=556;DPB=556.0;AC=1;AN=3;AF=0.25;RO=412;AO=143;PRO=0.0;PAO=0.0;QR=15686;QA=5484;PQR=0.0;PQA=0.0;SRF=207;SRR=205;SAF=72;SAR=71;SRP=3.03138;SAP=3.02549;AB=0.334895;ABP=104.113;RUN=1;RPP=4.24029;RPPR=12.3076;RPL=67.0;RPR=76.0;EPP=3.38993;EPPR=5.11853;DPRA=3.31008;ODDS=81.4432;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986014;PAIREDR=0.992718;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.062;Dels=0.0;FS= [...]
+chr7 27926450 . C CA 1659.73 PASS SOMATIC;DP=182;AC=1;AN=4;AF=0.5;MQ0=0;END=27926450;HOMLEN=3;HOMSEQ=AAA;SVLEN=1;SVTYPE=INS;BaseQRankSum=2.352;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.81;MQRankSum=0.702;QD=9.12;RPA=3,4;RU=A;ReadPosRankSum=0.955;SOR=0.593;STR GT:AD:DP:MM:MQS:NQSBQ:NQSMM:REnd:RStart:SC:GMIMUT:GMIMAF:GMICOV:GQ:PL:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:45,0:45:0.111111,0.0:59.1333,0.0:38.3702,0.0:0.0,0.0:0,0:0,0:4,41,0,0:0:0:45:.:.:.:.:.:.:0:.:0.00182088 0/1:125,56:181:0.2, [...]
+chr7 27926454 . GAC AGAT 1222.56 PASS SOMATIC;NS=2;DP=205;DPB=225.286;AC=1;AN=4;AF=0.25;RO=149;AO=53;PRO=13.0;PAO=10.0;QR=5664;QA=1954;PQR=457.5;PQA=367.5;SRF=10;SRR=139;SAF=3;SAR=50;SRP=245.53;SAP=93.5156;AB=0.325153;ABP=46.2932;RUN=1;RPP=3.05127;RPPR=3.37464;RPL=27.0;RPR=26.0;EPP=3.05127;EPPR=3.14146;DPRA=3.88095;ODDS=29.1126;GTI=0;TYPE=complex;CIGAR=1M1I5M1X;NUMALT=1;MEANALT=4.0;LEN=8;MQM=59.0189;MQMR=59.7383;PAIRED=0.981132;PAIREDR=0.973154;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:Q [...]
+chr7 27926456 . C T 1849.77 PASS SOMATIC;DP=167;AC=1;AN=3;AF=0.5;MQ0=0;VT=SNP;BaseQRankSum=2.249;Dels=0.0;FS=0.0;HaplotypeScore=8.8858;MLEAC=1;MLEAF=0.5;MQ=59.73;MQRankSum=-1.12;QD=11.08;ReadPosRankSum=1.215;SOR=0.585 GT:AD:BQ:DP:FA:SS:GMIMUT:GMIMAF:GMICOV:GQ:PL:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0:42,0:.:42:0.0:0:0:0:42:.:.:.:.:.:.:.:0:0.00182088 0/1:109,55:38.0:165:0.337:2:55:34:165:99.0:1878,0,4042:.:1:.:.:.:1:-0.0111333
+chr7 27926858 . TA T 1602.97 PASS SOMATIC;NS=2;DP=211;DPB=195.0;AC=1;AN=4;AF=0.25;RO=148;AO=63;PRO=7.5;PAO=2.5;QR=5559;QA=2362;PQR=247.0;PQA=59.0;SRF=102;SRR=46;SAF=46;SAR=17;SRP=49.022;SAP=31.9977;AB=0.396226;ABP=17.8828;RUN=1;RPP=4.69922;RPPR=8.87914;RPL=28.0;RPR=35.0;EPP=3.872;EPPR=6.76636;DPRA=3.05769;ODDS=34.0941;GTI=0;TYPE=del;CIGAR=1M1D1M;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.3175;MQMR=60.0;PAIRED=0.984127;PAIREDR=0.993243;technology.ILLUMINA=1.0;MQ0=0;END=27926859;HOMLEN=0;SVLEN=-1;S [...]
+chr7 27927027 . G GTATT 848.067 PASS SOMATIC;NS=2;DP=176;DPB=260.107;AC=1;AN=4;AF=0.25;RO=133;AO=37;PRO=80.5;PAO=79.5;QR=5102;QA=1420;PQR=2958.0;PQA=2920.0;SRF=35;SRR=98;SAF=8;SAR=29;SRP=67.8116;SAP=28.8919;AB=0.289062;ABP=52.4792;RUN=1;RPP=16.2152;RPPR=63.7625;RPL=26.0;RPR=11.0;EPP=5.88603;EPPR=11.6472;DPRA=2.66667;ODDS=29.0825;GTI=0;TYPE=ins;CIGAR=1M4I27M;NUMALT=1;MEANALT=2.0;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;END=27927027;HOMLEN=25;HOMSEQ=TATTTATTT [...]
+chr7 27928374 . T C 7725.65 REJECT NS=2;DP=462;DPB=508.0;AC=2;AN=4;AF=0.5;RO=240;AO=267;PRO=0.0;PAO=0.0;QR=9221;QA=10190;PQR=0.0;PQA=0.0;SRF=129;SRR=111;SAF=129;SAR=138;SRP=5.94179;SAP=3.66906;AB=0.525591;ABP=5.8999;RUN=1;RPP=3.01843;RPPR=9.12661;RPL=134.0;RPR=133.0;EPP=7.31258;EPPR=3.58936;DPRA=0.0;ODDS=258.904;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996255;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3125;Dels=0.0;FS=3.266;HaplotypeSc [...]
+chr7 27929551 . C CA 1750.21 REJECT NS=2;DP=152;DPB=221.68;AC=2;AN=2;AF=0.0;RO=38;AO=5;PRO=44.75;PAO=40.75;QR=1336;QA=175;PQR=1549.92;PQA=1414.92;SRF=36;SRR=2;SAF=4;SAR=1;SRP=69.0688;SAP=6.91895;AB=0.0328947;ABP=291.073;RUN=1;RPP=3.44459;RPPR=5.06748;RPL=2.0;RPR=3.0;EPP=6.91895;EPPR=3.23888;DPRA=0.0;ODDS=47.7775;GTI=0;TYPE=ins;CIGAR=1M1I24M;NUMALT=3;MEANALT=18.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr7 27929551 . CA C 1472.97 REJECT NS=2;DP=149;DPB=221.68;AC=2;AN=4;AF=0.5;RO=38;AO=63;PRO=44.75;PAO=44.75;QR=1336;QA=2193;PQR=1549.92;PQA=1575.92;SRF=36;SRR=2;SAF=49;SAR=14;SRP=69.0688;SAP=45.2334;AB=0.414474;ABP=12.6676;RUN=1;RPP=12.9715;RPPR=5.06748;RPL=23.0;RPR=40.0;EPP=3.32051;EPPR=3.23888;DPRA=0.0;ODDS=47.7775;GTI=0;TYPE=del;CIGAR=1M1D23M;NUMALT=3;MEANALT=18.5;LEN=1;MQM=60.3175;MQMR=60.0;PAIRED=0.984127;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.06 [...]
+chr7 27929551 . CAA C 1750.21 REJECT NS=2;DP=152;DPB=221.68;AC=2;AN=2;AF=0.0;RO=38;AO=8;PRO=44.75;PAO=37.75;QR=1336;QA=291;PQR=1549.92;PQA=1321.25;SRF=36;SRR=2;SAF=7;SAR=1;SRP=69.0688;SAP=12.7819;AB=0.0526316;ABP=267.244;RUN=1;RPP=7.35324;RPPR=5.06748;RPL=2.0;RPR=6.0;EPP=12.7819;EPPR=3.23888;DPRA=0.0;ODDS=47.7775;GTI=0;TYPE=del;CIGAR=1M2D22M;NUMALT=3;MEANALT=18.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr7 27931860 . T C 17936.85 REJECT NS=2;DP=475;DPB=551.0;AC=4;AN=4;AF=1.0;RO=0;AO=550;PRO=0.0;PAO=0.0;QR=0;QA=21006;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=293;SAR=257;SRP=0.0;SAP=8.12708;AB=0.0;ABP=0.0;RUN=1;RPP=3.78413;RPPR=0.0;RPL=282.0;RPR=268.0;EPP=6.10564;EPPR=0.0;DPRA=0.0;ODDS=98.4484;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=7.7702;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=25.605;SOR=0.828 [...]
+chr7 27932193 . T C 16752.5 REJECT NS=2;DP=443;DPB=506.0;AC=4;AN=4;AF=1.0;RO=0;AO=506;PRO=0.0;PAO=0.0;QR=0;QA=19322;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=199;SAR=307;SRP=0.0;SAP=53.0657;AB=0.0;ABP=0.0;RUN=1;RPP=6.37479;RPPR=0.0;RPL=239.0;RPR=267.0;EPP=6.8726;EPPR=0.0;DPRA=0.0;ODDS=82.2362;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994071;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8324;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.475;SOR=1.3 [...]
+chr7 27932307 . A C 3850.07 PASS SOMATIC;NS=2;DP=521;DPB=521.0;AC=1;AN=3;AF=0.25;RO=377;AO=144;PRO=0.0;PAO=0.0;QR=14506;QA=5581;PQR=0.0;PQA=0.0;SRF=213;SRR=164;SAF=81;SAR=63;SRP=16.8398;SAP=7.89611;AB=0.35122;ABP=81.84;RUN=1;RPP=3.0103;RPPR=7.20925;RPL=72.0;RPR=72.0;EPP=3.07062;EPPR=7.20925;DPRA=3.69369;ODDS=70.2522;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9867;PAIRED=0.993056;PAIREDR=0.992042;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.574;Dels=0.0;FS= [...]
+chr7 27932505 . G A 6959.700000000001 REJECT NS=2;DP=432;DPB=509.0;AC=2;AN=4;AF=0.5;RO=251;AO=258;PRO=0.0;PAO=0.0;QR=9651;QA=9831;PQR=0.0;PQA=0.0;SRF=112;SRR=139;SAF=123;SAR=135;SRP=9.31709;SAP=4.22228;AB=0.506876;ABP=3.21934;RUN=1;RPP=3.0103;RPPR=3.01895;RPL=129.0;RPR=129.0;EPP=17.8571;EPPR=16.1689;DPRA=0.0;ODDS=502.642;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988372;PAIREDR=0.992032;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.8105;Dels=0.0;FS=2.7 [...]
+chr7 27933232 . T C 2362.3199999999997 REJECT NS=2;DP=479;DPB=546.0;AC=2;AN=4;AF=0.5;RO=416;AO=130;PRO=0.0;PAO=0.0;QR=15711;QA=4860;PQR=0.0;PQA=0.0;SRF=181;SRR=235;SAF=60;SAR=70;SRP=18.2315;SAP=4.68066;AB=0.238095;ABP=328.318;RUN=1;RPP=4.68066;RPPR=4.0334;RPL=70.0;RPR=60.0;EPP=11.0949;EPPR=11.3621;DPRA=0.0;ODDS=280.616;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9519;PAIRED=0.992308;PAIREDR=0.990385;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.574;Dels=0.0;FS=0.0; [...]
+chr7 27934142 . C T 6618.31 REJECT NS=2;DP=422;DPB=479.0;AC=2;AN=4;AF=0.5;RO=236;AO=243;PRO=0.0;PAO=0.0;QR=8876;QA=9078;PQR=0.0;PQA=0.0;SRF=122;SRR=114;SAF=130;SAR=113;SRP=3.59917;SAP=5.59283;AB=0.507307;ABP=3.23243;RUN=1;RPP=12.7417;RPPR=3.15752;RPL=105.0;RPR=138.0;EPP=3.2337;EPPR=8.31016;DPRA=0.0;ODDS=300.303;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995885;PAIREDR=0.995763;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.098;Dels=0.0;FS=0.396;Haplotyp [...]
+chr7 27953035 . A G 1553.21 REJECT NS=2;DP=359;DPB=414.0;AC=2;AN=4;AF=0.5;RO=329;AO=84;PRO=0.0;PAO=0.0;QR=12477;QA=3157;PQR=0.0;PQA=0.0;SRF=168;SRR=161;SAF=41;SAR=43;SRP=3.33371;SAP=3.1137;AB=0.202899;ABP=320.423;RUN=1;RPP=11.386;RPPR=3.80893;RPL=51.0;RPR=33.0;EPP=9.62812;EPPR=3.33371;DPRA=0.0;ODDS=109.72;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990881;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3185;Dels=0.0;FS=7.2385;HaplotypeScore=0.9 [...]
+chr7 28031704 . T C 2595.0 PASS SOMATIC;NS=2;DP=393;DPB=393.0;AC=1;AN=3;AF=0.25;RO=290;AO=102;PRO=0.0;PAO=0.0;QR=11014;QA=3889;PQR=0.0;PQA=0.0;SRF=132;SRR=158;SAF=44;SAR=58;SRP=8.07208;SAP=7.18293;AB=0.33887;ABP=70.8887;RUN=1;RPP=33.7515;RPPR=4.08855;RPL=70.0;RPR=32.0;EPP=3.7767;EPPR=4.92719;DPRA=3.27174;ODDS=57.7529;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990196;PAIREDR=0.989655;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.037;Dels=0.0;FS=1. [...]
+chr7 28031751 . T G 1748.375 REJECT NS=2;DP=292;DPB=342.0;AC=2;AN=4;AF=0.5;RO=259;AO=82;PRO=0.0;PAO=0.0;QR=9790;QA=3159;PQR=0.0;PQA=0.0;SRF=113;SRR=146;SAF=42;SAR=40;SRP=12.1405;SAP=3.11623;AB=0.239766;ABP=204.183;RUN=1;RPP=5.65844;RPPR=3.2199;RPL=46.0;RPR=36.0;EPP=5.65844;EPPR=6.03695;DPRA=0.0;ODDS=117.711;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992278;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.961;Dels=0.0;FS=2.8565;HaplotypeScore=2. [...]
+chr7 28220228 . C T 581.819 REJECT NS=2;DP=181;DPB=214.0;AC=2;AN=4;AF=0.5;RO=176;AO=38;PRO=0.0;PAO=0.0;QR=6537;QA=1387;PQR=0.0;PQA=0.0;SRF=56;SRR=120;SAF=12;SAR=26;SRP=53.5464;SAP=14.2105;AB=0.17757;ABP=196.251;RUN=1;RPP=30.668;RPPR=163.354;RPL=30.0;RPR=8.0;EPP=3.23888;EPPR=24.7744;DPRA=0.0;ODDS=0.866563;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.943182;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.776;Dels=0.0;FS=2.6225;HaplotypeScore=0.0; [...]
+chr7 31500579 . A G 2854.35 PASS SOMATIC;NS=2;DP=393;DPB=393.0;AC=1;AN=3;AF=0.25;RO=282;AO=110;PRO=0.0;PAO=0.0;QR=10884;QA=4237;PQR=0.0;PQA=0.0;SRF=101;SRR=181;SAF=28;SAR=82;SRP=52.2919;SAP=60.5741;AB=0.358306;ABP=56.5474;RUN=1;RPP=18.487;RPPR=28.914;RPL=69.0;RPR=41.0;EPP=3.32615;EPPR=6.0904;DPRA=3.56977;ODDS=54.6627;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992908;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.617;Dels=0.0;FS=20.674; [...]
+chr7 45044595 . CA C 2654.27 REJECT NS=2;DP=220;DPB=296.053;AC=2;AN=3;AF=0.5;RO=29;AO=121;PRO=51.5833;PAO=40.5833;QR=1061;QA=3710;PQR=1779.83;PQA=1407.33;SRF=15;SRR=14;SAF=78;SAR=43;SRP=3.08518;SAP=24.9942;AB=0.510549;ABP=3.23936;RUN=1;RPP=103.957;RPPR=19.8579;RPL=23.0;RPR=98.0;EPP=3.02825;EPPR=4.88226;DPRA=0.0;ODDS=4.4024;GTI=0;TYPE=del;CIGAR=1M1D17M;NUMALT=3;MEANALT=17.5;LEN=1;MQM=59.8099;MQMR=60.0;PAIRED=0.975207;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum [...]
+chr7 45044595 . CAA C 2848.81 REJECT NS=2;DP=237;DPB=296.053;AC=2;AN=2;AF=0.25;RO=29;AO=36;PRO=51.5833;PAO=36.0833;QR=1061;QA=1223;PQR=1779.83;PQA=1249.83;SRF=15;SRR=14;SAF=25;SAR=11;SRP=3.08518;SAP=14.8328;AB=0.151899;ABP=252.455;RUN=1;RPP=3.25157;RPPR=19.8579;RPL=17.0;RPR=19.0;EPP=18.4519;EPPR=4.88226;DPRA=0.0;ODDS=4.4024;GTI=0;TYPE=del;CIGAR=1M2D16M;NUMALT=3;MEANALT=17.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.99;FS=1.3 [...]
+chr7 45044609 . AGGCT GGCC 2848.81 REJECT SOMATIC;NS=2;DP=237;DPB=296.053;AC=1;AN=3;AF=0.0;RO=29;AO=12;PRO=51.5833;PAO=10.75;QR=1061;QA=200;PQR=1779.83;PQA=383.0;SRF=15;SRR=14;SAF=12;SAR=0;SRP=3.08518;SAP=29.068;AB=0.0506329;ABP=418.696;RUN=1;RPP=21.1059;RPPR=19.8579;RPL=11.0;RPR=1.0;EPP=21.1059;EPPR=4.88226;DPRA=0.0;ODDS=4.4024;GTI=0;TYPE=complex;CIGAR=1M1D16M1X;NUMALT=3;MEANALT=17.5;LEN=18;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:Q [...]
+chr7 46516842 . T C 7856.1 REJECT NS=2;DP=299;DPB=343.0;AC=2;AN=4;AF=0.5;RO=82;AO=260;PRO=0.0;PAO=0.0;QR=3151;QA=9910;PQR=0.0;PQA=0.0;SRF=37;SRR=45;SAF=106;SAR=154;SRP=4.70511;SAP=22.2529;AB=0.758017;ABP=201.349;RUN=1;RPP=39.3908;RPPR=59.0449;RPL=163.0;RPR=97.0;EPP=17.7429;EPPR=3.434;DPRA=0.0;ODDS=153.622;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996154;PAIREDR=0.987805;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.989;Dels=0.0;FS=7.4945;HaplotypeScore [...]
+chr7 50436033 . A G 8587.76 REJECT NS=2;DP=316;DPB=362.0;AC=2;AN=4;AF=0.5;RO=81;AO=281;PRO=0.0;PAO=0.0;QR=3056;QA=10769;PQR=0.0;PQA=0.0;SRF=24;SRR=57;SAF=112;SAR=169;SRP=32.2045;SAP=28.1175;AB=0.776243;ABP=242.952;RUN=1;RPP=11.4257;RPPR=14.8328;RPL=157.0;RPR=124.0;EPP=26.3865;EPPR=6.2541;DPRA=0.0;ODDS=105.508;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987654;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0015;Dels=0.0;FS=6.3415;HaplotypeScore [...]
+chr7 50467767 . C A 3196.0 PASS SOMATIC;NS=2;DP=447;DPB=447.0;AC=1;AN=3;AF=0.25;RO=325;AO=121;PRO=0.0;PAO=0.0;QR=12421;QA=4615;PQR=0.0;PQA=0.0;SRF=134;SRR=191;SAF=56;SAR=65;SRP=24.7183;SAP=4.46393;AB=0.367781;ABP=52.9674;RUN=1;RPP=3.88966;RPPR=14.2418;RPL=64.0;RPR=57.0;EPP=14.2266;EPPR=3.07043;DPRA=2.78814;ODDS=74.5656;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.009;Dels=0.0;FS=6.092;Hapl [...]
+chr7 55214348 . C T 9235.41 REJECT NS=2;DP=352;DPB=403.0;AC=2;AN=4;AF=0.5;RO=100;AO=303;PRO=0.0;PAO=0.0;QR=3903;QA=11572;PQR=0.0;PQA=0.0;SRF=55;SRR=45;SAF=170;SAR=133;SRP=5.18177;SAP=12.8213;AB=0.751861;ABP=225.055;RUN=1;RPP=3.0748;RPPR=4.40004;RPL=153.0;RPR=150.0;EPP=12.8213;EPPR=10.0459;DPRA=0.0;ODDS=223.212;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993399;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.8935;Dels=0.0;FS=2.255;HaplotypeScor [...]
+chr7 55249063 . G A 5314.59 REJECT NS=2;DP=311;DPB=360.0;AC=2;AN=4;AF=0.5;RO=167;AO=193;PRO=0.0;PAO=0.0;QR=6433;QA=7199;PQR=0.0;PQA=0.0;SRF=96;SRR=71;SAF=112;SAR=81;SRP=11.1371;SAP=13.8227;AB=0.536111;ABP=7.08784;RUN=1;RPP=3.29158;RPPR=3.33537;RPL=99.0;RPR=94.0;EPP=8.96216;EPPR=5.20778;DPRA=0.0;ODDS=304.743;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.7125;Dels=0.0;FS=1.322;HaplotypeScore=5.8462 [...]
+chr7 55266417 . T C 12936.65 REJECT NS=2;DP=343;DPB=383.0;AC=4;AN=4;AF=1.0;RO=1;AO=381;PRO=0.0;PAO=0.0;QR=27;QA=14559;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=247;SAR=134;SRP=5.18177;SAP=75.786;AB=0.0;ABP=0.0;RUN=1;RPP=19.0199;RPPR=5.18177;RPL=164.0;RPR=217.0;EPP=8.48743;EPPR=5.18177;DPRA=0.0;ODDS=50.0625;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992126;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.64;Dels=0.0;FS=0.0;HaplotypeScore=6.7619;MLEAC=2;ML [...]
+chr7 55268949 . A G 2024.96 REJECT NS=2;DP=382;DPB=434.0;AC=2;AN=4;AF=0.5;RO=329;AO=105;PRO=0.0;PAO=0.0;QR=12678;QA=3979;PQR=0.0;PQA=0.0;SRF=177;SRR=152;SAF=54;SAR=51;SRP=7.13544;SAP=3.19643;AB=0.241935;ABP=254.061;RUN=1;RPP=3.19643;RPPR=7.13544;RPL=51.0;RPR=54.0;EPP=3.03098;EPPR=14.1053;DPRA=0.0;ODDS=224.206;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.364;Dels=0.0;FS=2.817;HaplotypeScore=8.762 [...]
+chr7 55371250 . A G 14633.45 REJECT NS=2;DP=384;DPB=439.0;AC=4;AN=4;AF=1.0;RO=0;AO=439;PRO=0.0;PAO=0.0;QR=0;QA=16858;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=178;SAR=261;SRP=0.0;SAP=37.0861;AB=0.0;ABP=0.0;RUN=1;RPP=3.41096;RPPR=0.0;RPL=224.0;RPR=215.0;EPP=40.4496;EPPR=0.0;DPRA=0.0;ODDS=71.6732;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995444;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.8909;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=24.945;SOR=1 [...]
+chr7 55372073 . T C 1434.81 REJECT NS=2;DP=343;DPB=389.0;AC=2;AN=4;AF=0.5;RO=314;AO=75;PRO=0.0;PAO=0.0;QR=11632;QA=2839;PQR=0.0;PQA=0.0;SRF=160;SRR=154;SAF=33;SAR=42;SRP=3.25926;SAP=5.35549;AB=0.192802;ABP=321.871;RUN=1;RPP=7.90335;RPPR=15.2093;RPL=31.0;RPR=44.0;EPP=9.52472;EPPR=7.68519;DPRA=0.0;ODDS=7.98706;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993631;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0475;Dels=0.0;FS=2.2495;HaplotypeScore= [...]
+chr7 55374032 . A G 1622.83 REJECT NS=2;DP=366;DPB=414.0;AC=2;AN=4;AF=0.5;RO=323;AO=91;PRO=0.0;PAO=0.0;QR=12415;QA=3446;PQR=0.0;PQA=0.0;SRF=157;SRR=166;SAF=50;SAR=41;SRP=3.55485;SAP=4.94315;AB=0.219807;ABP=285.323;RUN=1;RPP=3.60686;RPPR=7.91124;RPL=43.0;RPR=48.0;EPP=5.89764;EPPR=4.14646;DPRA=0.0;ODDS=163.447;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989011;PAIREDR=0.996904;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.5175;Dels=0.0;FS=5.184;HaplotypeS [...]
+chr7 55374827 . C T 9783.87 REJECT NS=2;DP=367;DPB=416.0;AC=2;AN=4;AF=0.5;RO=97;AO=318;PRO=0.0;PAO=0.0;QR=3598;QA=12286;PQR=0.0;PQA=0.0;SRF=42;SRR=55;SAF=119;SAR=199;SRP=6.79359;SAP=46.7129;AB=0.764423;ABP=255.653;RUN=1;RPP=7.62639;RPPR=3.56996;RPL=172.0;RPR=146.0;EPP=34.5854;EPPR=11.0918;DPRA=0.0;ODDS=156.551;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993711;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.0085;Dels=0.0;FS=4.034;HaplotypeScore [...]
+chr7 57259664 . T C 1518.095 REJECT NS=2;DP=310;DPB=352.0;AC=2;AN=4;AF=0.5;RO=273;AO=79;PRO=0.0;PAO=0.0;QR=10423;QA=3019;PQR=0.0;PQA=0.0;SRF=167;SRR=106;SAF=47;SAR=32;SRP=32.6075;SAP=9.19487;AB=0.224432;ABP=235.185;RUN=1;RPP=26.1269;RPPR=84.1502;RPL=25.0;RPR=54.0;EPP=3.03779;EPPR=3.40005;DPRA=0.0;ODDS=129.598;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987342;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.628;Dels=0.0;FS=5.26;HaplotypeScore=6. [...]
+chr7 62496232 . T A 8072.115 REJECT NS=2;DP=375;DPB=423.0;AC=3;AN=4;AF=0.75;RO=135;AO=287;PRO=0.0;PAO=0.0;QR=5198;QA=10963;PQR=0.0;PQA=0.0;SRF=63;SRR=72;SAF=127;SAR=160;SRP=4.31318;SAP=11.2498;AB=0.586626;ABP=24.4544;RUN=1;RPP=4.71267;RPPR=3.02638;RPL=136.0;RPR=151.0;EPP=5.1969;EPPR=27.4756;DPRA=0.0;ODDS=59.6537;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996516;PAIREDR=0.992593;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.248;Dels=0.0;FS=1.511;Haploty [...]
+chr7 64506904 . T G 13808.25 REJECT NS=2;DP=365;DPB=419.0;AC=4;AN=4;AF=1.0;RO=1;AO=418;PRO=0.0;PAO=0.0;QR=40;QA=16115;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=190;SAR=228;SRP=5.18177;SAP=10.5118;AB=0.0;ABP=0.0;RUN=1;RPP=7.68572;RPPR=5.18177;RPL=194.0;RPR=224.0;EPP=22.9795;EPPR=5.18177;DPRA=0.0;ODDS=64.2538;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.3086;MQMR=60.0;PAIRED=0.992823;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.577;Dels=0.0;FS=1.6825;HaplotypeScore=3.9658;M [...]
+chr7 66000932 . A G 7767.900000000001 REJECT NS=2;DP=333;DPB=380.0;AC=3;AN=4;AF=0.75;RO=102;AO=277;PRO=0.0;PAO=0.0;QR=3986;QA=10597;PQR=0.0;PQA=0.0;SRF=43;SRR=59;SAF=129;SAR=148;SRP=8.46027;SAP=5.84027;AB=0.63986;ABP=51.6027;RUN=1;RPP=28.48;RPPR=3.7767;RPL=167.0;RPR=110.0;EPP=40.333;EPPR=4.37279;DPRA=0.0;ODDS=59.6749;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99639;PAIREDR=0.990196;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.296;Dels=0.0;FS=0.4755;Hap [...]
+chr7 67501943 . T C 13165.599999999999 REJECT NS=2;DP=349;DPB=405.0;AC=4;AN=4;AF=1.0;RO=0;AO=405;PRO=0.0;PAO=0.0;QR=0;QA=15462;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=220;SAR=185;SRP=0.0;SAP=9.57833;AB=0.0;ABP=0.0;RUN=1;RPP=22.961;RPPR=0.0;RPL=172.0;RPR=233.0;EPP=15.8836;EPPR=0.0;DPRA=0.0;ODDS=72.3105;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.987654;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.7977;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32. [...]
+chr7 69006274 . T C 9836.735 REJECT NS=2;DP=261;DPB=295.0;AC=4;AN=4;AF=1.0;RO=0;AO=295;PRO=0.0;PAO=0.0;QR=0;QA=11273;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=95;SAR=200;SRP=0.0;SAP=84.1645;AB=0.0;ABP=0.0;RUN=1;RPP=72.2692;RPPR=0.0;RPL=196.0;RPR=99.0;EPP=23.6871;EPPR=0.0;DPRA=0.0;ODDS=46.7469;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99661;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.9327;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.735;SOR=1.55 [...]
+chr7 76751658 . C A 13081.849999999999 REJECT NS=2;DP=354;DPB=410.0;AC=4;AN=4;AF=1.0;RO=0;AO=409;PRO=0.0;PAO=0.0;QR=0;QA=15287;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=221;SAR=188;SRP=0.0;SAP=8.79204;AB=0.0;ABP=0.0;RUN=1;RPP=4.54467;RPPR=0.0;RPL=196.0;RPR=213.0;EPP=36.1452;EPPR=0.0;DPRA=0.0;ODDS=73.4806;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9853;MQMR=0.0;PAIRED=0.99511;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8656;MLEAC=2;MLEAF=1.0;MQ=59.98;QD [...]
+chr7 79500341 . T A 2247.8 PASS SOMATIC;NS=2;DP=326;DPB=326.0;AC=1;AN=3;AF=0.25;RO=238;AO=88;PRO=0.0;PAO=0.0;QR=9306;QA=3319;PQR=0.0;PQA=0.0;SRF=159;SRR=79;SAF=65;SAR=23;SRP=61.4028;SAP=46.5385;AB=0.377682;ABP=33.2898;RUN=1;RPP=9.32731;RPPR=33.7029;RPL=36.0;RPR=52.0;EPP=7.84676;EPPR=20.674;DPRA=2.50538;ODDS=59.0267;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9545;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991597;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-3.376;Dels=0.0;FS=5.178 [...]
+chr7 81346685 . T C 6236.67 REJECT NS=2;DP=248;DPB=288.0;AC=2;AN=4;AF=0.5;RO=77;AO=211;PRO=0.0;PAO=0.0;QR=2920;QA=8009;PQR=0.0;PQA=0.0;SRF=18;SRR=59;SAF=57;SAR=154;SRP=50.4161;SAP=99.8415;AB=0.732639;ABP=138.396;RUN=1;RPP=14.2176;RPPR=6.42261;RPL=122.0;RPR=89.0;EPP=20.31;EPPR=5.29458;DPRA=0.0;ODDS=159.379;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7725;Dels=0.0;FS=2.4075;HaplotypeScore=6.8234;M [...]
+chr7 82506874 . G A 12457.65 REJECT NS=2;DP=326;DPB=381.0;AC=4;AN=4;AF=1.0;RO=0;AO=381;PRO=0.0;PAO=0.0;QR=0;QA=14769;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=138;SAR=243;SRP=0.0;SAP=65.8462;AB=0.0;ABP=0.0;RUN=1;RPP=19.0199;RPPR=0.0;RPL=217.0;RPR=164.0;EPP=15.6003;EPPR=0.0;DPRA=0.0;ODDS=72.946;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994751;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.86;SOR=1.3 [...]
+chr7 82506898 . T C 4011.12 REJECT NS=2;DP=258;DPB=301.0;AC=2;AN=4;AF=0.5;RO=156;AO=145;PRO=0.0;PAO=0.0;QR=5984;QA=5555;PQR=0.0;PQA=0.0;SRF=45;SRR=111;SAF=41;SAR=104;SRP=63.6445;SAP=62.4487;AB=0.481728;ABP=3.88322;RUN=1;RPP=17.4019;RPPR=25.2818;RPL=88.0;RPR=57.0;EPP=21.3555;EPPR=12.42;DPRA=0.0;ODDS=227.33;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.695;Dels=0.0;FS=1.047;HaplotypeScore=2.9328;MLE [...]
+chr7 85512786 . CA C 12189.2 REJECT NS=2;DP=329;DPB=247.0;AC=4;AN=4;AF=1.0;RO=0;AO=365;PRO=5.5;PAO=5.5;QR=0;QA=13736;PQR=129.0;PQA=129.0;SRF=0;SRR=0;SAF=126;SAR=239;SRP=0.0;SAP=78.9761;AB=0.0;ABP=0.0;RUN=1;RPP=36.4748;RPPR=0.0;RPL=220.0;RPR=145.0;EPP=19.7217;EPPR=0.0;DPRA=0.0;ODDS=53.609;GTI=0;TYPE=del;CIGAR=1M1D1M;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.2192;MQMR=0.0;PAIRED=0.983562;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=85512787;HOMLEN=0;SVLEN=-1;SVTYPE=DEL;FS=0.0;MLEAC=2;MLEAF=1.0;MQ [...]
+chr7 86274196 . T G 726.853 REJECT NS=1;DP=58;DPB=58.0;AC=1;AN=4;AF=0.5;RO=29;AO=29;PRO=0.0;PAO=0.0;QR=1063;QA=1098;PQR=0.0;PQA=0.0;SRF=6;SRR=23;SAF=2;SAR=27;SRP=24.6501;SAP=49.8093;AB=0.5;ABP=3.0103;RUN=1;RPP=6.67934;RPPR=9.07545;RPL=18.0;RPR=11.0;EPP=6.67934;EPPR=3.68421;DPRA=0.0;ODDS=167.326;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.965517;technology.ILLUMINA=1.0;BaseQRankSum=1.365;FS=5.97;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.726;QD=1 [...]
+chr7 90012086 . A T 1795.82 REJECT NS=2;DP=317;DPB=367.0;AC=2;AN=4;AF=0.5;RO=279;AO=88;PRO=0.0;PAO=0.0;QR=10797;QA=3386;PQR=0.0;PQA=0.0;SRF=97;SRR=182;SAF=25;SAR=63;SRP=59.2429;SAP=38.6422;AB=0.239782;ABP=218.862;RUN=1;RPP=17.2236;RPPR=24.8729;RPL=56.0;RPR=32.0;EPP=3.89863;EPPR=11.486;DPRA=0.0;ODDS=149.663;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988636;PAIREDR=0.996416;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8465;Dels=0.0;FS=5.651;HaplotypeScor [...]
+chr7 95668664 . C A 10307.4 REJECT NS=2;DP=385;DPB=442.0;AC=2;AN=4;AF=0.5;RO=107;AO=335;PRO=0.0;PAO=0.0;QR=4131;QA=12882;PQR=0.0;PQA=0.0;SRF=48;SRR=59;SAF=183;SAR=152;SRP=5.46589;SAP=9.23951;AB=0.757919;ABP=258.399;RUN=1;RPP=14.9955;RPPR=4.65412;RPL=146.0;RPR=189.0;EPP=4.10576;EPPR=22.513;DPRA=0.0;ODDS=215.267;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991045;PAIREDR=0.990654;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.118;Dels=0.0;FS=5.428;HaplotypeS [...]
+chr7 95709666 . C A 6315.26 REJECT NS=2;DP=246;DPB=285.0;AC=2;AN=4;AF=0.5;RO=67;AO=217;PRO=0.0;PAO=0.0;QR=2498;QA=8227;PQR=0.0;PQA=0.0;SRF=55;SRR=12;SAF=181;SAR=36;SRP=62.9365;SAP=213.403;AB=0.761404;ABP=172.164;RUN=1;RPP=31.1194;RPPR=5.63551;RPL=82.0;RPR=135.0;EPP=3.50063;EPPR=3.30199;DPRA=0.0;ODDS=140.469;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9724;MQMR=60.0;PAIRED=0.986175;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1785;Dels=0.0;FS=1.052;HaplotypeScore [...]
+chr7 99382096 . C T 13355.599999999999 REJECT NS=2;DP=354;DPB=410.0;AC=4;AN=4;AF=1.0;RO=0;AO=410;PRO=0.0;PAO=0.0;QR=0;QA=15677;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=205;SAR=205;SRP=0.0;SAP=3.0103;AB=0.0;ABP=0.0;RUN=1;RPP=3.20097;RPPR=0.0;RPL=208.0;RPR=202.0;EPP=22.0769;EPPR=0.0;DPRA=0.0;ODDS=72.9657;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997561;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8043;MLEAC=2;MLEAF=1.0;MQ=59.925;QD=3 [...]
+chr7 101755060 . A G 5266.69 REJECT NS=2;DP=348;DPB=392.0;AC=2;AN=4;AF=0.5;RO=204;AO=188;PRO=0.0;PAO=0.0;QR=7833;QA=7144;PQR=0.0;PQA=0.0;SRF=77;SRR=127;SAF=78;SAR=110;SRP=29.6215;SAP=14.8379;AB=0.479592;ABP=4.4284;RUN=1;RPP=14.8379;RPPR=5.73528;RPL=110.0;RPR=78.0;EPP=17.9796;EPPR=29.6215;DPRA=0.0;ODDS=254.319;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1615;Dels=0.0;FS=1.591;HaplotypeScore=0.99 [...]
+chr7 101758584 . G A 8949.77 REJECT NS=2;DP=239;DPB=273.0;AC=4;AN=4;AF=1.0;RO=0;AO=273;PRO=0.0;PAO=0.0;QR=0;QA=10339;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=100;SAR=173;SRP=0.0;SAP=45.3978;AB=0.0;ABP=0.0;RUN=1;RPP=71.8054;RPPR=0.0;RPL=183.0;RPR=90.0;EPP=15.1085;EPPR=0.0;DPRA=0.0;ODDS=46.6708;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.799;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.865;SOR=1.294 GT [...]
+chr7 101837149 . G A 5456.285 REJECT NS=2;DP=380;DPB=438.0;AC=2;AN=4;AF=0.5;RO=240;AO=197;PRO=0.0;PAO=0.0;QR=9159;QA=7541;PQR=0.0;PQA=0.0;SRF=130;SRR=110;SAF=109;SAR=88;SRP=6.62942;SAP=7.87131;AB=0.449772;ABP=12.6084;RUN=1;RPP=3.28587;RPPR=5.32654;RPL=96.0;RPR=101.0;EPP=19.7758;EPPR=20.5268;DPRA=0.0;ODDS=308.234;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994924;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.758;Dels=0.0;FS=1.555;HaplotypeScor [...]
+chr7 101844851 . A G 5629.675 REJECT NS=2;DP=375;DPB=430.0;AC=2;AN=4;AF=0.5;RO=223;AO=205;PRO=0.0;PAO=0.0;QR=8232;QA=7634;PQR=0.0;PQA=0.0;SRF=104;SRR=119;SAF=98;SAR=107;SRP=5.20125;SAP=3.8683;AB=0.476744;ABP=5.03027;RUN=1;RPP=4.80044;RPPR=5.20125;RPL=109.0;RPR=96.0;EPP=3.02089;EPPR=4.65594;DPRA=0.0;ODDS=292.651;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995516;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.151;Dels=0.0;FS=2.075;HaplotypeScore [...]
+chr7 101892328 . C T 1532.63 REJECT NS=1;DP=133;DPB=133.0;AC=1;AN=4;AF=0.5;RO=75;AO=58;PRO=0.0;PAO=0.0;QR=2838;QA=2200;PQR=0.0;PQA=0.0;SRF=32;SRR=43;SAF=20;SAR=38;SRP=6.51361;SAP=15.1406;AB=0.43609;ABP=7.72876;RUN=1;RPP=10.3484;RPPR=11.3777;RPL=36.0;RPR=22.0;EPP=21.1309;EPPR=47.0478;DPRA=0.0;ODDS=352.902;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.792;FS=4.358;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-2.3 [...]
+chr7 101916647 . A G 2654.57 REJECT NS=1;DP=79;DPB=79.0;AC=2;AN=4;AF=1.0;RO=0;AO=79;PRO=0.0;PAO=0.0;QR=0;QA=3064;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=62;SAR=17;SRP=0.0;SAP=58.6715;AB=0.0;ABP=0.0;RUN=1;RPP=17.5509;RPPR=0.0;RPL=28.0;RPR=51.0;EPP=3.03779;EPPR=0.0;DPRA=0.0;ODDS=53.9467;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.02;SOR=2.584 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:A [...]
+chr7 101916798 . C A 1427.03 REJECT NS=1;DP=86;DPB=86.0;AC=1;AN=4;AF=0.5;RO=33;AO=53;PRO=0.0;PAO=0.0;QR=1239;QA=1963;PQR=0.0;PQA=0.0;SRF=14;SRR=19;SAF=21;SAR=32;SRP=4.65535;SAP=7.96781;AB=0.616279;ABP=13.1102;RUN=1;RPP=53.2;RPPR=26.7649;RPL=44.0;RPR=9.0;EPP=3.05127;EPPR=10.9724;DPRA=0.0;ODDS=184.85;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.969697;technology.ILLUMINA=1.0;BaseQRankSum=0.422;FS=0.858;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-1.773 [...]
+chr7 101917521 . G A 5687.030000000001 REJECT NS=2;DP=351;DPB=400.0;AC=2;AN=4;AF=0.5;RO=200;AO=200;PRO=0.0;PAO=0.0;QR=7642;QA=7621;PQR=0.0;PQA=0.0;SRF=103;SRR=97;SAF=104;SAR=96;SRP=3.40116;SAP=3.70517;AB=0.5;ABP=3.0103;RUN=1;RPP=3.18402;RPPR=3.05373;RPL=98.0;RPR=102.0;EPP=14.1282;EPPR=14.1282;DPRA=0.0;ODDS=285.546;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995;PAIREDR=0.995;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.179;Dels=0.0;FS=2.1695;HaplotypeS [...]
+chr7 101923315 . T TC 2574.29 REJECT NS=1;DP=81;DPB=102.4;AC=2;AN=4;AF=1.0;RO=0;AO=81;PRO=4.0;PAO=5.0;QR=0;QA=2999;PQR=111.5;PQA=144.5;SRF=0;SRR=0;SAF=72;SAR=9;SRP=0.0;SAP=109.412;AB=0.0;ABP=0.0;RUN=1;RPP=3.03711;RPPR=0.0;RPL=40.0;RPR=41.0;EPP=7.5409;EPPR=0.0;DPRA=0.0;ODDS=55.7197;GTI=0;TYPE=ins;CIGAR=1M1I4M;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.987654;PAIREDR=0.0;technology.ILLUMINA=1.0;END=101923315;HOMLEN=2;HOMSEQ=CC;SVLEN=1;SVTYPE=INS;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0; [...]
+chr7 101926087 . G T 2448.38 REJECT NS=2;DP=303;DPB=347.0;AC=2;AN=4;AF=0.5;RO=209;AO=133;PRO=0.0;PAO=0.0;QR=6270;QA=3896;PQR=0.0;PQA=0.0;SRF=94;SRR=115;SAF=41;SAR=92;SRP=7.59221;SAP=45.4765;AB=0.383285;ABP=44.068;RUN=1;RPP=27.8435;RPPR=121.963;RPL=86.0;RPR=47.0;EPP=33.1987;EPPR=64.6115;DPRA=0.0;ODDS=145.565;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.5;LEN=1;MQM=60.0;MQMR=59.8373;PAIRED=0.992481;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.4655;Dels=0.0;FS=4.0535;HaplotypeSco [...]
+chr7 101926095 . T C 73.77 PASS DP=61;AC=1;AN=4;AF=0.5;BaseQRankSum=-3.194;FS=63.595;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.374;QD=1.21;ReadPosRankSum=-3.942;SOR=4.395;ClippingRankSum=-1.314 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:53,8:61:99.0:102,0,3076:8:13:61:1:.:.:.:.:.:-0.00407189 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0173504
+chr7 106508978 . A G 8898.4 REJECT NS=2;DP=327;DPB=375.0;AC=2;AN=4;AF=0.5;RO=83;AO=291;PRO=0.0;PAO=0.0;QR=3204;QA=11100;PQR=0.0;PQA=0.0;SRF=41;SRR=42;SAF=141;SAR=150;SRP=3.03646;SAP=3.61473;AB=0.776;ABP=251.131;RUN=1;RPP=3.01776;RPPR=3.03646;RPL=145.0;RPR=146.0;EPP=13.2259;EPPR=4.29225;DPRA=0.0;ODDS=120.808;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989691;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.624;Dels=0.0;FS=2.744;HaplotypeScore=2.9 [...]
+chr7 106508987 . T C 9111.08 REJECT NS=2;DP=332;DPB=381.0;AC=2;AN=4;AF=0.5;RO=84;AO=297;PRO=0.0;PAO=0.0;QR=3180;QA=11352;PQR=0.0;PQA=0.0;SRF=40;SRR=44;SAF=149;SAR=148;SRP=3.42391;SAP=3.01761;AB=0.779528;ABP=261.586;RUN=1;RPP=4.24592;RPPR=3.1137;RPL=142.0;RPR=155.0;EPP=7.5799;EPPR=3.1137;DPRA=0.0;ODDS=108.814;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986532;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8;Dels=0.0;FS=2.0365;HaplotypeScore=7.8 [...]
+chr7 106512936 . C T 886.678 REJECT NS=2;DP=183;DPB=209.0;AC=2;AN=4;AF=0.5;RO=160;AO=49;PRO=0.0;PAO=0.0;QR=6189;QA=1878;PQR=0.0;PQA=0.0;SRF=100;SRR=60;SAF=36;SAR=13;SRP=24.725;SAP=26.4533;AB=0.23445;ABP=131.023;RUN=1;RPP=51.2702;RPPR=73.366;RPL=8.0;RPR=41.0;EPP=8.37251;EPPR=6.48466;DPRA=0.0;ODDS=88.0793;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1735;Dels=0.0;FS=4.353;HaplotypeScore=5.8962;MLEA [...]
+chr7 106519943 . T C 7610.835 REJECT NS=2;DP=204;DPB=237.0;AC=4;AN=4;AF=1.0;RO=0;AO=237;PRO=0.0;PAO=0.0;QR=0;QA=9077;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=176;SAR=61;SRP=0.0;SAP=124.182;AB=0.0;ABP=0.0;RUN=1;RPP=104.025;RPPR=0.0;RPL=66.0;RPR=171.0;EPP=3.45925;EPPR=0.0;DPRA=0.0;ODDS=44.2804;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.987342;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=25.74;SOR=2.48 [...]
+chr7 106522592 . A G 2102.7 PASS SOMATIC;NS=2;DP=398;DPB=398.0;AC=1;AN=3;AF=0.25;RO=309;AO=88;PRO=0.0;PAO=0.0;QR=11329;QA=3312;PQR=0.0;PQA=0.0;SRF=175;SRR=134;SAF=57;SAR=31;SRP=14.8234;SAP=19.6912;AB=0.298305;ABP=107.248;RUN=1;RPP=7.84676;RPPR=5.5472;RPL=51.0;RPR=37.0;EPP=9.32731;EPPR=30.9021;DPRA=2.86408;ODDS=64.4941;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996764;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.292;Dels=0.0;FS=7.069; [...]
+chr7 116212474 . C A 5545.95 REJECT NS=2;DP=369;DPB=419.0;AC=2;AN=4;AF=0.5;RO=224;AO=194;PRO=0.0;PAO=0.0;QR=8483;QA=7496;PQR=0.0;PQA=0.0;SRF=118;SRR=106;SAF=102;SAR=92;SRP=4.40625;SAP=4.12962;AB=0.463007;ABP=7.99069;RUN=1;RPP=6.63688;RPPR=15.5738;RPL=88.0;RPR=106.0;EPP=3.41325;EPPR=6.88793;DPRA=0.0;ODDS=278.123;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994845;PAIREDR=0.986607;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.842;Dels=0.0;FS=3.472;Haplotype [...]
+chr7 116212511 . T C 1972.495 REJECT NS=2;DP=367;DPB=421.0;AC=2;AN=4;AF=0.5;RO=322;AO=99;PRO=0.0;PAO=0.0;QR=12479;QA=3844;PQR=0.0;PQA=0.0;SRF=162;SRR=160;SAF=57;SAR=42;SRP=3.03727;SAP=7.94546;AB=0.235154;ABP=259.507;RUN=1;RPP=3.20771;RPPR=3.4419;RPL=51.0;RPR=48.0;EPP=4.78696;EPPR=3.1182;DPRA=0.0;ODDS=207.936;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993789;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.449;Dels=0.0;FS=1.083;HaplotypeScore=4. [...]
+chr7 116214871 . C CA 1446.39 REJECT NS=2;DP=273;DPB=356.13;AC=2;AN=3;AF=0.5;RO=57;AO=60;PRO=48.6667;PAO=45.1667;QR=1933;QA=1716;PQR=1681.5;PQA=1552.0;SRF=41;SRR=16;SAF=39;SAR=21;SRP=26.8203;SAP=14.7363;AB=0.21978;ABP=189.208;RUN=1;RPP=10.1038;RPPR=6.09608;RPL=23.0;RPR=37.0;EPP=3.0103;EPPR=3.0484;DPRA=0.0;ODDS=18.9735;GTI=0;TYPE=ins;CIGAR=1M1I22M;NUMALT=3;MEANALT=28.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.72;FS=5.1 [...]
+chr7 116214871 . C CAA 1446.39 REJECT SOMATIC;NS=2;DP=273;DPB=356.13;AC=1;AN=3;AF=0.0;RO=57;AO=15;PRO=48.6667;PAO=43.1667;QR=1933;QA=387;PQR=1681.5;PQA=1511.0;SRF=41;SRR=16;SAF=11;SAR=4;SRP=26.8203;SAP=10.1038;AB=0.0549451;ABP=472.693;RUN=1;RPP=4.31318;RPPR=6.09608;RPL=9.0;RPR=6.0;EPP=3.15506;EPPR=3.0484;DPRA=0.0;ODDS=18.9735;GTI=0;TYPE=ins;CIGAR=1M2I22M;NUMALT=3;MEANALT=28.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr7 116214871 . CA C 1446.39 REJECT NS=2;DP=273;DPB=356.13;AC=2;AN=2;AF=0.25;RO=57;AO=57;PRO=48.6667;PAO=35.0;QR=1933;QA=1716;PQR=1681.5;PQA=1203.5;SRF=41;SRR=16;SAF=40;SAR=17;SRP=26.8203;SAP=23.1631;AB=0.208791;ABP=204.098;RUN=1;RPP=4.877;RPPR=6.09608;RPL=25.0;RPR=32.0;EPP=7.61992;EPPR=3.0484;DPRA=0.0;ODDS=18.9735;GTI=0;TYPE=del;CIGAR=1M1D21M;NUMALT=3;MEANALT=28.0;LEN=1;MQM=60.1754;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.37;FS=3.927;ML [...]
+chr7 116312986 . T C 6003.765 REJECT NS=2;DP=360;DPB=411.0;AC=2;AN=4;AF=0.5;RO=201;AO=210;PRO=0.0;PAO=0.0;QR=7687;QA=8089;PQR=0.0;PQA=0.0;SRF=101;SRR=100;SAF=105;SAR=105;SRP=3.0211;SAP=3.0103;AB=0.510949;ABP=3.43825;RUN=1;RPP=6.36057;RPPR=9.76239;RPL=96.0;RPR=114.0;EPP=3.67208;EPPR=4.3175;DPRA=0.0;ODDS=333.731;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990476;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.258;Dels=0.0;FS=4.409;HaplotypeScore= [...]
+chr7 116314327 . A C 5617.5 REJECT NS=2;DP=355;DPB=405.0;AC=2;AN=4;AF=0.5;RO=204;AO=201;PRO=0.0;PAO=0.0;QR=7733;QA=7595;PQR=0.0;PQA=0.0;SRF=79;SRR=125;SAF=88;SAR=113;SRP=25.534;SAP=9.76239;AB=0.496296;ABP=3.05855;RUN=1;RPP=4.3175;RPPR=3.05288;RPL=106.0;RPR=95.0;EPP=3.10753;EPPR=3.69155;DPRA=0.0;ODDS=290.858;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99005;PAIREDR=0.995098;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8995;Dels=0.0;FS=2.636;HaplotypeScor [...]
+chr7 116314405 . G A 1571.755 REJECT NS=2;DP=351;DPB=402.0;AC=2;AN=4;AF=0.5;RO=316;AO=86;PRO=0.0;PAO=0.0;QR=11913;QA=3328;PQR=0.0;PQA=0.0;SRF=156;SRR=160;SAF=46;SAR=40;SRP=3.12025;SAP=3.91929;AB=0.21393;ABP=288.759;RUN=1;RPP=3.1113;RPPR=3.03779;RPL=44.0;RPR=42.0;EPP=3.1113;EPPR=12.9331;DPRA=0.0;ODDS=192.496;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990506;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.184;Dels=0.0;FS=3.6695;HaplotypeScore=4. [...]
+chr7 116315808 . C CT 470.661 REJECT NS=2;DP=153;DPB=350.224;AC=2;AN=2;AF=0.0;RO=94;AO=8;PRO=208.667;PAO=106.667;QR=3477;QA=198;PQR=7560.5;PQA=3709.5;SRF=29;SRR=65;SAF=2;SAR=6;SRP=32.9489;SAP=7.35324;AB=0.0522876;ABP=269.392;RUN=1;RPP=7.35324;RPPR=5.32038;RPL=6.0;RPR=2.0;EPP=3.0103;EPPR=3.0103;DPRA=0.0;ODDS=46.8758;GTI=0;TYPE=ins;CIGAR=1M1I48M;NUMALT=2;MEANALT=15.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr7 116315808 . CT C 470.661 REJECT NS=2;DP=153;DPB=350.224;AC=2;AN=4;AF=0.5;RO=94;AO=20;PRO=208.667;PAO=108.667;QR=3477;QA=659;PQR=7560.5;PQA=3896.0;SRF=29;SRR=65;SAF=8;SAR=12;SRP=32.9489;SAP=4.74748;AB=0.130719;ABP=184.236;RUN=1;RPP=3.44459;RPPR=5.32038;RPL=9.0;RPR=11.0;EPP=13.8677;EPPR=3.0103;DPRA=0.0;ODDS=46.8758;GTI=0;TYPE=del;CIGAR=1M1D47M;NUMALT=2;MEANALT=15.0;LEN=1;MQM=60.5;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.852;FS=1.229;MLE [...]
+chr7 116317042 . G GT 1968.02 REJECT NS=2;DP=119;DPB=286.588;AC=2;AN=3;AF=0.25;RO=49;AO=17;PRO=135.833;PAO=102.833;QR=1767;QA=490;PQR=4938.33;PQA=3582.33;SRF=26;SRR=23;SAF=9;SAR=8;SRP=3.40914;SAP=3.13803;AB=0.142857;ABP=134.85;RUN=1;RPP=9.26925;RPPR=19.0083;RPL=5.0;RPR=12.0;EPP=3.13803;EPPR=4.11819;DPRA=0.0;ODDS=23.0096;GTI=0;TYPE=ins;CIGAR=1M1I50M;NUMALT=2;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-1.785;FS= [...]
+chr7 116317042 . GT G 1968.02 REJECT NS=2;DP=119;DPB=286.588;AC=2;AN=3;AF=0.25;RO=49;AO=31;PRO=135.833;PAO=112.333;QR=1767;QA=1086;PQR=4938.33;PQA=4090.33;SRF=26;SRR=23;SAF=15;SAR=16;SRP=3.40914;SAP=3.08035;AB=0.260504;ABP=62.297;RUN=1;RPP=4.76149;RPPR=19.0083;RPL=13.0;RPR=18.0;EPP=14.8483;EPPR=4.11819;DPRA=0.0;ODDS=23.0096;GTI=0;TYPE=del;CIGAR=1M1D49M;NUMALT=2;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.967742;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.057; [...]
+chr7 116317877 . G A 5393.075000000001 REJECT NS=2;DP=368;DPB=429.0;AC=2;AN=4;AF=0.5;RO=233;AO=196;PRO=0.0;PAO=0.0;QR=8995;QA=7548;PQR=0.0;PQA=0.0;SRF=112;SRR=121;SAF=106;SAR=90;SRP=3.76519;SAP=5.84651;AB=0.456876;ABP=9.93978;RUN=1;RPP=4.60567;RPPR=3.24329;RPL=92.0;RPR=104.0;EPP=5.84651;EPPR=14.4268;DPRA=0.0;ODDS=332.819;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9796;MQMR=60.0;PAIRED=0.989796;PAIREDR=0.995708;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1285;Dels=0.0;FS=3 [...]
+chr7 116318023 . TTC T 33.0475 REJECT NS=2;DP=220;DPB=291.368;AC=1;AN=4;AF=0.25;RO=196;AO=15;PRO=78.5;PAO=68.5;QR=7315;QA=534;PQR=2795.0;PQA=2429.0;SRF=104;SRR=92;SAF=12;SAR=3;SRP=4.60567;SAP=14.7363;AB=0.157895;ABP=41.6397;RUN=1;RPP=3.15506;RPPR=3.18756;RPL=8.0;RPR=7.0;EPP=3.15506;EPPR=3.18756;DPRA=0.0;ODDS=7.60898;GTI=0;TYPE=del;CIGAR=1M2D16M;NUMALT=1;MEANALT=4.5;LEN=2;MQM=60.0;MQMR=59.898;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallH [...]
+chr7 116318027 . CTCTCTCTCTCTCTG C 853.73 PASS DP=116;AC=2;AN=4;AF=0.5;END=116318041;HOMLEN=13;HOMSEQ=TCTCTCTCTCTCT;SVLEN=-14;SVTYPE=DEL;BaseQRankSum=2.618;FS=6.869;MLEAC=1;MLEAF=0.5;MQ=60.65;MQRankSum=-0.109;QD=7.36;ReadPosRankSum=1.259;SOR=1.043;ClippingRankSum=1.747 GT:AD:GMIMUT:GMIMAF:GMICOV:DP:GQ:PL:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:59,41:41:41:100:97:99.0:891,0,3294:1:.:.:1:.:.:-0.00407189 0/1:235,44:44:16:279:.:.:.:.:.:.:1:.:.:-0.0173504
+chr7 116318486 . GT G 1557.79 REJECT NS=2;DP=308;DPB=359.647;AC=2;AN=4;AF=0.5;RO=229;AO=69;PRO=64.5;PAO=58.5;QR=8638;QA=2457;PQR=2293.0;PQA=2070.0;SRF=99;SRR=130;SAF=28;SAR=41;SRP=12.1229;SAP=8.32883;AB=0.224026;ABP=206.762;RUN=1;RPP=3.29354;RPPR=9.92298;RPL=33.0;RPR=36.0;EPP=3.29354;EPPR=3.09564;DPRA=0.0;ODDS=93.7573;GTI=0;TYPE=del;CIGAR=1M1D15M;NUMALT=1;MEANALT=4.0;LEN=1;MQM=60.2899;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991266;technology.ILLUMINA=1.0;BaseQRankSum=0.994;FS=1.855;MLEAC=1;MLEAF= [...]
+chr7 116318765 . CTTGGGACCAGCA C 726.338 REJECT NS=2;DP=355;DPB=351.5;AC=2;AN=4;AF=0.25;RO=282;AO=65;PRO=90.0;PAO=3.0;QR=10666;QA=2150;PQR=3315.5;PQA=109.5;SRF=131;SRR=151;SAF=30;SAR=35;SRP=6.0904;SAP=3.84548;AB=0.413793;ABP=8.62618;RUN=1;RPP=4.64726;RPPR=3.78033;RPL=29.0;RPR=36.0;EPP=5.71629;EPPR=4.98157;DPRA=0.0;ODDS=5.82746;GTI=0;TYPE=del;CIGAR=1M12D1M;NUMALT=1;MEANALT=4.5;LEN=12;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996454;technology.ILLUMINA=1.0;END=116318777;HOMLEN=10;HOMSEQ=TTGG [...]
+chr7 116319002 . A G 2435.625 REJECT NS=2;DP=400;DPB=462.0;AC=2;AN=4;AF=0.5;RO=348;AO=114;PRO=0.0;PAO=0.0;QR=13420;QA=4406;PQR=0.0;PQA=0.0;SRF=161;SRR=187;SAF=57;SAR=57;SRP=7.22845;SAP=3.0103;AB=0.246753;ABP=260.372;RUN=1;RPP=10.6295;RPPR=7.22845;RPL=47.0;RPR=67.0;EPP=6.74371;EPPR=3.11014;DPRA=0.0;ODDS=184.456;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991228;PAIREDR=0.994253;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4915;Dels=0.0;FS=2.499;Haplotype [...]
+chr7 116319211 . C T 1376.27 PASS DP=199;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=1.882;Dels=0.0;FS=2.0465;HaplotypeScore=3.8985;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.2925;QD=10.365;ReadPosRankSum=0.181;SOR=0.781;ClippingRankSum=-2.716 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:56,51:107:99.0:1964,0,4117:51:48:107:1:.:.:.:.:.:-0.00407189 0/1:252,39:291:99.0:845,0,9842:39:13:291:.:1:.:.:.:.:-0.0173504
+chr7 116319211 . CATC TATT 2032.56 REJECT NS=2;DP=388;DPB=396.25;AC=2;AN=4;AF=0.5;RO=298;AO=89;PRO=14.0;PAO=4.0;QR=11094;QA=3332;PQR=469.0;PQA=149.0;SRF=143;SRR=155;SAF=46;SAR=43;SRP=4.0596;SAP=3.22989;AB=0.229381;ABP=249.819;RUN=1;RPP=18.2594;RPPR=4.87573;RPL=57.0;RPR=32.0;EPP=7.13366;EPPR=7.93619;DPRA=0.0;ODDS=143.062;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=1;MEANALT=1.5;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=0.977528;PAIREDR=0.993289;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr7 116319214 . C T 1375.27 PASS DP=197;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.1305;Dels=0.0;FS=1.5655;HaplotypeScore=5.8957;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.8715;QD=10.5;ReadPosRankSum=0.5285;SOR=0.79;ClippingRankSum=0.215 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:55,52:107:99.0:2005,0,4039:52:49:107:1:.:.:.:.:.:-0.00407189 0/1:249,38:287:99.0:802,0,9526:38:13:287:.:1:.:.:.:.:-0.0173504
+chr7 116319926 . A G 3308.4 PASS SOMATIC;NS=2;DP=447;DPB=447.0;AC=1;AN=3;AF=0.25;RO=321;AO=125;PRO=0.0;PAO=0.0;QR=12257;QA=4785;PQR=0.0;PQA=0.0;SRF=164;SRR=157;SAF=55;SAR=70;SRP=3.34177;SAP=6.91895;AB=0.362319;ABP=59.8148;RUN=1;RPP=5.11229;RPPR=3.82883;RPL=68.0;RPR=57.0;EPP=8.03074;EPPR=12.2712;DPRA=3.38235;ODDS=64.6221;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=59.9533;PAIRED=0.992;PAIREDR=0.993769;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.777;Dels=0.0;FS [...]
+chr7 116320864 . C T 832.817 PASS SOMATIC;NS=2;DP=123;DPB=123.0;AC=1;AN=3;AF=0.25;RO=89;AO=34;PRO=0.0;PAO=0.0;QR=3346;QA=1295;PQR=0.0;PQA=0.0;SRF=65;SRR=24;SAF=25;SAR=9;SRP=44.0243;SAP=19.3602;AB=0.373626;ABP=15.6335;RUN=1;RPP=7.09778;RPPR=8.49998;RPL=13.0;RPR=21.0;EPP=23.7032;EPPR=48.1232;DPRA=2.84375;ODDS=20.9603;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.267;Dels=0.0;FS=0.0;HaplotypeS [...]
+chr7 116320886 . C T 771.223 PASS SOMATIC;NS=2;DP=133;DPB=133.0;AC=1;AN=3;AF=0.25;RO=100;AO=33;PRO=0.0;PAO=0.0;QR=3744;QA=1275;PQR=0.0;PQA=0.0;SRF=82;SRR=18;SAF=30;SAR=3;SRP=91.9538;SAP=50.9801;AB=0.336735;ABP=25.7;RUN=1;RPP=8.34028;RPPR=4.40004;RPL=12.0;RPR=21.0;EPP=10.9724;EPPR=20.0346;DPRA=2.8;ODDS=22.8502;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.15;Dels=0.0;FS=2.739;HaplotypeScore= [...]
+chr7 116321039 . T C 2239.2 PASS SOMATIC;NS=2;DP=337;DPB=337.0;AC=1;AN=3;AF=0.25;RO=250;AO=87;PRO=0.0;PAO=0.0;QR=9648;QA=3292;PQR=0.0;PQA=0.0;SRF=145;SRR=105;SAF=50;SAR=37;SRP=16.9077;SAP=7.22845;AB=0.356557;ABP=46.6177;RUN=1;RPP=8.62618;RPPR=3.0103;RPL=36.0;RPR=51.0;EPP=3.63429;EPPR=4.71273;DPRA=2.62366;ODDS=59.0228;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.133;Dels=0.0;FS=0.0;Haplo [...]
+chr7 116321802 . A G 2756.87 PASS SOMATIC;NS=2;DP=343;DPB=343.0;AC=1;AN=3;AF=0.25;RO=240;AO=103;PRO=0.0;PAO=0.0;QR=9201;QA=3892;PQR=0.0;PQA=0.0;SRF=109;SRR=131;SAF=49;SAR=54;SRP=7.38944;SAP=3.53736;AB=0.407115;ABP=21.9699;RUN=1;RPP=3.53736;RPPR=3.58936;RPL=54.0;RPR=49.0;EPP=9.10307;EPPR=4.78367;DPRA=2.81111;ODDS=57.1375;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990291;PAIREDR=0.979167;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.735;Dels=0.0;F [...]
+chr7 116321992 . C CA 208.996 REJECT NS=2;DP=344;DPB=407.312;AC=2;AN=3;AF=0.25;RO=258;AO=38;PRO=49.6667;PAO=36.6667;QR=9571;QA=1223;PQR=1709.83;PQA=1260.83;SRF=131;SRR=127;SAF=22;SAR=16;SRP=3.14496;SAP=5.06748;AB=0.110465;ABP=456.394;RUN=1;RPP=6.66752;RPPR=3.04397;RPL=15.0;RPR=23.0;EPP=3.0103;EPPR=4.22228;DPRA=0.0;ODDS=1.78188;GTI=1;TYPE=ins;CIGAR=1M1I15M;NUMALT=2;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.973684;PAIREDR=0.984496;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:Q [...]
+chr7 116321992 . CA C 208.996 REJECT NS=2;DP=344;DPB=407.312;AC=2;AN=3;AF=0.25;RO=258;AO=27;PRO=49.6667;PAO=31.6667;QR=9571;QA=985;PQR=1709.83;PQA=1107.33;SRF=131;SRR=127;SAF=12;SAR=15;SRP=3.14496;SAP=3.73412;AB=0.0784884;ABP=533.885;RUN=1;RPP=3.09072;RPPR=3.04397;RPL=13.0;RPR=14.0;EPP=3.73412;EPPR=4.22228;DPRA=0.0;ODDS=1.78188;GTI=1;TYPE=del;CIGAR=1M1D14M;NUMALT=2;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.962963;PAIREDR=0.984496;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO: [...]
+chr7 116324531 . C T 6372.700000000001 REJECT NS=2;DP=419;DPB=476.0;AC=2;AN=4;AF=0.5;RO=244;AO=231;PRO=0.0;PAO=0.0;QR=9272;QA=8626;PQR=0.0;PQA=0.0;SRF=124;SRR=120;SAF=114;SAR=117;SRP=3.15269;SAP=3.0949;AB=0.485294;ABP=3.90444;RUN=1;RPP=3.0197;RPPR=8.1364;RPL=115.0;RPR=116.0;EPP=3.47092;EPPR=12.1234;DPRA=0.0;ODDS=335.279;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995671;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.45;Dels=0.0;FS=3.601;Haplo [...]
+chr7 116325326 . T C 6278.07 REJECT NS=2;DP=402;DPB=460.0;AC=2;AN=4;AF=0.5;RO=235;AO=225;PRO=0.0;PAO=0.0;QR=8819;QA=8603;PQR=0.0;PQA=0.0;SRF=107;SRR=128;SAF=87;SAR=138;SRP=7.08528;SAP=28.1125;AB=0.48913;ABP=3.48236;RUN=1;RPP=4.64132;RPPR=3.46308;RPL=119.0;RPR=106.0;EPP=3.79203;EPPR=3.46308;DPRA=0.0;ODDS=373.412;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991489;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.4715;Dels=0.0;FS=4.424;HaplotypeScor [...]
+chr7 116327430 . C G 2160.03 PASS SOMATIC;NS=2;DP=431;DPB=431.0;AC=1;AN=3;AF=0.25;RO=341;AO=90;PRO=0.0;PAO=0.0;QR=12789;QA=3430;PQR=0.0;PQA=0.0;SRF=162;SRR=179;SAF=36;SAR=54;SRP=4.85064;SAP=10.8276;AB=0.28125;ABP=136.013;RUN=1;RPP=3.39634;RPPR=3.06761;RPL=43.0;RPR=47.0;EPP=3.0103;EPPR=6.99027;DPRA=2.88288;ODDS=70.2519;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988889;PAIREDR=0.985337;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.183;Dels=0.0;FS=3 [...]
+chr7 116327659 . T C 1746.05 REJECT NS=2;DP=360;DPB=410.0;AC=2;AN=4;AF=0.5;RO=318;AO=92;PRO=0.0;PAO=0.0;QR=12318;QA=3522;PQR=0.0;PQA=0.0;SRF=136;SRR=182;SAF=41;SAR=51;SRP=17.4595;SAP=5.3706;AB=0.22439;ABP=273.523;RUN=1;RPP=14.4341;RPPR=3.03761;RPL=57.0;RPR=35.0;EPP=3.0103;EPPR=3.25613;DPRA=0.0;ODDS=145.431;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987421;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.401;Dels=0.0;FS=1.47;HaplotypeScore=5.81 [...]
+chr7 116328284 . C CT 29.5936 REJECT NS=2;DP=329;DPB=407.952;AC=2;AN=3;AF=0.25;RO=260;AO=26;PRO=71.0;PAO=53.0;QR=9656;QA=808;PQR=2493.33;PQA=1853.33;SRF=128;SRR=132;SAF=8;SAR=18;SRP=3.14393;SAP=11.3621;AB=0.0790274;ABP=509.439;RUN=1;RPP=4.34659;RPPR=4.21296;RPL=11.0;RPR=15.0;EPP=4.34659;EPPR=9.55812;DPRA=0.0;ODDS=0.519661;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=2;MEANALT=8.5;LEN=1;MQM=60.0;MQMR=59.9885;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr7 116328284 . CT C 29.5936 REJECT NS=2;DP=329;DPB=407.952;AC=2;AN=3;AF=0.25;RO=260;AO=23;PRO=71.0;PAO=42.0;QR=9656;QA=787;PQR=2493.33;PQA=1460.33;SRF=128;SRR=132;SAF=9;SAR=14;SRP=3.14393;SAP=5.3706;AB=0.0699088;ABP=531.615;RUN=1;RPP=5.3706;RPPR=4.21296;RPL=9.0;RPR=14.0;EPP=3.10471;EPPR=9.55812;DPRA=0.0;ODDS=0.519661;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=2;MEANALT=8.5;LEN=1;MQM=59.8696;MQMR=59.9885;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr7 116329159 . G GAAATTTCATGT 787.099 REJECT NS=2;DP=327;DPB=412.692;AC=2;AN=4;AF=0.5;RO=271;AO=52;PRO=43.5;PAO=43.5;QR=10276;QA=1913;PQR=1469.0;PQA=1469.0;SRF=149;SRR=122;SAF=29;SAR=23;SRP=8.85164;SAP=4.51363;AB=0.159021;ABP=333.24;RUN=1;RPP=9.02361;RPPR=3.01831;RPL=20.0;RPR=32.0;EPP=3.17734;EPPR=4.36447;DPRA=0.0;ODDS=7.37314;GTI=0;TYPE=ins;CIGAR=1M11I12M;NUMALT=1;MEANALT=3.0;LEN=11;MQM=60.0;MQMR=60.0;PAIRED=0.980769;PAIREDR=0.98524;technology.ILLUMINA=1.0;END=116329159;HOMLEN=15;HOMS [...]
+chr7 116329401 . G T 1828.7150000000001 REJECT NS=2;DP=337;DPB=389.0;AC=2;AN=4;AF=0.5;RO=301;AO=88;PRO=0.0;PAO=0.0;QR=11244;QA=3376;PQR=0.0;PQA=0.0;SRF=131;SRR=170;SAF=36;SAR=52;SRP=13.9831;SAP=9.32731;AB=0.226221;ABP=256.269;RUN=1;RPP=5.47788;RPPR=3.19065;RPL=39.0;RPR=49.0;EPP=5.47788;EPPR=3.07523;DPRA=0.0;ODDS=106.168;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.973422;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.088;Dels=0.0;FS=2.754;Haplo [...]
+chr7 116330878 . C T 1669.0549999999998 REJECT NS=2;DP=366;DPB=418.0;AC=2;AN=4;AF=0.5;RO=326;AO=92;PRO=0.0;PAO=0.0;QR=12671;QA=3540;PQR=0.0;PQA=0.0;SRF=153;SRR=173;SAF=48;SAR=44;SRP=5.67468;SAP=3.38795;AB=0.220096;ABP=287.463;RUN=1;RPP=9.05266;RPPR=23.8991;RPL=38.0;RPR=54.0;EPP=3.38795;EPPR=3.25009;DPRA=0.0;ODDS=227.501;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.978261;PAIREDR=0.993865;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.173;Dels=0.0;FS=0.932; [...]
+chr7 116331101 . C A 2440.8050000000003 REJECT NS=2;DP=363;DPB=426.0;AC=2;AN=4;AF=0.5;RO=313;AO=113;PRO=0.0;PAO=0.0;QR=11737;QA=4328;PQR=0.0;PQA=0.0;SRF=157;SRR=156;SAF=56;SAR=57;SRP=3.01724;SAP=3.02952;AB=0.265258;ABP=206.904;RUN=1;RPP=11.4848;RPPR=4.57126;RPL=46.0;RPR=67.0;EPP=3.02952;EPPR=8.06782;DPRA=0.0;ODDS=196.927;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99115;PAIREDR=0.99361;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1935;Dels=0.0;FS=1.755; [...]
+chr7 116331370 . C T 2180.35 PASS SOMATIC;NS=2;DP=390;DPB=390.0;AC=1;AN=3;AF=0.25;RO=300;AO=90;PRO=0.0;PAO=0.0;QR=11355;QA=3319;PQR=0.0;PQA=0.0;SRF=150;SRR=150;SAF=48;SAR=42;SRP=3.0103;SAP=3.87889;AB=0.32491;ABP=76.7698;RUN=1;RPP=3.87889;RPPR=9.52472;RPL=42.0;RPR=48.0;EPP=5.42305;EPPR=3.27088;DPRA=2.45133;ODDS=71.2631;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.83;PAIRED=0.988889;PAIREDR=0.993333;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.863;Dels=0.0;FS [...]
+chr7 116332197 . A G 1699.6 REJECT NS=2;DP=382;DPB=438.0;AC=2;AN=4;AF=0.5;RO=353;AO=85;PRO=0.0;PAO=0.0;QR=13466;QA=3278;PQR=0.0;PQA=0.0;SRF=168;SRR=185;SAF=50;SAR=35;SRP=4.78808;SAP=8.75832;AB=0.194064;ABP=359.092;RUN=1;RPP=6.10145;RPPR=15.467;RPL=37.0;RPR=48.0;EPP=3.24022;EPPR=3.01645;DPRA=0.0;ODDS=39.1514;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988235;PAIREDR=0.991501;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6965;Dels=0.0;FS=4.6855;HaplotypeSc [...]
+chr7 116332324 . T A 1640.13 REJECT NS=2;DP=356;DPB=408.0;AC=2;AN=4;AF=0.5;RO=328;AO=80;PRO=0.0;PAO=0.0;QR=12571;QA=3116;PQR=0.0;PQA=0.0;SRF=162;SRR=166;SAF=35;SAR=45;SRP=3.11623;SAP=5.72464;AB=0.196078;ABP=330.349;RUN=1;RPP=3.44459;RPPR=3.24863;RPL=38.0;RPR=42.0;EPP=3.98746;EPPR=3.03678;DPRA=0.0;ODDS=17.8612;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.975;PAIREDR=0.990854;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.773;Dels=0.0;FS=6.292;HaplotypeScore [...]
+chr7 116332539 . C G 5644.55 REJECT NS=2;DP=375;DPB=427.0;AC=2;AN=4;AF=0.5;RO=222;AO=205;PRO=0.0;PAO=0.0;QR=8420;QA=7787;PQR=0.0;PQA=0.0;SRF=116;SRR=106;SAF=103;SAR=102;SRP=3.98844;SAP=3.02089;AB=0.480094;ABP=4.47999;RUN=1;RPP=6.07155;RPPR=4.41882;RPL=111.0;RPR=94.0;EPP=3.8683;EPPR=3.63631;DPRA=0.0;ODDS=325.783;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990244;PAIREDR=0.990991;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6645;Dels=0.0;FS=3.2;HaplotypeS [...]
+chr7 116333709 . A G 3094.0 PASS SOMATIC;NS=2;DP=439;DPB=439.0;AC=1;AN=3;AF=0.25;RO=320;AO=119;PRO=0.0;PAO=0.0;QR=12203;QA=4533;PQR=0.0;PQA=0.0;SRF=150;SRR=170;SAF=59;SAR=60;SRP=5.72464;SAP=3.02855;AB=0.348974;ABP=70.5679;RUN=1;RPP=3.46649;RPPR=9.11757;RPL=57.0;RPR=62.0;EPP=9.59771;EPPR=7.59754;DPRA=3.47959;ODDS=62.1418;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990625;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.17;Dels=0.0;FS=0.0; [...]
+chr7 116334058 . G A 1919.315 REJECT NS=2;DP=400;DPB=447.0;AC=2;AN=4;AF=0.5;RO=343;AO=104;PRO=0.0;PAO=0.0;QR=13074;QA=3938;PQR=0.0;PQA=0.0;SRF=188;SRR=155;SAF=56;SAR=48;SRP=9.90457;SAP=4.34659;AB=0.232662;ABP=280.497;RUN=1;RPP=3.0103;RPPR=3.77633;RPL=52.0;RPR=52.0;EPP=11.3621;EPPR=5.29573;DPRA=0.0;ODDS=222.231;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997085;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.885;Dels=0.0;FS=0.898;HaplotypeScore= [...]
+chr7 116336013 . G A 1083.62 REJECT NS=2;DP=220;DPB=254.0;AC=2;AN=4;AF=0.5;RO=189;AO=65;PRO=0.0;PAO=0.0;QR=7099;QA=2335;PQR=0.0;PQA=0.0;SRF=40;SRR=149;SAF=17;SAR=48;SRP=139.514;SAP=35.1147;AB=0.255906;ABP=134.461;RUN=1;RPP=7.05258;RPPR=12.6728;RPL=38.0;RPR=27.0;EPP=7.05258;EPPR=3.02179;DPRA=0.0;ODDS=137.061;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.969231;PAIREDR=0.989418;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.2005;Dels=0.0;FS=2.1005;HaplotypeS [...]
+chr7 116336880 . T C 1529.375 REJECT NS=2;DP=334;DPB=376.0;AC=2;AN=4;AF=0.5;RO=292;AO=84;PRO=0.0;PAO=0.0;QR=11294;QA=3184;PQR=0.0;PQA=0.0;SRF=142;SRR=150;SAF=41;SAR=43;SRP=3.48624;SAP=3.1137;AB=0.223404;ABP=252.868;RUN=1;RPP=3.1137;RPPR=3.12928;RPL=41.0;RPR=43.0;EPP=3.42391;EPPR=4.91406;DPRA=0.0;ODDS=168.384;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993151;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.519;Dels=0.0;FS=1.923;HaplotypeScore=5. [...]
+chr7 116336947 . C T 2416.68 PASS SOMATIC;NS=2;DP=374;DPB=374.0;AC=1;AN=3;AF=0.25;RO=281;AO=93;PRO=0.0;PAO=0.0;QR=10787;QA=3590;PQR=0.0;PQA=0.0;SRF=145;SRR=136;SAF=46;SAR=47;SRP=3.63624;SAP=3.03365;AB=0.334532;ABP=69.123;RUN=1;RPP=8.26386;RPPR=4.31627;RPL=54.0;RPR=39.0;EPP=5.83555;EPPR=3.01803;DPRA=2.89583;ODDS=60.8225;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989247;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.455;Dels=0.0;FS=0.459 [...]
+chr7 116336948 . G A 1800.065 REJECT NS=2;DP=319;DPB=368.0;AC=2;AN=4;AF=0.5;RO=281;AO=86;PRO=0.0;PAO=0.0;QR=10785;QA=3332;PQR=0.0;PQA=0.0;SRF=150;SRR=131;SAF=43;SAR=43;SRP=5.79999;SAP=3.0103;AB=0.233696;ABP=229.693;RUN=1;RPP=3.91929;RPPR=3.94535;RPL=46.0;RPR=40.0;EPP=3.0103;EPPR=3.63624;DPRA=0.0;ODDS=137.816;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996441;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.4205;Dels=0.0;FS=6.829;HaplotypeScore=4 [...]
+chr7 116337144 . G A 2118.1099999999997 REJECT NS=2;DP=369;DPB=423.0;AC=2;AN=4;AF=0.5;RO=318;AO=105;PRO=0.0;PAO=0.0;QR=12311;QA=3991;PQR=0.0;PQA=0.0;SRF=179;SRR=139;SAF=55;SAR=50;SRP=13.9359;SAP=3.52732;AB=0.248227;ABP=235.912;RUN=1;RPP=3.03098;RPPR=3.03761;RPL=52.0;RPR=53.0;EPP=5.51266;EPPR=3.11956;DPRA=0.0;ODDS=192.141;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990476;PAIREDR=0.981132;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.516;Dels=0.0;FS=0.656 [...]
+chr7 116337352 . T G 1740.7350000000001 REJECT NS=2;DP=404;DPB=460.0;AC=2;AN=4;AF=0.5;RO=367;AO=93;PRO=0.0;PAO=0.0;QR=14108;QA=3405;PQR=0.0;PQA=0.0;SRF=193;SRR=174;SAF=49;SAR=44;SRP=5.14627;SAP=3.59403;AB=0.202174;ABP=357.413;RUN=1;RPP=8.26386;RPPR=5.61962;RPL=39.0;RPR=54.0;EPP=5.83555;EPPR=4.01024;DPRA=0.0;ODDS=82.8818;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989247;PAIREDR=0.99455;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.151;Dels=0.0;FS=1.893; [...]
+chr7 116337649 . G A 3256.44 PASS SOMATIC;NS=2;DP=423;DPB=423.0;AC=1;AN=3;AF=0.25;RO=300;AO=123;PRO=0.0;PAO=0.0;QR=11245;QA=4640;PQR=0.0;PQA=0.0;SRF=154;SRR=146;SAF=51;SAR=72;SRP=3.47355;SAP=10.7958;AB=0.39172;ABP=34.9877;RUN=1;RPP=9.38348;RPPR=5.9056;RPL=71.0;RPR=52.0;EPP=3.16919;EPPR=12.3911;DPRA=2.88073;ODDS=68.9579;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8967;PAIRED=0.98374;PAIREDR=0.983333;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.56;Dels=0.0;FS [...]
+chr7 116364823 . CA C 2822.06 PASS SOMATIC;NS=2;DP=403;DPB=377.0;AC=1;AN=4;AF=0.25;RO=295;AO=108;PRO=15.0;PAO=6.0;QR=11183;QA=4122;PQR=396.5;PQA=73.5;SRF=165;SRR=130;SAF=57;SAR=51;SRP=12.0274;SAP=3.73412;AB=0.363636;ABP=50.9801;RUN=1;RPP=8.15749;RPPR=3.19432;RPL=46.0;RPR=62.0;EPP=12.7417;EPPR=15.384;DPRA=2.80189;ODDS=69.6376;GTI=0;TYPE=del;CIGAR=1M1D1M;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.1852;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986441;technology.ILLUMINA=1.0;MQ0=0;END=116364824;HOMLEN=0;SVLEN=- [...]
+chr7 116381121 . G T 369.183 REJECT NS=2;DP=74;DPB=168.849;AC=2;AN=2;AF=0.0;RO=18;AO=22;PRO=101.167;PAO=26.1667;QR=608;QA=273;PQR=3599.83;PQA=703.167;SRF=1;SRR=17;SAF=0;SAR=22;SRP=33.8935;SAP=50.7827;AB=0.297297;ABP=29.4201;RUN=1;RPP=3.40511;RPPR=4.9405;RPL=10.0;RPR=12.0;EPP=3.40511;EPPR=7.35324;DPRA=0.0;ODDS=13.0846;GTI=0;TYPE=snp;CIGAR=1X52M;NUMALT=3;MEANALT=12.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr7 116381121 . GT G 369.183 REJECT NS=2;DP=74;DPB=168.849;AC=2;AN=4;AF=0.5;RO=18;AO=9;PRO=101.167;PAO=59.1667;QR=608;QA=234;PQR=3599.83;PQA=1922.83;SRF=1;SRR=17;SAF=2;SAR=7;SRP=33.8935;SAP=9.04217;AB=0.121622;ABP=95.0338;RUN=1;RPP=14.8328;RPPR=4.9405;RPL=8.0;RPR=1.0;EPP=5.18177;EPPR=7.35324;DPRA=0.0;ODDS=13.0846;GTI=0;TYPE=del;CIGAR=1M1D51M;NUMALT=3;MEANALT=12.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.326;FS=1.179;M [...]
+chr7 116381121 . GTT G 369.183 REJECT NS=2;DP=74;DPB=168.849;AC=2;AN=2;AF=0.0;RO=18;AO=5;PRO=101.167;PAO=43.5;QR=608;QA=119;PQR=3599.83;PQA=1487.17;SRF=1;SRR=17;SAF=1;SAR=4;SRP=33.8935;SAP=6.91895;AB=0.0675676;ABP=123.204;RUN=1;RPP=3.44459;RPPR=4.9405;RPL=2.0;RPR=3.0;EPP=6.91895;EPPR=7.35324;DPRA=0.0;ODDS=13.0846;GTI=0;TYPE=del;CIGAR=1M2D50M;NUMALT=3;MEANALT=12.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr7 116397572 . A G 1639.7849999999999 REJECT NS=2;DP=351;DPB=399.0;AC=2;AN=4;AF=0.5;RO=318;AO=81;PRO=0.0;PAO=0.0;QR=11996;QA=3116;PQR=0.0;PQA=0.0;SRF=163;SRR=155;SAF=46;SAR=35;SRP=3.44733;SAP=6.2541;AB=0.203008;ABP=308.698;RUN=1;RPP=19.7655;RPPR=9.15598;RPL=28.0;RPR=53.0;EPP=3.03711;EPPR=6.94353;DPRA=0.0;ODDS=94.5103;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.975309;PAIREDR=0.993711;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.6635;Dels=0.0;FS=1.1625 [...]
+chr7 116416010 . G T 7900.83 REJECT NS=2;DP=333;DPB=387.0;AC=3;AN=4;AF=0.75;RO=103;AO=284;PRO=0.0;PAO=0.0;QR=3958;QA=10916;PQR=0.0;PQA=0.0;SRF=57;SRR=46;SAF=166;SAR=118;SRP=5.56125;SAP=20.6268;AB=0.632143;ABP=45.4781;RUN=1;RPP=3.13264;RPPR=5.56125;RPL=140.0;RPR=144.0;EPP=4.11133;EPPR=3.20004;DPRA=0.0;ODDS=67.6924;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989437;PAIREDR=0.990291;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.105;Dels=0.0;FS=0.749;Haploty [...]
+chr7 116416123 . G GT 105.719 REJECT NS=2;DP=335;DPB=384.882;AC=2;AN=3;AF=0.25;RO=264;AO=30;PRO=45.8333;PAO=36.8333;QR=9716;QA=1039;PQR=1615.83;PQA=1287.83;SRF=128;SRR=136;SAF=20;SAR=10;SRP=3.53672;SAP=10.2485;AB=0.1;ABP=350.446;RUN=1;RPP=5.61607;RPPR=36.701;RPL=12.0;RPR=18.0;EPP=3.29983;EPPR=4.19474;DPRA=0.0;ODDS=10.6201;GTI=0;TYPE=ins;CIGAR=1M1I16M;NUMALT=2;MEANALT=10.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996212;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr7 116416123 . GT G 105.719 REJECT NS=2;DP=335;DPB=384.882;AC=2;AN=2;AF=0.0;RO=264;AO=19;PRO=45.8333;PAO=34.3333;QR=9716;QA=663;PQR=1615.83;PQA=1188.33;SRF=128;SRR=136;SAF=11;SAR=8;SRP=3.53672;SAP=4.03889;AB=0.056;ABP=431.086;RUN=1;RPP=4.03889;RPPR=36.701;RPL=11.0;RPR=8.0;EPP=3.12459;EPPR=4.19474;DPRA=0.0;ODDS=10.6201;GTI=0;TYPE=del;CIGAR=1M1D15M;NUMALT=2;MEANALT=10.0;LEN=1;MQM=58.9474;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996212;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr7 116416327 . C T 1597.9650000000001 REJECT NS=2;DP=379;DPB=427.0;AC=2;AN=4;AF=0.5;RO=336;AO=90;PRO=0.0;PAO=0.0;QR=12602;QA=3345;PQR=0.0;PQA=0.0;SRF=153;SRR=183;SAF=52;SAR=38;SRP=8.82674;SAP=7.73928;AB=0.210773;ABP=313.266;RUN=1;RPP=9.18693;RPPR=7.3791;RPL=37.0;RPR=53.0;EPP=6.48466;EPPR=3.1137;DPRA=0.0;ODDS=154.989;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994048;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.286;Dels=0.0;FS=7.981;Haplot [...]
+chr7 116416423 . G A 2677.07 PASS SOMATIC;NS=2;DP=429;DPB=429.0;AC=1;AN=3;AF=0.25;RO=322;AO=106;PRO=0.0;PAO=0.0;QR=12030;QA=4006;PQR=0.0;PQA=0.0;SRF=174;SRR=148;SAF=66;SAR=40;SRP=7.56904;SAP=16.8586;AB=0.334385;ABP=78.5323;RUN=1;RPP=3.74778;RPPR=11.7501;RPL=56.0;RPR=50.0;EPP=7.02548;EPPR=3.1182;DPRA=2.83036;ODDS=70.7773;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993789;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.776;Dels=0.0;FS=10.3 [...]
+chr7 116417848 . G C 5084.52 REJECT NS=2;DP=390;DPB=442.0;AC=2;AN=4;AF=0.5;RO=243;AO=196;PRO=0.0;PAO=0.0;QR=8940;QA=7174;PQR=0.0;PQA=0.0;SRF=117;SRR=126;SAF=96;SAR=100;SRP=3.73412;SAP=3.18756;AB=0.443439;ABP=15.2924;RUN=1;RPP=5.18177;RPPR=4.5205;RPL=105.0;RPR=91.0;EPP=10.4997;EPPR=5.59283;DPRA=0.0;ODDS=294.766;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989796;PAIREDR=0.995885;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1285;Dels=0.0;FS=0.2045;Haploty [...]
+chr7 116435768 . C T 2251.12 PASS SOMATIC;NS=2;DP=377;DPB=377.0;AC=1;AN=3;AF=0.25;RO=289;AO=88;PRO=0.0;PAO=0.0;QR=11016;QA=3415;PQR=0.0;PQA=0.0;SRF=167;SRR=122;SAF=51;SAR=37;SRP=18.2256;SAP=7.84676;AB=0.315412;ABP=85.5807;RUN=1;RPP=4.58955;RPPR=3.37847;RPL=40.0;RPR=48.0;EPP=11.0053;EPPR=9.32936;DPRA=2.84694;ODDS=62.0583;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99654;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.424;Dels=0.0;FS=0.99 [...]
+chr7 116436022 . G A 3814.64 PASS SOMATIC;NS=2;DP=508;DPB=508.0;AC=1;AN=3;AF=0.25;RO=366;AO=141;PRO=0.0;PAO=0.0;QR=14074;QA=5412;PQR=0.0;PQA=0.0;SRF=168;SRR=198;SAF=63;SAR=78;SRP=8.34999;SAP=6.47542;AB=0.384196;ABP=45.7593;RUN=1;RPP=3.1489;RPPR=3.03403;RPL=69.0;RPR=72.0;EPP=4.25774;EPPR=11.5775;DPRA=2.60284;ODDS=88.3164;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992908;PAIREDR=0.994536;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.771;Dels=0.0;FS [...]
+chr7 116436097 . G A 2545.44 PASS SOMATIC;NS=2;DP=378;DPB=378.0;AC=1;AN=3;AF=0.25;RO=280;AO=98;PRO=0.0;PAO=0.0;QR=10727;QA=3749;PQR=0.0;PQA=0.0;SRF=126;SRR=154;SAF=39;SAR=59;SRP=9.09042;SAP=11.8735;AB=0.351254;ABP=56.6278;RUN=1;RPP=6.20103;RPPR=4.53033;RPL=55.0;RPR=43.0;EPP=10.1895;EPPR=3.28949;DPRA=2.81818;ODDS=62.7376;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989796;PAIREDR=0.992857;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.302;Dels=0.0;FS [...]
+chr7 116528581 . A G 5487.05 REJECT NS=2;DP=341;DPB=391.0;AC=2;AN=4;AF=0.5;RO=196;AO=195;PRO=0.0;PAO=0.0;QR=7259;QA=7429;PQR=0.0;PQA=0.0;SRF=67;SRR=129;SAF=73;SAR=122;SRP=45.5977;SAP=29.7472;AB=0.498721;ABP=3.01585;RUN=1;RPP=36.696;RPPR=28.5362;RPL=125.0;RPR=70.0;EPP=5.51585;EPPR=26.4533;DPRA=0.0;ODDS=298.498;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994898;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6535;Dels=0.0;FS=2.0735;HaplotypeScore [...]
+chr7 116534747 . T C 6967.1 REJECT NS=2;DP=412;DPB=464.0;AC=2;AN=4;AF=0.5;RO=219;AO=245;PRO=0.0;PAO=0.0;QR=8523;QA=9314;PQR=0.0;PQA=0.0;SRF=108;SRR=111;SAF=100;SAR=145;SRP=3.09954;SAP=20.9582;AB=0.528017;ABP=6.17391;RUN=1;RPP=3.44459;RPPR=3.49615;RPL=126.0;RPR=119.0;EPP=17.9093;EPPR=7.38299;DPRA=0.0;ODDS=318.402;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.8285;Dels=0.0;FS=5.738;HaplotypeScore=2 [...]
+chr7 124481245 . G A 5268.39 REJECT NS=2;DP=210;DPB=245.0;AC=2;AN=4;AF=0.5;RO=68;AO=176;PRO=0.0;PAO=0.0;QR=2576;QA=6782;PQR=0.0;PQA=0.0;SRF=14;SRR=54;SAF=53;SAR=123;SRP=54.1038;SAP=63.4661;AB=0.718367;ABP=104.485;RUN=1;RPP=44.515;RPPR=18.4661;RPL=117.0;RPR=59.0;EPP=12.6832;EPPR=6.20364;DPRA=0.0;ODDS=93.9864;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9886;MQMR=60.0;PAIRED=0.982955;PAIREDR=0.970588;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.2365;Dels=0.0;FS=5.0835;Haplotyp [...]
+chr7 124486980 . T C 11136.55 REJECT NS=2;DP=293;DPB=338.0;AC=4;AN=4;AF=1.0;RO=0;AO=338;PRO=0.0;PAO=0.0;QR=0;QA=13033;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=226;SAR=112;SRP=0.0;SAP=86.5028;AB=0.0;ABP=0.0;RUN=1;RPP=44.1269;RPPR=0.0;RPL=129.0;RPR=209.0;EPP=32.7171;EPPR=0.0;DPRA=0.0;ODDS=59.1927;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.985207;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.9;SOR=1.676 [...]
+chr7 124488721 . G A 19.1396 REJECT NS=1;DP=43;DPB=86.8667;AC=1;AN=4;AF=0.5;RO=7;AO=7;PRO=58.5;PAO=27.5;QR=233;QA=230;PQR=2113.0;PQA=981.0;SRF=7;SRR=0;SAF=1;SAR=6;SRP=18.2106;SAP=10.7656;AB=0.162791;ABP=45.4803;RUN=1;RPP=18.2106;RPPR=5.80219;RPL=0.0;RPR=7.0;EPP=10.7656;EPPR=5.80219;DPRA=0.0;ODDS=4.39479;GTI=0;TYPE=snp;CIGAR=1X29M;NUMALT=1;MEANALT=27.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.857143;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:Ca [...]
+chr7 124488721 . G GAAAAA 258.73 PASS DP=53;AC=1;AN=4;AF=0.5;BaseQRankSum=0.158;FS=21.553;MLEAC=1;MLEAF=0.5;MQ=59.23;MQRankSum=-0.683;QD=4.88;ReadPosRankSum=0.817;SOR=1.697;ClippingRankSum=-0.368 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:15,12:27:99.0:296,0,313:12:44:27:1:.:.:.:.:.:-0.00407189 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0173504
+chr7 124491972 . C A 2162.26 PASS SOMATIC;NS=2;DP=409;DPB=409.0;AC=1;AN=3;AF=0.25;RO=321;AO=88;PRO=0.0;PAO=0.0;QR=12236;QA=3417;PQR=0.0;PQA=0.0;SRF=145;SRR=176;SAF=38;SAR=50;SRP=9.51119;SAP=6.56362;AB=0.28115;ABP=133.222;RUN=1;RPP=7.84676;RPPR=19.2524;RPL=51.0;RPR=37.0;EPP=7.84676;EPPR=22.0124;DPRA=3.26042;ODDS=60.901;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996885;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.861;Dels=0.0;FS=0.967; [...]
+chr7 124499002 . AT CA 2312.575 REJECT NS=2;DP=329;DPB=380.5;AC=2;AN=4;AF=0.5;RO=280;AO=96;PRO=6.0;PAO=3.0;QR=10717;QA=3693;PQR=114.0;PQA=110.0;SRF=184;SRR=96;SAF=61;SAR=35;SRP=63.067;SAP=18.3011;AB=0.255319;ABP=198.535;RUN=1;RPP=4.45795;RPPR=29.099;RPL=44.0;RPR=52.0;EPP=10.339;EPPR=9.99003;DPRA=0.0;ODDS=233.925;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=1;MEANALT=1.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996429;technology.ILLUMINA=1.0;MQ0=0;JOINED;BaseQRankSum=-0.875;Dels=0.0;FS=1.4795;Hapl [...]
+chr7 128845018 . C T 4866.245000000001 REJECT NS=2;DP=227;DPB=262.0;AC=3;AN=4;AF=0.75;RO=79;AO=183;PRO=0.0;PAO=0.0;QR=3030;QA=6936;PQR=0.0;PQA=0.0;SRF=59;SRR=20;SAF=119;SAR=64;SRP=44.818;SAP=38.9049;AB=0.590674;ABP=16.793;RUN=1;RPP=165.444;RPPR=49.2159;RPL=33.0;RPR=150.0;EPP=8.24319;EPPR=5.23675;DPRA=0.0;ODDS=44.0273;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0546;MQMR=60.0;PAIRED=0.994536;PAIREDR=0.987342;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.392;Dels=0.0;FS=4.661; [...]
+chr7 128846328 . G C 8191.935 REJECT NS=2;DP=347;DPB=395.0;AC=3;AN=4;AF=0.75;RO=107;AO=288;PRO=0.0;PAO=0.0;QR=4065;QA=11013;PQR=0.0;PQA=0.0;SRF=54;SRR=53;SAF=131;SAR=157;SRP=3.03059;SAP=8.10723;AB=0.643333;ABP=56.5443;RUN=1;RPP=7.35324;RPPR=6.44001;RPL=156.0;RPR=132.0;EPP=9.79615;EPPR=4.65412;DPRA=0.0;ODDS=60.2529;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993056;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.452;Dels=0.0;FS=1.9945;HaplotypeS [...]
+chr7 132008454 . G C 2461.76 REJECT NS=2;DP=402;DPB=460.0;AC=2;AN=4;AF=0.5;RO=339;AO=121;PRO=0.0;PAO=0.0;QR=13036;QA=4614;PQR=0.0;PQA=0.0;SRF=139;SRR=200;SAF=58;SAR=63;SRP=26.8453;SAP=3.45895;AB=0.263043;ABP=227.352;RUN=1;RPP=6.04318;RPPR=3.17044;RPL=67.0;RPR=54.0;EPP=7.04816;EPPR=25.3079;DPRA=0.0;ODDS=259.167;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99705;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.619;Dels=0.0;FS=3.5395;HaplotypeScore [...]
+chr7 132008511 . T A 963.515 REJECT NS=2;DP=239;DPB=263.0;AC=2;AN=4;AF=0.5;RO=209;AO=54;PRO=0.0;PAO=0.0;QR=8019;QA=2055;PQR=0.0;PQA=0.0;SRF=54;SRR=155;SAF=17;SAR=37;SRP=108.997;SAP=19.0953;AB=0.205323;ABP=201.374;RUN=1;RPP=49.4959;RPPR=113.236;RPL=44.0;RPR=10.0;EPP=3.0103;EPPR=6.76103;DPRA=0.0;ODDS=79.9078;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0515;Dels=0.0;FS=1.526;HaplotypeScore=2.9995;M [...]
+chr7 139502073 . C T 5638.865 REJECT NS=2;DP=413;DPB=476.0;AC=2;AN=4;AF=0.5;RO=272;AO=204;PRO=0.0;PAO=0.0;QR=10516;QA=7822;PQR=0.0;PQA=0.0;SRF=146;SRR=126;SAF=116;SAR=88;SRP=6.20364;SAP=11.3556;AB=0.428571;ABP=24.1046;RUN=1;RPP=4.5431;RPPR=5.05404;RPL=108.0;RPR=96.0;EPP=9.14152;EPPR=15.7837;DPRA=0.0;ODDS=296.322;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996324;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7745;Dels=0.0;FS=4.674;HaplotypeSco [...]
+chr7 140482263 . C A 419.348 REJECT NS=2;DP=232;DPB=370.647;AC=2;AN=2;AF=0.0;RO=105;AO=10;PRO=105.583;PAO=42.9167;QR=3795;QA=173;PQR=3663.08;PQA=1516.75;SRF=31;SRR=74;SAF=2;SAR=8;SRP=41.2489;SAP=10.8276;AB=0.0431034;ABP=423.677;RUN=1;RPP=6.48466;RPPR=18.0865;RPL=3.0;RPR=7.0;EPP=3.0103;EPPR=8.98702;DPRA=0.0;ODDS=14.4183;GTI=0;TYPE=snp;CIGAR=1X33M;NUMALT=3;MEANALT=27.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr7 140482263 . C CA 419.348 REJECT NS=2;DP=232;DPB=370.647;AC=2;AN=3;AF=0.25;RO=105;AO=21;PRO=105.583;PAO=78.5833;QR=3795;QA=635;PQR=3663.08;PQA=2626.08;SRF=31;SRR=74;SAF=11;SAR=10;SRP=41.2489;SAP=3.1137;AB=0.0905172;ABP=340.899;RUN=1;RPP=8.07707;RPPR=18.0865;RPL=7.0;RPR=14.0;EPP=3.94093;EPPR=8.98702;DPRA=0.0;ODDS=14.4183;GTI=0;TYPE=ins;CIGAR=1M1I33M;NUMALT=3;MEANALT=27.5;LEN=1;MQM=59.0952;MQMR=60.0;PAIRED=0.952381;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO [...]
+chr7 140482263 . CA C 419.348 REJECT NS=2;DP=232;DPB=370.647;AC=2;AN=3;AF=0.25;RO=105;AO=28;PRO=105.583;PAO=72.9167;QR=3795;QA=844;PQR=3663.08;PQA=2411.08;SRF=31;SRR=74;SAF=9;SAR=19;SRP=41.2489;SAP=10.7656;AB=0.12069;ABP=292.939;RUN=1;RPP=10.7656;RPPR=18.0865;RPL=9.0;RPR=19.0;EPP=4.25114;EPPR=8.98702;DPRA=0.0;ODDS=14.4183;GTI=0;TYPE=del;CIGAR=1M1D32M;NUMALT=3;MEANALT=27.5;LEN=1;MQM=60.3571;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr7 140484450 . C CT 43.968 REJECT NS=2;DP=151;DPB=196.824;AC=2;AN=3;AF=0.25;RO=104;AO=19;PRO=34.8333;PAO=26.8333;QR=3770;QA=513;PQR=1186.5;PQA=887.5;SRF=22;SRR=82;SAF=4;SAR=15;SRP=78.1767;SAP=16.8392;AB=0.125828;ABP=186.636;RUN=1;RPP=12.2676;RPPR=6.01695;RPL=14.0;RPR=5.0;EPP=5.8675;EPPR=3.0103;DPRA=0.0;ODDS=2.42882;GTI=1;TYPE=ins;CIGAR=1M1I16M;NUMALT=2;MEANALT=6.5;LEN=1;MQM=60.0;MQMR=59.8077;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr7 140484450 . CT C 43.968 REJECT NS=2;DP=151;DPB=196.824;AC=2;AN=3;AF=0.25;RO=104;AO=13;PRO=34.8333;PAO=25.3333;QR=3770;QA=440;PQR=1186.5;PQA=857.0;SRF=22;SRR=82;SAF=3;SAR=10;SRP=78.1767;SAP=11.1951;AB=0.0860927;ABP=227.707;RUN=1;RPP=4.51363;RPPR=6.01695;RPL=8.0;RPR=5.0;EPP=7.18621;EPPR=3.0103;DPRA=0.0;ODDS=2.42882;GTI=1;TYPE=del;CIGAR=1M1D15M;NUMALT=2;MEANALT=6.5;LEN=1;MQM=59.8462;MQMR=59.8077;PAIRED=0.923077;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr7 140488689 . A G 1380.45 REJECT NS=2;DP=56;DPB=62.0;AC=2;AN=4;AF=0.5;RO=13;AO=49;PRO=0.0;PAO=0.0;QR=480;QA=1831;PQR=0.0;PQA=0.0;SRF=5;SRR=8;SAF=17;SAR=32;SRP=4.51363;SAP=12.9813;AB=0.790323;ABP=48.4011;RUN=1;RPP=10.4997;RPPR=4.51363;RPL=31.0;RPR=18.0;EPP=35.3165;EPPR=11.1951;DPRA=0.0;ODDS=11.5462;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.979592;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7165;Dels=0.0;FS=1.316;HaplotypeScore=0.0;MLEAC [...]
+chr7 140493351 . T C 7530.59 REJECT NS=2;DP=300;DPB=344.0;AC=2;AN=4;AF=0.5;RO=91;AO=253;PRO=0.0;PAO=0.0;QR=3457;QA=9522;PQR=0.0;PQA=0.0;SRF=39;SRR=52;SAF=92;SAR=161;SRP=7.04303;SAP=43.8735;AB=0.735465;ABP=168.673;RUN=1;RPP=3.43086;RPPR=5.89764;RPL=123.0;RPR=130.0;EPP=3.08755;EPPR=5.89764;DPRA=0.0;ODDS=145.102;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9231;PAIRED=0.992095;PAIREDR=0.956044;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0105;Dels=0.0;FS=4.3665;Haplot [...]
+chr7 140495573 . T C 15054.75 REJECT NS=2;DP=412;DPB=474.0;AC=4;AN=4;AF=1.0;RO=0;AO=474;PRO=0.0;PAO=0.0;QR=0;QA=17537;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=256;SAR=218;SRP=0.0;SAP=9.6255;AB=0.0;ABP=0.0;RUN=1;RPP=10.3402;RPPR=0.0;RPL=217.0;RPR=257.0;EPP=10.3402;EPPR=0.0;DPRA=0.0;ODDS=80.2569;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9494;MQMR=0.0;PAIRED=0.989451;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=10.7316;MLEAC=2;MLEAF=1.0;MQ=59.995;QD=27.93; [...]
+chr7 140496148 . T TA 667.667 REJECT NS=2;DP=176;DPB=227.286;AC=2;AN=2;AF=0.0;RO=73;AO=17;PRO=35.25;PAO=28.25;QR=2652;QA=524;PQR=1231.5;PQA=991.5;SRF=44;SRR=29;SAF=12;SAR=5;SRP=9.70319;SAP=9.26925;AB=0.0965909;ABP=251.792;RUN=1;RPP=9.26925;RPPR=39.4494;RPL=5.0;RPR=12.0;EPP=3.13803;EPPR=3.27802;DPRA=0.0;ODDS=33.0958;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=3;MEANALT=18.0;LEN=1;MQM=58.8235;MQMR=59.7534;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr7 140496148 . TA T 471.1985 REJECT NS=2;DP=161;DPB=227.286;AC=2;AN=4;AF=0.5;RO=73;AO=37;PRO=35.25;PAO=23.25;QR=2652;QA=1255;PQR=1231.5;PQA=805.5;SRF=44;SRR=29;SAF=28;SAR=9;SRP=9.70319;SAP=24.1968;AB=0.210227;ABP=131.374;RUN=1;RPP=19.9713;RPPR=39.4494;RPL=10.0;RPR=27.0;EPP=5.88603;EPPR=3.27802;DPRA=0.0;ODDS=33.0958;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=3;MEANALT=18.0;LEN=1;MQM=61.6216;MQMR=59.7534;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.476;F [...]
+chr7 140496148 . TAA T 667.667 REJECT NS=2;DP=176;DPB=227.286;AC=2;AN=2;AF=0.0;RO=73;AO=13;PRO=35.25;PAO=24.25;QR=2652;QA=377;PQR=1231.5;PQA=840.5;SRF=44;SRR=29;SAF=8;SAR=5;SRP=9.70319;SAP=4.51363;AB=0.0738636;ABP=280.613;RUN=1;RPP=4.51363;RPPR=39.4494;RPL=5.0;RPR=8.0;EPP=11.1951;EPPR=3.27802;DPRA=0.0;ODDS=33.0958;GTI=0;TYPE=del;CIGAR=1M2D18M;NUMALT=3;MEANALT=18.0;LEN=2;MQM=60.0;MQMR=59.7534;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr7 140497260 . CAA C 9401.04 REJECT NS=2;DP=358;DPB=354.0;AC=2;AN=4;AF=0.5;RO=88;AO=308;PRO=29.0;PAO=27.0;QR=3347;QA=11444;PQR=996.5;PQA=942.5;SRF=49;SRR=39;SAF=170;SAR=138;SRP=5.47788;SAP=10.2297;AB=0.77193;ABP=259.282;RUN=1;RPP=13.1908;RPPR=12.8806;RPL=173.0;RPR=135.0;EPP=3.71532;EPPR=7.84676;DPRA=0.0;ODDS=111.071;GTI=0;TYPE=del;CIGAR=1M2D6M;NUMALT=1;MEANALT=2.5;LEN=2;MQM=60.1623;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=140497262;HOMLEN=2;HOMSEQ=AA;SVLEN=-2; [...]
+chr7 140498072 . C CTTTTTTTTTTT 549.73 PASS DP=17;AC=2;AN=4;AF=1.0;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.29;QD=32.34;SOR=1.609 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:0,12:12:42.0:549,42,0:12:100:12:1:.:.:.:.:.:-0.00407189 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.014491
+chr7 140498359 . CT C 199.4215 REJECT NS=2;DP=54;DPB=91.25;AC=2;AN=4;AF=0.5;RO=20;AO=15;PRO=41.3333;PAO=29.3333;QR=686;QA=528;PQR=1411.17;PQA=981.167;SRF=18;SRR=2;SAF=14;SAR=1;SRP=30.8051;SAP=27.4756;AB=0.277778;ABP=26.1727;RUN=1;RPP=3.15506;RPPR=3.44459;RPL=8.0;RPR=7.0;EPP=4.31318;EPPR=3.44459;DPRA=0.0;ODDS=26.7217;GTI=0;TYPE=del;CIGAR=1M1D26M;NUMALT=2;MEANALT=9.0;LEN=1;MQM=59.2667;MQMR=59.85;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.1285;FS= [...]
+chr7 140498359 . CTT C 274.113 REJECT NS=2;DP=54;DPB=91.25;AC=2;AN=2;AF=0.0;RO=20;AO=4;PRO=41.3333;PAO=26.3333;QR=686;QA=149;PQR=1411.17;PQA=871.667;SRF=18;SRR=2;SAF=4;SAR=0;SRP=30.8051;SAP=11.6962;AB=0.111111;ABP=50.3001;RUN=1;RPP=5.18177;RPPR=3.44459;RPL=1.0;RPR=3.0;EPP=5.18177;EPPR=3.44459;DPRA=0.0;ODDS=26.7217;GTI=0;TYPE=del;CIGAR=1M2D25M;NUMALT=2;MEANALT=10.0;LEN=2;MQM=60.0;MQMR=59.85;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr7 140498812 . A AT 402.503 REJECT NS=2;DP=110;DPB=146.75;AC=2;AN=2;AF=0.0;RO=67;AO=10;PRO=30.5833;PAO=18.5833;QR=2413;QA=349;PQR=1055.5;PQA=636.5;SRF=38;SRR=29;SAF=8;SAR=2;SRP=5.63551;SAP=10.8276;AB=0.0909091;ABP=162.91;RUN=1;RPP=6.48466;RPPR=3.04271;RPL=7.0;RPR=3.0;EPP=3.0103;EPPR=42.7126;DPRA=0.0;ODDS=13.0621;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=3;MEANALT=6.5;LEN=1;MQM=60.0;MQMR=58.8209;PAIRED=1.0;PAIREDR=0.985075;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr7 140498812 . A ATT 402.503 REJECT NS=2;DP=110;DPB=146.75;AC=2;AN=2;AF=0.0;RO=67;AO=4;PRO=30.5833;PAO=19.5833;QR=2413;QA=147;PQR=1055.5;PQA=672.5;SRF=38;SRR=29;SAF=2;SAR=2;SRP=5.63551;SAP=3.0103;AB=0.0363636;ABP=208.392;RUN=1;RPP=11.6962;RPPR=3.04271;RPL=4.0;RPR=0.0;EPP=3.0103;EPPR=42.7126;DPRA=0.0;ODDS=13.0621;GTI=0;TYPE=ins;CIGAR=1M2I23M;NUMALT=3;MEANALT=6.5;LEN=2;MQM=60.0;MQMR=58.8209;PAIRED=1.0;PAIREDR=0.985075;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr7 140498812 . AT A 402.503 REJECT NS=2;DP=110;DPB=146.75;AC=2;AN=4;AF=0.5;RO=67;AO=21;PRO=30.5833;PAO=20.25;QR=2413;QA=752;PQR=1055.5;PQA=702.5;SRF=38;SRR=29;SAF=13;SAR=8;SRP=5.63551;SAP=5.59539;AB=0.190909;ABP=94.2911;RUN=1;RPP=3.1137;RPPR=3.04271;RPL=11.0;RPR=10.0;EPP=15.5221;EPPR=42.7126;DPRA=0.0;ODDS=13.0621;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=3;MEANALT=6.5;LEN=1;MQM=60.4762;MQMR=58.8209;PAIRED=1.0;PAIREDR=0.985075;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.192 [...]
+chr7 140499107 . C T 2045.98 REJECT NS=2;DP=461;DPB=520.0;AC=2;AN=4;AF=0.5;RO=410;AO=110;PRO=0.0;PAO=0.0;QR=15540;QA=4207;PQR=0.0;PQA=0.0;SRF=196;SRR=214;SAF=65;SAR=45;SRP=4.72629;SAP=10.9066;AB=0.211538;ABP=378.842;RUN=1;RPP=3.08926;RPPR=9.13279;RPL=54.0;RPR=56.0;EPP=4.2737;EPPR=16.251;DPRA=0.0;ODDS=196.895;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990244;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8365;Dels=0.0;FS=4.18;HaplotypeScore=6. [...]
+chr7 148504716 . AG A 2643.61 REJECT NS=2;DP=439;DPB=479.8;AC=2;AN=4;AF=0.5;RO=306;AO=122;PRO=55.5;PAO=32.5;QR=11137;QA=4248;PQR=1958.5;PQA=1099.5;SRF=156;SRR=150;SAF=53;SAR=69;SRP=3.26577;SAP=7.56683;AB=0.277904;ABP=191.097;RUN=1;RPP=11.625;RPPR=8.57381;RPL=72.0;RPR=50.0;EPP=4.14943;EPPR=4.82696;DPRA=0.0;ODDS=267.869;GTI=0;TYPE=del;CIGAR=1M1D13M;NUMALT=1;MEANALT=6.5;LEN=1;MQM=60.1639;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993464;technology.ILLUMINA=1.0;BaseQRankSum=0.314;FS=0.0;MLEAC=1;MLEAF=0. [...]
+chr7 148506396 . A C 1494.45 REJECT NS=2;DP=411;DPB=472.0;AC=2;AN=4;AF=0.5;RO=386;AO=86;PRO=0.0;PAO=0.0;QR=14939;QA=3248;PQR=0.0;PQA=0.0;SRF=167;SRR=219;SAF=45;SAR=41;SRP=18.2219;SAP=3.41429;AB=0.182203;ABP=417.062;RUN=1;RPP=13.1102;RPPR=3.0103;RPL=53.0;RPR=33.0;EPP=3.91929;EPPR=11.1336;DPRA=0.0;ODDS=105.704;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988372;PAIREDR=0.992228;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.7205;Dels=0.0;FS=4.82;HaplotypeSc [...]
+chr7 148508833 . A G 1226.17 REJECT NS=2;DP=229;DPB=266.0;AC=2;AN=4;AF=0.5;RO=204;AO=62;PRO=0.0;PAO=0.0;QR=7608;QA=2260;PQR=0.0;PQA=0.0;SRF=54;SRR=150;SAF=20;SAR=42;SRP=101.11;SAP=19.9618;AB=0.233083;ABP=167.618;RUN=1;RPP=9.87495;RPPR=67.7713;RPL=38.0;RPR=24.0;EPP=14.358;EPPR=3.3935;DPRA=0.0;ODDS=49.5267;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995098;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.842;Dels=0.0;FS=15.851;HaplotypeScore=4.88 [...]
+chr7 148543693 . T TA 1679.5 REJECT NS=2;DP=241;DPB=261.1;AC=2;AN=2;AF=0.0;RO=148;AO=10;PRO=25.5;PAO=11.5;QR=5499;QA=363;PQR=929.833;PQA=423.833;SRF=42;SRR=106;SAF=2;SAR=8;SRP=63.1073;SAP=10.8276;AB=0.0414938;ABP=443.08;RUN=1;RPP=10.8276;RPPR=16.2152;RPL=8.0;RPR=2.0;EPP=3.87889;EPPR=28.8919;DPRA=0.0;ODDS=170.442;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=2;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993243;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr7 148543693 . TA T 1679.5 REJECT NS=2;DP=241;DPB=261.1;AC=2;AN=4;AF=0.5;RO=148;AO=71;PRO=25.5;PAO=12.0;QR=5499;QA=2626;PQR=929.833;PQA=430.333;SRF=42;SRR=106;SAF=20;SAR=51;SRP=63.1073;SAP=32.4016;AB=0.294606;ABP=91.3198;RUN=1;RPP=16.4979;RPPR=16.2152;RPL=46.0;RPR=25.0;EPP=4.50892;EPPR=28.8919;DPRA=0.0;ODDS=170.442;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=2;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993243;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=1.176;FS=0.0;ML [...]
+chr7 150025915 . G T 2927.62 PASS SOMATIC;NS=2;DP=413;DPB=413.0;AC=1;AN=3;AF=0.25;RO=299;AO=113;PRO=0.0;PAO=0.0;QR=11443;QA=4271;PQR=0.0;PQA=0.0;SRF=156;SRR=143;SAF=54;SAR=59;SRP=4.23765;SAP=3.49071;AB=0.359873;ABP=56.5641;RUN=1;RPP=5.3355;RPPR=14.0565;RPL=62.0;RPR=51.0;EPP=15.0207;EPPR=15.2185;DPRA=3.17172;ODDS=62.1451;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.461;Dels=0.0;FS=6.325;Hap [...]
+chr7 150025966 . T C 1843.31 PASS SOMATIC;NS=2;DP=332;DPB=332.0;AC=1;AN=3;AF=0.25;RO=254;AO=78;PRO=0.0;PAO=0.0;QR=9713;QA=2903;PQR=0.0;PQA=0.0;SRF=104;SRR=150;SAF=25;SAR=53;SRP=21.1002;SAP=24.8364;AB=0.309524;ABP=82.4241;RUN=1;RPP=16.4846;RPPR=3.86521;RPL=50.0;RPR=28.0;EPP=3.0103;EPPR=7.14807;DPRA=3.15;ODDS=50.9218;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996063;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.88;Dels=0.0;FS=10.428;Ha [...]
+chr7 151168415 . CAAT C . PASS SOMATIC;AC=1;AN=4 GT:AD:DP:MM:MQS:NQSBQ:NQSMM:REnd:RStart:SC:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:45,0:45:0.0222222,0.0:60.0,0.0:38.3134,0.0:0.0,0.0:0,0:0,0:32,13,0,0:0:0:45:.:.:.:.:0:.:-0.00407189 0/1:86,53:139:0.0930233,0.0188679:60.0,60.0:37.7184,39.2585:0.00121359,0.0:73,11:27,11:64,22,36,17:53:38:139:.:.:.:.:1:.:-0.014491
+chr7 151168534 . G A 3220.88 PASS SOMATIC;NS=2;DP=428;DPB=428.0;AC=1;AN=3;AF=0.25;RO=308;AO=120;PRO=0.0;PAO=0.0;QR=11699;QA=4589;PQR=0.0;PQA=0.0;SRF=155;SRR=153;SAF=65;SAR=55;SRP=3.0385;SAP=4.81986;AB=0.382166;ABP=40.8797;RUN=1;RPP=3.66174;RPPR=3.71532;RPL=63.0;RPR=57.0;EPP=4.16842;EPPR=3.1231;DPRA=2.75439;ODDS=72.1231;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99026;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.859;Dels=0.0;FS=0.426; [...]
+chr7 151873853 . C T 5646.805 REJECT NS=2;DP=379;DPB=432.0;AC=2;AN=4;AF=0.5;RO=229;AO=203;PRO=0.0;PAO=0.0;QR=8727;QA=7743;PQR=0.0;PQA=0.0;SRF=119;SRR=110;SAF=102;SAR=101;SRP=3.77838;SAP=3.021;AB=0.469907;ABP=6.40825;RUN=1;RPP=3.53445;RPPR=6.43345;RPL=105.0;RPR=98.0;EPP=9.69587;EPPR=4.61283;DPRA=0.0;ODDS=308.747;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995074;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.7515;Dels=0.0;FS=0.656;HaplotypeSco [...]
+chr7 151875100 . TA T 83.272 REJECT NS=2;DP=29;DPB=40.8293;AC=2;AN=3;AF=0.25;RO=12;AO=6;PRO=20.1667;PAO=18.1667;QR=457;QA=135;PQR=712.333;PQA=621.333;SRF=0;SRR=12;SAF=0;SAR=6;SRP=29.068;SAP=16.0391;AB=0.206897;ABP=24.6501;RUN=1;RPP=8.80089;RPPR=3.73412;RPL=5.0;RPR=1.0;EPP=8.80089;EPPR=3.73412;DPRA=0.0;ODDS=1.67818;GTI=0;TYPE=del;CIGAR=1M1D39M;NUMALT=2;MEANALT=4.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.52;FS=7.368;MLE [...]
+chr7 151875100 . TAA T 83.272 REJECT NS=2;DP=29;DPB=40.8293;AC=2;AN=3;AF=0.25;RO=12;AO=7;PRO=20.1667;PAO=14.6667;QR=457;QA=148;PQR=712.333;PQA=509.333;SRF=0;SRR=12;SAF=0;SAR=7;SRP=29.068;SAP=18.2106;AB=0.241379;ABP=19.8579;RUN=1;RPP=10.7656;RPPR=3.73412;RPL=6.0;RPR=1.0;EPP=10.7656;EPPR=3.73412;DPRA=0.0;ODDS=1.67818;GTI=0;TYPE=del;CIGAR=1M2D38M;NUMALT=2;MEANALT=4.0;LEN=2;MQM=59.7143;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr7 151882622 . TAG T 43.73 PASS DP=64;AC=2;AN=4;AF=0.5;END=151882624;HOMLEN=2;HOMSEQ=AG;SVLEN=-2;SVTYPE=DEL;BaseQRankSum=-3.711;FS=4.502;MLEAC=1;MLEAF=0.5;MQ=59.2;MQRankSum=-4.016;QD=0.68;ReadPosRankSum=1.614;SOR=0.152;ClippingRankSum=-0.831 GT:AD:GMIMUT:GMIMAF:GMICOV:DP:GQ:PL:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:57,6:6:10:63:63:81.0:81,0,2375:1:.:.:.:.:.:-0.00407189 0/1:111,23:23:17:134:.:.:.:.:.:.:1:.:.:-0.014491
+chr7 151891358 . T TA 490.287 REJECT NS=2;DP=246;DPB=310.19;AC=2;AN=2;AF=0.0;RO=165;AO=15;PRO=62.5;PAO=45.5;QR=6127;QA=492;PQR=2191.17;PQA=1549.17;SRF=42;SRR=123;SAF=3;SAR=12;SRP=89.3559;SAP=14.7363;AB=0.0609756;ABP=414.849;RUN=1;RPP=3.15506;RPPR=3.12874;RPL=8.0;RPR=7.0;EPP=6.62942;EPPR=4.60271;DPRA=0.0;ODDS=32.7461;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=2;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=59.8788;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr7 151891358 . TA T 490.287 REJECT NS=2;DP=246;DPB=310.19;AC=2;AN=4;AF=0.5;RO=165;AO=35;PRO=62.5;PAO=41.0;QR=6127;QA=1247;PQR=2191.17;PQA=1420.67;SRF=42;SRR=123;SAF=17;SAR=18;SRP=89.3559;SAP=3.07234;AB=0.142276;ABP=276.439;RUN=1;RPP=3.07234;RPPR=3.12874;RPL=17.0;RPR=18.0;EPP=4.56135;EPPR=4.60271;DPRA=0.0;ODDS=32.7461;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=2;MEANALT=12.5;LEN=1;MQM=60.5714;MQMR=59.8788;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-1.226;FS=1 [...]
+chr7 151927021 . C A 1606.565 REJECT NS=2;DP=277;DPB=308.0;AC=2;AN=4;AF=0.5;RO=192;AO=116;PRO=0.0;PAO=0.0;QR=7414;QA=4495;PQR=0.0;PQA=0.0;SRF=140;SRR=52;SAF=87;SAR=29;SRP=90.593;SAP=65.983;AB=0.376623;ABP=43.7325;RUN=1;RPP=24.6501;RPPR=13.1891;RPL=41.0;RPR=75.0;EPP=5.70592;EPPR=52.2756;DPRA=0.0;ODDS=122.735;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=26.4828;MQMR=33.7604;PAIRED=1.0;PAIREDR=0.994792;technology.ILLUMINA=1.0;MQ0=16;BaseQRankSum=0.296;Dels=0.0;FS=5.106;HaplotypeSc [...]
+chr7 151927025 . A G 618.685 REJECT NS=2;DP=287;DPB=317.0;AC=2;AN=4;AF=0.5;RO=249;AO=68;PRO=0.0;PAO=0.0;QR=9617;QA=2554;PQR=0.0;PQA=0.0;SRF=172;SRR=77;SAF=52;SAR=16;SRP=81.7153;SAP=44.396;AB=0.214511;ABP=227.425;RUN=1;RPP=3.0103;RPPR=37.623;RPL=34.0;RPR=34.0;EPP=35.7101;EPPR=33.3673;DPRA=0.0;ODDS=19.4444;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=28.9706;MQMR=32.1888;PAIRED=0.985294;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=17;BaseQRankSum=-1.7625;Dels=0.0;FS=5.556;HaplotypeSco [...]
+chr7 151927026 . T C 1598.28 REJECT NS=2;DP=285;DPB=316.0;AC=2;AN=4;AF=0.5;RO=201;AO=115;PRO=0.0;PAO=0.0;QR=7793;QA=4421;PQR=0.0;PQA=0.0;SRF=138;SRR=63;SAF=83;SAR=32;SRP=63.7791;SAP=52.1233;AB=0.363924;ABP=53.8337;RUN=1;RPP=21.1563;RPPR=16.2444;RPL=42.0;RPR=73.0;EPP=8.4673;EPPR=57.47;DPRA=0.0;ODDS=122.922;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=26.5391;MQMR=34.408;PAIRED=1.0;PAIREDR=0.995025;technology.ILLUMINA=1.0;MQ0=17;BaseQRankSum=1.817;Dels=0.0;FS=4.992;HaplotypeScore [...]
+chr7 151927127 . A G 1966.17 REJECT NS=2;DP=257;DPB=292.0;AC=2;AN=4;AF=0.5;RO=155;AO=137;PRO=0.0;PAO=0.0;QR=5861;QA=5142;PQR=0.0;PQA=0.0;SRF=33;SRR=122;SAF=21;SAR=116;SRP=113.98;SAP=146.058;AB=0.469178;ABP=5.41974;RUN=1;RPP=47.5334;RPPR=20.1719;RPL=95.0;RPR=42.0;EPP=4.92817;EPPR=3.02431;DPRA=0.0;ODDS=112.216;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=26.3504;MQMR=31.2968;PAIRED=0.992701;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=12;BaseQRankSum=1.185;Dels=0.0;FS=4.891;HaplotypeS [...]
+chr7 151932897 . C A 79.77 PASS SOMATIC;DP=291;AC=1;AN=4;AF=0.5;MQ0=30;BaseQRankSum=1.395;Dels=0.0;FS=4.956;HaplotypeScore=4.5962;MLEAC=1;MLEAF=0.5;MQ=41.1;MQRankSum=-5.345;QD=0.27;ReadPosRankSum=1.755;SOR=0.368 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00407189 0/1:261,30:291:99.0:108,0,7696:30:10:291:.:1:.:.:.:.:-0.014491
+chr7 151932908 . T C 138.9445 REJECT NS=2;DP=318;DPB=343.0;AC=2;AN=4;AF=0.5;RO=276;AO=67;PRO=0.0;PAO=0.0;QR=10573;QA=2595;PQR=0.0;PQA=0.0;SRF=180;SRR=96;SAF=8;SAR=59;SRP=58.5245;SAP=87.3088;AB=0.195335;ABP=279.547;RUN=1;RPP=3.30199;RPPR=3.13618;RPL=35.0;RPR=32.0;EPP=3.82055;EPPR=3.51383;DPRA=0.0;ODDS=15.7011;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=20.1642;MQMR=43.7174;PAIRED=0.985075;PAIREDR=0.978261;technology.ILLUMINA=1.0;MQ0=31;BaseQRankSum=1.311;Dels=0.0;FS=40.0155;Hap [...]
+chr7 151932945 . C T 425.78 REJECT NS=2;DP=365;DPB=398.0;AC=2;AN=4;AF=0.5;RO=313;AO=85;PRO=0.0;PAO=0.0;QR=12084;QA=3205;PQR=0.0;PQA=0.0;SRF=150;SRR=163;SAF=27;SAR=58;SRP=4.18276;SAP=27.5607;AB=0.213568;ABP=286.633;RUN=1;RPP=154.477;RPPR=10.5654;RPL=4.0;RPR=81.0;EPP=21.6339;EPPR=11.5089;DPRA=0.0;ODDS=28.284;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=25.4118;MQMR=40.8403;PAIRED=1.0;PAIREDR=0.980831;technology.ILLUMINA=1.0;MQ0=33;BaseQRankSum=-0.4905;Dels=0.0;FS=11.487;Haplotype [...]
+chr7 151932965 . C T 834.589 REJECT NS=2;DP=373;DPB=412.0;AC=2;AN=4;AF=0.5;RO=307;AO=104;PRO=0.0;PAO=0.0;QR=11729;QA=4017;PQR=0.0;PQA=0.0;SRF=134;SRR=173;SAF=33;SAR=71;SRP=13.7686;SAP=33.1604;AB=0.252427;ABP=222.35;RUN=1;RPP=136.639;RPPR=3.01737;RPL=12.0;RPR=92.0;EPP=21.8019;EPPR=13.7686;DPRA=0.0;ODDS=45.7666;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=24.8846;MQMR=45.0879;PAIRED=1.0;PAIREDR=0.980456;technology.ILLUMINA=1.0;MQ0=30;BaseQRankSum=0.7005;Dels=0.0;FS=8.844;Haplotyp [...]
+chr7 151933033 . G A 122.369 REJECT NS=2;DP=255;DPB=281.0;AC=2;AN=4;AF=0.5;RO=226;AO=55;PRO=0.0;PAO=0.0;QR=8555;QA=2072;PQR=0.0;PQA=0.0;SRF=75;SRR=151;SAF=14;SAR=41;SRP=58.5078;SAP=31.7922;AB=0.19573;ABP=228.975;RUN=1;RPP=57.0602;RPPR=70.8064;RPL=46.0;RPR=9.0;EPP=20.4216;EPPR=3.97113;DPRA=0.0;ODDS=6.94342;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=22.2545;MQMR=59.3717;PAIRED=1.0;PAIREDR=0.99115;technology.ILLUMINA=1.0;MQ0=20;BaseQRankSum=-1.2405;Dels=0.0;FS=5.1095;HaplotypeSc [...]
+chr7 151944961 . T A 470.894 REJECT NS=2;DP=297;DPB=297.0;AC=2;AN=4;AF=0.5;RO=248;AO=49;PRO=0.0;PAO=0.0;QR=9472;QA=1894;PQR=0.0;PQA=0.0;SRF=210;SRR=38;SAF=43;SAR=6;SRP=262.046;SAP=63.6786;AB=0.164983;ABP=292.547;RUN=1;RPP=26.4533;RPPR=133.334;RPL=13.0;RPR=36.0;EPP=19.0083;EPPR=41.1512;DPRA=0.0;ODDS=52.282;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=35.0;MQMR=32.0766;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=108;BaseQRankSum=1.3215;Dels=0.0;FS=1.523;HaplotypeScore=0.0; [...]
+chr7 151944981 . C A 64.77 PASS SOMATIC;DP=443;AC=1;AN=4;AF=0.5;MQ0=110;BaseQRankSum=2.548;Dels=0.0;FS=31.148;HaplotypeScore=2.8995;MLEAC=1;MLEAF=0.5;MQ=37.18;MQRankSum=-7.882;QD=0.15;ReadPosRankSum=5.352;SOR=4.946 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00407189 0/1:347,96:443:93.0:93,0,10262:96:22:443:.:1:.:.:.:.:-0.014491
+chr7 151945007 . C T 6095.9 REJECT NS=2;DP=521;DPB=548.0;AC=2;AN=4;AF=0.5;RO=286;AO=262;PRO=0.0;PAO=0.0;QR=10792;QA=9944;PQR=0.0;PQA=0.0;SRF=210;SRR=76;SAF=178;SAR=84;SRP=139.342;SAP=76.2436;AB=0.478102;ABP=5.29272;RUN=1;RPP=76.2436;RPPR=4.10363;RPL=84.0;RPR=178.0;EPP=12.5913;EPPR=23.5406;DPRA=0.0;ODDS=340.333;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=45.5573;MQMR=44.5699;PAIRED=0.98855;PAIREDR=0.996503;technology.ILLUMINA=1.0;MQ0=94;BaseQRankSum=0.9465;Dels=0.0;FS=2.833;Hap [...]
+chr7 151945071 . G GT 714.149 REJECT NS=2;DP=732;DPB=778.667;AC=2;AN=4;AF=0.5;RO=642;AO=86;PRO=15.5;PAO=17.5;QR=24303;QA=3020;PQR=383.0;PQA=458.0;SRF=343;SRR=299;SAF=40;SAR=46;SRP=9.55854;SAP=3.91929;AB=0.117486;ABP=933.302;RUN=1;RPP=3.0103;RPPR=30.4074;RPL=43.0;RPR=43.0;EPP=3.41429;EPPR=3.0103;DPRA=0.0;ODDS=65.2523;GTI=0;TYPE=ins;CIGAR=1M1I2M;NUMALT=1;MEANALT=3.0;LEN=1;MQM=51.0;MQMR=47.1931;PAIRED=1.0;PAIREDR=0.993769;technology.ILLUMINA=1.0;END=151945071;HOMLEN=1;HOMSEQ=T;SVLEN=1;SVTYP [...]
+chr7 151945101 . G C 863.269 REJECT NS=2;DP=751;DPB=852.0;AC=2;AN=4;AF=0.5;RO=667;AO=184;PRO=0.0;PAO=0.0;QR=25191;QA=7050;PQR=0.0;PQA=0.0;SRF=310;SRR=357;SAF=83;SAR=101;SRP=10.2019;SAP=6.83398;AB=0.215962;ABP=600.053;RUN=1;RPP=320.423;RPPR=19.4217;RPL=10.0;RPR=174.0;EPP=10.9881;EPPR=9.60285;DPRA=0.0;ODDS=4.32688;GTI=1;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=22.75;MQMR=45.7331;PAIRED=0.994565;PAIREDR=0.998501;technology.ILLUMINA=1.0;MQ0=1;BaseQRankSum=2.948;Dels=0.0;FS=1.285;Hapl [...]
+chr7 151945140 . C T 3090.49 REJECT NS=2;DP=698;DPB=780.0;AC=2;AN=4;AF=0.5;RO=576;AO=204;PRO=0.0;PAO=0.0;QR=22199;QA=7855;PQR=0.0;PQA=0.0;SRF=263;SRR=313;SAF=77;SAR=127;SRP=12.4351;SAP=29.6215;AB=0.261538;ABP=388.263;RUN=1;RPP=12.5903;RPPR=36.3213;RPL=117.0;RPR=87.0;EPP=23.618;EPPR=3.9754;DPRA=0.0;ODDS=133.897;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=33.4118;MQMR=35.5521;PAIRED=1.0;PAIREDR=0.998264;technology.ILLUMINA=1.0;MQ0=17;BaseQRankSum=0.951;Dels=0.0;FS=9.427;Haplotyp [...]
+chr7 151945167 . G T 3582.36 REJECT NS=2;DP=593;DPB=663.0;AC=2;AN=4;AF=0.5;RO=445;AO=218;PRO=0.0;PAO=0.0;QR=16664;QA=8277;PQR=0.0;PQA=0.0;SRF=202;SRR=243;SAF=53;SAR=165;SRP=11.2131;SAP=127.96;AB=0.328808;ABP=171.779;RUN=1;RPP=76.681;RPPR=102.796;RPL=152.0;RPR=66.0;EPP=5.56029;EPPR=3.60075;DPRA=0.0;ODDS=239.712;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=32.6376;MQMR=38.1685;PAIRED=1.0;PAIREDR=0.997753;technology.ILLUMINA=1.0;MQ0=32;BaseQRankSum=3.299;Dels=0.0;FS=36.6785;Haplot [...]
+chr7 151945204 . G A 2633.77 REJECT NS=2;DP=401;DPB=431.0;AC=2;AN=4;AF=0.5;RO=268;AO=163;PRO=0.0;PAO=0.0;QR=10225;QA=6292;PQR=0.0;PQA=0.0;SRF=146;SRR=122;SAF=8;SAR=155;SRP=7.67735;SAP=290.884;AB=0.37819;ABP=58.5567;RUN=1;RPP=70.1661;RPPR=4.59839;RPL=117.0;RPR=46.0;EPP=43.3091;EPPR=3.04271;DPRA=0.0;ODDS=178.764;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=31.9018;MQMR=48.7649;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=45;BaseQRankSum=2.052;Dels=0.0;FS=137.279;HaplotypeSc [...]
+chr7 151945225 . T C 85.8389 REJECT NS=2;DP=389;DPB=389.0;AC=1;AN=4;AF=0.25;RO=367;AO=22;PRO=0.0;PAO=0.0;QR=14158;QA=816;PQR=0.0;PQA=0.0;SRF=129;SRR=238;SAF=0;SAR=22;SRP=73.308;SAP=50.7827;AB=0.151163;ABP=93.9091;RUN=1;RPP=3.0103;RPPR=4.01024;RPL=11.0;RPR=11.0;EPP=3.0103;EPPR=3.06355;DPRA=0.0;ODDS=19.7651;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=34.6818;MQMR=40.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.577;FS=21.464;MLEAC=1;MLEAF=0.5;MQ=41.65;MQRankSu [...]
+chr7 151945256 . G A 49.77 PASS SOMATIC;DP=353;AC=1;AN=4;AF=0.5;MQ0=67;BaseQRankSum=3.236;Dels=0.0;FS=43.694;HaplotypeScore=2.9304;MLEAC=1;MLEAF=0.5;MQ=35.85;MQRankSum=-3.06;QD=0.14;ReadPosRankSum=0.376;SOR=5.391 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00407189 0/1:324,29:353:78.0:78,0,8468:29:8:353:.:1:.:.:.:.:-0.014491
+chr7 151945334 . T C 82.77 PASS SOMATIC;DP=269;AC=1;AN=4;AF=0.5;MQ0=32;BaseQRankSum=-0.693;Dels=0.0;FS=42.288;HaplotypeScore=11.8359;MLEAC=1;MLEAF=0.5;MQ=46.89;MQRankSum=-7.341;QD=0.31;ReadPosRankSum=-1.108;SOR=6.274 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00407189 0/1:211,57:269:99.0:111,0,8097:57:21:268:.:1:.:.:.:.:-0.014491
+chr7 151962113 . G T 40.77 PASS DP=64;AC=1;AN=4;AF=0.5;BaseQRankSum=-0.802;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=42.42;MQRankSum=-2.0;QD=0.64;ReadPosRankSum=-1.127;SOR=0.737;ClippingRankSum=-0.335 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:56,8:64:69.0:69,0,1983:8:13:64:1:.:.:.:.:.:-0.00407189 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.014491
+chr7 151962176 . T A 1527.94 REJECT NS=2;DP=434;DPB=489.0;AC=2;AN=4;AF=0.5;RO=353;AO=136;PRO=0.0;PAO=0.0;QR=13753;QA=5219;PQR=0.0;PQA=0.0;SRF=222;SRR=131;SAF=93;SAR=43;SRP=53.9507;SAP=42.9271;AB=0.278119;ABP=212.116;RUN=1;RPP=4.03217;RPPR=3.50857;RPL=64.0;RPR=72.0;EPP=21.4678;EPPR=43.3702;DPRA=0.0;ODDS=51.422;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=27.4265;MQMR=33.5071;PAIRED=0.970588;PAIREDR=0.985836;technology.ILLUMINA=1.0;MQ0=3;BaseQRankSum=-0.8065;Dels=0.0;FS=1.1955;Ha [...]
+chr7 151970775 . C G 8.45592 REJECT SOMATIC;NS=2;DP=358;DPB=358.0;AC=1;AN=4;AF=0.25;RO=301;AO=56;PRO=0.0;PAO=0.0;QR=11584;QA=2127;PQR=0.0;PQA=0.0;SRF=244;SRR=57;SAF=48;SAR=8;SRP=255.283;SAP=65.0524;AB=0.162791;ABP=257.83;RUN=1;RPP=4.40625;RPPR=37.3571;RPL=31.0;RPR=25.0;EPP=6.88793;EPPR=6.19176;DPRA=0.0;ODDS=1.78129;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=22.1071;MQMR=46.5781;PAIRED=1.0;PAIREDR=0.990033;technology.ILLUMINA=1.0;MQ0=16;BaseQRankSum=0.984;Dels=0.0;FS=12.483;Ha [...]
+chr7 151970777 . G A . PASS SOMATIC;AC=1;AN=3;VT=SNP GT:AD:BQ:DP:FA:SS:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0:103,0:.:98:0.0:0:0:0:103:.:.:.:.:.:0:-0.00407189 0/1:241,8:37.0:250:0.032:2:8:3:249:.:.:.:.:.:1:-0.014491
+chr7 151970856 . T A 9382.96 REJECT NS=2;DP=484;DPB=542.5;AC=2;AN=4;AF=0.5;RO=85;AO=425;PRO=6.0;PAO=8.0;QR=3267;QA=12170;PQR=205.0;PQA=277.0;SRF=43;SRR=42;SAF=226;SAR=199;SRP=3.03585;SAP=6.73501;AB=0.798872;ABP=415.77;RUN=1;RPP=15.2778;RPPR=3.03585;RPL=237.0;RPR=188.0;EPP=34.8977;EPPR=6.10145;DPRA=0.0;ODDS=84.335;GTI=0;TYPE=snp;CIGAR=1X3M;NUMALT=2;MEANALT=3.5;LEN=1;MQM=34.2518;MQMR=51.6235;PAIRED=0.992941;PAIREDR=0.976471;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=8;BaseQRankSum=-0.42 [...]
+chr7 151970856 . TGCC AGCT 9382.96 REJECT NS=2;DP=532;DPB=542.5;AC=2;AN=2;AF=0.0;RO=85;AO=15;PRO=6.0;PAO=6.0;QR=3267;QA=588;PQR=205.0;PQA=212.0;SRF=43;SRR=42;SAF=8;SAR=7;SRP=3.03585;SAP=3.15506;AB=0.0281955;ABP=1031.62;RUN=1;RPP=3.15506;RPPR=3.03585;RPL=8.0;RPR=7.0;EPP=4.31318;EPPR=6.10145;DPRA=0.0;ODDS=84.335;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=2;MEANALT=3.5;LEN=4;MQM=30.6667;MQMR=51.6235;PAIRED=1.0;PAIREDR=0.976471;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr7 151970931 . G A 2595.92 REJECT NS=2;DP=234;DPB=242.0;AC=2;AN=4;AF=0.5;RO=72;AO=170;PRO=0.0;PAO=0.0;QR=2729;QA=6497;PQR=0.0;PQA=0.0;SRF=27;SRR=45;SAF=49;SAR=121;SRP=12.7819;SAP=69.2274;AB=0.702479;ABP=89.1872;RUN=1;RPP=48.9944;RPPR=7.35324;RPL=115.0;RPR=55.0;EPP=3.47014;EPPR=6.02623;DPRA=0.0;ODDS=143.574;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=24.7765;MQMR=51.8611;PAIRED=1.0;PAIREDR=0.986111;technology.ILLUMINA=1.0;MQ0=58;BaseQRankSum=1.3635;Dels=0.0;FS=6.792;Haplotype [...]
+chr7 152055766 . G GA 199.538 REJECT NS=2;DP=183;DPB=234.875;AC=2;AN=4;AF=0.5;RO=118;AO=29;PRO=52.6667;PAO=33.6667;QR=4372;QA=684;PQR=1903.83;PQA=1124.83;SRF=17;SRR=101;SAF=1;SAR=28;SRP=132.857;SAP=57.5966;AB=0.15847;ABP=188.416;RUN=1;RPP=3.08518;RPPR=21.8543;RPL=14.0;RPR=15.0;EPP=3.68421;EPPR=3.08391;DPRA=0.0;ODDS=10.4373;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=2;MEANALT=6.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr7 152055766 . GA G 199.538 REJECT NS=2;DP=183;DPB=234.875;AC=2;AN=2;AF=0.0;RO=118;AO=18;PRO=52.6667;PAO=23.6667;QR=4372;QA=501;PQR=1903.83;PQA=852.333;SRF=17;SRR=101;SAF=2;SAR=16;SRP=132.857;SAP=26.6552;AB=0.0983607;ABP=259.422;RUN=1;RPP=10.7311;RPPR=21.8543;RPL=13.0;RPR=5.0;EPP=4.9405;EPPR=3.08391;DPRA=0.0;ODDS=10.4373;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=2;MEANALT=6.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr7 153023667 . T C 9850.08 REJECT NS=2;DP=355;DPB=404.0;AC=2;AN=4;AF=0.5;RO=84;AO=320;PRO=0.0;PAO=0.0;QR=3228;QA=12286;PQR=0.0;PQA=0.0;SRF=49;SRR=35;SAF=182;SAR=138;SRP=8.07707;SAP=16.1477;AB=0.792079;ABP=302.372;RUN=1;RPP=4.34033;RPPR=3.1137;RPL=153.0;RPR=167.0;EPP=32.5695;EPPR=17.9004;DPRA=0.0;ODDS=129.662;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996875;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2965;Dels=0.0;FS=3.0165;HaplotypeScor [...]
+chr7 155595590 . G C 95.7182 REJECT NS=1;DP=69;DPB=70.25;AC=1;AN=3;AF=0.0;RO=57;AO=4;PRO=1.5;PAO=1.5;QR=1787;QA=44;PQR=17.5;PQA=17.5;SRF=39;SRR=18;SAF=4;SAR=0;SRP=19.8106;SAP=11.6962;AB=0.057971;ABP=120.112;RUN=1;RPP=11.6962;RPPR=39.6206;RPL=4.0;RPR=0.0;EPP=11.6962;EPPR=3.0484;DPRA=0.0;ODDS=22.0399;GTI=0;TYPE=snp;CIGAR=1X3M;NUMALT=2;MEANALT=4.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.982456;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallH [...]
+chr7 155595590 . GGCT CGCC 95.7182 REJECT NS=1;DP=69;DPB=70.25;AC=1;AN=4;AF=0.5;RO=57;AO=5;PRO=1.5;PAO=0.0;QR=1787;QA=34;PQR=17.5;PQA=0.0;SRF=39;SRR=18;SAF=5;SAR=0;SRP=19.8106;SAP=13.8677;AB=0.0724638;ABP=112.56;RUN=1;RPP=6.91895;RPPR=39.6206;RPL=4.0;RPR=1.0;EPP=6.91895;EPPR=3.0484;DPRA=0.0;ODDS=22.0399;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=2;MEANALT=4.0;LEN=4;MQM=56.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.982456;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr7 157501344 . T C 8114.275 REJECT NS=2;DP=216;DPB=243.0;AC=4;AN=4;AF=1.0;RO=0;AO=243;PRO=0.0;PAO=0.0;QR=0;QA=9273;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=161;SAR=82;SRP=0.0;SAP=58.7805;AB=0.0;ABP=0.0;RUN=1;RPP=121.19;RPPR=0.0;RPL=64.0;RPR=179.0;EPP=3.01924;EPPR=0.0;DPRA=0.0;ODDS=36.7591;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995885;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9464;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.445;SOR=1.54 [...]
+chr8 4500949 . C A 13555.75 REJECT NS=2;DP=356;DPB=405.0;AC=4;AN=4;AF=1.0;RO=0;AO=405;PRO=0.0;PAO=0.0;QR=0;QA=15613;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=215;SAR=190;SRP=0.0;SAP=6.36134;AB=0.0;ABP=0.0;RUN=1;RPP=84.1269;RPPR=0.0;RPL=141.0;RPR=264.0;EPP=81.5104;EPPR=0.0;DPRA=0.0;ODDS=64.8392;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.990123;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9638;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.055;SOR=0. [...]
+chr8 8119486 . T C 14100.45 REJECT NS=2;DP=380;DPB=432.0;AC=4;AN=4;AF=1.0;RO=1;AO=429;PRO=0.0;PAO=0.0;QR=16;QA=16245;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=275;SAR=154;SRP=5.18177;SAP=77.1188;AB=0.0;ABP=0.0;RUN=1;RPP=3.62277;RPPR=5.18177;RPL=209.0;RPR=220.0;EPP=77.1188;EPPR=5.18177;DPRA=0.0;ODDS=68.5533;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=59.965;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.721;Dels=0.0;FS=0.0;HaplotypeScore=5.799;MLEAC=2;MLEAF [...]
+chr8 19528128 . C T 1092.28 REJECT NS=1;DP=100;DPB=100.0;AC=1;AN=4;AF=0.5;RO=50;AO=50;PRO=0.0;PAO=0.0;QR=1711;QA=1656;PQR=0.0;PQA=0.0;SRF=14;SRR=36;SAF=14;SAR=36;SRP=24.0302;SAP=24.0302;AB=0.5;ABP=3.0103;RUN=1;RPP=53.2147;RPPR=53.2147;RPL=42.0;RPR=8.0;EPP=11.5225;EPPR=17.0814;DPRA=0.0;ODDS=251.506;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.62;PAIRED=0.98;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.724;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.715;QD=1 [...]
+chr8 27255080 . A G 849.038 REJECT;LowQual NS=2;DP=249;DPB=277.0;AC=2;AN=4;AF=0.375;RO=227;AO=49;PRO=0.0;PAO=0.0;QR=8497;QA=1815;PQR=0.0;PQA=0.0;SRF=137;SRR=90;SAF=32;SAR=17;SRP=24.1415;SAP=12.9813;AB=0.571429;ABP=5.49198;RUN=1;RPP=26.4533;RPPR=96.7663;RPL=13.0;RPR=36.0;EPP=3.05462;EPPR=3.09639;DPRA=0.0;ODDS=10.8791;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.699;Dels=0.0;FS=3.675;HaplotypeScore [...]
+chr8 27255128 . T C 2040.925 REJECT NS=2;DP=361;DPB=411.0;AC=2;AN=4;AF=0.5;RO=314;AO=97;PRO=0.0;PAO=0.0;QR=11699;QA=3638;PQR=0.0;PQA=0.0;SRF=167;SRR=147;SAF=50;SAR=47;SRP=5.77651;SAP=3.21178;AB=0.23601;ABP=251.8;RUN=1;RPP=17.0017;RPPR=4.00613;RPL=36.0;RPR=61.0;EPP=4.82359;EPPR=6.35741;DPRA=0.0;ODDS=95.16;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989691;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.4665;Dels=0.0;FS=1.3425;HaplotypeScore=6.81 [...]
+chr8 27255146 . G A 2397.8 REJECT NS=2;DP=382;DPB=440.0;AC=2;AN=4;AF=0.5;RO=331;AO=109;PRO=0.0;PAO=0.0;QR=12674;QA=4146;PQR=0.0;PQA=0.0;SRF=165;SRR=166;SAF=55;SAR=54;SRP=3.01686;SAP=3.03022;AB=0.247727;ABP=246.235;RUN=1;RPP=33.3113;RPPR=3.54169;RPL=35.0;RPR=74.0;EPP=11.7958;EPPR=9.31479;DPRA=0.0;ODDS=122.75;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.981651;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1725;Dels=0.0;FS=2.806;HaplotypeScore=5. [...]
+chr8 27255263 . A G 1767.195 REJECT NS=2;DP=342;DPB=390.0;AC=2;AN=4;AF=0.5;RO=303;AO=87;PRO=0.0;PAO=0.0;QR=11654;QA=3358;PQR=0.0;PQA=0.0;SRF=130;SRR=173;SAF=41;SAR=46;SRP=16.2613;SAP=3.63429;AB=0.223077;ABP=262.785;RUN=1;RPP=3.03526;RPPR=3.0748;RPL=43.0;RPR=44.0;EPP=5.03202;EPPR=3.59079;DPRA=0.0;ODDS=111.362;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990099;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3745;Dels=0.0;FS=4.0575;HaplotypeScore= [...]
+chr8 27277537 . G A 11000.5 REJECT NS=2;DP=392;DPB=449.0;AC=2;AN=4;AF=0.5;RO=84;AO=365;PRO=0.0;PAO=0.0;QR=3193;QA=13666;PQR=0.0;PQA=0.0;SRF=46;SRR=38;SAF=194;SAR=171;SRP=4.66476;SAP=6.15745;AB=0.812918;ABP=384.885;RUN=1;RPP=3.73016;RPPR=6.73282;RPL=177.0;RPR=188.0;EPP=12.0591;EPPR=4.66476;DPRA=0.0;ODDS=91.7242;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99726;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.254;Dels=0.0;FS=2.323;HaplotypeScore= [...]
+chr8 27291557 . T C 10579.349999999999 REJECT NS=2;DP=284;DPB=320.0;AC=4;AN=4;AF=1.0;RO=0;AO=319;PRO=0.0;PAO=0.0;QR=0;QA=12068;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=213;SAR=106;SRP=0.0;SAP=80.9451;AB=0.0;ABP=0.0;RUN=1;RPP=93.0345;RPPR=0.0;RPL=102.0;RPR=217.0;EPP=4.1607;EPPR=0.0;DPRA=0.0;ODDS=48.548;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996865;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9133;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.8 [...]
+chr8 27293335 . G T 1225.1799999999998 REJECT NS=2;DP=318;DPB=358.0;AC=2;AN=4;AF=0.5;RO=285;AO=73;PRO=0.0;PAO=0.0;QR=11019;QA=2747;PQR=0.0;PQA=0.0;SRF=112;SRR=173;SAF=27;SAR=46;SRP=31.3613;SAP=13.7487;AB=0.203911;ABP=275.621;RUN=1;RPP=3.75395;RPPR=9.41805;RPL=39.0;RPR=34.0;EPP=5.41974;EPPR=33.2509;DPRA=0.0;ODDS=121.953;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992982;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.3535;Dels=0.0;FS=1.2005;Hap [...]
+chr8 27293865 . C T 7551.78 REJECT NS=2;DP=282;DPB=322.0;AC=2;AN=4;AF=0.5;RO=74;AO=248;PRO=0.0;PAO=0.0;QR=2858;QA=9535;PQR=0.0;PQA=0.0;SRF=40;SRR=34;SAF=115;SAR=133;SRP=4.06669;SAP=5.84722;AB=0.770186;ABP=207.183;RUN=1;RPP=50.9578;RPPR=17.2129;RPL=161.0;RPR=87.0;EPP=43.4978;EPPR=12.5178;DPRA=0.0;ODDS=118.164;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995968;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.733;Dels=0.0;FS=2.9165;HaplotypeScore= [...]
+chr8 27308538 . G A 10601.1 REJECT NS=2;DP=397;DPB=452.0;AC=2;AN=4;AF=0.5;RO=100;AO=352;PRO=0.0;PAO=0.0;QR=3750;QA=13222;PQR=0.0;PQA=0.0;SRF=47;SRR=53;SAF=189;SAR=163;SRP=3.79203;SAP=7.18051;AB=0.778761;ABP=308.093;RUN=1;RPP=3.0103;RPPR=3.09716;RPL=176.0;RPR=176.0;EPP=3.6272;EPPR=4.40004;DPRA=0.0;ODDS=153.04;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994318;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.295;Dels=0.0;FS=5.4235;HaplotypeScore= [...]
+chr8 27308585 . A C 1714.67 REJECT NS=2;DP=362;DPB=411.0;AC=2;AN=4;AF=0.5;RO=323;AO=88;PRO=0.0;PAO=0.0;QR=12375;QA=3348;PQR=0.0;PQA=0.0;SRF=144;SRR=179;SAF=39;SAR=49;SRP=11.2458;SAP=5.47788;AB=0.214112;ABP=294.785;RUN=1;RPP=7.84676;RPPR=23.3468;RPL=51.0;RPR=37.0;EPP=3.40511;EPPR=38.8362;DPRA=0.0;ODDS=120.774;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993808;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2015;Dels=0.0;FS=4.6185;HaplotypeScore= [...]
+chr8 27311703 . T C 14205.95 REJECT NS=2;DP=378;DPB=437.0;AC=4;AN=4;AF=1.0;RO=0;AO=437;PRO=0.0;PAO=0.0;QR=0;QA=16567;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=237;SAR=200;SRP=0.0;SAP=9.81292;AB=0.0;ABP=0.0;RUN=1;RPP=7.78555;RPPR=0.0;RPL=203.0;RPR=234.0;EPP=6.11595;EPPR=0.0;DPRA=0.0;ODDS=76.3819;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.990847;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.9436;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.345;SOR=0 [...]
+chr8 27312040 . C T 9957.48 REJECT NS=2;DP=366;DPB=415.0;AC=2;AN=4;AF=0.5;RO=86;AO=329;PRO=0.0;PAO=0.0;QR=3289;QA=12409;PQR=0.0;PQA=0.0;SRF=48;SRR=38;SAF=185;SAR=144;SRP=5.53527;SAP=14.1053;AB=0.792771;ABP=311.982;RUN=1;RPP=8.56109;RPPR=3.0103;RPL=150.0;RPR=179.0;EPP=7.82186;EPPR=3.41429;DPRA=0.0;ODDS=68.1335;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987842;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.973;Dels=0.0;FS=5.5495;HaplotypeScore [...]
+chr8 27312135 . G A 9040.56 REJECT NS=2;DP=315;DPB=356.0;AC=2;AN=4;AF=0.5;RO=61;AO=295;PRO=0.0;PAO=0.0;QR=2356;QA=11327;PQR=0.0;PQA=0.0;SRF=22;SRR=39;SAF=88;SAR=207;SRP=13.2981;SAP=107.248;AB=0.828652;ABP=337.002;RUN=1;RPP=12.0274;RPPR=13.2981;RPL=165.0;RPR=130.0;EPP=9.20084;EPPR=4.7546;DPRA=0.0;ODDS=32.754;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2935;Dels=0.0;FS=2.1565;HaplotypeScore=4.965; [...]
+chr8 27315876 . A G 14700.9 REJECT NS=2;DP=390;DPB=441.0;AC=4;AN=4;AF=1.0;RO=2;AO=438;PRO=0.0;PAO=0.0;QR=75;QA=16770;PQR=0.0;PQA=0.0;SRF=0;SRR=2;SAF=239;SAR=199;SRP=7.35324;SAP=10.9426;AB=0.0;ABP=0.0;RUN=1;RPP=3.98201;RPPR=3.0103;RPL=212.0;RPR=226.0;EPP=37.9918;EPPR=3.0103;DPRA=0.0;ODDS=66.3124;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995434;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.966;Dels=0.0;FS=3.1605;HaplotypeScore=6.8482;MLEAC=2; [...]
+chr8 27315900 . A G 14661.95 REJECT NS=2;DP=385;DPB=441.0;AC=4;AN=4;AF=1.0;RO=0;AO=441;PRO=0.0;PAO=0.0;QR=0;QA=16888;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=221;SAR=220;SRP=0.0;SAP=3.01522;AB=0.0;ABP=0.0;RUN=1;RPP=3.40914;RPPR=0.0;RPL=225.0;RPR=216.0;EPP=45.5977;EPPR=0.0;DPRA=0.0;ODDS=73.5067;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995465;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.9118;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.91;SOR=0. [...]
+chr8 28561355 . C G 5173.555 REJECT NS=2;DP=314;DPB=364.0;AC=2;AN=4;AF=0.5;RO=175;AO=188;PRO=0.0;PAO=0.0;QR=6653;QA=7128;PQR=0.0;PQA=0.0;SRF=127;SRR=48;SAF=132;SAR=56;SRP=80.4512;SAP=69.7253;AB=0.516484;ABP=3.86934;RUN=1;RPP=39.2323;RPPR=52.2593;RPL=66.0;RPR=122.0;EPP=7.63045;EPPR=6.59633;DPRA=0.0;ODDS=291.566;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994681;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.064;Dels=0.0;FS=2.424;HaplotypeScore [...]
+chr8 30027689 . C CA 917.348 REJECT NS=2;DP=215;DPB=269.9;AC=2;AN=2;AF=0.0;RO=112;AO=19;PRO=32.1667;PAO=30.1667;QR=4064;QA=554;PQR=1127.17;PQA=1027.17;SRF=83;SRR=29;SAF=13;SAR=6;SRP=59.5461;SAP=8.61041;AB=0.0883721;ABP=319.429;RUN=1;RPP=3.12459;RPPR=37.211;RPL=9.0;RPR=10.0;EPP=3.12459;EPPR=4.25114;DPRA=0.0;ODDS=64.0096;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=3;MEANALT=12.0;LEN=1;MQM=59.5789;MQMR=60.0;PAIRED=1.0;PAIREDR=0.982143;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr8 30027689 . CA C 661.039 REJECT NS=2;DP=199;DPB=269.9;AC=2;AN=4;AF=0.5;RO=112;AO=48;PRO=32.1667;PAO=22.1667;QR=4064;QA=1688;PQR=1127.17;PQA=774.667;SRF=83;SRR=29;SAF=33;SAR=15;SRP=59.5461;SAP=17.6677;AB=0.223256;ABP=146.035;RUN=1;RPP=21.1059;RPPR=37.211;RPL=14.0;RPR=34.0;EPP=3.19126;EPPR=4.25114;DPRA=0.0;ODDS=64.0096;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=3;MEANALT=12.0;LEN=1;MQM=60.4167;MQMR=60.0;PAIRED=0.979167;PAIREDR=0.982143;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRank [...]
+chr8 30027689 . CAA C 917.348 REJECT NS=2;DP=215;DPB=269.9;AC=2;AN=2;AF=0.0;RO=112;AO=11;PRO=32.1667;PAO=20.5;QR=4064;QA=370;PQR=1127.17;PQA=717.0;SRF=83;SRR=29;SAF=6;SAR=5;SRP=59.5461;SAP=3.20771;AB=0.0511628;ABP=379.22;RUN=1;RPP=3.20771;RPPR=37.211;RPL=5.0;RPR=6.0;EPP=7.94546;EPPR=4.25114;DPRA=0.0;ODDS=64.0096;GTI=0;TYPE=del;CIGAR=1M2D17M;NUMALT=3;MEANALT=12.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.982143;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr8 30921935 . G A 7144.595 REJECT NS=2;DP=319;DPB=371.0;AC=3;AN=4;AF=0.75;RO=109;AO=262;PRO=0.0;PAO=0.0;QR=4187;QA=10149;PQR=0.0;PQA=0.0;SRF=41;SRR=68;SAF=88;SAR=174;SRP=17.5333;SAP=64.3088;AB=0.59176;ABP=22.5373;RUN=1;RPP=12.5913;RPPR=4.62396;RPL=148.0;RPR=114.0;EPP=3.83911;EPPR=3.03022;DPRA=0.0;ODDS=65.8886;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992366;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.4;Dels=0.0;FS=1.823;HaplotypeScore=6 [...]
+chr8 30921970 . A T 4674.35 REJECT NS=2;DP=223;DPB=260.0;AC=3;AN=4;AF=0.75;RO=75;AO=184;PRO=0.0;PAO=0.0;QR=2873;QA=6791;PQR=0.0;PQA=0.0;SRF=25;SRR=50;SAF=50;SAR=134;SRP=21.1059;SAP=86.2815;AB=0.59893;ABP=18.9073;RUN=1;RPP=34.9215;RPPR=15.7786;RPL=118.0;RPR=66.0;EPP=3.76559;EPPR=3.03925;DPRA=0.0;ODDS=45.8863;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.98913;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.492;Dels=0.0;FS=2.4725;HaplotypeScore=4.8 [...]
+chr8 30924557 . C T 11867.099999999999 REJECT NS=2;DP=309;DPB=357.0;AC=4;AN=4;AF=1.0;RO=0;AO=357;PRO=0.0;PAO=0.0;QR=0;QA=13903;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=244;SAR=113;SRP=0.0;SAP=107.393;AB=0.0;ABP=0.0;RUN=1;RPP=44.913;RPPR=0.0;RPL=137.0;RPR=220.0;EPP=14.2569;EPPR=0.0;DPRA=0.0;ODDS=63.0127;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994398;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8994;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28. [...]
+chr8 30925751 . T A 5078.695 REJECT NS=2;DP=229;DPB=266.0;AC=3;AN=4;AF=0.75;RO=77;AO=189;PRO=0.0;PAO=0.0;QR=2969;QA=7313;PQR=0.0;PQA=0.0;SRF=56;SRR=21;SAF=145;SAR=44;SRP=37.5565;SAP=120.212;AB=0.598958;ABP=19.3416;RUN=1;RPP=115.617;RPPR=17.9286;RPL=45.0;RPR=144.0;EPP=7.15793;EPPR=6.42261;DPRA=0.0;ODDS=47.1804;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987013;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.417;Dels=0.0;FS=2.027;HaplotypeScore=0 [...]
+chr8 30933816 . C CT 448.309 REJECT NS=2;DP=233;DPB=263.4;AC=2;AN=3;AF=0.25;RO=166;AO=20;PRO=32.5;PAO=17.5;QR=6242;QA=703;PQR=1156.67;PQA=613.667;SRF=43;SRR=123;SAF=8;SAR=12;SRP=86.7297;SAP=4.74748;AB=0.0858369;ABP=350.157;RUN=1;RPP=18.6449;RPPR=86.7297;RPL=16.0;RPR=4.0;EPP=4.74748;EPPR=3.06262;DPRA=0.0;ODDS=2.15673;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=2;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.95;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr8 30933816 . CT C 448.309 REJECT NS=2;DP=233;DPB=263.4;AC=2;AN=3;AF=0.25;RO=166;AO=31;PRO=32.5;PAO=17.0;QR=6242;QA=1134;PQR=1156.67;PQA=603.667;SRF=43;SRR=123;SAF=5;SAR=26;SRP=86.7297;SAP=33.9012;AB=0.133047;ABP=275.525;RUN=1;RPP=18.771;RPPR=86.7297;RPL=23.0;RPR=8.0;EPP=4.76149;EPPR=3.06262;DPRA=0.0;ODDS=2.15673;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=2;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr8 30941317 . T C 535.595 PASS SOMATIC;NS=2;DP=273;DPB=273.0;AC=1;AN=3;AF=0.25;RO=214;AO=59;PRO=0.0;PAO=0.0;QR=8315;QA=2260;PQR=0.0;PQA=0.0;SRF=72;SRR=142;SAF=18;SAR=41;SRP=52.7309;SAP=22.4799;AB=0.282297;ABP=89.0484;RUN=1;RPP=26.0132;RPPR=92.6698;RPL=42.0;RPR=17.0;EPP=7.46366;EPPR=9.86972;DPRA=3.26562;ODDS=40.9566;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=25.3729;MQMR=48.8411;PAIRED=1.0;PAIREDR=0.995327;technology.ILLUMINA=1.0;MQ0=11;VT=SNP;BaseQRankSum=1.429;Dels=0.0;FS= [...]
+chr8 30946403 . C A 6135.25 REJECT NS=2;DP=274;DPB=317.0;AC=3;AN=4;AF=0.75;RO=89;AO=228;PRO=0.0;PAO=0.0;QR=3371;QA=8678;PQR=0.0;PQA=0.0;SRF=60;SRR=29;SAF=147;SAR=81;SRP=26.4573;SAP=44.4969;AB=0.616379;ABP=30.3035;RUN=1;RPP=58.0209;RPPR=20.7969;RPL=76.0;RPR=152.0;EPP=14.02;EPPR=8.49998;DPRA=0.0;ODDS=54.0369;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986842;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.446;Dels=0.0;FS=1.2105;HaplotypeScore=3.8 [...]
+chr8 30954270 . G T 91.4608 REJECT NS=2;DP=271;DPB=281.4;AC=2;AN=2;AF=0.0;RO=225;AO=14;PRO=9.5;PAO=9.5;QR=7660;QA=227;PQR=241.0;PQA=241.0;SRF=156;SRR=69;SAF=13;SAR=1;SRP=76.0586;SAP=25.3454;AB=0.0516605;ABP=476.159;RUN=1;RPP=5.49198;RPPR=109.412;RPL=9.0;RPR=5.0;EPP=8.59409;EPPR=3.09716;DPRA=0.0;ODDS=1.62468;GTI=0;TYPE=snp;CIGAR=1X4M;NUMALT=3;MEANALT=4.0;LEN=1;MQM=60.0;MQMR=59.9556;PAIRED=1.0;PAIREDR=0.986667;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr8 30954270 . GTTTG TTTTT 91.4608 REJECT NS=2;DP=271;DPB=281.4;AC=2;AN=3;AF=0.25;RO=225;AO=13;PRO=9.5;PAO=0.0;QR=7660;QA=193;PQR=241.0;PQA=0.0;SRF=156;SRR=69;SAF=13;SAR=0;SRP=76.0586;SAP=31.2394;AB=0.0479705;ABP=483.979;RUN=1;RPP=16.5402;RPPR=109.412;RPL=11.0;RPR=2.0;EPP=16.5402;EPPR=3.09716;DPRA=0.0;ODDS=1.62468;GTI=0;TYPE=complex;CIGAR=1X3M1X;NUMALT=3;MEANALT=4.0;LEN=5;MQM=60.0;MQMR=59.9556;PAIRED=1.0;PAIREDR=0.986667;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr8 30954274 . G T 91.4608 REJECT NS=2;DP=271;DPB=281.4;AC=2;AN=3;AF=0.25;RO=225;AO=17;PRO=9.5;PAO=0.0;QR=7660;QA=298;PQR=241.0;PQA=0.0;SRF=156;SRR=69;SAF=17;SAR=0;SRP=76.0586;SAP=39.9253;AB=0.0627306;ABP=453.082;RUN=1;RPP=18.4661;RPPR=109.412;RPL=14.0;RPR=3.0;EPP=18.4661;EPPR=3.09716;DPRA=0.0;ODDS=1.62468;GTI=0;TYPE=snp;CIGAR=4M1X;NUMALT=3;MEANALT=4.0;LEN=1;MQM=58.8235;MQMR=59.9556;PAIRED=1.0;PAIREDR=0.986667;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr8 30958353 . CT C 8393.029999999999 REJECT NS=2;DP=251;DPB=283.182;AC=4;AN=4;AF=1.0;RO=0;AO=290;PRO=24.5;PAO=24.5;QR=0;QA=10793;PQR=668.5;PQA=668.5;SRF=0;SRR=0;SAF=217;SAR=73;SRP=0.0;SAP=158.278;AB=0.0;ABP=0.0;RUN=1;RPP=48.5663;RPPR=0.0;RPL=106.0;RPR=184.0;EPP=4.92719;EPPR=0.0;DPRA=0.0;ODDS=54.777;GTI=0;TYPE=del;CIGAR=1M1D9M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.1379;MQMR=0.0;PAIRED=0.996552;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.14;QD=32.785;RPA=7,6;RU=T [...]
+chr8 30999122 . C T 2912.18 PASS SOMATIC;NS=2;DP=427;DPB=427.0;AC=1;AN=3;AF=0.25;RO=314;AO=112;PRO=0.0;PAO=0.0;QR=11931;QA=4302;PQR=0.0;PQA=0.0;SRF=141;SRR=173;SAF=50;SAR=62;SRP=10.0918;SAP=5.80219;AB=0.336336;ABP=80.4856;RUN=1;RPP=3.0103;RPPR=4.00613;RPL=56.0;RPR=56.0;EPP=5.80219;EPPR=3.70185;DPRA=3.54255;ODDS=59.649;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.631;Dels=0.0;FS=0.423;Haplo [...]
+chr8 31005017 . T TC 8557.65 REJECT NS=2;DP=242;DPB=362.0;AC=4;AN=4;AF=1.0;RO=0;AO=267;PRO=5.0;PAO=5.0;QR=0;QA=9812;PQR=177.5;PQA=177.5;SRF=0;SRR=0;SAF=93;SAR=174;SRP=0.0;SAP=56.37;AB=0.0;ABP=0.0;RUN=1;RPP=160.145;RPPR=0.0;RPL=203.0;RPR=64.0;EPP=16.6816;EPPR=0.0;DPRA=0.0;ODDS=44.1939;GTI=0;TYPE=ins;CIGAR=1M1I2M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996255;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=31005017;HOMLEN=0;SVLEN=1;SVTYPE=INS;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.18;Q [...]
+chr8 31024638 . C T 2735.68 PASS SOMATIC;NS=2;DP=424;DPB=424.0;AC=1;AN=3;AF=0.25;RO=318;AO=106;PRO=0.0;PAO=0.0;QR=12285;QA=4075;PQR=0.0;PQA=0.0;SRF=159;SRR=159;SAF=48;SAR=58;SRP=3.0103;SAP=5.05886;AB=0.334385;ABP=78.5323;RUN=1;RPP=8.25461;RPPR=9.15598;RPL=61.0;RPR=45.0;EPP=14.81;EPPR=3.44733;DPRA=2.96262;ODDS=67.7003;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.971698;PAIREDR=0.990566;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.139;Dels=0.0;FS=1. [...]
+chr8 31502726 . G T 9124.07 REJECT NS=2;DP=347;DPB=401.0;AC=2;AN=4;AF=0.5;RO=101;AO=300;PRO=0.0;PAO=0.0;QR=3914;QA=11530;PQR=0.0;PQA=0.0;SRF=63;SRR=38;SAF=186;SAR=114;SRP=16.4476;SAP=40.5333;AB=0.74813;ABP=217.455;RUN=1;RPP=61.6401;RPPR=14.3837;RPL=105.0;RPR=195.0;EPP=4.429;EPPR=4.75178;DPRA=0.0;ODDS=229.005;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993333;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1045;Dels=0.0;FS=2.488;HaplotypeScore=3 [...]
+chr8 37501860 . A C 8131.2300000000005 REJECT NS=2;DP=367;DPB=414.0;AC=3;AN=4;AF=0.75;RO=123;AO=291;PRO=0.0;PAO=0.0;QR=4745;QA=10972;PQR=0.0;PQA=0.0;SRF=59;SRR=64;SAF=126;SAR=165;SRP=3.45166;SAP=14.3602;AB=0.615625;ABP=40.1696;RUN=1;RPP=3.61473;RPPR=3.87536;RPL=150.0;RPR=141.0;EPP=88.4439;EPPR=24.6368;DPRA=0.0;ODDS=59.5499;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996564;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.075;Dels=0.0;FS=3.4755; [...]
+chr8 37686749 . A G 2363.79 PASS SOMATIC;NS=2;DP=302;DPB=302.0;AC=1;AN=3;AF=0.25;RO=214;AO=88;PRO=0.0;PAO=0.0;QR=7989;QA=3399;PQR=0.0;PQA=0.0;SRF=129;SRR=85;SAF=59;SAR=29;SRP=22.655;SAP=25.2185;AB=0.394619;ABP=24.5205;RUN=1;RPP=19.6912;RPPR=64.7451;RPL=31.0;RPR=57.0;EPP=3.0103;EPPR=7.06913;DPRA=2.82278;ODDS=49.295;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9579;PAIRED=1.0;PAIREDR=0.990654;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.992;Dels=0.0;FS=2.481;H [...]
+chr8 37693302 . T C 9375.86 REJECT NS=2;DP=255;DPB=301.0;AC=4;AN=4;AF=1.0;RO=1;AO=300;PRO=0.0;PAO=0.0;QR=15;QA=11274;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=113;SAR=187;SRP=5.18177;SAP=42.6469;AB=0.0;ABP=0.0;RUN=1;RPP=81.2991;RPPR=5.18177;RPL=202.0;RPR=98.0;EPP=5.35549;EPPR=5.18177;DPRA=0.0;ODDS=58.8373;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993333;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9242;MLEAC=2;MLEAF=1.0;MQ=60.0;QD= [...]
+chr8 37699195 . C G 1343.87 PASS SOMATIC;NS=2;DP=288;DPB=288.0;AC=1;AN=3;AF=0.25;RO=229;AO=58;PRO=0.0;PAO=0.0;QR=8554;QA=2193;PQR=0.0;PQA=0.0;SRF=92;SRR=137;SAF=27;SAR=31;SRP=22.2122;SAP=3.60933;AB=0.271028;ABP=100.463;RUN=1;RPP=5.40641;RPPR=3.09564;RPL=33.0;RPR=25.0;EPP=4.35811;EPPR=14.6263;DPRA=2.89189;ODDS=47.1303;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995633;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.476;Dels=0.0;FS=1.201;H [...]
+chr8 37985897 . A G 13984.349999999999 REJECT NS=2;DP=372;DPB=431.0;AC=4;AN=4;AF=1.0;RO=1;AO=429;PRO=0.0;PAO=0.0;QR=34;QA=16319;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=218;SAR=211;SRP=5.18177;SAP=3.25832;AB=0.0;ABP=0.0;RUN=1;RPP=3.05586;RPPR=5.18177;RPL=216.0;RPR=213.0;EPP=5.24251;EPPR=5.18177;DPRA=0.0;ODDS=76.0165;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997669;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8658;MLEAC=2;MLEAF=1.0 [...]
+chr8 38171513 . G GCAAAA 4629.18 REJECT NS=2;DP=331;DPB=476.667;AC=2;AN=4;AF=0.5;RO=186;AO=159;PRO=73.0;PAO=81.0;QR=7059;QA=5752;PQR=2510.0;PQA=2770.0;SRF=97;SRR=89;SAF=81;SAR=78;SRP=3.75747;SAP=3.13321;AB=0.458213;ABP=8.27315;RUN=1;RPP=3.6795;RPPR=4.69144;RPL=83.0;RPR=76.0;EPP=4.6628;EPPR=4.17776;DPRA=0.0;ODDS=222.73;GTI=0;TYPE=ins;CIGAR=1M5I17M;NUMALT=1;MEANALT=2.0;LEN=5;MQM=60.5031;MQMR=60.0;PAIRED=0.993711;PAIREDR=0.973118;technology.ILLUMINA=1.0;MQ0=0;END=38171513;HOMLEN=10;HOMSEQ=C [...]
+chr8 38176435 . T G 3178.47 PASS SOMATIC;NS=2;DP=386;DPB=386.0;AC=1;AN=3;AF=0.25;RO=269;AO=116;PRO=0.0;PAO=0.0;QR=10289;QA=4524;PQR=0.0;PQA=0.0;SRF=132;SRR=137;SAF=57;SAR=59;SRP=3.21211;SAP=3.08518;AB=0.379085;ABP=41.8697;RUN=1;RPP=3.30981;RPPR=3.01837;RPL=56.0;RPR=60.0;EPP=12.0706;EPPR=20.8422;DPRA=3.825;ODDS=50.2547;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991379;PAIREDR=0.992565;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.068;Dels=0.0;FS=0 [...]
+chr8 38276794 . CA C 5507.469999999999 REJECT NS=2;DP=373;DPB=419.429;AC=2;AN=4;AF=0.5;RO=210;AO=206;PRO=31.0;PAO=28.0;QR=7953;QA=7601;PQR=1034.0;PQA=897.0;SRF=127;SRR=83;SAF=123;SAR=83;SRP=23.0292;SAP=19.8761;AB=0.488152;ABP=3.52487;RUN=1;RPP=3.38978;RPPR=3.67208;RPL=100.0;RPR=106.0;EPP=4.52822;EPPR=10.0004;DPRA=0.0;ODDS=363.691;GTI=0;TYPE=del;CIGAR=1M1D5M;NUMALT=1;MEANALT=4.0;LEN=1;MQM=60.2427;MQMR=60.0;PAIRED=0.995146;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=38276795;HOMLEN=2;HOM [...]
+chr8 38286811 . C G 5098.795 REJECT NS=2;DP=351;DPB=405.0;AC=2;AN=4;AF=0.5;RO=215;AO=189;PRO=0.0;PAO=0.0;QR=8261;QA=7174;PQR=0.0;PQA=0.0;SRF=117;SRR=98;SAF=96;SAR=93;SRP=6.65635;SAP=3.1137;AB=0.466667;ABP=6.91895;RUN=1;RPP=24.254;RPPR=11.5043;RPL=73.0;RPR=116.0;EPP=11.386;EPPR=5.28277;DPRA=0.0;ODDS=316.699;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.973545;PAIREDR=0.990698;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.789;Dels=0.0;FS=1.9115;HaplotypeSco [...]
+chr8 38424739 . C T 8099.96 REJECT NS=2;DP=355;DPB=408.0;AC=3;AN=4;AF=0.75;RO=114;AO=294;PRO=0.0;PAO=0.0;QR=4210;QA=11094;PQR=0.0;PQA=0.0;SRF=65;SRR=49;SAF=189;SAR=105;SRP=7.88659;SAP=55.1256;AB=0.62623;ABP=45.2223;RUN=1;RPP=6.5851;RPPR=4.9151;RPL=136.0;RPR=158.0;EPP=4.90111;EPPR=3.31507;DPRA=0.0;ODDS=65.2212;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993197;PAIREDR=0.982456;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.087;Dels=0.0;FS=1.361;HaplotypeSc [...]
+chr8 38424961 . T C 9024.635 REJECT NS=2;DP=393;DPB=448.0;AC=3;AN=4;AF=0.75;RO=128;AO=320;PRO=0.0;PAO=0.0;QR=4896;QA=12269;PQR=0.0;PQA=0.0;SRF=48;SRR=80;SAF=132;SAR=188;SRP=20.3821;SAP=24.2907;AB=0.622419;ABP=47.138;RUN=1;RPP=6.91895;RPPR=9.79615;RPL=172.0;RPR=148.0;EPP=8.33041;EPPR=5.45321;DPRA=0.0;ODDS=68.9633;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984375;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.98;Dels=0.0;FS=2.219;HaplotypeScore [...]
+chr8 38426012 . A G 13391.599999999999 REJECT NS=2;DP=351;DPB=401.0;AC=4;AN=4;AF=1.0;RO=0;AO=400;PRO=0.0;PAO=0.0;QR=0;QA=15451;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=172;SAR=228;SRP=0.0;SAP=20.0346;AB=0.0;ABP=0.0;RUN=1;RPP=6.68009;RPPR=0.0;RPL=213.0;RPR=187.0;EPP=6.68009;EPPR=0.0;DPRA=0.0;ODDS=66.0857;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.9875;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.3 [...]
+chr8 41806890 . G A 1468.89 PASS SOMATIC;NS=2;DP=238;DPB=238.0;AC=1;AN=3;AF=0.25;RO=176;AO=61;PRO=0.0;PAO=0.0;QR=6724;QA=2308;PQR=0.0;PQA=0.0;SRF=46;SRR=130;SAF=14;SAR=47;SRP=90.0666;SAP=41.7764;AB=0.331522;ABP=48.3752;RUN=1;RPP=25.259;RPPR=31.4368;RPL=43.0;RPR=18.0;EPP=3.90025;EPPR=4.78696;DPRA=3.40741;ODDS=34.7008;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994318;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.318;Dels=0.0;FS=0.0;Hapl [...]
+chr8 48732074 . T A 51.5935 REJECT NS=2;DP=66;DPB=110.379;AC=2;AN=2;AF=0.0;RO=34;AO=3;PRO=34.75;PAO=1.0;QR=1283;QA=42;PQR=1226.0;PQA=16.0;SRF=0;SRR=34;SAF=0;SAR=3;SRP=76.8404;SAP=9.52472;AB=0.0454545;ABP=121.454;RUN=1;RPP=3.73412;RPPR=7.09778;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=7.09778;DPRA=0.0;ODDS=1.62704;GTI=0;TYPE=snp;CIGAR=1X28M;NUMALT=4;MEANALT=5.5;LEN=1;MQM=59.6667;MQMR=59.7647;PAIRED=1.0;PAIREDR=0.941176;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr8 48732074 . T TA 51.5935 REJECT NS=2;DP=66;DPB=110.379;AC=2;AN=4;AF=0.5;RO=34;AO=7;PRO=34.75;PAO=26.25;QR=1283;QA=141;PQR=1226.0;PQA=892.5;SRF=0;SRR=34;SAF=0;SAR=7;SRP=76.8404;SAP=18.2106;AB=0.106061;ABP=91.9749;RUN=1;RPP=5.80219;RPPR=7.09778;RPL=2.0;RPR=5.0;EPP=5.80219;EPPR=7.09778;DPRA=0.0;ODDS=1.62704;GTI=0;TYPE=ins;CIGAR=1M1I28M;NUMALT=4;MEANALT=5.5;LEN=1;MQM=60.0;MQMR=59.7647;PAIRED=1.0;PAIREDR=0.941176;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr8 48732074 . T TAA 51.5935 REJECT NS=2;DP=66;DPB=110.379;AC=2;AN=2;AF=0.0;RO=34;AO=4;PRO=34.75;PAO=24.25;QR=1283;QA=87;PQR=1226.0;PQA=836.5;SRF=0;SRR=34;SAF=0;SAR=4;SRP=76.8404;SAP=11.6962;AB=0.0606061;ABP=113.69;RUN=1;RPP=11.6962;RPPR=7.09778;RPL=4.0;RPR=0.0;EPP=11.6962;EPPR=7.09778;DPRA=0.0;ODDS=1.62704;GTI=0;TYPE=ins;CIGAR=1M2I28M;NUMALT=4;MEANALT=5.5;LEN=2;MQM=55.0;MQMR=59.7647;PAIRED=1.0;PAIREDR=0.941176;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr8 48732074 . TA T 51.5935 REJECT NS=2;DP=66;DPB=110.379;AC=2;AN=2;AF=0.0;RO=34;AO=13;PRO=34.75;PAO=18.75;QR=1283;QA=334;PQR=1226.0;PQA=631.0;SRF=0;SRR=34;SAF=0;SAR=13;SRP=76.8404;SAP=31.2394;AB=0.19697;ABP=55.6521;RUN=1;RPP=16.5402;RPPR=7.09778;RPL=11.0;RPR=2.0;EPP=16.5402;EPPR=7.09778;DPRA=0.0;ODDS=1.62704;GTI=0;TYPE=del;CIGAR=1M1D27M;NUMALT=4;MEANALT=5.5;LEN=1;MQM=56.0769;MQMR=59.7647;PAIRED=1.0;PAIREDR=0.941176;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr8 48805816 . A AG 12344.25 REJECT NS=2;DP=335;DPB=517.333;AC=4;AN=4;AF=1.0;RO=0;AO=371;PRO=12.5;PAO=19.5;QR=0;QA=13604;PQR=347.5;PQA=587.5;SRF=0;SRR=0;SAF=231;SAR=140;SRP=0.0;SAP=51.4792;AB=0.0;ABP=0.0;RUN=1;RPP=6.10655;RPPR=0.0;RPL=174.0;RPR=197.0;EPP=8.63506;EPPR=0.0;DPRA=0.0;ODDS=60.9323;GTI=0;TYPE=ins;CIGAR=1M1I2M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.2156;MQMR=0.0;PAIRED=0.994609;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=48805816;HOMLEN=1;HOMSEQ=G;SVLEN=1;SVTYPE=INS;FS=0.0;MLEAC= [...]
+chr8 48846519 . T C 12557.15 REJECT NS=2;DP=332;DPB=375.0;AC=4;AN=4;AF=1.0;RO=0;AO=375;PRO=0.0;PAO=0.0;QR=0;QA=14428;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=264;SAR=111;SRP=0.0;SAP=138.562;AB=0.0;ABP=0.0;RUN=1;RPP=32.2007;RPPR=0.0;RPL=152.0;RPR=223.0;EPP=42.9017;EPPR=0.0;DPRA=0.0;ODDS=56.1211;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.984;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.866;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.42;SOR=1.9655 [...]
+chr8 48852225 . C T 2064.175 REJECT NS=2;DP=320;DPB=377.0;AC=2;AN=4;AF=0.5;RO=282;AO=95;PRO=0.0;PAO=0.0;QR=10729;QA=3639;PQR=0.0;PQA=0.0;SRF=92;SRR=190;SAF=41;SAR=54;SRP=76.9636;SAP=6.87324;AB=0.251989;ABP=204.427;RUN=1;RPP=3.21602;RPPR=30.7312;RPL=49.0;RPR=46.0;EPP=8.15326;EPPR=10.8954;DPRA=0.0;ODDS=102.002;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9579;MQMR=60.0;PAIRED=0.978947;PAIREDR=0.996454;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.78;Dels=0.0;FS=5.592;HaplotypeS [...]
+chr8 51010911 . A G 9615.3 REJECT NS=2;DP=349;DPB=397.0;AC=2;AN=4;AF=0.5;RO=79;AO=318;PRO=0.0;PAO=0.0;QR=3023;QA=12065;PQR=0.0;PQA=0.0;SRF=30;SRR=49;SAF=135;SAR=183;SRP=12.9331;SAP=18.7432;AB=0.801008;ABP=315.445;RUN=1;RPP=65.942;RPPR=15.1321;RPL=207.0;RPR=111.0;EPP=22.9223;EPPR=6.33623;DPRA=0.0;ODDS=62.6804;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993711;PAIREDR=0.987342;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.256;Dels=0.0;FS=1.97;HaplotypeSco [...]
+chr8 57078933 . G T 4925.12 REJECT NS=2;DP=318;DPB=361.0;AC=2;AN=4;AF=0.5;RO=189;AO=172;PRO=0.0;PAO=0.0;QR=7246;QA=6628;PQR=0.0;PQA=0.0;SRF=90;SRR=99;SAF=84;SAR=88;SRP=3.94093;SAP=3.2123;AB=0.476454;ABP=4.74868;RUN=1;RPP=3.0608;RPPR=3.94093;RPL=85.0;RPR=87.0;EPP=3.0608;EPPR=7.15793;DPRA=0.0;ODDS=237.705;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988372;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6855;Dels=0.0;FS=2.0815;HaplotypeScore=3.846 [...]
+chr8 61504093 . A G 5332.91 REJECT NS=2;DP=216;DPB=247.0;AC=2;AN=4;AF=0.5;RO=65;AO=182;PRO=0.0;PAO=0.0;QR=2486;QA=6907;PQR=0.0;PQA=0.0;SRF=43;SRR=22;SAF=112;SAR=70;SRP=17.7429;SAP=24.0569;AB=0.736842;ABP=123.356;RUN=1;RPP=127.142;RPPR=53.8228;RPL=40.0;RPR=142.0;EPP=4.20342;EPPR=4.64726;DPRA=0.0;ODDS=131.271;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994505;PAIREDR=0.984615;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.2205;Dels=0.0;FS=4.684;HaplotypeSc [...]
+chr8 61504193 . G A 8043.17 REJECT NS=2;DP=315;DPB=357.0;AC=2;AN=4;AF=0.5;RO=92;AO=264;PRO=0.0;PAO=0.0;QR=3467;QA=10108;PQR=0.0;PQA=0.0;SRF=37;SRR=55;SAF=131;SAR=133;SRP=10.6577;SAP=3.0432;AB=0.739496;ABP=180.87;RUN=1;RPP=9.45891;RPPR=3.0103;RPL=146.0;RPR=118.0;EPP=20.415;EPPR=3.86001;DPRA=0.0;ODDS=179.163;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992424;PAIREDR=0.98913;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5765;Dels=0.0;FS=6.56;HaplotypeScore= [...]
+chr8 67491249 . A G 1121.6399999999999 REJECT NS=2;DP=34;DPB=41.0;AC=4;AN=4;AF=1.0;RO=0;AO=41;PRO=0.0;PAO=0.0;QR=0;QA=1539;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=41;SAR=0;SRP=0.0;SAP=92.0407;AB=0.0;ABP=0.0;RUN=1;RPP=14.9269;RPPR=0.0;RPL=13.0;RPR=28.0;EPP=14.9269;EPPR=0.0;DPRA=0.0;ODDS=13.08;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=42.7805;MQMR=0.0;PAIRED=0.97561;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=44.035;QD=29.53;SOR=5. [...]
+chr8 67491498 . A T 6127.405000000001 REJECT NS=2;DP=386;DPB=448.0;AC=2;AN=4;AF=0.5;RO=225;AO=223;PRO=0.0;PAO=0.0;QR=8624;QA=8410;PQR=0.0;PQA=0.0;SRF=151;SRR=74;SAF=147;SAR=76;SRP=60.231;SAP=52.0973;AB=0.497768;ABP=3.02969;RUN=1;RPP=80.1414;RPPR=30.1199;RPL=67.0;RPR=156.0;EPP=14.9388;EPPR=46.3336;DPRA=0.0;ODDS=335.297;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8834;MQMR=59.9378;PAIRED=0.995516;PAIREDR=0.995556;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.565;Dels=0.0;FS=0. [...]
+chr8 67491891 . T TA 251.887 REJECT NS=2;DP=255;DPB=330.1;AC=2;AN=2;AF=0.0;RO=168;AO=23;PRO=58.6667;PAO=46.6667;QR=6111;QA=829;PQR=1985.17;PQA=1549.17;SRF=159;SRR=9;SAF=22;SAR=1;SRP=293.832;SAP=44.6459;AB=0.0901961;ABP=374.979;RUN=1;RPP=37.093;RPPR=55.9529;RPL=2.0;RPR=21.0;EPP=30.2953;EPPR=59.3135;DPRA=0.0;ODDS=22.3836;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=2;MEANALT=16.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.913043;PAIREDR=0.988095;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr8 67491891 . TA T 251.887 REJECT NS=2;DP=255;DPB=330.1;AC=2;AN=4;AF=0.5;RO=168;AO=28;PRO=58.6667;PAO=45.6667;QR=6111;QA=1052;PQR=1985.17;PQA=1512.67;SRF=159;SRR=9;SAF=26;SAR=2;SRP=293.832;SAP=47.6806;AB=0.109804;ABP=340.236;RUN=1;RPP=14.1779;RPPR=55.9529;RPL=8.0;RPR=20.0;EPP=14.1779;EPPR=59.3135;DPRA=0.0;ODDS=22.3836;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=2;MEANALT=16.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988095;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.561;FS=9. [...]
+chr8 67509142 . A T 2398.07 PASS SOMATIC;NS=2;DP=428;DPB=428.0;AC=1;AN=3;AF=0.25;RO=331;AO=97;PRO=0.0;PAO=0.0;QR=12733;QA=3654;PQR=0.0;PQA=0.0;SRF=199;SRR=132;SAF=62;SAR=35;SRP=32.4597;SAP=19.3299;AB=0.325503;ABP=81.8245;RUN=1;RPP=12.8827;RPPR=24.3248;RPL=38.0;RPR=59.0;EPP=6.79359;EPPR=67.3082;DPRA=2.29231;ODDS=82.1254;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993958;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.482;Dels=0.0;FS=2.78; [...]
+chr8 68864728 . G A 3505.65 REJECT NS=1;DP=105;DPB=105.0;AC=2;AN=4;AF=1.0;RO=0;AO=105;PRO=0.0;PAO=0.0;QR=0;QA=3974;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=70;SAR=35;SRP=0.0;SAP=28.3441;AB=0.0;ABP=0.0;RUN=1;RPP=13.9504;RPPR=0.0;RPL=41.0;RPR=64.0;EPP=4.68544;EPPR=0.0;DPRA=0.0;ODDS=70.1305;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.990476;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.37;SOR=1.542 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr8 68968166 . C A 6088.575000000001 REJECT NS=2;DP=384;DPB=444.0;AC=2;AN=4;AF=0.5;RO=226;AO=218;PRO=0.0;PAO=0.0;QR=8597;QA=8472;PQR=0.0;PQA=0.0;SRF=116;SRR=110;SAF=117;SAR=101;SRP=3.3562;SAP=5.56029;AB=0.490991;ABP=3.3233;RUN=1;RPP=3.05014;RPPR=6.12338;RPL=110.0;RPR=108.0;EPP=3.6478;EPPR=9.5055;DPRA=0.0;ODDS=367.015;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990826;PAIREDR=0.99115;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.026;Dels=0.0;FS=1.833;Hap [...]
+chr8 68968171 . G A 6123.405000000001 REJECT NS=2;DP=388;DPB=449.0;AC=2;AN=4;AF=0.5;RO=227;AO=222;PRO=0.0;PAO=0.0;QR=8647;QA=8480;PQR=0.0;PQA=0.0;SRF=121;SRR=106;SAF=118;SAR=104;SRP=5.16264;SAP=4.92746;AB=0.494432;ABP=3.13121;RUN=1;RPP=4.41882;RPPR=11.0553;RPL=105.0;RPR=117.0;EPP=5.51434;EPPR=8.07069;DPRA=0.0;ODDS=375.916;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990991;PAIREDR=0.991189;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.065;Dels=0.0;FS=0.54 [...]
+chr8 68972907 . C G 2221.23 PASS SOMATIC;NS=2;DP=327;DPB=327.0;AC=1;AN=3;AF=0.25;RO=243;AO=83;PRO=0.0;PAO=0.0;QR=9460;QA=3265;PQR=0.0;PQA=0.0;SRF=160;SRR=83;SAF=53;SAR=30;SRP=55.9924;SAP=16.8502;AB=0.350211;ABP=49.1976;RUN=1;RPP=14.5479;RPPR=26.2531;RPL=31.0;RPR=52.0;EPP=3.24576;EPPR=22.7501;DPRA=2.63333;ODDS=57.1592;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987952;PAIREDR=0.983539;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=4.115;Dels=0.0;FS=4. [...]
+chr8 68993013 . AT GC 1584.865 REJECT NS=2;DP=358;DPB=410.0;AC=2;AN=4;AF=0.5;RO=329;AO=74;PRO=7.0;PAO=3.0;QR=12326;QA=2752;PQR=127.0;PQA=113.0;SRF=170;SRR=159;SAF=33;SAR=41;SRP=3.80893;SAP=4.88833;AB=0.182716;ABP=357.143;RUN=1;RPP=10.5224;RPPR=3.0697;RPL=29.0;RPR=45.0;EPP=3.12768;EPPR=29.2066;DPRA=0.0;ODDS=154.219;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=1;MEANALT=2.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990881;technology.ILLUMINA=1.0;MQ0=0;JOINED;BaseQRankSum=1.5495;Dels=0.0;FS=2.857;Hap [...]
+chr8 68995468 . C T 1042.9 REJECT NS=2;DP=310;DPB=352.0;AC=2;AN=4;AF=0.5;RO=285;AO=67;PRO=0.0;PAO=0.0;QR=10811;QA=2419;PQR=0.0;PQA=0.0;SRF=209;SRR=76;SAF=45;SAR=22;SRP=137.786;SAP=20.1552;AB=0.190341;ABP=296.184;RUN=1;RPP=12.3768;RPPR=71.7736;RPL=25.0;RPR=42.0;EPP=6.93191;EPPR=3.38364;DPRA=0.0;ODDS=101.993;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.4925;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989474;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.351;Dels=0.0;FS=3.5365;HaplotypeScore [...]
+chr8 68995633 . A G 1111.56 REJECT NS=2;DP=278;DPB=313.0;AC=2;AN=4;AF=0.5;RO=250;AO=63;PRO=0.0;PAO=0.0;QR=9648;QA=2387;PQR=0.0;PQA=0.0;SRF=59;SRR=191;SAF=21;SAR=42;SRP=154.353;SAP=18.2106;AB=0.201278;ABP=245.612;RUN=1;RPP=12.9715;RPPR=64.2979;RPL=40.0;RPR=23.0;EPP=3.872;EPPR=8.88196;DPRA=0.0;ODDS=92.1273;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.547;Dels=0.0;FS=4.8795;HaplotypeScore=4.8992; [...]
+chr8 68999938 . C T 1138.92 REJECT NS=2;DP=256;DPB=294.0;AC=2;AN=4;AF=0.5;RO=233;AO=61;PRO=0.0;PAO=0.0;QR=8862;QA=2365;PQR=0.0;PQA=0.0;SRF=169;SRR=64;SAF=42;SAR=19;SRP=105.759;SAP=21.8416;AB=0.207483;ABP=221.517;RUN=1;RPP=13.2981;RPPR=64.1564;RPL=22.0;RPR=39.0;EPP=13.2981;EPPR=5.10722;DPRA=0.0;ODDS=94.8984;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991416;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.651;Dels=0.0;FS=0.8865;HaplotypeScore=4.8 [...]
+chr8 69002965 . A G 1243.8 REJECT NS=2;DP=239;DPB=272.0;AC=2;AN=4;AF=0.5;RO=203;AO=67;PRO=0.0;PAO=0.0;QR=7784;QA=2558;PQR=0.0;PQA=0.0;SRF=65;SRR=138;SAF=21;SAR=46;SRP=60.0141;SAP=23.2666;AB=0.246324;ABP=155.045;RUN=1;RPP=3.82055;RPPR=28.6936;RPL=36.0;RPR=31.0;EPP=23.2666;EPPR=14.6592;DPRA=0.0;ODDS=171.169;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.2985;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995074;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.095;Dels=0.0;FS=0.8765;HaplotypeScore= [...]
+chr8 69009268 . C T 1407.365 REJECT NS=2;DP=326;DPB=371.0;AC=2;AN=4;AF=0.5;RO=296;AO=75;PRO=0.0;PAO=0.0;QR=11316;QA=2860;PQR=0.0;PQA=0.0;SRF=194;SRR=102;SAF=52;SAR=23;SRP=65.1027;SAP=27.3597;AB=0.202156;ABP=288.878;RUN=1;RPP=9.52472;RPPR=8.76177;RPL=30.0;RPR=45.0;EPP=6.51361;EPPR=4.06669;DPRA=0.0;ODDS=93.3375;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993243;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1225;Dels=0.0;FS=2.1865;HaplotypeScore [...]
+chr8 69020496 . T C 6038.8 REJECT NS=2;DP=370;DPB=422.0;AC=2;AN=4;AF=0.5;RO=205;AO=217;PRO=0.0;PAO=0.0;QR=7928;QA=8291;PQR=0.0;PQA=0.0;SRF=83;SRR=122;SAF=100;SAR=117;SRP=19.1216;SAP=5.90226;AB=0.514218;ABP=3.75128;RUN=1;RPP=13.9077;RPPR=4.80044;RPL=92.0;RPR=125.0;EPP=3.82085;EPPR=5.39362;DPRA=0.0;ODDS=298.514;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990244;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.253;Dels=0.0;FS=5.468;HaplotypeScore= [...]
+chr8 69136871 . T A 4540.76 REJECT NS=2;DP=298;DPB=341.0;AC=2;AN=4;AF=0.5;RO=174;AO=167;PRO=0.0;PAO=0.0;QR=6628;QA=6372;PQR=0.0;PQA=0.0;SRF=72;SRR=102;SAF=49;SAR=118;SRP=14.2421;SAP=64.9168;AB=0.489736;ABP=3.32233;RUN=1;RPP=20.8112;RPPR=12.7944;RPL=102.0;RPR=65.0;EPP=11.1371;EPPR=12.7944;DPRA=0.0;ODDS=251.231;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994253;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.915;Dels=0.0;FS=8.722;HaplotypeScore=3 [...]
+chr8 69143520 . A C 3097.0299999999997 REJECT NS=2;DP=248;DPB=292.0;AC=2;AN=4;AF=0.5;RO=169;AO=123;PRO=0.0;PAO=0.0;QR=6527;QA=4640;PQR=0.0;PQA=0.0;SRF=113;SRR=56;SAF=86;SAR=37;SRP=44.7565;SAP=45.3981;AB=0.421233;ABP=18.746;RUN=1;RPP=60.3689;RPPR=33.8606;RPL=33.0;RPR=90.0;EPP=3.16919;EPPR=9.80739;DPRA=0.0;ODDS=219.241;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.98374;PAIREDR=0.988166;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4085;Dels=0.0;FS=0.9485;H [...]
+chr8 69143589 . A G 5395.02 REJECT NS=2;DP=342;DPB=396.0;AC=2;AN=4;AF=0.5;RO=201;AO=195;PRO=0.0;PAO=0.0;QR=7677;QA=7466;PQR=0.0;PQA=0.0;SRF=95;SRR=106;SAF=121;SAR=74;SRP=4.3175;SAP=27.6092;AB=0.492424;ABP=3.20771;RUN=1;RPP=3.9123;RPPR=3.28038;RPL=102.0;RPR=93.0;EPP=29.7472;EPPR=4.83607;DPRA=0.0;ODDS=334.104;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989744;PAIREDR=0.985075;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6705;Dels=0.0;FS=13.959;HaplotypeSc [...]
+chr8 71037103 . T TA 430.163 REJECT NS=2;DP=172;DPB=210.6;AC=2;AN=4;AF=0.5;RO=133;AO=25;PRO=43.1667;PAO=22.1667;QR=4940;QA=879;PQR=1557.5;PQA=774.5;SRF=20;SRR=113;SAF=3;SAR=22;SRP=144.221;SAP=34.3664;AB=0.145349;ABP=190.918;RUN=1;RPP=3.09716;RPPR=16.7412;RPL=13.0;RPR=12.0;EPP=3.09716;EPPR=3.02663;DPRA=0.0;ODDS=10.9229;GTI=0;TYPE=ins;CIGAR=1M1I24M;NUMALT=2;MEANALT=4.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992481;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr8 71037103 . TA T 430.163 REJECT NS=2;DP=172;DPB=210.6;AC=2;AN=2;AF=0.0;RO=133;AO=9;PRO=43.1667;PAO=13.6667;QR=4940;QA=322;PQR=1557.5;PQA=478.0;SRF=20;SRR=113;SAF=3;SAR=6;SRP=144.221;SAP=5.18177;AB=0.0523256;ABP=302.421;RUN=1;RPP=3.25157;RPPR=16.7412;RPL=5.0;RPR=4.0;EPP=5.18177;EPPR=3.02663;DPRA=0.0;ODDS=10.9229;GTI=0;TYPE=del;CIGAR=1M1D23M;NUMALT=2;MEANALT=4.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992481;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr8 71075113 . T C 3592.79 REJECT NS=2;DP=275;DPB=318.0;AC=2;AN=4;AF=0.5;RO=160;AO=155;PRO=0.0;PAO=0.0;QR=5887;QA=5401;PQR=0.0;PQA=0.0;SRF=21;SRR=139;SAF=26;SAR=129;SRP=191.983;SAP=151.637;AB=0.487421;ABP=3.44733;RUN=1;RPP=109.048;RPPR=179.388;RPL=121.0;RPR=34.0;EPP=33.9573;EPPR=98.7722;DPRA=0.0;ODDS=203.818;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=59.7871;MQMR=59.9375;PAIRED=0.987097;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.509;Dels=0.0;FS=1.6435;Haplotyp [...]
+chr8 77694368 . GTTTC TTTTT 105.62 REJECT SOMATIC;NS=2;DP=238;DPB=261.4;AC=1;AN=4;AF=0.25;RO=198;AO=18;PRO=44.0;PAO=0.0;QR=7131;QA=240;PQR=1087.0;PQA=0.0;SRF=126;SRR=72;SAF=18;SAR=0;SRP=34.9902;SAP=42.0968;AB=0.0706522;ABP=297.622;RUN=1;RPP=10.7311;RPPR=263.104;RPL=13.0;RPR=5.0;EPP=10.7311;EPPR=39.9034;DPRA=0.0;ODDS=9.40273;GTI=0;TYPE=complex;CIGAR=1X3M1X;NUMALT=1;MEANALT=4.5;LEN=5;MQM=56.1111;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989899;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr8 77745635 . G A 2910.02 PASS SOMATIC;NS=2;DP=411;DPB=411.0;AC=1;AN=3;AF=0.25;RO=303;AO=108;PRO=0.0;PAO=0.0;QR=11643;QA=4202;PQR=0.0;PQA=0.0;SRF=112;SRR=191;SAF=38;SAR=70;SRP=47.7369;SAP=23.5991;AB=0.369863;ABP=45.9638;RUN=1;RPP=8.15749;RPPR=17.5226;RPL=62.0;RPR=46.0;EPP=3.332;EPPR=13.9107;DPRA=2.45378;ODDS=74.2979;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990099;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.748;Dels=0.0;FS=0.0;Ha [...]
+chr8 77765865 . C T 4059.5 PASS SOMATIC;NS=2;DP=438;DPB=438.0;AC=1;AN=3;AF=0.25;RO=290;AO=148;PRO=0.0;PAO=0.0;QR=11091;QA=5603;PQR=0.0;PQA=0.0;SRF=134;SRR=156;SAF=68;SAR=80;SRP=6.63441;SAP=5.12308;AB=0.43787;ABP=14.3431;RUN=1;RPP=4.47751;RPPR=4.47792;RPL=79.0;RPR=69.0;EPP=10.1116;EPPR=4.47792;DPRA=3.38;ODDS=63.3722;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993103;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.372;Dels=0.0;FS=0.399;Ha [...]
+chr8 80678865 . C A 3901.9300000000003 REJECT NS=2;DP=269;DPB=309.0;AC=2;AN=4;AF=0.5;RO=167;AO=142;PRO=0.0;PAO=0.0;QR=6307;QA=5438;PQR=0.0;PQA=0.0;SRF=106;SRR=61;SAF=90;SAR=52;SRP=29.341;SAP=25.092;AB=0.459547;ABP=7.40244;RUN=1;RPP=32.6157;RPPR=8.74455;RPL=49.0;RPR=93.0;EPP=14.9993;EPPR=6.76812;DPRA=0.0;ODDS=225.16;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988024;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.3955;Dels=0.0;FS=0.689;Haplotype [...]
+chr8 87027866 . T C 12658.75 REJECT NS=2;DP=339;DPB=385.0;AC=4;AN=4;AF=1.0;RO=0;AO=382;PRO=0.0;PAO=0.0;QR=0;QA=14569;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=244;SAR=138;SRP=0.0;SAP=66.8811;AB=0.0;ABP=0.0;RUN=1;RPP=10.3774;RPPR=0.0;RPL=173.0;RPR=209.0;EPP=35.8439;EPPR=0.0;DPRA=0.0;ODDS=59.8904;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992147;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=10.6246;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.85;SOR=1 [...]
+chr8 90955624 . T A 971.9 REJECT NS=2;DP=219;DPB=245.0;AC=2;AN=4;AF=0.5;RO=188;AO=57;PRO=0.0;PAO=0.0;QR=7077;QA=2124;PQR=0.0;PQA=0.0;SRF=54;SRR=134;SAF=18;SAR=39;SRP=76.9328;SAP=19.8106;AB=0.232653;ABP=155.111;RUN=1;RPP=60.9543;RPPR=147.898;RPL=48.0;RPR=9.0;EPP=3.35316;EPPR=21.4909;DPRA=0.0;ODDS=109.789;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.982456;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.075;Dels=0.0;FS=0.886;HaplotypeScore=4.8572 [...]
+chr8 90958422 . T C 1666.48 REJECT NS=2;DP=375;DPB=431.0;AC=2;AN=4;AF=0.5;RO=347;AO=84;PRO=0.0;PAO=0.0;QR=13201;QA=3213;PQR=0.0;PQA=0.0;SRF=194;SRR=153;SAF=40;SAR=44;SRP=13.5297;SAP=3.42391;AB=0.194896;ABP=351.499;RUN=1;RPP=4.66476;RPPR=3.06662;RPL=46.0;RPR=38.0;EPP=3.42391;EPPR=3.31693;DPRA=0.0;ODDS=54.2045;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991354;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.245;Dels=0.0;FS=3.514;HaplotypeScore=11 [...]
+chr8 90958530 . T C 708.0554999999999 REJECT NS=2;DP=280;DPB=315.0;AC=2;AN=4;AF=0.5;RO=265;AO=50;PRO=0.0;PAO=0.0;QR=10223;QA=1886;PQR=0.0;PQA=0.0;SRF=92;SRR=173;SAF=19;SAR=31;SRP=56.7727;SAP=9.26414;AB=0.15873;ABP=321.665;RUN=1;RPP=24.0302;RPPR=39.7942;RPL=36.0;RPR=14.0;EPP=3.70517;EPPR=5.37843;DPRA=0.0;ODDS=53.0269;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.98;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988679;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4765;Dels=0.0;FS=1.3715;Haplot [...]
+chr8 90967711 . A G 1667.8049999999998 REJECT NS=2;DP=366;DPB=414.0;AC=2;AN=4;AF=0.5;RO=326;AO=88;PRO=0.0;PAO=0.0;QR=12669;QA=3415;PQR=0.0;PQA=0.0;SRF=145;SRR=181;SAF=39;SAR=49;SRP=11.6429;SAP=5.47788;AB=0.21256;ABP=300.114;RUN=1;RPP=25.2185;RPPR=5.16845;RPL=59.0;RPR=29.0;EPP=3.40511;EPPR=5.67468;DPRA=0.0;ODDS=134.018;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988636;PAIREDR=0.98773;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1735;Dels=0.0;FS=4.5925; [...]
+chr8 90970935 . G A 1615.28 REJECT NS=2;DP=263;DPB=310.0;AC=2;AN=4;AF=0.5;RO=233;AO=77;PRO=0.0;PAO=0.0;QR=8818;QA=2867;PQR=0.0;PQA=0.0;SRF=169;SRR=64;SAF=56;SAR=21;SRP=105.759;SAP=37.5565;AB=0.248387;ABP=173.478;RUN=1;RPP=37.5565;RPPR=76.831;RPL=21.0;RPR=56.0;EPP=3.71532;EPPR=4.58532;DPRA=0.0;ODDS=63.5381;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987013;PAIREDR=0.991416;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4495;Dels=0.0;FS=1.5485;HaplotypeSco [...]
+chr8 90990479 . C G 2567.7200000000003 REJECT NS=2;DP=404;DPB=467.0;AC=2;AN=4;AF=0.5;RO=346;AO=121;PRO=0.0;PAO=0.0;QR=13164;QA=4630;PQR=0.0;PQA=0.0;SRF=192;SRR=154;SAF=62;SAR=59;SRP=12.0727;SAP=3.17181;AB=0.259101;ABP=238.408;RUN=1;RPP=5.18177;RPPR=7.93063;RPL=55.0;RPR=66.0;EPP=7.04816;EPPR=6.62524;DPRA=0.0;ODDS=190.67;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983471;PAIREDR=0.991329;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2365;Dels=0.0;FS=1.754; [...]
+chr8 90995019 . C T 1642.98 REJECT NS=2;DP=417;DPB=479.0;AC=2;AN=4;AF=0.5;RO=391;AO=87;PRO=0.0;PAO=0.0;QR=15104;QA=3339;PQR=0.0;PQA=0.0;SRF=178;SRR=213;SAF=47;SAR=40;SRP=9.81351;SAP=4.23331;AB=0.181628;ABP=424.725;RUN=1;RPP=4.23331;RPPR=4.25987;RPL=47.0;RPR=40.0;EPP=12.0207;EPPR=87.0313;DPRA=0.0;ODDS=40.7584;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988506;PAIREDR=0.997442;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.337;Dels=0.0;FS=5.0665;HaplotypeSc [...]
+chr8 93088151 . C T 5888.91 REJECT NS=2;DP=230;DPB=259.0;AC=2;AN=4;AF=0.5;RO=65;AO=194;PRO=0.0;PAO=0.0;QR=2487;QA=7614;PQR=0.0;PQA=0.0;SRF=39;SRR=26;SAF=125;SAR=69;SRP=8.65613;SAP=38.112;AB=0.749035;ABP=142.529;RUN=1;RPP=153.625;RPPR=43.9342;RPL=39.0;RPR=155.0;EPP=6.63688;EPPR=3.84548;DPRA=0.0;ODDS=130.623;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984536;PAIREDR=0.969231;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.67;Dels=0.0;FS=2.5015;HaplotypeScore [...]
+chr8 108970367 . A G 5921.435 REJECT NS=2;DP=364;DPB=417.0;AC=2;AN=4;AF=0.5;RO=206;AO=211;PRO=0.0;PAO=0.0;QR=8002;QA=8077;PQR=0.0;PQA=0.0;SRF=100;SRR=106;SAF=118;SAR=93;SRP=3.38978;SAP=9.44239;AB=0.505995;ABP=3.14048;RUN=1;RPP=9.44239;RPPR=11.2745;RPL=93.0;RPR=118.0;EPP=3.8439;EPPR=4.52822;DPRA=0.0;ODDS=329.258;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990291;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.128;Dels=0.0;FS=4.651;HaplotypeScor [...]
+chr8 109009081 . T C 5315.97 REJECT NS=2;DP=325;DPB=363.0;AC=2;AN=4;AF=0.5;RO=174;AO=189;PRO=0.0;PAO=0.0;QR=6640;QA=7242;PQR=0.0;PQA=0.0;SRF=106;SRR=68;SAF=105;SAR=84;SRP=21.031;SAP=8.07707;AB=0.520661;ABP=4.35625;RUN=1;RPP=144.57;RPPR=91.0673;RPL=39.0;RPR=150.0;EPP=3.94093;EPPR=8.00219;DPRA=0.0;ODDS=208.958;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989418;PAIREDR=0.988506;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.638;Dels=0.0;FS=3.5535;HaplotypeSc [...]
+chr8 109500880 . G A 5649.98 REJECT NS=2;DP=372;DPB=434.0;AC=2;AN=4;AF=0.5;RO=225;AO=209;PRO=0.0;PAO=0.0;QR=8535;QA=8053;PQR=0.0;PQA=0.0;SRF=99;SRR=126;SAF=102;SAR=107;SRP=10.0459;SAP=3.27005;AB=0.481567;ABP=4.29117;RUN=1;RPP=7.59221;RPPR=3.79203;RPL=94.0;RPR=115.0;EPP=17.234;EPPR=10.0459;DPRA=0.0;ODDS=402.936;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995215;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6155;Dels=0.0;FS=9.314;HaplotypeScore [...]
+chr8 117000266 . G GA 51.0858 REJECT NS=2;DP=222;DPB=247.176;AC=2;AN=2;AF=0.0;RO=175;AO=20;PRO=30.5;PAO=16.5;QR=6602;QA=658;PQR=1098.67;PQA=584.667;SRF=25;SRR=150;SAF=5;SAR=15;SRP=196.892;SAP=13.8677;AB=0.0988372;ABP=243.438;RUN=1;RPP=13.8677;RPPR=43.3252;RPL=15.0;RPR=5.0;EPP=3.0103;EPPR=4.51172;DPRA=0.0;ODDS=10.3552;GTI=0;TYPE=ins;CIGAR=1M1I16M;NUMALT=2;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988571;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr8 117000266 . GA G 51.0858 REJECT NS=2;DP=222;DPB=247.176;AC=2;AN=3;AF=0.25;RO=175;AO=19;PRO=30.5;PAO=15.0;QR=6602;QA=699;PQR=1098.67;PQA=535.667;SRF=25;SRR=150;SAF=3;SAR=16;SRP=196.892;SAP=22.325;AB=0.0988372;ABP=243.438;RUN=1;RPP=5.8675;RPPR=43.3252;RPL=12.0;RPR=7.0;EPP=3.12459;EPPR=4.51172;DPRA=0.0;ODDS=10.3552;GTI=0;TYPE=del;CIGAR=1M1D15M;NUMALT=2;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988571;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr8 117864952 . T TA 424.774 REJECT NS=2;DP=152;DPB=191.68;AC=2;AN=3;AF=0.25;RO=84;AO=19;PRO=25.5667;PAO=12.0667;QR=3147;QA=593;PQR=906.667;PQA=405.417;SRF=7;SRR=77;SAF=4;SAR=15;SRP=129.68;SAP=16.8392;AB=0.125;ABP=188.671;RUN=1;RPP=4.03889;RPPR=6.73282;RPL=11.0;RPR=8.0;EPP=5.8675;EPPR=3.1137;DPRA=0.0;ODDS=12.0227;GTI=0;TYPE=ins;CIGAR=1M1I24M;NUMALT=5;MEANALT=11.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988095;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr8 117864952 . T TAA 424.774 REJECT NS=2;DP=152;DPB=191.68;AC=2;AN=2;AF=0.0;RO=84;AO=5;PRO=25.5667;PAO=11.5667;QR=3147;QA=142;PQR=906.667;PQA=383.917;SRF=7;SRR=77;SAF=0;SAR=5;SRP=129.68;SAP=13.8677;AB=0.0328947;ABP=291.073;RUN=1;RPP=3.44459;RPPR=6.73282;RPL=3.0;RPR=2.0;EPP=3.44459;EPPR=3.1137;DPRA=0.0;ODDS=12.0227;GTI=0;TYPE=ins;CIGAR=1M2I24M;NUMALT=5;MEANALT=11.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988095;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr8 117864952 . TA T 424.774 REJECT NS=2;DP=152;DPB=191.68;AC=2;AN=3;AF=0.25;RO=84;AO=16;PRO=25.5667;PAO=18.1667;QR=3147;QA=548;PQR=906.667;PQA=612.667;SRF=7;SRR=77;SAF=5;SAR=11;SRP=129.68;SAP=7.89611;AB=0.105263;ABP=208.729;RUN=1;RPP=5.18177;RPPR=6.73282;RPL=6.0;RPR=10.0;EPP=7.89611;EPPR=3.1137;DPRA=0.0;ODDS=12.0227;GTI=0;TYPE=del;CIGAR=1M1D23M;NUMALT=5;MEANALT=11.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988095;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr8 117864967 . G A 424.774 REJECT NS=2;DP=152;DPB=191.68;AC=2;AN=2;AF=0.0;RO=84;AO=4;PRO=25.5667;PAO=15.5667;QR=3147;QA=82;PQR=906.667;PQA=480.917;SRF=7;SRR=77;SAF=3;SAR=1;SRP=129.68;SAP=5.18177;AB=0.0263158;ABP=299.245;RUN=1;RPP=3.0103;RPPR=6.73282;RPL=2.0;RPR=2.0;EPP=5.18177;EPPR=3.1137;DPRA=0.0;ODDS=12.0227;GTI=0;TYPE=snp;CIGAR=15M1X9M;NUMALT=5;MEANALT=11.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988095;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr8 117864967 . GAAAAATTTC AGAAAAATTTA 424.774 REJECT NS=2;DP=152;DPB=191.68;AC=2;AN=2;AF=0.0;RO=84;AO=2;PRO=25.5667;PAO=12.0667;QR=3147;QA=32;PQR=906.667;PQA=405.417;SRF=7;SRR=77;SAF=2;SAR=0;SRP=129.68;SAP=7.35324;AB=0.0571429;ABP=62.6327;RUN=1;RPP=7.35324;RPPR=6.73282;RPL=2.0;RPR=0.0;EPP=7.35324;EPPR=3.1137;DPRA=0.0;ODDS=12.0227;GTI=0;TYPE=complex;CIGAR=1M1I23M1X;NUMALT=5;MEANALT=8.0;LEN=26;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988095;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ: [...]
+chr8 123041540 . A G 5817.280000000001 REJECT NS=2;DP=383;DPB=443.0;AC=2;AN=4;AF=0.5;RO=234;AO=209;PRO=0.0;PAO=0.0;QR=9124;QA=8103;PQR=0.0;PQA=0.0;SRF=130;SRR=104;SAF=112;SAR=97;SRP=9.28344;SAP=5.34801;AB=0.471783;ABP=6.07389;RUN=1;RPP=5.34801;RPPR=3.15878;RPL=97.0;RPR=112.0;EPP=10.5845;EPPR=3.15878;DPRA=0.0;ODDS=368.661;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985646;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.9755;Dels=0.0;FS=5.807;Hap [...]
+chr8 128649634 . A C 1797.325 REJECT NS=2;DP=394;DPB=449.0;AC=2;AN=4;AF=0.5;RO=358;AO=90;PRO=0.0;PAO=0.0;QR=13731;QA=3431;PQR=0.0;PQA=0.0;SRF=167;SRR=191;SAF=42;SAR=48;SRP=6.50407;SAP=3.87889;AB=0.200445;ABP=352.966;RUN=1;RPP=5.42305;RPPR=3.22866;RPL=40.0;RPR=50.0;EPP=7.73928;EPPR=19.4116;DPRA=0.0;ODDS=88.7736;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988889;PAIREDR=0.997207;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.198;Dels=0.0;FS=3.3075;Haplotype [...]
+chr8 128650439 . CAAAAAA C 64.1957 REJECT NS=1;DP=25;DPB=53.1316;AC=1;AN=3;AF=0.0;RO=0;AO=3;PRO=31.0333;PAO=17.0333;QR=0;QA=57;PQR=917.967;PQA=536.967;SRF=0;SRR=0;SAF=2;SAR=1;SRP=0.0;SAP=3.73412;AB=0.12;ABP=34.3664;RUN=1;RPP=3.73412;RPPR=0.0;RPL=1.0;RPR=2.0;EPP=3.73412;EPPR=0.0;DPRA=0.0;ODDS=14.7816;GTI=0;TYPE=del;CIGAR=1M6D31M;NUMALT=4;MEANALT=11.0;LEN=6;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC [...]
+chr8 128650439 . CAAAAAAA C 64.1957 REJECT NS=1;DP=25;DPB=53.1316;AC=1;AN=4;AF=0.5;RO=0;AO=9;PRO=31.0333;PAO=15.5333;QR=0;QA=192;PQR=917.967;PQA=492.467;SRF=0;SRR=0;SAF=4;SAR=5;SRP=0.0;SAP=3.25157;AB=0.36;ABP=7.26639;RUN=1;RPP=9.04217;RPPR=0.0;RPL=2.0;RPR=7.0;EPP=3.25157;EPPR=0.0;DPRA=0.0;ODDS=14.7816;GTI=0;TYPE=del;CIGAR=1M7D30M;NUMALT=4;MEANALT=11.0;LEN=7;MQM=61.1111;MQMR=0.0;PAIRED=0.888889;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.547;FS=5.401;MLEAC=1;MLEAF [...]
+chr8 128650439 . CAAAAAAAAA C 64.1957 REJECT NS=1;DP=25;DPB=53.1316;AC=1;AN=3;AF=0.0;RO=0;AO=4;PRO=31.0333;PAO=10.2;QR=0;QA=87;PQR=917.967;PQA=353.8;SRF=0;SRR=0;SAF=1;SAR=3;SRP=0.0;SAP=5.18177;AB=0.16;ABP=28.1125;RUN=1;RPP=11.6962;RPPR=0.0;RPL=0.0;RPR=4.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=14.7816;GTI=0;TYPE=del;CIGAR=1M9D28M;NUMALT=4;MEANALT=11.0;LEN=9;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:C [...]
+chr8 128650439 . CAAAAAAAAAA C 64.1957 REJECT NS=1;DP=25;DPB=53.1316;AC=1;AN=3;AF=0.0;RO=0;AO=2;PRO=31.0333;PAO=10.2;QR=0;QA=71;PQR=917.967;PQA=353.8;SRF=0;SRR=0;SAF=1;SAR=1;SRP=0.0;SAP=3.0103;AB=0.08;ABP=41.3151;RUN=1;RPP=7.35324;RPPR=0.0;RPL=0.0;RPR=2.0;EPP=3.0103;EPPR=0.0;DPRA=0.0;ODDS=14.7816;GTI=0;TYPE=del;CIGAR=1M10D27M;NUMALT=4;MEANALT=11.0;LEN=10;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC: [...]
+chr8 128650460 . A AAAAAAAAAAAG 653.73 PASS DP=71;AC=1;AN=4;AF=0.5;BaseQRankSum=-0.069;FS=2.615;MLEAC=1;MLEAF=0.5;MQ=55.36;MQRankSum=-0.363;QD=9.21;ReadPosRankSum=-3.282;SOR=1.125;ClippingRankSum=0.45 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:49,13:62:99.0:691,0,1826:13:21:62:1:.:.:.:.:.:-0.00044971 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00653895
+chr8 128650492 . C G 1257.97 REJECT NS=1;DP=133;DPB=133.0;AC=1;AN=4;AF=0.5;RO=82;AO=51;PRO=0.0;PAO=0.0;QR=2978;QA=1946;PQR=0.0;PQA=0.0;SRF=38;SRR=44;SAF=30;SAR=21;SRP=3.96363;SAP=6.45911;AB=0.383459;ABP=18.7004;RUN=1;RPP=49.3776;RPPR=15.8273;RPL=9.0;RPR=42.0;EPP=25.534;EPPR=5.65844;DPRA=0.0;ODDS=289.657;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.5098;MQMR=59.878;PAIRED=0.980392;PAIREDR=0.963415;technology.ILLUMINA=1.0;BaseQRankSum=0.844;FS=12.101;MLEAC=1;MLEAF=0.5;MQ=59.89 [...]
+chr8 128653001 . T C 1596.135 REJECT NS=2;DP=347;DPB=403.0;AC=2;AN=4;AF=0.5;RO=317;AO=86;PRO=0.0;PAO=0.0;QR=12097;QA=3324;PQR=0.0;PQA=0.0;SRF=155;SRR=162;SAF=41;SAR=45;SRP=3.34595;SAP=3.41429;AB=0.2134;ABP=290.534;RUN=1;RPP=4.62628;RPPR=5.48318;RPL=47.0;RPR=39.0;EPP=3.91929;EPPR=3.01715;DPRA=0.0;ODDS=167.605;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996845;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.285;Dels=0.0;FS=4.2505;HaplotypeScore=7 [...]
+chr8 128653726 . T C 1188.04 REJECT NS=2;DP=363;DPB=411.0;AC=2;AN=4;AF=0.5;RO=342;AO=69;PRO=0.0;PAO=0.0;QR=13180;QA=2629;PQR=0.0;PQA=0.0;SRF=196;SRR=146;SAF=38;SAR=31;SRP=18.8836;SAP=4.55236;AB=0.167883;ABP=396.776;RUN=1;RPP=3.29354;RPPR=17.6392;RPL=36.0;RPR=33.0;EPP=12.1053;EPPR=35.9253;DPRA=0.0;ODDS=26.9064;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985507;PAIREDR=0.997076;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.602;Dels=0.0;FS=3.456;HaplotypeSc [...]
+chr8 128750540 . A G 2205.58 PASS SOMATIC;NS=2;DP=390;DPB=390.0;AC=1;AN=3;AF=0.25;RO=301;AO=88;PRO=0.0;PAO=0.0;QR=11448;QA=3412;PQR=0.0;PQA=0.0;SRF=131;SRR=170;SAF=41;SAR=47;SRP=13.9831;SAP=3.89863;AB=0.294314;ABP=112.884;RUN=1;RPP=3.109;RPPR=5.0952;RPL=43.0;RPR=45.0;EPP=4.58955;EPPR=3.07523;DPRA=3.28571;ODDS=57.1103;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993355;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.991;Dels=0.0;FS=2.152;H [...]
+chr8 128751902 . A AT 636.159 REJECT NS=2;DP=270;DPB=393.276;AC=2;AN=4;AF=0.5;RO=169;AO=30;PRO=114.333;PAO=84.3333;QR=6258;QA=1108;PQR=4071.17;PQA=2952.17;SRF=95;SRR=74;SAF=12;SAR=18;SRP=8.67669;SAP=5.61607;AB=0.111111;ABP=357.684;RUN=1;RPP=4.16842;RPPR=17.0028;RPL=13.0;RPR=17.0;EPP=4.16842;EPPR=6.72365;DPRA=0.0;ODDS=14.8648;GTI=0;TYPE=ins;CIGAR=1M1I28M;NUMALT=2;MEANALT=16.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994083;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:Q [...]
+chr8 128751902 . AT A 636.159 REJECT NS=2;DP=270;DPB=393.276;AC=2;AN=2;AF=0.0;RO=169;AO=22;PRO=114.333;PAO=71.3333;QR=6258;QA=759;PQR=4071.17;PQA=2444.67;SRF=95;SRR=74;SAF=14;SAR=8;SRP=8.67669;SAP=6.56362;AB=0.0814815;ABP=413.789;RUN=1;RPP=3.40511;RPPR=17.0028;RPL=12.0;RPR=10.0;EPP=3.40511;EPPR=6.72365;DPRA=0.0;ODDS=14.8648;GTI=0;TYPE=del;CIGAR=1M1D27M;NUMALT=2;MEANALT=16.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994083;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr8 128752212 . C T 481.051 REJECT NS=2;DP=140;DPB=239.107;AC=2;AN=2;AF=0.0;RO=59;AO=21;PRO=67.85;PAO=19.1;QR=2047;QA=282;PQR=2370.68;PQA=532.033;SRF=20;SRR=39;SAF=0;SAR=21;SRP=16.2968;SAP=48.6112;AB=0.15;ABP=151.973;RUN=1;RPP=8.07707;RPPR=22.4799;RPL=7.0;RPR=14.0;EPP=8.07707;EPPR=3.93042;DPRA=0.0;ODDS=14.9122;GTI=0;TYPE=snp;CIGAR=1X27M;NUMALT=5;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=59.3729;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr8 128752212 . C CT 481.051 REJECT NS=2;DP=140;DPB=239.107;AC=2;AN=2;AF=0.0;RO=59;AO=10;PRO=67.85;PAO=32.85;QR=2047;QA=205;PQR=2370.68;PQA=1114.68;SRF=20;SRR=39;SAF=2;SAR=8;SRP=16.2968;SAP=10.8276;AB=0.0714286;ABP=226.362;RUN=1;RPP=3.87889;RPPR=22.4799;RPL=6.0;RPR=4.0;EPP=3.87889;EPPR=3.93042;DPRA=0.0;ODDS=14.9122;GTI=0;TYPE=ins;CIGAR=1M1I27M;NUMALT=5;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=59.3729;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr8 128752212 . CT C 481.051 REJECT NS=2;DP=140;DPB=239.107;AC=2;AN=4;AF=0.5;RO=59;AO=22;PRO=67.85;PAO=44.85;QR=2047;QA=503;PQR=2370.68;PQA=1456.18;SRF=20;SRR=39;SAF=4;SAR=18;SRP=16.2968;SAP=22.3561;AB=0.157143;ABP=145.955;RUN=1;RPP=3.0103;RPPR=22.4799;RPL=11.0;RPR=11.0;EPP=4.58955;EPPR=3.93042;DPRA=0.0;ODDS=14.9122;GTI=0;TYPE=del;CIGAR=1M1D26M;NUMALT=5;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=59.3729;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.343;FS=1.744; [...]
+chr8 128752212 . CTT C 481.051 REJECT NS=2;DP=140;DPB=239.107;AC=2;AN=2;AF=0.0;RO=59;AO=6;PRO=67.85;PAO=28.85;QR=2047;QA=191;PQR=2370.68;PQA=960.183;SRF=20;SRR=39;SAF=2;SAR=4;SRP=16.2968;SAP=4.45795;AB=0.0428571;ABP=257.135;RUN=1;RPP=8.80089;RPPR=22.4799;RPL=5.0;RPR=1.0;EPP=3.0103;EPPR=3.93042;DPRA=0.0;ODDS=14.9122;GTI=0;TYPE=del;CIGAR=1M2D25M;NUMALT=5;MEANALT=12.5;LEN=2;MQM=60.0;MQMR=59.3729;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.13;FS=0.0; [...]
+chr8 128752212 . CTTT C 481.051 REJECT NS=2;DP=140;DPB=239.107;AC=2;AN=2;AF=0.0;RO=59;AO=6;PRO=67.85;PAO=23.5;QR=2047;QA=177;PQR=2370.68;PQA=788.233;SRF=20;SRR=39;SAF=3;SAR=3;SRP=16.2968;SAP=3.0103;AB=0.0428571;ABP=257.135;RUN=1;RPP=4.45795;RPPR=22.4799;RPL=4.0;RPR=2.0;EPP=8.80089;EPPR=3.93042;DPRA=0.0;ODDS=14.9122;GTI=0;TYPE=del;CIGAR=1M3D24M;NUMALT=5;MEANALT=12.5;LEN=3;MQM=60.0;MQMR=59.3729;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr8 135001704 . A G 3043.605 REJECT NS=2;DP=207;DPB=240.0;AC=2;AN=4;AF=0.5;RO=125;AO=115;PRO=0.0;PAO=0.0;QR=4751;QA=4358;PQR=0.0;PQA=0.0;SRF=67;SRR=58;SAF=71;SAR=44;SRP=4.41741;SAP=16.7755;AB=0.479167;ABP=3.91508;RUN=1;RPP=64.3591;RPPR=48.1943;RPL=29.0;RPR=86.0;EPP=7.25883;EPPR=3.02767;DPRA=0.0;ODDS=204.166;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.3825;Dels=0.0;FS=3.7545;HaplotypeScore=5.876 [...]
+chr9 2029018 . G A 1836.98 PASS SOMATIC;NS=2;DP=296;DPB=296.0;AC=1;AN=3;AF=0.25;RO=220;AO=76;PRO=0.0;PAO=0.0;QR=8400;QA=2831;PQR=0.0;PQA=0.0;SRF=178;SRR=42;SAF=61;SAR=15;SRP=185.572;SAP=63.4687;AB=0.353488;ABP=43.0967;RUN=1;RPP=16.8392;RPPR=11.8936;RPL=27.0;RPR=49.0;EPP=3.0103;EPPR=6.20829;DPRA=2.65432;ODDS=51.5642;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986364;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.742;Dels=0.0;FS=1.371;Hap [...]
+chr9 2029199 . G A 10416.585 REJECT NS=2;DP=411;DPB=473.0;AC=3;AN=4;AF=0.75;RO=109;AO=364;PRO=0.0;PAO=0.0;QR=4165;QA=13955;PQR=0.0;PQA=0.0;SRF=49;SRR=60;SAF=177;SAR=187;SRP=5.42083;SAP=3.60686;AB=0.688571;ABP=111.112;RUN=1;RPP=3.03416;RPPR=8.76769;RPL=181.0;RPR=183.0;EPP=21.7184;EPPR=13.5489;DPRA=0.0;ODDS=77.6787;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9451;MQMR=60.0;PAIRED=0.994505;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.026;Dels=0.0;FS=1.5575;Haplotyp [...]
+chr9 2039776 . ACAG A 3082.6 REJECT NS=2;DP=173;DPB=288.439;AC=2;AN=3;AF=0.625;RO=32;AO=111;PRO=95.8333;PAO=90.8333;QR=1225;QA=3923;PQR=3523.5;PQA=3334.5;SRF=15;SRR=17;SAF=71;SAR=40;SRP=3.28173;SAP=21.8102;AB=0.596899;ABP=13.531;RUN=1;RPP=6.31642;RPPR=3.28173;RPL=49.0;RPR=62.0;EPP=6.31642;EPPR=7.35324;DPRA=0.0;ODDS=6.7038;GTI=0;TYPE=del;CIGAR=1M3D37M;NUMALT=2;MEANALT=8.0;LEN=3;MQM=60.7207;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.336; [...]
+chr9 2039776 . ACAGCAG A 3082.6 REJECT NS=2;DP=173;DPB=288.439;AC=2;AN=2;AF=0.0;RO=32;AO=14;PRO=95.8333;PAO=80.3333;QR=1225;QA=464;PQR=3523.5;PQA=2936.0;SRF=15;SRR=17;SAF=9;SAR=5;SRP=3.28173;SAP=5.49198;AB=0.0852713;ABP=195.733;RUN=1;RPP=5.49198;RPPR=3.28173;RPL=9.0;RPR=5.0;EPP=3.63072;EPPR=7.35324;DPRA=0.0;ODDS=6.7038;GTI=0;TYPE=del;CIGAR=1M6D34M;NUMALT=2;MEANALT=8.0;LEN=6;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60. [...]
+chr9 2073514 . A T 2998.88 REJECT NS=2;DP=214;DPB=247.0;AC=2;AN=4;AF=0.5;RO=134;AO=113;PRO=0.0;PAO=0.0;QR=5046;QA=4311;PQR=0.0;PQA=0.0;SRF=82;SRR=52;SAF=71;SAR=42;SRP=17.5948;SAP=19.1714;AB=0.45749;ABP=6.8873;RUN=1;RPP=99.881;RPPR=96.6105;RPL=21.0;RPR=92.0;EPP=7.33403;EPPR=24.012;DPRA=0.0;ODDS=183.326;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99115;PAIREDR=0.992537;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.268;Dels=0.0;FS=0.757;HaplotypeScore=0.966 [...]
+chr9 2086804 . G A 2875.13 REJECT NS=2;DP=184;DPB=211.0;AC=2;AN=4;AF=0.5;RO=100;AO=109;PRO=0.0;PAO=0.0;QR=3789;QA=4172;PQR=0.0;PQA=0.0;SRF=85;SRR=15;SAF=89;SAR=20;SRP=109.412;SAP=97.8578;AB=0.516588;ABP=3.51458;RUN=1;RPP=47.0175;RPPR=61.7269;RPL=31.0;RPR=78.0;EPP=13.5489;EPPR=28.1125;DPRA=0.0;ODDS=123.464;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.088;Dels=0.0;FS=3.437;HaplotypeScore=3.8904;M [...]
+chr9 2096706 . A T 776.518 REJECT NS=2;DP=440;DPB=440.0;AC=1;AN=4;AF=0.25;RO=385;AO=55;PRO=0.0;PAO=0.0;QR=14807;QA=2095;PQR=0.0;PQA=0.0;SRF=190;SRR=195;SAF=26;SAR=29;SRP=3.1513;SAP=3.36563;AB=0.302752;ABP=39.8456;RUN=1;RPP=4.94488;RPPR=4.27934;RPL=31.0;RPR=24.0;EPP=3.04978;EPPR=15.4695;DPRA=0.0;ODDS=31.7006;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.98961;technology.ILLUMINA=1.0;BaseQRankSum=-1.242;FS=0.778;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankS [...]
+chr9 2096774 . G A 1488.025 REJECT NS=2;DP=280;DPB=327.0;AC=2;AN=4;AF=0.5;RO=257;AO=70;PRO=0.0;PAO=0.0;QR=9941;QA=2729;PQR=0.0;PQA=0.0;SRF=98;SRR=159;SAF=33;SAR=37;SRP=34.4502;SAP=3.50664;AB=0.214067;ABP=235.225;RUN=1;RPP=9.09042;RPPR=40.9392;RPL=42.0;RPR=28.0;EPP=7.47733;EPPR=4.03267;DPRA=0.0;ODDS=60.7403;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988327;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7205;Dels=0.0;FS=3.9615;HaplotypeScore=1. [...]
+chr9 2101545 . T A 4917.825000000001 REJECT NS=2;DP=319;DPB=365.0;AC=2;AN=4;AF=0.5;RO=184;AO=181;PRO=0.0;PAO=0.0;QR=7095;QA=6862;PQR=0.0;PQA=0.0;SRF=123;SRR=61;SAF=116;SAR=65;SRP=48.3752;SAP=34.2147;AB=0.49589;ABP=3.06384;RUN=1;RPP=53.698;RPPR=40.0197;RPL=58.0;RPR=123.0;EPP=19.4343;EPPR=16.6528;DPRA=0.0;ODDS=266.612;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983425;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6405;Dels=0.0;FS=3.0495;Haploty [...]
+chr9 2157934 . C T 6791.455 REJECT NS=2;DP=316;DPB=360.0;AC=3;AN=4;AF=0.75;RO=113;AO=246;PRO=0.0;PAO=0.0;QR=4308;QA=9449;PQR=0.0;PQA=0.0;SRF=32;SRR=81;SAF=83;SAR=163;SRP=49.1493;SAP=59.5039;AB=0.583942;ABP=19.7798;RUN=1;RPP=51.3476;RPPR=3.95191;RPL=160.0;RPR=86.0;EPP=20.0996;EPPR=11.4848;DPRA=0.0;ODDS=54.6874;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995935;PAIREDR=0.99115;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.331;Dels=0.0;FS=1.848;HaplotypeSc [...]
+chr9 4502848 . C G 5931.46 REJECT NS=2;DP=361;DPB=418.0;AC=2;AN=4;AF=0.5;RO=202;AO=216;PRO=0.0;PAO=0.0;QR=7763;QA=8276;PQR=0.0;PQA=0.0;SRF=114;SRR=88;SAF=120;SAR=96;SRP=10.2772;SAP=8.80089;AB=0.516746;ABP=4.0285;RUN=1;RPP=12.0581;RPPR=3.0103;RPL=93.0;RPR=123.0;EPP=4.01561;EPPR=3.1823;DPRA=0.0;ODDS=332.088;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.896;Dels=0.0;FS=2.487;HaplotypeScore=1.9664;MLE [...]
+chr9 5064525 . C CA 183.355 REJECT NS=2;DP=115;DPB=201.0;AC=2;AN=3;AF=0.25;RO=59;AO=14;PRO=43.9833;PAO=39.9833;QR=2081;QA=385;PQR=1509.42;PQA=1350.42;SRF=42;SRR=17;SAF=9;SAR=5;SRP=26.0132;SAP=5.49198;AB=0.121739;ABP=145.931;RUN=1;RPP=8.59409;RPPR=71.062;RPL=4.0;RPR=10.0;EPP=5.49198;EPPR=13.6468;DPRA=0.0;ODDS=9.4066;GTI=0;TYPE=ins;CIGAR=1M1I31M;NUMALT=4;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr9 5064525 . CA C 183.355 PASS SOMATIC;NS=2;DP=115;DPB=201.0;AC=2;AN=3;AF=0.25;RO=59;AO=14;PRO=43.9833;PAO=37.15;QR=2081;QA=457;PQR=1509.42;PQA=1246.75;SRF=42;SRR=17;SAF=11;SAR=3;SRP=26.0132;SAP=12.937;AB=0.121739;ABP=145.931;RUN=1;RPP=18.5208;RPPR=71.062;RPL=2.0;RPR=12.0;EPP=5.49198;EPPR=13.6468;DPRA=0.0;ODDS=9.4066;GTI=0;TYPE=del;CIGAR=1M1D30M;NUMALT=4;MEANALT=11.5;LEN=1;MQM=60.7143;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.387;FS [...]
+chr9 5064525 . CAA C 183.355 REJECT NS=2;DP=115;DPB=201.0;AC=2;AN=2;AF=0.0;RO=59;AO=5;PRO=43.9833;PAO=36.9;QR=2081;QA=126;PQR=1509.42;PQA=1261.5;SRF=42;SRR=17;SAF=2;SAR=3;SRP=26.0132;SAP=3.44459;AB=0.0574713;ABP=150.995;RUN=1;RPP=3.44459;RPPR=71.062;RPL=3.0;RPR=2.0;EPP=3.44459;EPPR=13.6468;DPRA=0.0;ODDS=9.4066;GTI=0;TYPE=del;CIGAR=1M2D29M;NUMALT=4;MEANALT=17.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr9 5064541 . G A 183.355 REJECT NS=2;DP=115;DPB=201.0;AC=2;AN=2;AF=0.0;RO=59;AO=5;PRO=43.9833;PAO=28.9833;QR=2081;QA=70;PQR=1509.42;PQA=798.917;SRF=42;SRR=17;SAF=5;SAR=0;SRP=26.0132;SAP=13.8677;AB=0.0434783;ABP=211.188;RUN=1;RPP=6.91895;RPPR=71.062;RPL=4.0;RPR=1.0;EPP=6.91895;EPPR=13.6468;DPRA=0.0;ODDS=9.4066;GTI=0;TYPE=snp;CIGAR=16M1X15M;NUMALT=4;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr9 5068174 . C A 180.73 REJECT NS=2;DP=169;DPB=236.926;AC=2;AN=2;AF=0.0;RO=63;AO=8;PRO=38.7167;PAO=25.2167;QR=2216;QA=182;PQR=1279.73;PQA=850.9;SRF=42;SRR=21;SAF=2;SAR=6;SRP=18.2106;SAP=7.35324;AB=0.0473373;ABP=303.791;RUN=1;RPP=7.35324;RPPR=45.2334;RPL=2.0;RPR=6.0;EPP=3.0103;EPPR=3.872;DPRA=0.0;ODDS=2.97827;GTI=0;TYPE=snp;CIGAR=1X26M;NUMALT=4;MEANALT=23.0;LEN=1;MQM=58.75;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984127;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr9 5068174 . C CA 180.73 REJECT NS=2;DP=169;DPB=236.926;AC=2;AN=4;AF=0.5;RO=63;AO=18;PRO=38.7167;PAO=35.7167;QR=2216;QA=536;PQR=1279.73;PQA=1189.73;SRF=42;SRR=21;SAF=13;SAR=5;SRP=18.2106;SAP=10.7311;AB=0.106509;ABP=230.295;RUN=1;RPP=20.3821;RPPR=45.2334;RPL=3.0;RPR=15.0;EPP=7.35324;EPPR=3.872;DPRA=0.0;ODDS=2.97827;GTI=0;TYPE=ins;CIGAR=1M1I26M;NUMALT=4;MEANALT=23.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984127;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr9 5068174 . CA C 180.73 REJECT NS=2;DP=169;DPB=236.926;AC=2;AN=2;AF=0.0;RO=63;AO=16;PRO=38.7167;PAO=32.05;QR=2216;QA=474;PQR=1279.73;PQA=1061.4;SRF=42;SRR=21;SAF=6;SAR=10;SRP=18.2106;SAP=5.18177;AB=0.0946746;ABP=244.172;RUN=1;RPP=3.0103;RPPR=45.2334;RPL=8.0;RPR=8.0;EPP=5.18177;EPPR=3.872;DPRA=0.0;ODDS=2.97827;GTI=0;TYPE=del;CIGAR=1M1D25M;NUMALT=4;MEANALT=23.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984127;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr9 5068190 . C A 180.73 REJECT NS=2;DP=169;DPB=236.926;AC=2;AN=2;AF=0.0;RO=63;AO=10;PRO=38.7167;PAO=25.3;QR=2216;QA=156;PQR=1279.73;PQA=706.233;SRF=42;SRR=21;SAF=10;SAR=0;SRP=18.2106;SAP=24.725;AB=0.0591716;ABP=288.27;RUN=1;RPP=3.87889;RPPR=45.2334;RPL=4.0;RPR=6.0;EPP=3.87889;EPPR=3.872;DPRA=0.0;ODDS=2.97827;GTI=0;TYPE=snp;CIGAR=16M1X10M;NUMALT=4;MEANALT=23.0;LEN=1;MQM=58.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984127;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr9 5070905 . C T 2548.6 PASS SOMATIC;NS=2;DP=461;DPB=461.0;AC=1;AN=3;AF=0.25;RO=358;AO=103;PRO=0.0;PAO=0.0;QR=13682;QA=3919;PQR=0.0;PQA=0.0;SRF=163;SRR=195;SAF=54;SAR=49;SRP=9.22144;SAP=3.53736;AB=0.304734;ABP=114.95;RUN=1;RPP=9.10307;RPPR=4.97554;RPL=43.0;RPR=60.0;EPP=5.56125;EPPR=3.10735;DPRA=2.74797;ODDS=77.7305;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994413;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.976;Dels=0.0;FS=7.094;H [...]
+chr9 5071049 . G A 3475.53 PASS SOMATIC;NS=2;DP=507;DPB=507.0;AC=1;AN=3;AF=0.25;RO=374;AO=133;PRO=0.0;PAO=0.0;QR=14268;QA=5069;PQR=0.0;PQA=0.0;SRF=210;SRR=164;SAF=79;SAR=54;SRP=15.296;SAP=13.2146;AB=0.354667;ABP=71.8083;RUN=1;RPP=6.68384;RPPR=5.82044;RPL=59.0;RPR=74.0;EPP=3.41847;EPPR=4.14829;DPRA=2.84091;ODDS=83.2821;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991979;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.82;Dels=0.0;FS=2.349;H [...]
+chr9 5072846 . G A 3368.96 PASS SOMATIC;NS=2;DP=470;DPB=470.0;AC=1;AN=3;AF=0.25;RO=341;AO=129;PRO=0.0;PAO=0.0;QR=13059;QA=4889;PQR=0.0;PQA=0.0;SRF=170;SRR=171;SAF=69;SAR=60;SRP=3.01667;SAP=4.37378;AB=0.365439;ABP=58.5274;RUN=1;RPP=6.79775;RPPR=3.5261;RPL=72.0;RPR=57.0;EPP=17.167;EPPR=5.30913;DPRA=3.01709;ODDS=73.9909;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994135;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.243;Dels=0.0;FS=1.321; [...]
+chr9 5079498 . G GT 206.977 REJECT NS=2;DP=385;DPB=447.778;AC=2;AN=3;AF=0.25;RO=285;AO=33;PRO=57.6667;PAO=40.6667;QR=10545;QA=1161;PQR=1998.83;PQA=1391.83;SRF=120;SRR=165;SAF=19;SAR=14;SRP=18.4392;SAP=4.65535;AB=0.0947368;ABP=409.579;RUN=1;RPP=3.0761;RPPR=3.62746;RPL=16.0;RPR=17.0;EPP=3.60252;EPPR=17.0982;DPRA=0.0;ODDS=7.78822;GTI=0;TYPE=ins;CIGAR=1M1I17M;NUMALT=2;MEANALT=10.0;LEN=1;MQM=60.303;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989474;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR: [...]
+chr9 5079498 . GT G 206.977 REJECT NS=2;DP=385;DPB=447.778;AC=2;AN=2;AF=0.0;RO=285;AO=28;PRO=57.6667;PAO=35.6667;QR=10545;QA=998;PQR=1998.83;PQA=1191.33;SRF=120;SRR=165;SAF=13;SAR=15;SRP=18.4392;SAP=3.32051;AB=0.077193;ABP=445.541;RUN=1;RPP=4.25114;RPPR=3.62746;RPL=16.0;RPR=12.0;EPP=3.32051;EPPR=17.0982;DPRA=0.0;ODDS=7.78822;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=2;MEANALT=10.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.964286;PAIREDR=0.989474;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR [...]
+chr9 5079828 . A T 234.747 REJECT NS=2;DP=309;DPB=358.647;AC=2;AN=2;AF=0.0;RO=229;AO=11;PRO=34.4167;PAO=19.0833;QR=8576;QA=379;PQR=1197.17;PQA=633.5;SRF=158;SRR=71;SAF=10;SAR=1;SRP=74.7827;SAP=19.0002;AB=0.0355987;ABP=581.852;RUN=1;RPP=26.8965;RPPR=85.0237;RPL=0.0;RPR=11.0;EPP=19.0002;EPPR=23.9569;DPRA=0.0;ODDS=25.2507;GTI=0;TYPE=snp;CIGAR=1X16M;NUMALT=3;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995633;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr9 5079828 . A AT 234.747 REJECT NS=2;DP=309;DPB=358.647;AC=2;AN=3;AF=0.25;RO=229;AO=27;PRO=34.4167;PAO=31.4167;QR=8576;QA=968;PQR=1197.17;PQA=1086.17;SRF=158;SRR=71;SAF=15;SAR=12;SRP=74.7827;SAP=3.73412;AB=0.0873786;ABP=459.968;RUN=1;RPP=9.52472;RPPR=85.0237;RPL=9.0;RPR=18.0;EPP=5.02092;EPPR=23.9569;DPRA=0.0;ODDS=25.2507;GTI=0;TYPE=ins;CIGAR=1M1I16M;NUMALT=3;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995633;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.818;FS [...]
+chr9 5079828 . AT A 234.747 PASS SOMATIC;NS=2;DP=309;DPB=358.647;AC=2;AN=3;AF=0.25;RO=229;AO=25;PRO=34.4167;PAO=27.0833;QR=8576;QA=842;PQR=1197.17;PQA=920.167;SRF=158;SRR=71;SAF=13;SAR=12;SRP=74.7827;SAP=3.09716;AB=0.0809061;ABP=474.417;RUN=1;RPP=10.0459;RPPR=85.0237;RPL=8.0;RPR=17.0;EPP=5.18177;EPPR=23.9569;DPRA=0.0;ODDS=25.2507;GTI=0;TYPE=del;CIGAR=1M1D15M;NUMALT=3;MEANALT=9.5;LEN=1;MQM=62.4;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995633;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR: [...]
+chr9 5350821 . C T 3230.09 REJECT NS=2;DP=209;DPB=242.0;AC=2;AN=4;AF=0.5;RO=125;AO=117;PRO=0.0;PAO=0.0;QR=4733;QA=4483;PQR=0.0;PQA=0.0;SRF=89;SRR=36;SAF=78;SAR=39;SRP=51.8076;SAP=31.2394;AB=0.483471;ABP=3.58457;RUN=1;RPP=37.327;RPPR=3.44459;RPL=37.0;RPR=80.0;EPP=3.17734;EPPR=9.28151;DPRA=0.0;ODDS=191.01;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.108;Dels=0.0;FS=3.5105;HaplotypeScore=6.798;MLEAC [...]
+chr9 5350828 . C G 3681.105 REJECT NS=2;DP=229;DPB=266.0;AC=2;AN=4;AF=0.5;RO=133;AO=133;PRO=0.0;PAO=0.0;QR=5102;QA=5094;PQR=0.0;PQA=0.0;SRF=90;SRR=43;SAF=87;SAR=46;SRP=39.0763;SAP=30.4558;AB=0.5;ABP=3.0103;RUN=1;RPP=36.0722;RPPR=4.33278;RPL=44.0;RPR=89.0;EPP=3.81032;EPPR=5.76954;DPRA=0.0;ODDS=221.899;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2615;Dels=0.0;FS=3.4385;HaplotypeScore=5.8315;MLEAC= [...]
+chr9 5350875 . A C 4971.105 REJECT NS=2;DP=279;DPB=326.0;AC=2;AN=4;AF=0.5;RO=152;AO=173;PRO=0.0;PAO=0.0;QR=5809;QA=6732;PQR=0.0;PQA=0.0;SRF=85;SRR=67;SAF=101;SAR=72;SRP=7.63896;SAP=13.5664;AB=0.530675;ABP=5.67468;RUN=1;RPP=5.13156;RPPR=3.9246;RPL=80.0;RPR=93.0;EPP=3.62534;EPPR=9.92473;DPRA=0.0;ODDS=307.372;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99422;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8635;Dels=0.0;FS=2.016;HaplotypeScore=0.0; [...]
+chr9 5352625 . C G 6313.610000000001 REJECT NS=2;DP=384;DPB=443.0;AC=2;AN=4;AF=0.5;RO=218;AO=225;PRO=0.0;PAO=0.0;QR=8367;QA=8522;PQR=0.0;PQA=0.0;SRF=97;SRR=121;SAF=108;SAR=117;SRP=8.74777;SAP=3.79203;AB=0.507901;ABP=3.25049;RUN=1;RPP=7.26639;RPPR=6.23763;RPL=102.0;RPR=123.0;EPP=3.79203;EPPR=18.9477;DPRA=0.0;ODDS=329.9;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.977778;PAIREDR=0.995413;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.78;Dels=0.0;FS=2.129;Ha [...]
+chr9 5557672 . T C 15798.65 REJECT NS=2;DP=416;DPB=466.0;AC=4;AN=4;AF=1.0;RO=0;AO=466;PRO=0.0;PAO=0.0;QR=0;QA=17787;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=226;SAR=240;SRP=0.0;SAP=3.92362;AB=0.0;ABP=0.0;RUN=1;RPP=4.87422;RPPR=0.0;RPL=223.0;RPR=243.0;EPP=39.0959;EPPR=0.0;DPRA=0.0;ODDS=66.7056;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995708;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.6812;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.63;SOR=0.8 [...]
+chr9 8319806 . C T 781.3205 REJECT NS=2;DP=213;DPB=239.0;AC=2;AN=4;AF=0.5;RO=194;AO=45;PRO=0.0;PAO=0.0;QR=7417;QA=1742;PQR=0.0;PQA=0.0;SRF=119;SRR=75;SAF=30;SAR=15;SRP=24.6803;SAP=13.8677;AB=0.188285;ABP=204.721;RUN=1;RPP=62.1226;RPPR=78.2731;RPL=5.0;RPR=40.0;EPP=6.91895;EPPR=4.62211;DPRA=0.0;ODDS=55.9602;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994845;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.346;Dels=0.0;FS=2.1365;HaplotypeScore=4.93 [...]
+chr9 8331574 . A AAACTTACCATTCCTGAACTGT 226.634 REJECT NS=2;DP=265;DPB=454.2;AC=2;AN=3;AF=0.25;RO=219;AO=19;PRO=3.33333;PAO=4.83333;QR=8340;QA=620;PQR=96.6667;PQA=143.167;SRF=135;SRR=84;SAF=11;SAR=8;SRP=28.8003;SAP=4.03889;AB=0.0716981;ABP=425.251;RUN=1;RPP=3.12459;RPPR=21.3439;RPL=10.0;RPR=9.0;EPP=4.03889;EPPR=16.5845;DPRA=0.0;ODDS=17.8063;GTI=0;TYPE=ins;CIGAR=1M21I4M;NUMALT=2;MEANALT=4.0;LEN=21;MQM=60.0;MQMR=59.9635;PAIRED=1.0;PAIREDR=0.990868;technology.ILLUMINA=1.0;SPLITMULTIALLELIC; [...]
+chr9 8331574 . A AAACTTACCATTCTTGAACTGT 226.634 PASS SOMATIC;NS=2;DP=265;DPB=454.2;AC=2;AN=3;AF=0.25;RO=219;AO=22;PRO=3.33333;PAO=4.83333;QR=8340;QA=729;PQR=96.6667;PQA=143.167;SRF=135;SRR=84;SAF=16;SAR=6;SRP=28.8003;SAP=12.8806;AB=0.105263;ABP=285.873;RUN=1;RPP=4.58955;RPPR=21.3439;RPL=13.0;RPR=9.0;EPP=17.2236;EPPR=16.5845;DPRA=0.0;ODDS=17.8063;GTI=0;TYPE=ins;CIGAR=1M21I4M;NUMALT=2;MEANALT=5.0;LEN=21;MQM=60.0;MQMR=59.9635;PAIRED=1.0;PAIREDR=0.990868;technology.ILLUMINA=1.0;SPLITMULTIALL [...]
+chr9 8341280 . G GA 113.078 REJECT NS=2;DP=124;DPB=166.154;AC=2;AN=2;AF=0.0;RO=85;AO=5;PRO=54.1667;PAO=21.1667;QR=3132;QA=159;PQR=1781.5;PQA=706.5;SRF=9;SRR=76;SAF=0;SAR=5;SRP=117.69;SAP=13.8677;AB=0.0403226;ABP=230.595;RUN=1;RPP=6.91895;RPPR=37.9838;RPL=1.0;RPR=4.0;EPP=6.91895;EPPR=16.5245;DPRA=0.0;ODDS=4.0855;GTI=0;TYPE=ins;CIGAR=1M1I25M;NUMALT=2;MEANALT=10.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr9 8341280 . GA G 113.078 REJECT NS=2;DP=124;DPB=166.154;AC=2;AN=4;AF=0.5;RO=85;AO=16;PRO=54.1667;PAO=18.6667;QR=3132;QA=560;PQR=1781.5;PQA=642.0;SRF=9;SRR=76;SAF=2;SAR=14;SRP=117.69;SAP=22.5536;AB=0.129032;ABP=151.231;RUN=1;RPP=11.6962;RPPR=37.9838;RPL=12.0;RPR=4.0;EPP=5.18177;EPPR=16.5245;DPRA=0.0;ODDS=4.0855;GTI=0;TYPE=del;CIGAR=1M1D24M;NUMALT=2;MEANALT=10.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr9 8389364 . C G 2960.32 PASS SOMATIC;NS=2;DP=382;DPB=382.0;AC=1;AN=3;AF=0.25;RO=269;AO=113;PRO=0.0;PAO=0.0;QR=10212;QA=4253;PQR=0.0;PQA=0.0;SRF=108;SRR=161;SAF=48;SAR=65;SRP=25.6856;SAP=8.56389;AB=0.389655;ABP=33.6805;RUN=1;RPP=13.1759;RPPR=4.37453;RPL=68.0;RPR=45.0;EPP=15.0207;EPPR=3.08295;DPRA=3.15217;ODDS=58.3805;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9823;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992565;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.393;Dels=0.0;FS=0 [...]
+chr9 8436703 . C G 5456.05 REJECT NS=2;DP=225;DPB=265.0;AC=3;AN=4;AF=0.75;RO=64;AO=201;PRO=0.0;PAO=0.0;QR=2468;QA=7726;PQR=0.0;PQA=0.0;SRF=20;SRR=44;SAF=42;SAR=159;SRP=22.5536;SAP=150.897;AB=0.655914;ABP=42.2836;RUN=1;RPP=57.47;RPPR=33.5466;RPL=136.0;RPR=65.0;EPP=3.88537;EPPR=6.40323;DPRA=0.0;ODDS=50.1981;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.841;Dels=0.0;FS=4.1895;HaplotypeScore=5.8793;ML [...]
+chr9 8460277 . T C 4921.735000000001 REJECT NS=2;DP=314;DPB=359.0;AC=2;AN=4;AF=0.5;RO=179;AO=180;PRO=0.0;PAO=0.0;QR=6846;QA=6755;PQR=0.0;PQA=0.0;SRF=93;SRR=86;SAF=105;SAR=75;SRP=3.60473;SAP=13.8677;AB=0.501393;ABP=3.01635;RUN=1;RPP=5.37479;RPPR=3.31358;RPL=97.0;RPR=83.0;EPP=3.0103;EPPR=6.5162;DPRA=0.0;ODDS=281.67;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.7821;PAIRED=0.994444;PAIREDR=0.988827;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.4685;Dels=0.0;FS=7.6265;Ha [...]
+chr9 8460591 . A G 4028.07 REJECT NS=2;DP=247;DPB=275.0;AC=2;AN=4;AF=0.5;RO=130;AO=144;PRO=0.0;PAO=0.0;QR=4939;QA=5504;PQR=0.0;PQA=0.0;SRF=35;SRR=95;SAF=39;SAR=105;SRP=63.1434;SAP=68.6973;AB=0.523636;ABP=4.34477;RUN=1;RPP=57.2971;RPPR=27.1303;RPL=102.0;RPR=42.0;EPP=3.55317;EPPR=3.0103;DPRA=0.0;ODDS=166.581;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992308;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0455;Dels=0.0;FS=2.0135;HaplotypeScore=4. [...]
+chr9 8470974 . G A 6844.015 REJECT NS=2;DP=290;DPB=326.0;AC=3;AN=4;AF=0.75;RO=87;AO=239;PRO=0.0;PAO=0.0;QR=3397;QA=9143;PQR=0.0;PQA=0.0;SRF=49;SRR=38;SAF=152;SAR=87;SRP=6.03039;SAP=41.3972;AB=0.65748;ABP=57.7246;RUN=1;RPP=114.955;RPPR=44.9671;RPL=64.0;RPR=175.0;EPP=7.01708;EPPR=3.03526;DPRA=0.0;ODDS=45.9292;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.1255;MQMR=60.0;PAIRED=0.995816;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.384;Dels=0.0;FS=2.314;HaplotypeScore [...]
+chr9 8484397 . TA T 992.606 REJECT NS=2;DP=198;DPB=219.067;AC=2;AN=4;AF=0.5;RO=139;AO=47;PRO=28.0;PAO=22.0;QR=5241;QA=1677;PQR=1019.0;PQA=799.0;SRF=27;SRR=112;SAF=7;SAR=40;SRP=115.88;SAP=53.3238;AB=0.237374;ABP=121.63;RUN=1;RPP=10.8184;RPPR=57.3908;RPL=30.0;RPR=17.0;EPP=3.0565;EPPR=4.27569;DPRA=0.0;ODDS=70.8701;GTI=0;TYPE=del;CIGAR=1M1D13M;NUMALT=1;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992806;technology.ILLUMINA=1.0;BaseQRankSum=-0.526;FS=2.712;MLEAC=1;MLEAF=0.5;MQ=60 [...]
+chr9 8497250 . T C 5528.85 REJECT NS=2;DP=354;DPB=405.0;AC=2;AN=4;AF=0.5;RO=209;AO=196;PRO=0.0;PAO=0.0;QR=7833;QA=7484;PQR=0.0;PQA=0.0;SRF=95;SRR=114;SAF=105;SAR=91;SRP=6.76103;SAP=5.18177;AB=0.483951;ABP=3.91642;RUN=1;RPP=8.37251;RPPR=7.59221;RPL=87.0;RPR=109.0;EPP=7.44188;EPPR=5.34801;DPRA=0.0;ODDS=291.17;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994898;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.952;Dels=0.0;FS=5.153;HaplotypeScore=3.8 [...]
+chr9 21869079 . T G 1616.65 REJECT NS=2;DP=369;DPB=411.0;AC=2;AN=4;AF=0.5;RO=321;AO=90;PRO=0.0;PAO=0.0;QR=12224;QA=3457;PQR=0.0;PQA=0.0;SRF=130;SRR=191;SAF=34;SAR=56;SRP=28.1818;SAP=14.688;AB=0.218978;ABP=284.937;RUN=1;RPP=5.42305;RPPR=22.0124;RPL=50.0;RPR=40.0;EPP=3.87889;EPPR=6.58883;DPRA=0.0;ODDS=175.211;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.561;Dels=0.0;FS=3.9375;HaplotypeScore=4.8239; [...]
+chr9 21905632 . GT G 5824.55 REJECT NS=2;DP=374;DPB=366.667;AC=2;AN=4;AF=0.5;RO=222;AO=208;PRO=9.0;PAO=6.0;QR=8510;QA=7873;PQR=312.0;PQA=209.0;SRF=114;SRR=108;SAF=97;SAR=111;SRP=3.36243;SAP=5.0565;AB=0.483721;ABP=4.00009;RUN=1;RPP=5.0565;RPPR=3.04943;RPL=111.0;RPR=97.0;EPP=23.2217;EPPR=27.4638;DPRA=0.0;ODDS=344.861;GTI=0;TYPE=del;CIGAR=1M1D1M;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0481;MQMR=60.0;PAIRED=0.995192;PAIREDR=0.990991;technology.ILLUMINA=1.0;MQ0=0;END=21905633;HOMLEN=0;SVLEN=-1;SVTY [...]
+chr9 21909979 . A G 5782.425 REJECT NS=2;DP=374;DPB=427.0;AC=2;AN=4;AF=0.5;RO=223;AO=204;PRO=0.0;PAO=0.0;QR=8512;QA=7870;PQR=0.0;PQA=0.0;SRF=119;SRR=104;SAF=90;SAR=114;SRP=5.20125;SAP=9.14152;AB=0.477752;ABP=4.84613;RUN=1;RPP=3.3935;RPPR=3.48744;RPL=99.0;RPR=105.0;EPP=8.16222;EPPR=26.3901;DPRA=0.0;ODDS=324.783;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990196;PAIREDR=0.995516;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.333;Dels=0.0;FS=7.5565;Haplotype [...]
+chr9 21968199 . C G 11336.3 REJECT NS=2;DP=342;DPB=387.0;AC=4;AN=4;AF=1.0;RO=4;AO=383;PRO=0.0;PAO=0.0;QR=36;QA=13104;PQR=0.0;PQA=0.0;SRF=4;SRR=0;SAF=167;SAR=216;SRP=11.6962;SAP=16.6231;AB=0.0;ABP=0.0;RUN=1;RPP=4.64883;RPPR=11.6962;RPL=183.0;RPR=200.0;EPP=38.3945;EPPR=11.6962;DPRA=0.0;ODDS=55.9331;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9922;MQMR=60.0;PAIRED=0.997389;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.851;Dels=0.0;FS=0.0;HaplotypeScore=30.7695;MLEAC [...]
+chr9 22088260 . C T 3637.34 PASS SOMATIC;NS=2;DP=427;DPB=427.0;AC=1;AN=3;AF=0.25;RO=296;AO=130;PRO=0.0;PAO=0.0;QR=11342;QA=5063;PQR=0.0;PQA=0.0;SRF=116;SRR=180;SAF=52;SAR=78;SRP=33.0588;SAP=14.302;AB=0.414013;ABP=23.1759;RUN=1;RPP=6.28421;RPPR=3.03964;RPL=72.0;RPR=58.0;EPP=3.61163;EPPR=18.5334;DPRA=2.77876;ODDS=71.4788;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986486;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.538;Dels=0.0;FS=0.426 [...]
+chr9 22102437 . G A 1626.55 REJECT NS=1;DP=119;DPB=119.0;AC=1;AN=4;AF=0.5;RO=62;AO=57;PRO=0.0;PAO=0.0;QR=2403;QA=2225;PQR=0.0;PQA=0.0;SRF=33;SRR=29;SAF=33;SAR=24;SRP=3.57068;SAP=6.09608;AB=0.478992;ABP=3.46649;RUN=1;RPP=3.9627;RPPR=6.51267;RPL=26.0;RPR=31.0;EPP=3.0484;EPPR=3.0103;DPRA=0.0;ODDS=374.527;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.964912;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=0.341;FS=0.693;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0. [...]
+chr9 22103813 . A G 2386.12 PASS SOMATIC;NS=2;DP=441;DPB=441.0;AC=1;AN=3;AF=0.25;RO=341;AO=100;PRO=0.0;PAO=0.0;QR=13035;QA=3722;PQR=0.0;PQA=0.0;SRF=199;SRR=142;SAF=61;SAR=39;SRP=23.6998;SAP=13.5202;AB=0.302115;ABP=115.592;RUN=1;RPP=6.13722;RPPR=4.08648;RPL=44.0;RPR=56.0;EPP=3.09716;EPPR=3.5261;DPRA=3.00909;ODDS=69.6088;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.96;PAIREDR=0.997067;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.058;Dels=0.0;FS=0.0; [...]
+chr9 22513841 . T C 7623.63 REJECT NS=2;DP=320;DPB=371.0;AC=3;AN=4;AF=0.75;RO=96;AO=275;PRO=0.0;PAO=0.0;QR=3673;QA=10547;PQR=0.0;PQA=0.0;SRF=57;SRR=39;SAF=156;SAR=119;SRP=10.339;SAP=13.8203;AB=0.645756;ABP=53.0183;RUN=1;RPP=12.6832;RPPR=3.37221;RPL=120.0;RPR=155.0;EPP=17.6105;EPPR=23.3679;DPRA=0.0;ODDS=63.4192;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.2182;MQMR=60.0;PAIRED=0.992727;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.287;Dels=0.0;FS=0.2375;HaplotypeSc [...]
+chr9 22513910 . C CA 6942.305 REJECT NS=2;DP=307;DPB=445.333;AC=3;AN=4;AF=0.75;RO=93;AO=257;PRO=5.5;PAO=5.5;QR=3551;QA=9499;PQR=200.5;PQA=200.5;SRF=31;SRR=62;SAF=82;SAR=175;SRP=25.4488;SAP=76.0884;AB=0.631373;ABP=41.2367;RUN=1;RPP=10.1162;RPPR=4.90158;RPL=143.0;RPR=114.0;EPP=50.5377;EPPR=22.6469;DPRA=0.0;ODDS=60.8491;GTI=0;TYPE=ins;CIGAR=1M1I2M;NUMALT=1;MEANALT=2.5;LEN=1;MQM=60.1556;MQMR=60.0;PAIRED=0.996109;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=22513910;HOMLEN=1;HOMSEQ=A;SVLEN=1 [...]
+chr9 27004338 . G A 5715.92 REJECT NS=2;DP=372;DPB=428.0;AC=2;AN=4;AF=0.5;RO=217;AO=211;PRO=0.0;PAO=0.0;QR=8164;QA=8025;PQR=0.0;PQA=0.0;SRF=121;SRR=96;SAF=114;SAR=97;SRP=9.26454;SAP=5.9845;AB=0.492991;ABP=3.19295;RUN=1;RPP=23.8503;RPPR=11.426;RPL=128.0;RPR=83.0;EPP=29.7781;EPPR=23.274;DPRA=0.0;ODDS=363.663;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990521;PAIREDR=0.990783;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.028;Dels=0.0;FS=0.4305;HaplotypeScor [...]
+chr9 30042002 . T G 1406.22 REJECT NS=1;DP=92;DPB=92.0;AC=1;AN=4;AF=0.5;RO=42;AO=50;PRO=0.0;PAO=0.0;QR=1615;QA=1916;PQR=0.0;PQA=0.0;SRF=25;SRR=17;SAF=31;SAR=19;SRP=6.31921;SAP=9.26414;AB=0.543478;ABP=4.52089;RUN=1;RPP=9.26414;RPPR=4.87156;RPL=19.0;RPR=31.0;EPP=11.5225;EPPR=16.2459;DPRA=0.0;ODDS=262.189;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=0.216;FS=0.793;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.114;Q [...]
+chr9 35074917 . T C 6645.515 REJECT NS=2;DP=283;DPB=320.0;AC=3;AN=4;AF=0.75;RO=89;AO=231;PRO=0.0;PAO=0.0;QR=3414;QA=8933;PQR=0.0;PQA=0.0;SRF=63;SRR=26;SAF=154;SAR=77;SRP=36.4119;SAP=58.7448;AB=0.639676;ABP=44.8661;RUN=1;RPP=67.7691;RPPR=15.9171;RPL=74.0;RPR=157.0;EPP=3.0949;EPPR=5.96253;DPRA=0.0;ODDS=46.5514;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995671;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.979;Dels=0.0;FS=1.615;HaplotypeScore=3. [...]
+chr9 36840623 . G A 10777.95 REJECT NS=2;DP=287;DPB=328.0;AC=4;AN=4;AF=1.0;RO=0;AO=327;PRO=0.0;PAO=0.0;QR=0;QA=12545;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=90;SAR=237;SRP=0.0;SAP=146.507;AB=0.0;ABP=0.0;RUN=1;RPP=84.829;RPPR=0.0;RPL=219.0;RPR=108.0;EPP=12.1013;EPPR=0.0;DPRA=0.0;ODDS=54.8595;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.185;SOR=2.0045 G [...]
+chr9 37920272 . A AAAAAC 1751.83 REJECT NS=2;DP=91;DPB=351.106;AC=2;AN=2;AF=0.5;RO=2;AO=33;PRO=153.417;PAO=153.417;QR=78;QA=1230;PQR=5570.58;PQA=5570.58;SRF=2;SRR=0;SAF=28;SAR=5;SRP=7.35324;SAP=37.8197;AB=0.362637;ABP=17.9243;RUN=1;RPP=6.23461;RPPR=7.35324;RPL=20.0;RPR=13.0;EPP=3.0761;EPPR=7.35324;DPRA=0.0;ODDS=8.64631;GTI=0;TYPE=ins;CIGAR=1M5I65M;NUMALT=3;MEANALT=4.5;LEN=5;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;END=37920272;HOMLEN=60;HO [...]
+chr9 37920272 . AAAAAC A 1751.83 REJECT SOMATIC;NS=2;DP=91;DPB=351.106;AC=1;AN=3;AF=0.25;RO=2;AO=35;PRO=153.417;PAO=138.917;QR=78;QA=1206;PQR=5570.58;PQA=5048.58;SRF=2;SRR=0;SAF=29;SAR=6;SRP=7.35324;SAP=35.8306;AB=0.448718;ABP=4.79202;RUN=1;RPP=3.07234;RPPR=7.35324;RPL=17.0;RPR=18.0;EPP=3.56868;EPPR=7.35324;DPRA=0.0;ODDS=8.64631;GTI=0;TYPE=del;CIGAR=1M5D60M;NUMALT=3;MEANALT=7.0;LEN=5;MQM=60.2857;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;END=37920277 [...]
+chr9 37920272 . AAAAACAAAACAAAAC A 1751.83 REJECT NS=2;DP=91;DPB=351.106;AC=2;AN=3;AF=0.25;RO=2;AO=16;PRO=153.417;PAO=116.25;QR=78;QA=521;PQR=5570.58;PQA=4203.25;SRF=2;SRR=0;SAF=11;SAR=5;SRP=7.35324;SAP=7.89611;AB=0.175824;ABP=86.0751;RUN=1;RPP=3.0103;RPPR=7.35324;RPL=8.0;RPR=8.0;EPP=3.55317;EPPR=7.35324;DPRA=0.0;ODDS=8.64631;GTI=0;TYPE=del;CIGAR=1M15D50M;NUMALT=3;MEANALT=4.5;LEN=15;MQM=61.25;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;END=37920287;HOMLEN=4 [...]
+chr9 71111910 . C T 3179.03 PASS SOMATIC;NS=2;DP=466;DPB=466.0;AC=1;AN=3;AF=0.25;RO=346;AO=120;PRO=0.0;PAO=0.0;QR=13072;QA=4654;PQR=0.0;PQA=0.0;SRF=182;SRR=164;SAF=61;SAR=59;SRP=5.0437;SAP=3.08268;AB=0.35503;ABP=64.711;RUN=1;RPP=3.0103;RPPR=9.43685;RPL=60.0;RPR=60.0;EPP=41.3006;EPPR=43.1763;DPRA=2.64062;ODDS=80.7385;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991667;PAIREDR=0.99422;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.245;Dels=0.0;FS=1.34 [...]
+chr9 71115991 . T C 2621.8 PASS SOMATIC;NS=2;DP=342;DPB=342.0;AC=1;AN=3;AF=0.25;RO=243;AO=99;PRO=0.0;PAO=0.0;QR=9230;QA=3782;PQR=0.0;PQA=0.0;SRF=163;SRR=80;SAF=64;SAR=35;SRP=64.5711;SAP=21.4568;AB=0.388235;ABP=30.6774;RUN=1;RPP=10.9285;RPPR=67.5736;RPL=40.0;RPR=59.0;EPP=14.6134;EPPR=3.01924;DPRA=2.93103;ODDS=55.22;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.983539;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.397;Dels=0.0;FS=0.491;Hapl [...]
+chr9 71117523 . C T 4535.925 REJECT NS=2;DP=282;DPB=322.0;AC=2;AN=4;AF=0.5;RO=156;AO=166;PRO=0.0;PAO=0.0;QR=6027;QA=6327;PQR=0.0;PQA=0.0;SRF=50;SRR=106;SAF=41;SAR=125;SRP=46.6625;SAP=95.311;AB=0.515528;ABP=3.68467;RUN=1;RPP=4.89399;RPPR=5.01474;RPL=89.0;RPR=77.0;EPP=35.7132;EPPR=17.2641;DPRA=0.0;ODDS=228.086;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993976;PAIREDR=0.99359;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.082;Dels=0.0;FS=8.6105;HaplotypeSco [...]
+chr9 71142594 . AG A 4746.66 REJECT NS=2;DP=348;DPB=370.8;AC=2;AN=4;AF=0.5;RO=212;AO=182;PRO=15.5;PAO=13.5;QR=7996;QA=6705;PQR=377.0;PQA=303.0;SRF=95;SRR=117;SAF=80;SAR=102;SRP=7.96781;SAP=8.78498;AB=0.458438;ABP=8.96681;RUN=1;RPP=9.88265;RPPR=6.32897;RPL=103.0;RPR=79.0;EPP=3.77389;EPPR=7.10742;DPRA=0.0;ODDS=329.873;GTI=0;TYPE=del;CIGAR=1M1D3M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.1648;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995283;technology.ILLUMINA=1.0;MQ0=0;END=71142595;HOMLEN=1;HOMSEQ=G;SVLEN=-1 [...]
+chr9 72002554 . G A 3546.38 PASS SOMATIC;NS=2;DP=484;DPB=484.0;AC=1;AN=3;AF=0.25;RO=351;AO=133;PRO=0.0;PAO=0.0;QR=13404;QA=5116;PQR=0.0;PQA=0.0;SRF=173;SRR=178;SAF=67;SAR=66;SRP=3.16496;SAP=3.02663;AB=0.361413;ABP=64.4016;RUN=1;RPP=6.68384;RPPR=14.4492;RPL=59.0;RPR=74.0;EPP=4.33278;EPPR=23.1103;DPRA=3.17241;ODDS=73.2932;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.609;Dels=0.0;FS=0.817;Hap [...]
+chr9 85511305 . A C 2306.04 REJECT NS=1;DP=69;DPB=69.0;AC=2;AN=4;AF=1.0;RO=0;AO=69;PRO=0.0;PAO=0.0;QR=0;QA=2628;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=45;SAR=24;SRP=0.0;SAP=16.8888;AB=0.0;ABP=0.0;RUN=1;RPP=12.1053;RPPR=0.0;RPL=26.0;RPR=43.0;EPP=10.0912;EPPR=0.0;DPRA=0.0;ODDS=47.6568;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=38.09;SOR=1.478 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:AD [...]
+chr9 87478172 . T G 2649.17 PASS SOMATIC;NS=2;DP=439;DPB=439.0;AC=1;AN=3;AF=0.25;RO=336;AO=103;PRO=0.0;PAO=0.0;QR=12794;QA=3990;PQR=0.0;PQA=0.0;SRF=157;SRR=179;SAF=52;SAR=51;SRP=6.13825;SAP=3.03138;AB=0.315951;ABP=98.9281;RUN=1;RPP=7.75381;RPPR=12.3425;RPL=44.0;RPR=59.0;EPP=3.03138;EPPR=3.94093;DPRA=2.88496;ODDS=71.5024;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.985119;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.483;Dels=0.0;FS=0.43 [...]
+chr9 87479105 . G A 5131.6 REJECT NS=2;DP=303;DPB=352.0;AC=2;AN=4;AF=0.5;RO=166;AO=186;PRO=0.0;PAO=0.0;QR=6372;QA=7039;PQR=0.0;PQA=0.0;SRF=79;SRR=87;SAF=95;SAR=91;SRP=3.84749;SAP=3.19709;AB=0.528409;ABP=5.47788;RUN=1;RPP=3.0103;RPPR=3.06262;RPL=93.0;RPR=93.0;EPP=3.057;EPPR=3.2196;DPRA=0.0;ODDS=309.573;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983871;PAIREDR=0.993976;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.5105;Dels=0.0;FS=3.4925;HaplotypeScore=1 [...]
+chr9 87479651 . C T 172.764 REJECT NS=2;DP=46;DPB=105.633;AC=2;AN=2;AF=0.0;RO=5;AO=7;PRO=49.0667;PAO=22.15;QR=153;QA=28;PQR=1709.63;PQA=502.05;SRF=1;SRR=4;SAF=0;SAR=7;SRP=6.91895;SAP=18.2106;AB=0.0810811;ABP=59.4099;RUN=1;RPP=18.2106;RPPR=6.91895;RPL=0.0;RPR=7.0;EPP=18.2106;EPPR=13.8677;DPRA=0.0;ODDS=4.14484;GTI=0;TYPE=snp;CIGAR=1X29M;NUMALT=4;MEANALT=8.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV [...]
+chr9 87479651 . CTTTTT C 172.764 REJECT NS=2;DP=46;DPB=105.633;AC=2;AN=2;AF=0.0;RO=5;AO=3;PRO=49.0667;PAO=29.5667;QR=153;QA=69;PQR=1709.63;PQA=1011.13;SRF=1;SRR=4;SAF=1;SAR=2;SRP=6.91895;SAP=3.73412;AB=0.0810811;ABP=59.4099;RUN=1;RPP=9.52472;RPPR=6.91895;RPL=3.0;RPR=0.0;EPP=3.73412;EPPR=13.8677;DPRA=4.11111;ODDS=4.14484;GTI=0;TYPE=del;CIGAR=1M5D24M;NUMALT=4;MEANALT=13.0;LEN=5;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr9 87479651 . CTTTTTT C 172.764 REJECT NS=2;DP=46;DPB=105.633;AC=2;AN=3;AF=0.25;RO=5;AO=14;PRO=49.0667;PAO=25.5667;QR=153;QA=356;PQR=1709.63;PQA=867.633;SRF=1;SRR=4;SAF=7;SAR=7;SRP=6.91895;SAP=3.0103;AB=0.378378;ABP=7.76406;RUN=1;RPP=5.49198;RPPR=6.91895;RPL=9.0;RPR=5.0;EPP=3.63072;EPPR=13.8677;DPRA=4.11111;ODDS=4.14484;GTI=0;TYPE=del;CIGAR=1M6D23M;NUMALT=4;MEANALT=13.0;LEN=6;MQM=58.9286;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr9 87479651 . CTTTTTTT C 172.764 REJECT NS=2;DP=46;DPB=105.633;AC=2;AN=2;AF=0.0;RO=5;AO=5;PRO=49.0667;PAO=22.65;QR=153;QA=137;PQR=1709.63;PQA=730.55;SRF=1;SRR=4;SAF=1;SAR=4;SRP=6.91895;SAP=6.91895;AB=0.135135;ABP=45.7942;RUN=1;RPP=3.44459;RPPR=6.91895;RPL=3.0;RPR=2.0;EPP=3.44459;EPPR=13.8677;DPRA=4.11111;ODDS=4.14484;GTI=0;TYPE=del;CIGAR=1M7D22M;NUMALT=4;MEANALT=13.0;LEN=7;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr9 87563370 . T C 2354.83 PASS SOMATIC;NS=2;DP=314;DPB=314.0;AC=1;AN=3;AF=0.25;RO=226;AO=88;PRO=0.0;PAO=0.0;QR=8492;QA=3409;PQR=0.0;PQA=0.0;SRF=153;SRR=73;SAF=56;SAR=32;SRP=64.5033;SAP=17.2236;AB=0.372881;ABP=36.1345;RUN=1;RPP=7.84676;RPPR=28.9911;RPL=37.0;RPR=51.0;EPP=5.47788;EPPR=3.04873;DPRA=3.02564;ODDS=49.6121;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988636;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=4.589;Dels=0.0;FS=5.014;H [...]
+chr9 87563460 . C A 3041.79 PASS SOMATIC;NS=2;DP=408;DPB=408.0;AC=1;AN=3;AF=0.25;RO=292;AO=116;PRO=0.0;PAO=0.0;QR=11117;QA=4388;PQR=0.0;PQA=0.0;SRF=159;SRR=133;SAF=62;SAR=54;SRP=8.03741;SAP=4.20835;AB=0.370607;ABP=48.528;RUN=1;RPP=3.08518;RPPR=12.6481;RPL=59.0;RPR=57.0;EPP=6.67934;EPPR=3.27802;DPRA=3.29474;ODDS=60.2151;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.512;Dels=0.0;FS=1.944;Hap [...]
+chr9 93464044 . G A 1973.975 REJECT NS=2;DP=327;DPB=384.0;AC=2;AN=4;AF=0.5;RO=288;AO=96;PRO=0.0;PAO=0.0;QR=11003;QA=3599;PQR=0.0;PQA=0.0;SRF=135;SRR=153;SAF=43;SAR=53;SRP=5.45321;SAP=5.27225;AB=0.25;ABP=211.472;RUN=1;RPP=3.0103;RPPR=4.09604;RPL=48.0;RPR=48.0;EPP=18.3011;EPPR=6.65958;DPRA=0.0;ODDS=159.775;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996528;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.245;Dels=0.0;FS=2.7175;HaplotypeScore=2.932 [...]
+chr9 93464111 . A G 4840.715 REJECT NS=2;DP=225;DPB=265.0;AC=3;AN=4;AF=0.75;RO=75;AO=190;PRO=0.0;PAO=0.0;QR=2882;QA=7078;PQR=0.0;PQA=0.0;SRF=23;SRR=52;SAF=60;SAR=130;SRP=27.3597;SAP=59.0114;AB=0.6;ABP=19.0792;RUN=1;RPP=49.8227;RPPR=6.51361;RPL=127.0;RPR=63.0;EPP=3.74174;EPPR=6.51361;DPRA=0.0;ODDS=45.0288;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994737;PAIREDR=0.986667;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-3.364;Dels=0.0;FS=0.299;HaplotypeScore= [...]
+chr9 93466407 . A G 8279.46 REJECT NS=2;DP=358;DPB=403.0;AC=3;AN=4;AF=0.75;RO=112;AO=291;PRO=0.0;PAO=0.0;QR=4358;QA=10995;PQR=0.0;PQA=0.0;SRF=61;SRR=51;SAF=172;SAR=119;SRP=4.94911;SAP=23.9714;AB=0.644444;ABP=60.0959;RUN=1;RPP=15.5541;RPPR=3.08785;RPL=125.0;RPR=166.0;EPP=6.30109;EPPR=5.80219;DPRA=0.0;ODDS=55.8289;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993127;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.141;Dels=0.0;FS=1.6235;HaplotypeSco [...]
+chr9 93466631 . G A 5550.535 REJECT NS=2;DP=365;DPB=422.0;AC=2;AN=4;AF=0.5;RO=217;AO=205;PRO=0.0;PAO=0.0;QR=8271;QA=7908;PQR=0.0;PQA=0.0;SRF=90;SRR=127;SAF=93;SAR=112;SRP=16.7096;SAP=6.83421;AB=0.485782;ABP=3.75128;RUN=1;RPP=4.80044;RPPR=5.90226;RPL=96.0;RPR=109.0;EPP=10.7323;EPPR=4.70145;DPRA=0.0;ODDS=330.934;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9415;MQMR=60.0;PAIRED=0.995122;PAIREDR=0.995392;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.3575;Dels=0.0;FS=1.568;Haplot [...]
+chr9 93469911 . G T 8600.345000000001 REJECT NS=2;DP=347;DPB=406.0;AC=3;AN=4;AF=0.75;RO=100;AO=306;PRO=0.0;PAO=0.0;QR=3868;QA=11803;PQR=0.0;PQA=0.0;SRF=51;SRR=49;SAF=181;SAR=125;SRP=3.09716;SAP=25.2643;AB=0.667774;ABP=76.6023;RUN=1;RPP=4.40118;RPPR=6.13722;RPL=160.0;RPR=146.0;EPP=16.7488;EPPR=3.09716;DPRA=0.0;ODDS=66.5013;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.941176;PAIREDR=0.94;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.887;Dels=0.0;FS=1.3845;H [...]
+chr9 93606309 . G A 10294.9 REJECT NS=2;DP=396;DPB=451.0;AC=2;AN=4;AF=0.5;RO=109;AO=342;PRO=0.0;PAO=0.0;QR=4160;QA=12887;PQR=0.0;PQA=0.0;SRF=56;SRR=53;SAF=173;SAR=169;SRP=3.1896;SAP=3.11189;AB=0.758315;ABP=264.401;RUN=1;RPP=5.06748;RPPR=3.03022;RPL=180.0;RPR=162.0;EPP=13.1692;EPPR=11.7958;DPRA=0.0;ODDS=257.372;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994152;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1095;Dels=0.0;FS=0.787;HaplotypeScor [...]
+chr9 93639849 . G A 1603.5549999999998 REJECT NS=2;DP=305;DPB=348.0;AC=2;AN=4;AF=0.5;RO=266;AO=82;PRO=0.0;PAO=0.0;QR=10226;QA=3161;PQR=0.0;PQA=0.0;SRF=161;SRR=105;SAF=55;SAR=27;SRP=28.6108;SAP=23.7717;AB=0.235632;ABP=214.267;RUN=1;RPP=15.8273;RPPR=26.8149;RPL=30.0;RPR=52.0;EPP=3.434;EPPR=25.0842;DPRA=0.0;ODDS=134.877;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.97561;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7695;Dels=0.0;FS=3.1235;Haploty [...]
+chr9 93650015 . T A 4038.93 REJECT NS=2;DP=275;DPB=312.0;AC=2;AN=4;AF=0.5;RO=159;AO=152;PRO=0.0;PAO=0.0;QR=6088;QA=5636;PQR=0.0;PQA=0.0;SRF=108;SRR=51;SAF=110;SAR=42;SRP=47.3821;SAP=69.0688;AB=0.487179;ABP=3.45573;RUN=1;RPP=57.9257;RPPR=88.244;RPL=45.0;RPR=107.0;EPP=9.92473;EPPR=3.02396;DPRA=0.0;ODDS=156.098;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986842;PAIREDR=0.993711;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.2235;Dels=0.0;FS=3.1225;Haplotype [...]
+chr9 93657761 . A T 2179.66 REJECT NS=2;DP=163;DPB=186.0;AC=2;AN=4;AF=0.5;RO=102;AO=84;PRO=0.0;PAO=0.0;QR=3854;QA=3227;PQR=0.0;PQA=0.0;SRF=77;SRR=25;SAF=63;SAR=21;SRP=60.5756;SAP=48.6112;AB=0.451613;ABP=6.79286;RUN=1;RPP=96.0734;RPPR=84.845;RPL=12.0;RPR=72.0;EPP=20.4855;EPPR=24.8102;DPRA=0.0;ODDS=112.178;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.5;Dels=0.0;FS=0.0;HaplotypeScore=5.8324;MLEAC=1; [...]
+chr9 93754036 . T C 6199.73 REJECT NS=2;DP=363;DPB=409.0;AC=2;AN=4;AF=0.5;RO=193;AO=216;PRO=0.0;PAO=0.0;QR=7435;QA=8298;PQR=0.0;PQA=0.0;SRF=93;SRR=100;SAF=100;SAR=116;SRP=3.56161;SAP=5.5839;AB=0.528117;ABP=5.81888;RUN=1;RPP=9.8062;RPPR=12.4725;RPL=95.0;RPR=121.0;EPP=4.01561;EPPR=3.02155;DPRA=0.0;ODDS=253.903;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990741;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9855;Dels=0.0;FS=6.008;HaplotypeScore=0 [...]
+chr9 93754829 . A C 5680.045 REJECT NS=2;DP=359;DPB=411.0;AC=2;AN=4;AF=0.5;RO=212;AO=199;PRO=0.0;PAO=0.0;QR=8261;QA=7706;PQR=0.0;PQA=0.0;SRF=91;SRR=121;SAF=83;SAR=116;SRP=12.2288;SAP=14.8934;AB=0.484185;ABP=3.90319;RUN=1;RPP=3.89417;RPPR=5.01789;RPL=104.0;RPR=95.0;EPP=6.16385;EPPR=19.3988;DPRA=0.0;ODDS=314.112;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.98995;PAIREDR=0.990566;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.208;Dels=0.0;FS=0.794;HaplotypeSc [...]
+chr9 97885616 . T C 818.786 PASS SOMATIC;NS=2;DP=171;DPB=171.0;AC=1;AN=3;AF=0.25;RO=127;AO=44;PRO=0.0;PAO=0.0;QR=4735;QA=1602;PQR=0.0;PQA=0.0;SRF=127;SRR=0;SAF=44;SAR=0;SRP=278.787;SAP=98.5551;AB=0.346457;ABP=29.0167;RUN=1;RPP=53.5464;RPPR=126.545;RPL=6.0;RPR=38.0;EPP=53.5464;EPPR=126.545;DPRA=2.88636;ODDS=28.46;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.977273;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.519;Dels=0.0;FS=0.0;Haplotyp [...]
+chr9 98209594 . G A 6934.56 REJECT NS=2;DP=411;DPB=469.0;AC=2;AN=4;AF=0.5;RO=225;AO=243;PRO=0.0;PAO=0.0;QR=8422;QA=9214;PQR=0.0;PQA=0.0;SRF=107;SRR=118;SAF=147;SAR=96;SRP=4.17807;SAP=26.2531;AB=0.518124;ABP=4.34837;RUN=1;RPP=3.01924;RPPR=3.79203;RPL=122.0;RPR=121.0;EPP=5.02092;EPPR=3.4832;DPRA=0.0;ODDS=354.476;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995556;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.429;Dels=0.0;FS=13.454;HaplotypeScore [...]
+chr9 98232223 . GA G 3594.585 REJECT NS=2;DP=278;DPB=308.0;AC=2;AN=4;AF=0.5;RO=149;AO=142;PRO=23.0;PAO=20.0;QR=5608;QA=5259;PQR=844.0;PQA=740.0;SRF=44;SRR=105;SAF=49;SAR=93;SRP=57.2388;SAP=32.6157;AB=0.47651;ABP=4.43852;RUN=1;RPP=13.3477;RPPR=25.1768;RPL=84.0;RPR=58.0;EPP=38.2432;EPPR=5.47325;DPRA=0.0;ODDS=207.58;GTI=0;TYPE=del;CIGAR=1M1D10M;NUMALT=1;MEANALT=4.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986577;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8255;FS=3.4325;MLEAC=1;MLEAF= [...]
+chr9 103503843 . A G 1781.925 REJECT NS=2;DP=341;DPB=394.0;AC=2;AN=4;AF=0.5;RO=301;AO=93;PRO=0.0;PAO=0.0;QR=11557;QA=3576;PQR=0.0;PQA=0.0;SRF=181;SRR=120;SAF=65;SAR=28;SRP=29.8543;SAP=34.9753;AB=0.236041;ABP=241.453;RUN=1;RPP=20.0318;RPPR=28.1229;RPL=33.0;RPR=60.0;EPP=6.95631;EPPR=45.7833;DPRA=0.0;ODDS=176.713;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9103;PAIRED=1.0;PAIREDR=0.996678;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6535;Dels=0.0;FS=7.029;HaplotypeSc [...]
+chr9 114010861 . G A 2637.56 PASS SOMATIC;NS=2;DP=384;DPB=384.0;AC=1;AN=3;AF=0.25;RO=283;AO=100;PRO=0.0;PAO=0.0;QR=10921;QA=3858;PQR=0.0;PQA=0.0;SRF=158;SRR=125;SAF=50;SAR=50;SRP=11.3662;SAP=3.0103;AB=0.347222;ABP=61.3988;RUN=1;RPP=6.13722;RPPR=9.46333;RPL=44.0;RPR=56.0;EPP=3.35774;EPPR=7.80595;DPRA=3.0;ODDS=60.7578;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992933;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.21;Dels=0.0;FS=5.762;Hap [...]
+chr9 127951863 . G A 2483.98 REJECT NS=1;DP=73;DPB=73.0;AC=2;AN=4;AF=1.0;RO=0;AO=73;PRO=0.0;PAO=0.0;QR=0;QA=2808;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=45;SAR=28;SRP=0.0;SAP=11.607;AB=0.0;ABP=0.0;RUN=1;RPP=8.03741;RPPR=0.0;RPL=30.0;RPR=43.0;EPP=3.27802;EPPR=0.0;DPRA=0.0;ODDS=50.2012;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.986301;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.93;SOR=1.308 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMIC [...]
+chr9 130549571 . G A 10721.3 REJECT NS=2;DP=380;DPB=431.0;AC=2;AN=4;AF=0.5;RO=87;AO=344;PRO=0.0;PAO=0.0;QR=3342;QA=13321;PQR=0.0;PQA=0.0;SRF=44;SRR=43;SAF=158;SAR=186;SRP=3.03526;SAP=7.95924;AB=0.798144;ABP=335.78;RUN=1;RPP=12.1254;RPPR=6.03039;RPL=191.0;RPR=153.0;EPP=18.7913;EPPR=6.03039;DPRA=0.0;ODDS=118.518;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991279;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.25;Dels=0.0;FS=2.912;HaplotypeScore=4 [...]
+chr9 132048664 . G A 9197.62 REJECT NS=2;DP=346;DPB=398.0;AC=2;AN=4;AF=0.5;RO=94;AO=301;PRO=0.0;PAO=0.0;QR=3609;QA=11488;PQR=0.0;PQA=0.0;SRF=49;SRR=45;SAF=152;SAR=149;SRP=3.37991;SAP=3.07523;AB=0.756281;ABP=230.066;RUN=1;RPP=5.61462;RPPR=3.37991;RPL=160.0;RPR=141.0;EPP=4.2295;EPPR=10.4949;DPRA=0.0;ODDS=138.564;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993355;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.5015;Dels=0.0;FS=6.4065;HaplotypeSco [...]
+chr9 133710804 . T C 6079.505 REJECT NS=2;DP=172;DPB=200.0;AC=4;AN=4;AF=1.0;RO=0;AO=199;PRO=0.0;PAO=0.0;QR=0;QA=7447;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=179;SAR=20;SRP=0.0;SAP=278.875;AB=0.0;ABP=0.0;RUN=1;RPP=85.6026;RPPR=0.0;RPL=56.0;RPR=143.0;EPP=27.1147;EPPR=0.0;DPRA=0.0;ODDS=38.6175;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.89;SOR=4.22 GT:G [...]
+chr9 133710819 . T TC 7950.61 REJECT NS=2;DP=216;DPB=342.667;AC=4;AN=4;AF=1.0;RO=0;AO=247;PRO=5.0;PAO=12.0;QR=0;QA=9061;PQR=89.5;PQA=312.5;SRF=0;SRR=0;SAF=216;SAR=31;SRP=0.0;SAP=303.895;AB=0.0;ABP=0.0;RUN=1;RPP=31.5735;RPPR=0.0;RPL=95.0;RPR=152.0;EPP=3.08942;EPPR=0.0;DPRA=0.0;ODDS=44.8589;GTI=0;TYPE=ins;CIGAR=1M1I2M;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=133710819;HOMLEN=0;SVLEN=1;SVTYPE=INS;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;Q [...]
+chr9 133761001 . A G 1561.4650000000001 REJECT NS=2;DP=329;DPB=374.0;AC=2;AN=4;AF=0.5;RO=292;AO=82;PRO=0.0;PAO=0.0;QR=11368;QA=3098;PQR=0.0;PQA=0.0;SRF=123;SRR=169;SAF=35;SAR=47;SRP=18.746;SAP=6.82362;AB=0.219251;ABP=259.058;RUN=1;RPP=3.96363;RPPR=3.04005;RPL=44.0;RPR=38.0;EPP=6.82362;EPPR=26.3313;DPRA=0.0;ODDS=118.55;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.885;Dels=0.0;FS=0.685;HaplotypeSc [...]
+chr9 135003565 . T C 1561.46 REJECT NS=2;DP=348;DPB=396.0;AC=2;AN=4;AF=0.5;RO=315;AO=81;PRO=0.0;PAO=0.0;QR=12127;QA=3089;PQR=0.0;PQA=0.0;SRF=155;SRR=160;SAF=36;SAR=45;SRP=3.18264;SAP=5.18177;AB=0.204545;ABP=303.266;RUN=1;RPP=4.32391;RPPR=12.4476;RPL=44.0;RPR=37.0;EPP=19.7655;EPPR=28.6612;DPRA=0.0;ODDS=103.305;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2215;Dels=0.0;FS=1.0755;HaplotypeScore=2.99 [...]
+chr9 135777121 . A G 741.854 PASS SOMATIC;NS=2;DP=195;DPB=195.0;AC=1;AN=3;AF=0.25;RO=159;AO=36;PRO=0.0;PAO=0.0;QR=6096;QA=1371;PQR=0.0;PQA=0.0;SRF=50;SRR=109;SAF=13;SAR=23;SRP=50.5505;SAP=9.04217;AB=0.241611;ABP=89.4174;RUN=1;RPP=37.7539;RPPR=116.104;RPL=30.0;RPR=6.0;EPP=3.25157;EPPR=4.6628;DPRA=3.23913;ODDS=29.6935;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.401;Dels=0.0;FS=1.639;Haplot [...]
+chr9 135782221 . T C 2285.11 PASS SOMATIC;NS=2;DP=334;DPB=334.0;AC=1;AN=3;AF=0.25;RO=246;AO=88;PRO=0.0;PAO=0.0;QR=9437;QA=3430;PQR=0.0;PQA=0.0;SRF=77;SRR=169;SAF=20;SAR=68;SRP=77.7231;SAP=59.8634;AB=0.349206;ABP=52.7818;RUN=1;RPP=7.84676;RPPR=48.7701;RPL=51.0;RPR=37.0;EPP=5.47788;EPPR=21.6885;DPRA=3.07317;ODDS=52.1478;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988636;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.87;Dels=0.0;FS=3.447;H [...]
+chr9 135786112 . T C 1617.8 PASS SOMATIC;NS=2;DP=238;DPB=238.0;AC=1;AN=3;AF=0.25;RO=171;AO=67;PRO=0.0;PAO=0.0;QR=6501;QA=2486;PQR=0.0;PQA=0.0;SRF=55;SRR=116;SAF=22;SAR=45;SRP=50.262;SAP=20.1552;AB=0.372881;ABP=27.8534;RUN=1;RPP=57.4916;RPPR=132.549;RPL=54.0;RPR=13.0;EPP=8.4876;EPPR=12.2676;DPRA=0.0;ODDS=37.1307;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.3731;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988304;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.182;Dels=0.0;FS=0.0;Haplot [...]
+chr9 135786904 . A G 2544.86 PASS SOMATIC;NS=2;DP=404;DPB=404.0;AC=1;AN=3;AF=0.25;RO=297;AO=106;PRO=0.0;PAO=0.0;QR=11385;QA=3809;PQR=0.0;PQA=0.0;SRF=103;SRR=194;SAF=42;SAR=64;SRP=63.5556;SAP=12.9253;AB=0.350993;ABP=61.2518;RUN=1;RPP=4.32138;RPPR=11.9667;RPL=57.0;RPR=49.0;EPP=5.96022;EPPR=5.6497;DPRA=2.96078;ODDS=64.6219;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990566;PAIREDR=0.986532;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.601;Dels=0.0;F [...]
+chr9 135918481 . G T 1646.795 REJECT NS=2;DP=413;DPB=467.0;AC=2;AN=4;AF=0.5;RO=378;AO=89;PRO=0.0;PAO=0.0;QR=14501;QA=3344;PQR=0.0;PQA=0.0;SRF=196;SRR=182;SAF=54;SAR=35;SRP=4.13625;SAP=11.8182;AB=0.190578;ABP=391.369;RUN=1;RPP=3.22989;RPPR=3.0103;RPL=43.0;RPR=46.0;EPP=3.0347;EPPR=3.0103;DPRA=0.0;ODDS=109.791;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997354;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.982;Dels=0.0;FS=4.098;HaplotypeScore=8. [...]
+chr9 139391636 . G A 8575.75 REJECT NS=2;DP=331;DPB=378.0;AC=3;AN=4;AF=0.75;RO=82;AO=296;PRO=0.0;PAO=0.0;QR=3161;QA=11357;PQR=0.0;PQA=0.0;SRF=39;SRR=43;SAF=133;SAR=163;SRP=3.434;SAP=9.61275;AB=0.711268;ABP=113.113;RUN=1;RPP=3.12768;RPPR=3.434;RPL=150.0;RPR=146.0;EPP=6.56095;EPPR=3.96363;DPRA=0.0;ODDS=59.6552;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993243;PAIREDR=0.987805;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.831;Dels=0.0;FS=1.4725;HaplotypeS [...]
+chr9 139397707 . G A 6805.73 REJECT NS=2;DP=294;DPB=332.0;AC=3;AN=4;AF=0.75;RO=91;AO=241;PRO=0.0;PAO=0.0;QR=3457;QA=9066;PQR=0.0;PQA=0.0;SRF=47;SRR=44;SAF=105;SAR=136;SRP=3.22506;SAP=11.6692;AB=0.649805;ABP=53.1063;RUN=1;RPP=5.03761;RPPR=3.03416;RPL=128.0;RPR=113.0;EPP=5.03761;EPPR=4.17955;DPRA=0.0;ODDS=44.9661;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991701;PAIREDR=0.978022;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.505;Dels=0.0;FS=4.756;Haplotyp [...]
+chr9 139400299 . C A 1215.63 REJECT NS=2;DP=250;DPB=289.0;AC=2;AN=4;AF=0.5;RO=228;AO=61;PRO=0.0;PAO=0.0;QR=8597;QA=2302;PQR=0.0;PQA=0.0;SRF=83;SRR=145;SAF=19;SAR=42;SRP=39.6206;SAP=21.8416;AB=0.211073;ABP=212.561;RUN=1;RPP=4.7546;RPPR=21.4488;RPL=27.0;RPR=34.0;EPP=3.33068;EPPR=3.0484;DPRA=0.0;ODDS=35.1214;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.02;Dels=0.0;FS=0.902;HaplotypeScore=3.9327;MLE [...]
+chr9 139402663 . T C 7479.83 REJECT NS=2;DP=330;DPB=382.0;AC=3;AN=4;AF=0.75;RO=104;AO=277;PRO=0.0;PAO=0.0;QR=3961;QA=10330;PQR=0.0;PQA=0.0;SRF=63;SRR=41;SAF=156;SAR=121;SRP=13.116;SAP=12.6134;AB=0.62724;ABP=42.2447;RUN=1;RPP=3.95885;RPPR=7.10269;RPL=133.0;RPR=144.0;EPP=4.77413;EPPR=4.34659;DPRA=0.0;ODDS=64.5014;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990385;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.277;Dels=0.0;FS=1.726;HaplotypeScor [...]
+chr9 139405261 . C T 720.244 REJECT NS=1;DP=67;DPB=67.0;AC=1;AN=4;AF=0.5;RO=39;AO=28;PRO=0.0;PAO=0.0;QR=1534;QA=1060;PQR=0.0;PQA=0.0;SRF=16;SRR=23;SAF=13;SAR=15;SRP=5.73856;SAP=3.32051;AB=0.41791;ABP=6.93191;RUN=1;RPP=5.80219;RPPR=19.1015;RPL=17.0;RPR=11.0;EPP=7.97367;EPPR=3.51141;DPRA=0.0;ODDS=165.842;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.948718;technology.ILLUMINA=1.0;BaseQRankSum=0.426;FS=0.952;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0. [...]
+chr9 139407452 . C T 2231.525 REJECT NS=2;DP=184;DPB=211.0;AC=2;AN=4;AF=0.5;RO=107;AO=101;PRO=0.0;PAO=0.0;QR=3655;QA=3366;PQR=0.0;PQA=0.0;SRF=75;SRR=32;SAF=69;SAR=32;SRP=40.5342;SAP=32.4434;AB=0.478673;ABP=3.8439;RUN=1;RPP=77.8508;RPPR=73.6542;RPL=21.0;RPR=80.0;EPP=3.0318;EPPR=5.46589;DPRA=0.0;ODDS=124.33;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=59.802;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990654;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2175;Dels=0.0;FS=0.3385;HaplotypeScore=3 [...]
+chr9 139407932 . A G 7109.39 REJECT NS=2;DP=387;DPB=450.0;AC=2;AN=4;AF=0.5;RO=205;AO=245;PRO=0.0;PAO=0.0;QR=7765;QA=9464;PQR=0.0;PQA=0.0;SRF=96;SRR=109;SAF=105;SAR=140;SRP=4.80044;SAP=13.8677;AB=0.544444;ABP=10.7311;RUN=1;RPP=5.57175;RPPR=3.10563;RPL=131.0;RPR=114.0;EPP=4.50817;EPPR=5.39362;DPRA=0.0;ODDS=405.209;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995918;PAIREDR=0.995122;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.5355;Dels=0.0;FS=2.5225;Haplot [...]
+chr9 139410177 . T C 3126.27 REJECT NS=2;DP=204;DPB=237.0;AC=2;AN=4;AF=0.5;RO=123;AO=114;PRO=0.0;PAO=0.0;QR=4620;QA=4349;PQR=0.0;PQA=0.0;SRF=29;SRR=94;SAF=26;SAR=88;SRP=77.5995;SAP=76.2308;AB=0.481013;ABP=3.75245;RUN=1;RPP=13.982;RPPR=29.8624;RPL=69.0;RPR=45.0;EPP=4.22937;EPPR=10.7958;DPRA=0.0;ODDS=166.48;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991228;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6835;Dels=0.0;FS=4.628;HaplotypeScore=4.83 [...]
+chr9 139410424 . A G 9366.705 REJECT NS=2;DP=252;DPB=292.0;AC=4;AN=4;AF=1.0;RO=0;AO=292;PRO=0.0;PAO=0.0;QR=0;QA=11028;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=171;SAR=121;SRP=0.0;SAP=21.6017;AB=0.0;ABP=0.0;RUN=1;RPP=74.4309;RPPR=0.0;RPL=97.0;RPR=195.0;EPP=33.4704;EPPR=0.0;DPRA=0.0;ODDS=53.5157;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993151;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.605;SOR=1.04 [...]
+chr9 139411714 . T C 1441.32 REJECT NS=1;DP=95;DPB=95.0;AC=1;AN=4;AF=0.5;RO=40;AO=54;PRO=0.0;PAO=0.0;QR=1544;QA=1965;PQR=0.0;PQA=0.0;SRF=23;SRR=17;SAF=33;SAR=21;SRP=4.96463;SAP=8.80089;AB=0.568421;ABP=6.87324;RUN=1;RPP=10.8919;RPPR=10.8276;RPL=20.0;RPR=34.0;EPP=13.3047;EPPR=8.43898;DPRA=0.0;ODDS=247.229;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.975;technology.ILLUMINA=1.0;BaseQRankSum=0.032;FS=1.751;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.3; [...]
+chr9 139412197 . G A 4742.015 REJECT NS=2;DP=296;DPB=344.0;AC=2;AN=4;AF=0.5;RO=171;AO=173;PRO=0.0;PAO=0.0;QR=6476;QA=6594;PQR=0.0;PQA=0.0;SRF=113;SRR=58;SAF=123;SAR=50;SRP=41.4238;SAP=69.8992;AB=0.502907;ABP=3.03555;RUN=1;RPP=30.7374;RPPR=36.0395;RPL=63.0;RPR=110.0;EPP=13.5664;EPPR=28.7251;DPRA=0.0;ODDS=295.07;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2475;Dels=0.0;FS=2.3505;HaplotypeScore=8.8 [...]
+chr9 139418260 . A G 6680.84 REJECT NS=2;DP=391;DPB=453.0;AC=2;AN=4;AF=0.5;RO=211;AO=241;PRO=0.0;PAO=0.0;QR=8072;QA=9184;PQR=0.0;PQA=0.0;SRF=115;SRR=96;SAF=129;SAR=112;SRP=6.72547;SAP=5.61426;AB=0.532009;ABP=7.04166;RUN=1;RPP=6.263;RPPR=5.32585;RPL=130.0;RPR=111.0;EPP=14.0479;EPPR=6.72547;DPRA=0.0;ODDS=364.083;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995261;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.8395;Dels=0.0;FS=2.6545;HaplotypeScor [...]
+chr10 3000970 . T C 14873.9 REJECT NS=2;DP=399;DPB=455.0;AC=4;AN=4;AF=1.0;RO=3;AO=452;PRO=0.0;PAO=0.0;QR=119;QA=17226;PQR=0.0;PQA=0.0;SRF=1;SRR=2;SAF=244;SAR=208;SRP=3.73412;SAP=9.23647;AB=0.0;ABP=0.0;RUN=1;RPP=16.0007;RPPR=3.73412;RPL=252.0;RPR=200.0;EPP=4.93196;EPPR=9.52472;DPRA=0.0;ODDS=66.7112;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997788;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.251;Dels=0.0;FS=0.0;HaplotypeScore=6.8322;MLEAC=2 [...]
+chr10 6014203 . T A 8609.48 REJECT NS=2;DP=328;DPB=375.0;AC=2;AN=4;AF=0.5;RO=92;AO=283;PRO=0.0;PAO=0.0;QR=3560;QA=10890;PQR=0.0;PQA=0.0;SRF=51;SRR=41;SAF=163;SAR=120;SRP=5.3706;SAP=17.1978;AB=0.754667;ABP=214.257;RUN=1;RPP=50.8978;RPPR=21.515;RPL=102.0;RPR=181.0;EPP=48.5038;EPPR=7.63648;DPRA=0.0;ODDS=176.229;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992933;PAIREDR=0.98913;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1455;Dels=0.0;FS=0.873;HaplotypeSc [...]
+chr10 6014272 . C G 9284.72 REJECT NS=2;DP=378;DPB=435.0;AC=2;AN=4;AF=0.5;RO=119;AO=316;PRO=0.0;PAO=0.0;QR=4453;QA=11851;PQR=0.0;PQA=0.0;SRF=39;SRR=80;SAF=105;SAR=211;SRP=33.6846;SAP=80.2213;AB=0.726437;ABP=196.741;RUN=1;RPP=40.64;RPPR=7.11603;RPL=195.0;RPR=121.0;EPP=21.5915;EPPR=3.90444;DPRA=0.0;ODDS=277.328;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996835;PAIREDR=0.991597;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.8995;Dels=0.0;FS=4.419;Haplotype [...]
+chr10 8100647 . C T 1879.595 REJECT NS=2;DP=397;DPB=453.0;AC=2;AN=4;AF=0.5;RO=351;AO=102;PRO=0.0;PAO=0.0;QR=13345;QA=3765;PQR=0.0;PQA=0.0;SRF=175;SRR=176;SAF=50;SAR=52;SRP=3.01649;SAP=3.09546;AB=0.225166;ABP=300.214;RUN=1;RPP=3.35092;RPPR=3.51141;RPL=49.0;RPR=53.0;EPP=11.5259;EPPR=5.24364;DPRA=0.0;ODDS=164.654;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994302;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.0575;Dels=0.0;FS=0.0;HaplotypeScore= [...]
+chr10 19509564 . G A 5714.735000000001 REJECT NS=2;DP=361;DPB=410.0;AC=2;AN=4;AF=0.5;RO=212;AO=198;PRO=0.0;PAO=0.0;QR=8117;QA=7705;PQR=0.0;PQA=0.0;SRF=98;SRR=114;SAF=96;SAR=102;SRP=5.63246;SAP=3.40511;AB=0.482927;ABP=4.04837;RUN=1;RPP=5.81786;RPPR=4.03458;RPL=91.0;RPR=107.0;EPP=24.2425;EPPR=21.0786;DPRA=0.0;ODDS=308.417;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989899;PAIREDR=0.995283;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1195;Dels=0.0;FS=1.894 [...]
+chr10 43595968 . A G 13662.3 REJECT NS=2;DP=365;DPB=418.0;AC=4;AN=4;AF=1.0;RO=0;AO=417;PRO=0.0;PAO=0.0;QR=0;QA=15786;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=180;SAR=237;SRP=0.0;SAP=19.929;AB=0.0;ABP=0.0;RUN=1;RPP=3.26546;RPPR=0.0;RPL=212.0;RPR=205.0;EPP=11.7639;EPPR=0.0;DPRA=0.0;ODDS=69.1397;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997602;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.946;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.185;SOR=1.0 [...]
+chr10 43596179 . G A 1294.44 PASS SOMATIC;NS=2;DP=202;DPB=202.0;AC=1;AN=3;AF=0.25;RO=148;AO=54;PRO=0.0;PAO=0.0;QR=5622;QA=1988;PQR=0.0;PQA=0.0;SRF=46;SRR=102;SAF=15;SAR=39;SRP=49.022;SAP=26.1727;AB=0.362416;ABP=27.5086;RUN=1;RPP=22.4731;RPPR=24.1968;RPL=38.0;RPR=16.0;EPP=3.0103;EPPR=10.1116;DPRA=2.81132;ODDS=34.103;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.468;Dels=0.0;FS=2.334;Haploty [...]
+chr10 43610366 . G A 14289.7 REJECT NS=2;DP=381;DPB=434.0;AC=4;AN=4;AF=1.0;RO=0;AO=434;PRO=0.0;PAO=0.0;QR=0;QA=16525;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=213;SAR=221;SRP=0.0;SAP=3.33052;AB=0.0;ABP=0.0;RUN=1;RPP=5.01166;RPPR=0.0;RPL=227.0;RPR=207.0;EPP=11.8363;EPPR=0.0;DPRA=0.0;ODDS=70.4926;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997696;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9973;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.805;SOR=0 [...]
+chr10 43610455 . T C 13695.7 REJECT NS=2;DP=361;DPB=406.0;AC=4;AN=4;AF=1.0;RO=0;AO=406;PRO=0.0;PAO=0.0;QR=0;QA=15475;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=170;SAR=236;SRP=0.0;SAP=26.3082;AB=0.0;ABP=0.0;RUN=1;RPP=16.3814;RPPR=0.0;RPL=228.0;RPR=178.0;EPP=4.7432;EPPR=0.0;DPRA=0.0;ODDS=60.4914;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997537;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8291;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.175;SOR=1. [...]
+chr10 43610558 . C T 11529.099999999999 REJECT NS=2;DP=302;DPB=343.0;AC=4;AN=4;AF=1.0;RO=0;AO=343;PRO=0.0;PAO=0.0;QR=0;QA=13183;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=179;SAR=164;SRP=0.0;SAP=4.43474;AB=0.0;ABP=0.0;RUN=1;RPP=9.90457;RPPR=0.0;RPL=188.0;RPR=155.0;EPP=3.06728;EPPR=0.0;DPRA=0.0;ODDS=54.9024;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.7286;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.17; [...]
+chr10 43611708 . A G 15950.5 REJECT NS=2;DP=420;DPB=480.0;AC=4;AN=4;AF=1.0;RO=0;AO=479;PRO=0.0;PAO=0.0;QR=0;QA=18373;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=233;SAR=246;SRP=0.0;SAP=3.77644;AB=0.0;ABP=0.0;RUN=1;RPP=6.31511;RPPR=0.0;RPL=226.0;RPR=253.0;EPP=10.6309;EPPR=0.0;DPRA=0.0;ODDS=77.9498;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9875;MQMR=0.0;PAIRED=0.995825;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.7173;MLEAC=2;MLEAF=1.0;MQ=59.99;QD=31.565;S [...]
+chr10 43611865 . T C 14664.75 REJECT NS=2;DP=388;DPB=453.0;AC=4;AN=4;AF=1.0;RO=0;AO=453;PRO=0.0;PAO=0.0;QR=0;QA=17323;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=240;SAR=213;SRP=0.0;SAP=6.50479;AB=0.0;ABP=0.0;RUN=1;RPP=12.7172;RPPR=0.0;RPL=249.0;RPR=204.0;EPP=11.8736;EPPR=0.0;DPRA=0.0;ODDS=83.8629;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8797;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.23;SOR=0.8305 [...]
+chr10 43613843 . G T 3839.52 REJECT NS=1;DP=114;DPB=114.0;AC=2;AN=4;AF=1.0;RO=0;AO=114;PRO=0.0;PAO=0.0;QR=0;QA=4339;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=49;SAR=65;SRP=0.0;SAP=7.88659;AB=0.0;ABP=0.0;RUN=1;RPP=4.9151;RPPR=0.0;RPL=52.0;RPR=62.0;EPP=27.6965;EPPR=0.0;DPRA=0.0;ODDS=75.6992;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.86;SOR=1.015 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV [...]
+chr10 43615505 . G A 857.3665 REJECT NS=2;DP=215;DPB=244.0;AC=2;AN=4;AF=0.5;RO=195;AO=49;PRO=0.0;PAO=0.0;QR=7463;QA=1865;PQR=0.0;PQA=0.0;SRF=126;SRR=69;SAF=30;SAR=19;SRP=39.1904;SAP=8.37251;AB=0.20082;ABP=192.712;RUN=1;RPP=26.4533;RPPR=72.5086;RPL=13.0;RPR=36.0;EPP=3.40914;EPPR=5.51585;DPRA=0.0;ODDS=84.9378;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994872;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0785;Dels=0.0;FS=2.331;HaplotypeScore=4 [...]
+chr10 43622217 . T C 10035.485 REJECT NS=2;DP=263;DPB=307.0;AC=4;AN=4;AF=1.0;RO=0;AO=307;PRO=0.0;PAO=0.0;QR=0;QA=11888;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=127;SAR=180;SRP=0.0;SAP=22.8789;AB=0.0;ABP=0.0;RUN=1;RPP=47.1541;RPPR=0.0;RPL=193.0;RPR=114.0;EPP=21.4077;EPPR=0.0;DPRA=0.0;ODDS=57.9967;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.990228;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.16;SOR=1 [...]
+chr10 45006398 . G A 5575.855 REJECT NS=2;DP=344;DPB=389.0;AC=2;AN=4;AF=0.5;RO=194;AO=193;PRO=0.0;PAO=0.0;QR=7540;QA=7503;PQR=0.0;PQA=0.0;SRF=105;SRR=89;SAF=101;SAR=92;SRP=5.87575;SAP=3.92164;AB=0.496144;ABP=3.06054;RUN=1;RPP=16.793;RPPR=40.6641;RPL=79.0;RPR=114.0;EPP=12.4725;EPPR=3.72666;DPRA=0.0;ODDS=284.103;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994845;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.038;Dels=0.0;FS=0.692;HaplotypeScore [...]
+chr10 45006477 . C G 5048.375 REJECT NS=2;DP=332;DPB=376.0;AC=2;AN=4;AF=0.5;RO=193;AO=183;PRO=0.0;PAO=0.0;QR=7446;QA=6977;PQR=0.0;PQA=0.0;SRF=74;SRR=119;SAF=68;SAR=115;SRP=25.7939;SAP=29.2222;AB=0.486702;ABP=3.58782;RUN=1;RPP=21.0584;RPPR=23.8137;RPL=111.0;RPR=72.0;EPP=27.0389;EPPR=21.9235;DPRA=0.0;ODDS=271.536;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983607;PAIREDR=0.994819;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1375;Dels=0.0;FS=0.462;Haploty [...]
+chr10 52568616 . T C 6261.41 REJECT NS=2;DP=173;DPB=201.0;AC=4;AN=4;AF=1.0;RO=0;AO=201;PRO=0.0;PAO=0.0;QR=0;QA=7561;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=162;SAR=39;SRP=0.0;SAP=166.454;AB=0.0;ABP=0.0;RUN=1;RPP=145.885;RPPR=0.0;RPL=43.0;RPR=158.0;EPP=21.1707;EPPR=0.0;DPRA=0.0;ODDS=39.2195;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.985075;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.56;SOR=3.1055 G [...]
+chr10 55511027 . A G 3993.3 REJECT NS=1;DP=118;DPB=118.0;AC=2;AN=4;AF=1.0;RO=0;AO=118;PRO=0.0;PAO=0.0;QR=0;QA=4502;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=59;SAR=59;SRP=0.0;SAP=3.0103;AB=0.0;ABP=0.0;RUN=1;RPP=3.08391;RPPR=0.0;RPL=60.0;RPR=58.0;EPP=26.8597;EPPR=0.0;DPRA=0.0;ODDS=78.191;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.983051;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.61;SOR=0.693 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr10 60025964 . TGA T . PASS SOMATIC;AC=1;AN=4 GT:AD:DP:MM:MQS:NQSBQ:NQSMM:REnd:RStart:SC:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:37,0:37:0.108108,0.0:60.0,0.0:38.4033,0.0:0.0,0.0:0,0:0,0:9,28,0,0:0:0:37:.:.:.:.:0:.:-0.000266909 0/1:82,39:121:0.158537,0.025641:60.0,60.0:37.8314,38.5692:0.002574,0.0:26,11:74,11:29,53,15,24:39:32:121:.:.:.:.:1:.:-0.00804187
+chr10 63760087 . C T 654.113 REJECT NS=2;DP=209;DPB=252.1;AC=2;AN=2;AF=0.0;RO=126;AO=8;PRO=41.3333;PAO=0.0;QR=4612;QA=100;PQR=1442.33;PQA=0.0;SRF=44;SRR=82;SAF=0;SAR=8;SRP=27.8961;SAP=20.3821;AB=0.0382775;ABP=390.021;RUN=1;RPP=3.0103;RPPR=30.5846;RPL=4.0;RPR=4.0;EPP=3.0103;EPPR=3.0103;DPRA=0.0;ODDS=41.6352;GTI=0;TYPE=snp;CIGAR=1X19M;NUMALT=3;MEANALT=8.5;LEN=1;MQM=60.0;MQMR=59.9524;PAIRED=1.0;PAIREDR=0.992063;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr10 63760087 . C CT 654.113 REJECT NS=2;DP=209;DPB=252.1;AC=2;AN=2;AF=0.0;RO=126;AO=22;PRO=41.3333;PAO=22.3333;QR=4612;QA=637;PQR=1442.33;PQA=803.333;SRF=44;SRR=82;SAF=8;SAR=14;SRP=27.8961;SAP=6.56362;AB=0.105263;ABP=285.873;RUN=1;RPP=12.8806;RPPR=30.5846;RPL=16.0;RPR=6.0;EPP=3.40511;EPPR=3.0103;DPRA=0.0;ODDS=41.6352;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=3;MEANALT=8.5;LEN=1;MQM=60.0;MQMR=59.9524;PAIRED=1.0;PAIREDR=0.992063;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr10 63760087 . CT C 509.92150000000004 REJECT NS=2;DP=209;DPB=252.1;AC=2;AN=4;AF=0.5;RO=126;AO=37;PRO=41.3333;PAO=23.3333;QR=4612;QA=1255;PQR=1442.33;PQA=811.333;SRF=44;SRR=82;SAF=12;SAR=25;SRP=27.8961;SAP=12.9286;AB=0.177033;ABP=192.365;RUN=1;RPP=7.76406;RPPR=30.5846;RPL=23.0;RPR=14.0;EPP=3.06899;EPPR=3.0103;DPRA=0.0;ODDS=41.6352;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=3;MEANALT=8.5;LEN=1;MQM=60.0;MQMR=59.9524;PAIRED=0.972973;PAIREDR=0.992063;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0= [...]
+chr10 64506292 . G T 1603.975 REJECT NS=2;DP=376;DPB=427.0;AC=2;AN=4;AF=0.5;RO=334;AO=93;PRO=0.0;PAO=0.0;QR=12895;QA=3517;PQR=0.0;PQA=0.0;SRF=163;SRR=171;SAF=42;SAR=51;SRP=3.42639;SAP=4.90158;AB=0.217799;ABP=298.376;RUN=1;RPP=11.4393;RPPR=3.42639;RPL=56.0;RPR=37.0;EPP=6.95631;EPPR=5.11676;DPRA=0.0;ODDS=193.47;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997006;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.1805;Dels=0.0;FS=2.169;HaplotypeScore [...]
+chr10 72010700 . C T 5760.74 REJECT NS=2;DP=412;DPB=463.0;AC=2;AN=4;AF=0.5;RO=250;AO=212;PRO=0.0;PAO=0.0;QR=9347;QA=7875;PQR=0.0;PQA=0.0;SRF=122;SRR=128;SAF=108;SAR=104;SRP=3.32299;SAP=3.17418;AB=0.457883;ABP=10.1438;RUN=1;RPP=7.10742;RPPR=4.71273;RPL=116.0;RPR=96.0;EPP=11.0407;EPPR=3.32299;DPRA=0.0;ODDS=234.398;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.707;Dels=0.0;FS=1.363;HaplotypeScore= [...]
+chr10 79527618 . G A 1966.1 PASS SOMATIC;NS=2;DP=280;DPB=280.0;AC=1;AN=3;AF=0.25;RO=205;AO=75;PRO=0.0;PAO=0.0;QR=8020;QA=2882;PQR=0.0;PQA=0.0;SRF=135;SRR=70;SAF=48;SAR=27;SRP=47.7638;SAP=15.7786;AB=0.376884;ABP=29.2098;RUN=1;RPP=24.117;RPPR=24.4602;RPL=24.0;RPR=51.0;EPP=6.51361;EPPR=22.5959;DPRA=2.45679;ODDS=51.5493;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986667;PAIREDR=0.990244;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.109;Dels=0.0;FS=0.5 [...]
+chr10 88635779 . C A 1542.51 REJECT NS=2;DP=310;DPB=360.0;AC=2;AN=4;AF=0.5;RO=279;AO=81;PRO=0.0;PAO=0.0;QR=10631;QA=3054;PQR=0.0;PQA=0.0;SRF=156;SRR=123;SAF=48;SAR=33;SRP=11.486;SAP=9.04217;AB=0.225;ABP=239.484;RUN=1;RPP=7.5409;RPPR=24.8729;RPL=34.0;RPR=47.0;EPP=3.68051;EPPR=35.8937;DPRA=0.0;ODDS=57.2549;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=45.4691;MQMR=58.6774;PAIRED=0.987654;PAIREDR=0.989247;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.618;Dels=0.0;FS=4.4085;Haplotype [...]
+chr10 88683122 . T C 1436.345 REJECT NS=2;DP=282;DPB=330.0;AC=2;AN=4;AF=0.5;RO=254;AO=75;PRO=0.0;PAO=0.0;QR=9888;QA=2865;PQR=0.0;PQA=0.0;SRF=158;SRR=96;SAF=48;SAR=27;SRP=35.8731;SAP=15.7786;AB=0.227273;ABP=216.209;RUN=1;RPP=9.52472;RPPR=29.8203;RPL=30.0;RPR=45.0;EPP=18.3264;EPPR=29.8203;DPRA=0.0;ODDS=127.241;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984252;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.102;Dels=0.0;FS=1.2095;HaplotypeScore= [...]
+chr10 89523233 . G T 1872.15 REJECT NS=1;DP=63;DPB=63.0;AC=2;AN=4;AF=1.0;RO=0;AO=63;PRO=0.0;PAO=0.0;QR=0;QA=2336;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=1;SAR=62;SRP=0.0;SAP=131.265;AB=0.0;ABP=0.0;RUN=1;RPP=24.5527;RPPR=0.0;RPL=44.0;RPR=19.0;EPP=21.2438;EPPR=0.0;DPRA=0.0;ODDS=43.8838;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.984127;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.57;SOR=6.901 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMIC [...]
+chr10 89525860 . C T 3981.435 REJECT NS=2;DP=270;DPB=307.0;AC=2;AN=4;AF=0.5;RO=158;AO=149;PRO=0.0;PAO=0.0;QR=5972;QA=5626;PQR=0.0;PQA=0.0;SRF=127;SRR=31;SAF=111;SAR=38;SRP=129.67;SAP=80.6732;AB=0.485342;ABP=3.58323;RUN=1;RPP=32.5219;RPPR=37.369;RPL=52.0;RPR=97.0;EPP=3.02487;EPPR=3.2302;DPRA=0.0;ODDS=210.57;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993289;PAIREDR=0.987342;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.784;Dels=0.0;FS=5.9175;HaplotypeScor [...]
+chr10 89534244 . G T 5561.450000000001 REJECT NS=2;DP=372;DPB=429.0;AC=2;AN=4;AF=0.5;RO=226;AO=202;PRO=0.0;PAO=0.0;QR=8644;QA=7679;PQR=0.0;PQA=0.0;SRF=97;SRR=129;SAF=101;SAR=101;SRP=12.8492;SAP=3.0103;AB=0.470862;ABP=6.17387;RUN=1;RPP=7.31025;RPPR=7.66071;RPL=111.0;RPR=91.0;EPP=4.08529;EPPR=12.8492;DPRA=0.0;ODDS=333.442;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99115;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1825;Dels=0.0;FS=6.655;Haplo [...]
+chr10 96798749 . T C 2116.5950000000003 REJECT NS=2;DP=380;DPB=432.0;AC=2;AN=4;AF=0.5;RO=332;AO=100;PRO=0.0;PAO=0.0;QR=12859;QA=3857;PQR=0.0;PQA=0.0;SRF=155;SRR=177;SAF=50;SAR=50;SRP=6.17594;SAP=3.0103;AB=0.231481;ABP=273.56;RUN=1;RPP=7.26639;RPPR=8.89682;RPL=43.0;RPR=57.0;EPP=13.5202;EPPR=26.5564;DPRA=0.0;ODDS=134.825;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99;PAIREDR=0.990964;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6805;Dels=0.0;FS=10.319;Hap [...]
+chr10 96827030 . C T 1319.92 REJECT NS=1;DP=93;DPB=93.0;AC=1;AN=4;AF=0.5;RO=46;AO=47;PRO=0.0;PAO=0.0;QR=1760;QA=1806;PQR=0.0;PQA=0.0;SRF=28;SRR=18;SAF=27;SAR=20;SRP=7.73089;SAP=5.27418;AB=0.505376;ABP=3.03365;RUN=1;RPP=4.16534;RPPR=18.305;RPL=21.0;RPR=26.0;EPP=5.27418;EPPR=4.70971;DPRA=0.0;ODDS=290.762;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.8696;PAIRED=1.0;PAIREDR=0.978261;technology.ILLUMINA=1.0;BaseQRankSum=-0.833;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.48;MQRankSum [...]
+chr10 101620771 . C G 5938.645 REJECT NS=2;DP=379;DPB=436.0;AC=2;AN=4;AF=0.5;RO=219;AO=217;PRO=0.0;PAO=0.0;QR=8272;QA=8232;PQR=0.0;PQA=0.0;SRF=114;SRR=105;SAF=117;SAR=100;SRP=3.81345;SAP=5.90226;AB=0.497706;ABP=3.03022;RUN=1;RPP=3.26047;RPPR=13.8082;RPL=106.0;RPR=111.0;EPP=8.30389;EPPR=3.02022;DPRA=0.0;ODDS=352.459;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.981567;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.04;Dels=0.0;FS=2.3685;HaplotypeS [...]
+chr10 104264107 . C T 7224.865 REJECT NS=2;DP=331;DPB=378.0;AC=3;AN=4;AF=0.75;RO=102;AO=276;PRO=0.0;PAO=0.0;QR=3842;QA=9958;PQR=0.0;PQA=0.0;SRF=34;SRR=68;SAF=106;SAR=170;SRP=27.6203;SAP=35.2362;AB=0.644599;ABP=55.1332;RUN=1;RPP=81.6868;RPPR=24.8102;RPL=188.0;RPR=88.0;EPP=6.15736;EPPR=8.46027;DPRA=0.0;ODDS=57.6304;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985507;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.668;Dels=0.0;FS=2.1935;HaplotypeS [...]
+chr10 104378750 . G A 1195.38 PASS SOMATIC;NS=2;DP=223;DPB=223.0;AC=1;AN=3;AF=0.25;RO=170;AO=51;PRO=0.0;PAO=0.0;QR=6035;QA=1958;PQR=0.0;PQA=0.0;SRF=106;SRR=64;SAF=31;SAR=20;SRP=25.5425;SAP=8.16222;AB=0.310976;ABP=53.9075;RUN=1;RPP=67.7713;RPPR=72.9573;RPL=6.0;RPR=45.0;EPP=5.09662;EPPR=4.28764;DPRA=2.77966;ODDS=37.0506;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=59.9294;PAIRED=1.0;PAIREDR=0.994118;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.574;Dels=0.0;FS=0.0 [...]
+chr10 104387019 . T C 4303.945 REJECT NS=2;DP=273;DPB=315.0;AC=2;AN=4;AF=0.5;RO=158;AO=157;PRO=0.0;PAO=0.0;QR=6049;QA=6004;PQR=0.0;PQA=0.0;SRF=54;SRR=104;SAF=50;SAR=107;SRP=37.369;SAP=47.9473;AB=0.498413;ABP=3.01719;RUN=1;RPP=4.68386;RPPR=8.5077;RPL=84.0;RPR=73.0;EPP=14.6422;EPPR=20.8219;DPRA=0.0;ODDS=251.107;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9125;Dels=0.0;FS=1.6415;HaplotypeScore=5.93 [...]
+chr10 104389932 . T G 10011.635 REJECT NS=2;DP=266;DPB=302.0;AC=4;AN=4;AF=1.0;RO=0;AO=302;PRO=0.0;PAO=0.0;QR=0;QA=11575;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=77;SAR=225;SRP=0.0;SAP=160.507;AB=0.0;ABP=0.0;RUN=1;RPP=66.5438;RPPR=0.0;RPL=198.0;RPR=104.0;EPP=16.9307;EPPR=0.0;DPRA=0.0;ODDS=48.6435;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.045;SOR=2.16 [...]
+chr10 104849468 . G A 2243.965 REJECT NS=2;DP=314;DPB=366.0;AC=2;AN=4;AF=0.5;RO=257;AO=109;PRO=0.0;PAO=0.0;QR=9723;QA=4044;PQR=0.0;PQA=0.0;SRF=179;SRR=78;SAF=72;SAR=37;SRP=89.2017;SAP=27.4145;AB=0.297814;ABP=132.966;RUN=1;RPP=7.4927;RPPR=55.7424;RPL=47.0;RPR=62.0;EPP=10.2021;EPPR=3.22153;DPRA=0.0;ODDS=195.759;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8899;MQMR=60.0;PAIRED=0.981651;PAIREDR=0.996109;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.813;Dels=0.0;FS=2.363;Haploty [...]
+chr10 104851285 . G A 1198.335 REJECT NS=2;DP=243;DPB=275.0;AC=2;AN=4;AF=0.5;RO=212;AO=62;PRO=0.0;PAO=0.0;QR=8177;QA=2368;PQR=0.0;PQA=0.0;SRF=147;SRR=65;SAF=43;SAR=19;SRP=71.8828;SAP=23.184;AB=0.225455;ABP=183.053;RUN=1;RPP=26.6864;RPPR=53.2;RPL=18.0;RPR=44.0;EPP=8.05372;EPPR=3.17418;DPRA=0.0;ODDS=89.5439;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.967742;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1185;Dels=0.0;FS=0.0;HaplotypeScore=6.898 [...]
+chr10 104851396 . G T 1776.545 REJECT NS=2;DP=325;DPB=360.0;AC=2;AN=4;AF=0.5;RO=275;AO=85;PRO=0.0;PAO=0.0;QR=10535;QA=3250;PQR=0.0;PQA=0.0;SRF=92;SRR=183;SAF=26;SAR=59;SRP=68.3993;SAP=30.8307;AB=0.236111;ABP=220.761;RUN=1;RPP=16.5245;RPPR=68.3993;RPL=54.0;RPR=31.0;EPP=5.07959;EPPR=7.94546;DPRA=0.0;ODDS=104.19;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.976471;PAIREDR=0.992727;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.637;Dels=0.0;FS=1.9555;HaplotypeS [...]
+chr10 104855656 . T C 846.481 REJECT NS=2;DP=266;DPB=303.0;AC=2;AN=4;AF=0.5;RO=251;AO=52;PRO=0.0;PAO=0.0;QR=9703;QA=2035;PQR=0.0;PQA=0.0;SRF=157;SRR=94;SAF=35;SAR=17;SRP=37.3472;SAP=16.5402;AB=0.171617;ABP=286.814;RUN=1;RPP=27.0635;RPPR=74.6516;RPL=14.0;RPR=38.0;EPP=4.51363;EPPR=23.782;DPRA=0.0;ODDS=85.2191;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.98008;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.682;Dels=0.0;FS=1.327;HaplotypeScore=3.89 [...]
+chr10 104855670 . G A 1040.24 REJECT NS=2;DP=317;DPB=363.0;AC=2;AN=4;AF=0.5;RO=300;AO=63;PRO=0.0;PAO=0.0;QR=11346;QA=2426;PQR=0.0;PQA=0.0;SRF=175;SRR=125;SAF=38;SAR=25;SRP=21.1059;SAP=8.83536;AB=0.173554;ABP=339.014;RUN=1;RPP=12.9715;RPPR=40.5333;RPL=23.0;RPR=40.0;EPP=5.80219;EPPR=47.0478;DPRA=0.0;ODDS=91.9675;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.98;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.685;Dels=0.0;FS=0.429;HaplotypeScore=1.96 [...]
+chr10 104860395 . T G 9107.62 REJECT NS=2;DP=244;DPB=272.0;AC=4;AN=4;AF=1.0;RO=0;AO=272;PRO=0.0;PAO=0.0;QR=0;QA=10341;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=174;SAR=98;SRP=0.0;SAP=49.1222;AB=0.0;ABP=0.0;RUN=1;RPP=110.434;RPPR=0.0;RPL=78.0;RPR=194.0;EPP=3.52123;EPPR=0.0;DPRA=0.0;ODDS=38.6158;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992647;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8656;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.545;SOR=1. [...]
+chr10 104899197 . C G 5687.09 REJECT NS=2;DP=364;DPB=411.0;AC=2;AN=4;AF=0.5;RO=208;AO=201;PRO=0.0;PAO=0.0;QR=7839;QA=7660;PQR=0.0;PQA=0.0;SRF=90;SRR=118;SAF=82;SAR=119;SRP=11.1951;SAP=17.8001;AB=0.489051;ABP=3.43825;RUN=1;RPP=3.88537;RPPR=7.18621;RPL=105.0;RPR=96.0;EPP=22.9857;EPPR=7.18621;DPRA=0.0;ODDS=233.355;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=59.9602;MQMR=60.0;PAIRED=0.995025;PAIREDR=0.990385;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.581;Dels=0.0;FS=2.1335;Haplo [...]
+chr10 111003099 . A G 5596.49 REJECT NS=2;DP=212;DPB=244.0;AC=2;AN=4;AF=0.5;RO=54;AO=190;PRO=0.0;PAO=0.0;QR=2077;QA=7211;PQR=0.0;PQA=0.0;SRF=36;SRR=18;SAF=130;SAR=60;SRP=16.0391;SAP=59.0114;AB=0.778689;ABP=167.615;RUN=1;RPP=108.338;RPPR=39.2015;RPL=47.0;RPR=143.0;EPP=7.58182;EPPR=3.17115;DPRA=0.0;ODDS=73.8532;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989474;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1945;Dels=0.0;FS=0.0;HaplotypeScore=5 [...]
+chr10 111003232 . G T 7330.69 REJECT NS=2;DP=276;DPB=323.0;AC=2;AN=4;AF=0.5;RO=77;AO=246;PRO=0.0;PAO=0.0;QR=2930;QA=9353;PQR=0.0;PQA=0.0;SRF=27;SRR=50;SAF=78;SAR=168;SRP=17.9286;SAP=74.51;AB=0.76161;ABP=195.021;RUN=1;RPP=59.5039;RPPR=11.1604;RPL=163.0;RPR=83.0;EPP=20.0996;EPPR=15.4469;DPRA=0.0;ODDS=72.1841;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99187;PAIREDR=0.987013;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.7875;Dels=0.0;FS=0.8615;HaplotypeSco [...]
+chr10 112356331 . G A 9514.835 REJECT NS=2;DP=254;DPB=296.0;AC=4;AN=4;AF=1.0;RO=0;AO=296;PRO=0.0;PAO=0.0;QR=0;QA=11336;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=98;SAR=198;SRP=0.0;SAP=76.3709;AB=0.0;ABP=0.0;RUN=1;RPP=79.3346;RPPR=0.0;RPL=199.0;RPR=97.0;EPP=4.44817;EPPR=0.0;DPRA=0.0;ODDS=56.703;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=35.29;SOR=1.6265 GT [...]
+chr10 112361870 . A G 13516.15 REJECT NS=2;DP=356;DPB=410.0;AC=4;AN=4;AF=1.0;RO=0;AO=410;PRO=0.0;PAO=0.0;QR=0;QA=15770;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=211;SAR=199;SRP=0.0;SAP=3.77296;AB=0.0;ABP=0.0;RUN=1;RPP=3.20097;RPPR=0.0;RPL=208.0;RPR=202.0;EPP=3.34926;EPPR=0.0;DPRA=0.0;ODDS=72.8328;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.3634;MQMR=0.0;PAIRED=0.997561;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=2;Dels=0.0;FS=0.0;HaplotypeScore=2.8995;MLEAC=2;MLEAF=1.0;MQ=58.545;QD=30.25 [...]
+chr10 114003865 . A C 957.386 REJECT NS=1;DP=72;DPB=72.0;AC=1;AN=4;AF=0.5;RO=36;AO=36;PRO=0.0;PAO=0.0;QR=1402;QA=1362;PQR=0.0;PQA=0.0;SRF=28;SRR=8;SAF=26;SAR=10;SRP=27.1378;SAP=18.4519;AB=0.5;ABP=3.0103;RUN=1;RPP=14.8328;RPPR=18.4519;RPL=11.0;RPR=25.0;EPP=3.25157;EPPR=3.0103;DPRA=0.0;ODDS=220.446;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.972222;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.435;FS=2.38;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=1.339;QD [...]
+chr10 114905753 . G T 336.818 REJECT NS=2;DP=334;DPB=341.0;AC=2;AN=2;AF=0.0;RO=256;AO=43;PRO=7.0;PAO=7.0;QR=8961;QA=753;PQR=122.5;PQA=122.5;SRF=146;SRR=110;SAF=43;SAR=0;SRP=14.0034;SAP=96.3836;AB=0.128743;ABP=402.873;RUN=1;RPP=39.8243;RPPR=155.319;RPL=35.0;RPR=8.0;EPP=39.8243;EPPR=8.74434;DPRA=0.0;ODDS=25.6435;GTI=0;TYPE=snp;CIGAR=1X2M;NUMALT=2;MEANALT=3.0;LEN=1;MQM=59.6977;MQMR=59.9219;PAIRED=0.976744;PAIREDR=0.996094;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr10 114905753 . GTA TTT 336.818 REJECT NS=2;DP=334;DPB=341.0;AC=2;AN=4;AF=0.5;RO=256;AO=29;PRO=7.0;PAO=0.0;QR=8961;QA=398;PQR=122.5;PQA=0.0;SRF=146;SRR=110;SAF=29;SAR=0;SRP=14.0034;SAP=65.983;AB=0.0868263;ABP=498.262;RUN=1;RPP=30.0414;RPPR=155.319;RPL=24.0;RPR=5.0;EPP=30.0414;EPPR=8.74434;DPRA=0.0;ODDS=25.6435;GTI=0;TYPE=complex;CIGAR=1X1M1X;NUMALT=2;MEANALT=3.0;LEN=3;MQM=59.1034;MQMR=59.9219;PAIRED=1.0;PAIREDR=0.996094;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr10 114919603 . C CT . PASS SOMATIC;AC=1;AN=4 GT:AD:DP:MM:MQS:NQSBQ:NQSMM:REnd:RStart:SC:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:10,0:10:2.4,0.0:60.0,0.0:28.403,0.0:0.0895522,0.0:0,0:0,0:9,1,0,0:0:0:10:.:.:.:.:0:.:-0.000266909 0/1:13,25:41:5.61538,3.0:57.7692,67.6:24.381,30.4044:0.0952381,0.08:91,8:8,8:13,0,18,7:25:66:38:.:.:.:.:1:.:-0.00804187
+chr10 114925491 . C T 4954.715 REJECT NS=2;DP=345;DPB=394.0;AC=2;AN=4;AF=0.5;RO=208;AO=186;PRO=0.0;PAO=0.0;QR=7913;QA=7039;PQR=0.0;PQA=0.0;SRF=93;SRR=115;SAF=88;SAR=98;SRP=8.06315;SAP=4.17776;AB=0.472081;ABP=5.67779;RUN=1;RPP=10.9023;RPPR=4.51363;RPL=106.0;RPR=80.0;EPP=4.17776;EPPR=8.06315;DPRA=0.0;ODDS=283.879;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.11;Dels=0.0;FS=0.6995;HaplotypeScore=2.94 [...]
+chr10 123239112 . G A 12392.9 REJECT NS=2;DP=325;DPB=368.0;AC=4;AN=4;AF=1.0;RO=0;AO=368;PRO=0.0;PAO=0.0;QR=0;QA=14184;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=221;SAR=147;SRP=0.0;SAP=35.3228;AB=0.0;ABP=0.0;RUN=1;RPP=14.4341;RPPR=0.0;RPL=162.0;RPR=206.0;EPP=35.3228;EPPR=0.0;DPRA=0.0;ODDS=57.3998;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991848;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.966;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.57;SOR=1. [...]
+chr10 123240287 . T C 15441.099999999999 REJECT NS=2;DP=406;DPB=464.0;AC=4;AN=4;AF=1.0;RO=0;AO=464;PRO=0.0;PAO=0.0;QR=0;QA=17796;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=268;SAR=196;SRP=0.0;SAP=27.2709;AB=0.0;ABP=0.0;RUN=1;RPP=13.7928;RPPR=0.0;RPL=256.0;RPR=208.0;EPP=3.30981;EPPR=0.0;DPRA=0.0;ODDS=76.084;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991379;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=7.8629;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=3 [...]
+chr10 123240903 . GACAC G 6390.45 REJECT NS=2;DP=250;DPB=352.146;AC=2;AN=2;AF=0.5;RO=0;AO=190;PRO=94.8333;PAO=101.833;QR=0;QA=6668;PQR=3420.5;PQA=3641.5;SRF=0;SRR=0;SAF=130;SAR=60;SRP=0.0;SAP=59.0114;AB=0.76;ABP=149.802;RUN=1;RPP=5.93607;RPPR=0.0;RPL=87.0;RPR=103.0;EPP=3.74174;EPPR=0.0;DPRA=0.0;ODDS=15.8033;GTI=0;TYPE=del;CIGAR=1M4D36M;NUMALT=2;MEANALT=9.0;LEN=4;MQM=60.5263;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.338;FS=0.0;MLEAC=1;M [...]
+chr10 123240903 . GACACAC G 6390.45 REJECT NS=2;DP=250;DPB=352.146;AC=2;AN=2;AF=0.5;RO=0;AO=33;PRO=94.8333;PAO=88.3333;QR=0;QA=1055;PQR=3420.5;PQA=3183.0;SRF=0;SRR=0;SAF=18;SAR=15;SRP=0.0;SAP=3.60252;AB=0.132;ABP=297.08;RUN=1;RPP=3.60252;RPPR=0.0;RPL=18.0;RPR=15.0;EPP=3.60252;EPPR=0.0;DPRA=0.0;ODDS=15.8033;GTI=0;TYPE=del;CIGAR=1M6D34M;NUMALT=2;MEANALT=9.0;LEN=6;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.338;FS=0.0;MLEAC=1;MLEAF [...]
+chr10 123241332 . G A 7412.67 REJECT NS=2;DP=225;DPB=256.0;AC=4;AN=4;AF=1.0;RO=0;AO=253;PRO=0.0;PAO=0.0;QR=0;QA=8842;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=40;SAR=213;SRP=0.0;SAP=259.888;AB=0.0;ABP=0.0;RUN=1;RPP=159.434;RPPR=0.0;RPL=194.0;RPR=59.0;EPP=62.1379;EPPR=0.0;DPRA=0.0;ODDS=42.235;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9763;MQMR=0.0;PAIRED=0.98419;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=15.3822;MLEAC=2;MLEAF=1.0;MQ=59.93;QD=29.885;SOR= [...]
+chr10 123241368 . TGAGAC GAGAT 4259.36 REJECT SOMATIC;NS=2;DP=109;DPB=171.9;AC=1;AN=3;AF=0.25;RO=0;AO=15;PRO=30.75;PAO=28.9167;QR=0;QA=473;PQR=1077.42;PQA=1025.58;SRF=0;SRR=0;SAF=3;SAR=12;SRP=0.0;SAP=14.7363;AB=0.1625;ABP=82.1605;RUN=1;RPP=6.62942;RPPR=0.0;RPL=5.0;RPR=10.0;EPP=4.31318;EPPR=0.0;DPRA=0.0;ODDS=9.02944;GTI=0;TYPE=complex;CIGAR=1M1D17M1X;NUMALT=3;MEANALT=7.5;LEN=19;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr10 123241369 . GAGAC TGAGAT 4259.36 REJECT NS=2;DP=109;DPB=171.9;AC=0;AN=4;AF=0.0;RO=0;AO=8;PRO=30.75;PAO=29.9167;QR=0;QA=184;PQR=1077.42;PQA=1063.25;SRF=0;SRR=0;SAF=0;SAR=8;SRP=0.0;SAP=20.3821;AB=0.0875;ABP=121.247;RUN=1;RPP=4.09604;RPPR=0.0;RPL=5.0;RPR=3.0;EPP=4.09604;EPPR=0.0;DPRA=0.0;ODDS=9.02944;GTI=0;TYPE=complex;CIGAR=1M1I18M1X;NUMALT=3;MEANALT=7.5;LEN=21;MQM=57.5;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr10 123241373 . C T 4139.065 REJECT NS=2;DP=104;DPB=171.9;AC=3;AN=3;AF=0.875;RO=0;AO=74;PRO=30.75;PAO=37.4167;QR=0;QA=2616;PQR=1077.42;PQA=1324.75;SRF=0;SRR=0;SAF=9;SAR=65;SRP=0.0;SAP=95.0338;AB=0.625;ABP=13.8677;RUN=1;RPP=26.0162;RPPR=0.0;RPL=51.0;RPR=23.0;EPP=29.4201;EPPR=0.0;DPRA=0.0;ODDS=9.02944;GTI=0;TYPE=snp;CIGAR=19M1X;NUMALT=3;MEANALT=7.5;LEN=1;MQM=59.2027;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=7.7321;MLEAC [...]
+chr10 123241496 . T C 3724.5 REJECT NS=2;DP=105;DPB=120.0;AC=4;AN=4;AF=1.0;RO=0;AO=120;PRO=0.0;PAO=0.0;QR=0;QA=4381;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=74;SAR=46;SRP=0.0;SAP=17.1973;AB=0.0;ABP=0.0;RUN=1;RPP=4.16842;RPPR=0.0;RPL=64.0;RPR=56.0;EPP=5.61607;EPPR=0.0;DPRA=0.0;ODDS=23.0959;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9083;MQMR=0.0;PAIRED=0.975;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=59.945;QD=27.59;SOR=1.313 GT [...]
+chr10 123242026 . T C 16354.35 REJECT NS=2;DP=441;DPB=500.0;AC=4;AN=4;AF=1.0;RO=0;AO=500;PRO=0.0;PAO=0.0;QR=0;QA=18685;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=265;SAR=235;SRP=0.0;SAP=6.91895;AB=0.0;ABP=0.0;RUN=1;RPP=3.16665;RPPR=0.0;RPL=247.0;RPR=253.0;EPP=7.45748;EPPR=0.0;DPRA=0.0;ODDS=76.6031;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.8631;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.295;SOR=0. [...]
+chr10 123242724 . T C 12418.849999999999 REJECT NS=2;DP=328;DPB=375.0;AC=4;AN=4;AF=1.0;RO=0;AO=375;PRO=0.0;PAO=0.0;QR=0;QA=14295;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=210;SAR=165;SRP=0.0;SAP=14.7363;AB=0.0;ABP=0.0;RUN=1;RPP=15.8017;RPPR=0.0;RPL=164.0;RPR=211.0;EPP=5.1007;EPPR=0.0;DPRA=0.0;ODDS=61.3787;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.986667;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29 [...]
+chr10 123242780 . G C 13334.55 REJECT NS=2;DP=350;DPB=409.0;AC=4;AN=4;AF=1.0;RO=0;AO=408;PRO=0.0;PAO=0.0;QR=0;QA=15773;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=208;SAR=200;SRP=0.0;SAP=3.35092;AB=0.0;ABP=0.0;RUN=1;RPP=4.37279;RPPR=0.0;RPL=212.0;RPR=196.0;EPP=3.09546;EPPR=0.0;DPRA=0.0;ODDS=76.7081;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.982843;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9973;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.395;SOR [...]
+chr10 123243197 . G A 14974.0 REJECT NS=2;DP=390;DPB=441.0;AC=4;AN=4;AF=1.0;RO=0;AO=441;PRO=0.0;PAO=0.0;QR=0;QA=17015;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=221;SAR=220;SRP=0.0;SAP=3.01522;AB=0.0;ABP=0.0;RUN=1;RPP=12.9813;RPPR=0.0;RPL=243.0;RPR=198.0;EPP=3.6061;EPPR=0.0;DPRA=0.0;ODDS=67.345;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995465;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9662;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.255;SOR=0. [...]
+chr10 123298158 . T C 16363.4 REJECT NS=2;DP=437;DPB=495.0;AC=4;AN=4;AF=1.0;RO=0;AO=495;PRO=0.0;PAO=0.0;QR=0;QA=18700;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=225;SAR=270;SRP=0.0;SAP=11.8936;AB=0.0;ABP=0.0;RUN=1;RPP=3.36563;RPPR=0.0;RPL=252.0;RPR=243.0;EPP=3.75167;EPPR=0.0;DPRA=0.0;ODDS=76.035;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99798;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8459;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.27;SOR=0.8 [...]
+chr10 129009160 . G A 5032.84 REJECT NS=2;DP=373;DPB=427.0;AC=2;AN=4;AF=0.5;RO=237;AO=189;PRO=0.0;PAO=0.0;QR=9089;QA=7294;PQR=0.0;PQA=0.0;SRF=129;SRR=108;SAF=94;SAR=95;SRP=7.05089;SAP=3.02179;AB=0.442623;ABP=15.2204;RUN=1;RPP=10.1911;RPPR=3.75245;RPL=82.0;RPR=107.0;EPP=30.596;EPPR=11.8153;DPRA=0.0;ODDS=359.425;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989418;PAIREDR=0.991561;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0715;Dels=0.0;FS=3.0645;Haplotyp [...]
+chr10 131166609 . G A 13453.349999999999 REJECT NS=2;DP=352;DPB=408.0;AC=4;AN=4;AF=1.0;RO=0;AO=408;PRO=0.0;PAO=0.0;QR=0;QA=15779;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=219;SAR=189;SRP=0.0;SAP=7.80031;AB=0.0;ABP=0.0;RUN=1;RPP=15.2727;RPPR=0.0;RPL=180.0;RPR=228.0;EPP=9.16281;EPPR=0.0;DPRA=0.0;ODDS=74.2389;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997549;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8574;MLEAC=2;MLEAF=1.0;MQ=60.0;QD= [...]
+chr10 131166636 . G A 15286.25 REJECT NS=2;DP=400;DPB=458.0;AC=4;AN=4;AF=1.0;RO=0;AO=457;PRO=0.0;PAO=0.0;QR=0;QA=17663;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=218;SAR=239;SRP=0.0;SAP=5.10575;AB=0.0;ABP=0.0;RUN=1;RPP=6.4742;RPPR=0.0;RPL=215.0;RPR=242.0;EPP=26.963;EPPR=0.0;DPRA=0.0;ODDS=76.711;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995624;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.655;SOR=0.8 [...]
+chr10 131170360 . T C 13292.75 REJECT NS=2;DP=350;DPB=405.0;AC=4;AN=4;AF=1.0;RO=0;AO=404;PRO=0.0;PAO=0.0;QR=0;QA=15564;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=223;SAR=181;SRP=0.0;SAP=12.4917;AB=0.0;ABP=0.0;RUN=1;RPP=3.54779;RPPR=0.0;RPL=207.0;RPR=197.0;EPP=9.97621;EPPR=0.0;DPRA=0.0;ODDS=72.9691;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992574;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.51;SOR= [...]
+chr10 131664108 . T C 8226.85 REJECT NS=2;DP=332;DPB=381.0;AC=2;AN=4;AF=0.5;RO=110;AO=271;PRO=0.0;PAO=0.0;QR=4172;QA=10409;PQR=0.0;PQA=0.0;SRF=59;SRR=51;SAF=169;SAR=102;SRP=4.2737;SAP=38.9798;AB=0.711286;ABP=150.745;RUN=1;RPP=4.81318;RPPR=4.98437;RPL=143.0;RPR=128.0;EPP=7.24908;EPPR=23.2247;DPRA=0.0;ODDS=234.721;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99631;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0025;Dels=0.0;FS=4.1985;HaplotypeSco [...]
+chr11 2169014 . A G 4951.99 REJECT NS=1;DP=149;DPB=149.0;AC=2;AN=4;AF=1.0;RO=0;AO=149;PRO=0.0;PAO=0.0;QR=0;QA=5586;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=50;SAR=99;SRP=0.0;SAP=38.0016;AB=0.0;ABP=0.0;RUN=1;RPP=5.47325;RPPR=0.0;RPL=81.0;RPR=68.0;EPP=3.37464;EPPR=0.0;DPRA=0.0;ODDS=97.4315;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993289;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.67;SOR=1.593 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr11 14316128 . T TA 191.489 REJECT NS=2;DP=247;DPB=315.167;AC=2;AN=2;AF=0.0;RO=188;AO=16;PRO=87.6667;PAO=30.6667;QR=6993;QA=595;PQR=3102.0;PQA=1089.0;SRF=61;SRR=127;SAF=3;SAR=13;SRP=53.3238;SAP=16.582;AB=0.0647773;ABP=409.392;RUN=1;RPP=3.55317;RPPR=3.74952;RPL=7.0;RPR=9.0;EPP=3.0103;EPPR=5.27418;DPRA=0.0;ODDS=23.1721;GTI=0;TYPE=ins;CIGAR=1M1I29M;NUMALT=2;MEANALT=11.0;LEN=1;MQM=60.0;MQMR=59.9947;PAIRED=1.0;PAIREDR=0.989362;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr11 14316128 . TA T 191.489 REJECT NS=2;DP=247;DPB=315.167;AC=2;AN=4;AF=0.5;RO=188;AO=24;PRO=87.6667;PAO=27.6667;QR=6993;QA=925;PQR=3102.0;PQA=1000.0;SRF=61;SRR=127;SAF=14;SAR=10;SRP=53.3238;SAP=4.45795;AB=0.097166;ABP=351.158;RUN=1;RPP=4.45795;RPPR=3.74952;RPL=10.0;RPR=14.0;EPP=8.80089;EPPR=5.27418;DPRA=0.0;ODDS=23.1721;GTI=0;TYPE=del;CIGAR=1M1D28M;NUMALT=2;MEANALT=11.0;LEN=1;MQM=60.0;MQMR=59.9947;PAIRED=1.0;PAIREDR=0.989362;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO: [...]
+chr11 14378347 . C T 349.908 REJECT NS=2;DP=135;DPB=201.792;AC=2;AN=2;AF=0.0;RO=37;AO=20;PRO=31.2262;PAO=2.0;QR=1343;QA=245;PQR=1118.65;PQA=14.0;SRF=4;SRR=33;SAF=0;SAR=20;SRP=52.3673;SAP=46.4397;AB=0.148148;ABP=148.177;RUN=1;RPP=3.0103;RPPR=4.47751;RPL=10.0;RPR=10.0;EPP=3.0103;EPPR=3.5385;DPRA=0.0;ODDS=4.97385;GTI=0;TYPE=snp;CIGAR=1X23M;NUMALT=7;MEANALT=11.5;LEN=1;MQM=57.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr11 14378347 . C CT 349.908 REJECT NS=2;DP=135;DPB=201.792;AC=2;AN=3;AF=0.25;RO=37;AO=9;PRO=31.2262;PAO=20.2262;QR=1343;QA=290;PQR=1118.65;PQA=733.655;SRF=4;SRR=33;SAF=4;SAR=5;SRP=52.3673;SAP=3.25157;AB=0.0666667;ABP=223.198;RUN=1;RPP=14.8328;RPPR=4.47751;RPL=8.0;RPR=1.0;EPP=5.18177;EPPR=3.5385;DPRA=0.0;ODDS=4.97385;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=7;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr11 14378347 . CT C 349.908 REJECT NS=2;DP=135;DPB=201.792;AC=2;AN=3;AF=0.25;RO=37;AO=26;PRO=31.2262;PAO=24.8929;QR=1343;QA=558;PQR=1118.65;PQA=859.655;SRF=4;SRR=33;SAF=4;SAR=22;SRP=52.3673;SAP=30.0702;AB=0.192593;ABP=113.82;RUN=1;RPP=15.0369;RPPR=4.47751;RPL=19.0;RPR=7.0;EPP=8.35546;EPPR=3.5385;DPRA=0.0;ODDS=4.97385;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=7;MEANALT=11.5;LEN=1;MQM=59.8462;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr11 14378347 . CTT C 349.908 REJECT NS=2;DP=135;DPB=201.792;AC=2;AN=2;AF=0.0;RO=37;AO=17;PRO=31.2262;PAO=15.6429;QR=1343;QA=334;PQR=1118.65;PQA=567.905;SRF=4;SRR=33;SAF=2;SAR=15;SRP=52.3673;SAP=24.5973;AB=0.125926;ABP=167.093;RUN=1;RPP=4.1599;RPPR=4.47751;RPL=10.0;RPR=7.0;EPP=3.13803;EPPR=3.5385;DPRA=0.0;ODDS=4.97385;GTI=0;TYPE=del;CIGAR=1M2D21M;NUMALT=7;MEANALT=11.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=0.941176;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.79;F [...]
+chr11 14378347 . CTTT C 349.908 REJECT NS=2;DP=135;DPB=201.792;AC=2;AN=2;AF=0.0;RO=37;AO=3;PRO=31.2262;PAO=14.6429;QR=1343;QA=46;PQR=1118.65;PQA=529.905;SRF=4;SRR=33;SAF=0;SAR=3;SRP=52.3673;SAP=9.52472;AB=0.0769231;ABP=63.6445;RUN=1;RPP=3.73412;RPPR=4.47751;RPL=1.0;RPR=2.0;EPP=3.73412;EPPR=3.5385;DPRA=0.0;ODDS=4.97385;GTI=0;TYPE=del;CIGAR=1M3D20M;NUMALT=7;MEANALT=10.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.146;FS=2.197;MLE [...]
+chr11 14378347 . CTTTT C 349.908 REJECT NS=2;DP=135;DPB=201.792;AC=2;AN=2;AF=0.0;RO=37;AO=7;PRO=31.2262;PAO=13.1429;QR=1343;QA=136;PQR=1118.65;PQA=474.571;SRF=4;SRR=33;SAF=1;SAR=6;SRP=52.3673;SAP=10.7656;AB=0.0518519;ABP=238.511;RUN=1;RPP=3.32051;RPPR=4.47751;RPL=4.0;RPR=3.0;EPP=3.32051;EPPR=3.5385;DPRA=0.0;ODDS=4.97385;GTI=0;TYPE=del;CIGAR=1M4D19M;NUMALT=7;MEANALT=11.5;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr11 14378366 . G T 349.908 REJECT NS=2;DP=135;DPB=201.792;AC=2;AN=2;AF=0.0;RO=37;AO=6;PRO=31.2262;PAO=20.2262;QR=1343;QA=60;PQR=1118.65;PQA=733.655;SRF=4;SRR=33;SAF=6;SAR=0;SRP=52.3673;SAP=16.0391;AB=0.0444444;ABP=246.36;RUN=1;RPP=16.0391;RPPR=4.47751;RPL=6.0;RPR=0.0;EPP=16.0391;EPPR=3.5385;DPRA=0.0;ODDS=4.97385;GTI=0;TYPE=snp;CIGAR=19M1X4M;NUMALT=7;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr11 55511545 . G A 4934.77 REJECT NS=2;DP=358;DPB=401.0;AC=2;AN=4;AF=0.5;RO=225;AO=176;PRO=0.0;PAO=0.0;QR=8624;QA=6767;PQR=0.0;PQA=0.0;SRF=98;SRR=127;SAF=78;SAR=98;SRP=11.1268;SAP=7.94546;AB=0.438903;ABP=16.0121;RUN=1;RPP=5.42853;RPPR=5.79944;RPL=95.0;RPR=81.0;EPP=3.05965;EPPR=6.49431;DPRA=0.0;ODDS=252.878;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994318;PAIREDR=0.995556;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.72;Dels=0.0;FS=1.7035;HaplotypeSco [...]
+chr11 55578940 . G A 3470.15 REJECT NS=2;DP=223;DPB=250.0;AC=2;AN=4;AF=0.5;RO=125;AO=125;PRO=0.0;PAO=0.0;QR=4744;QA=4800;PQR=0.0;PQA=0.0;SRF=98;SRR=27;SAF=87;SAR=38;SRP=90.5814;SAP=44.7199;AB=0.5;ABP=3.0103;RUN=1;RPP=21.9282;RPPR=17.62;RPL=46.0;RPR=79.0;EPP=3.86152;EPPR=6.91895;DPRA=0.0;ODDS=158.138;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=55.712;MQMR=55.84;PAIRED=0.992;PAIREDR=0.992;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5875;Dels=0.0;FS=4.5945;HaplotypeScore=4.8486; [...]
+chr11 55578987 . T C 2725.77 PASS DP=162;AC=2;AN=4;AF=0.5;MQ0=5;BaseQRankSum=1.7355;Dels=0.0;FS=2.6175;HaplotypeScore=5.8632;MLEAC=1;MLEAF=0.5;MQ=48.785;MQRankSum=0.478;QD=18.595;ReadPosRankSum=-0.4265;SOR=1.0315;ClippingRankSum=-1.736 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:35,40:75:99.0:1670,0,1373:40:53:75:1:.:.:.:.:.:-0.00409698 0/1:141,108:249:99.0:3838,0,5097:108:43:249:.:1:.:.:.:.:-0.0109317
+chr11 55578987 . TGGAC CGGAT 3932.34 REJECT NS=2;DP=305;DPB=318.0;AC=2;AN=4;AF=0.5;RO=162;AO=141;PRO=14.0;PAO=11.0;QR=6199;QA=5261;PQR=493.0;PQA=409.0;SRF=105;SRR=57;SAF=99;SAR=42;SRP=33.8935;SAP=53.0466;AB=0.462295;ABP=6.77656;RUN=1;RPP=3.39531;RPPR=5.63751;RPL=73.0;RPR=68.0;EPP=12.6356;EPPR=3.86817;DPRA=0.0;ODDS=227.179;GTI=0;TYPE=complex;CIGAR=1X3M1X;NUMALT=1;MEANALT=2.0;LEN=5;MQM=48.8652;MQMR=47.7963;PAIRED=0.992908;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr11 55578991 . C T 2696.27 PASS DP=160;AC=2;AN=4;AF=0.5;MQ0=5;BaseQRankSum=-0.383;Dels=0.0;FS=2.707;HaplotypeScore=3.8969;MLEAC=1;MLEAF=0.5;MQ=49.0;MQRankSum=1.468;QD=18.255;ReadPosRankSum=-0.733;SOR=1.069;ClippingRankSum=-0.508 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:36,44:80:99.0:1713,0,1363:44:55:80:1:.:.:.:.:.:-0.00409698 0/1:133,107:240:99.0:3736,0,4871:107:45:240:.:1:.:.:.:.:-0.0109317
+chr11 55579102 . C T 5216.605 REJECT NS=2;DP=342;DPB=385.0;AC=2;AN=4;AF=0.5;RO=199;AO=185;PRO=0.0;PAO=0.0;QR=7557;QA=7050;PQR=0.0;PQA=0.0;SRF=107;SRR=92;SAF=80;SAR=105;SRP=5.46548;SAP=10.3464;AB=0.480519;ABP=4.27934;RUN=1;RPP=3.58545;RPPR=13.4967;RPL=96.0;RPR=89.0;EPP=6.40249;EPPR=6.16385;DPRA=0.0;ODDS=263.663;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.6541;MQMR=57.1407;PAIRED=0.989189;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.625;Dels=0.0;FS=7.35;HaplotypeS [...]
+chr11 55579419 . T C 6429.395 REJECT NS=2;DP=391;DPB=448.0;AC=2;AN=4;AF=0.5;RO=220;AO=228;PRO=0.0;PAO=0.0;QR=8395;QA=8743;PQR=0.0;PQA=0.0;SRF=90;SRR=130;SAF=114;SAR=114;SRP=18.8028;SAP=3.0103;AB=0.508929;ABP=3.32051;RUN=1;RPP=14.02;RPPR=6.20829;RPL=131.0;RPR=97.0;EPP=3.35316;EPPR=4.94488;DPRA=0.0;ODDS=368.183;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995614;PAIREDR=0.990909;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0435;Dels=0.0;FS=9.7925;Haplotype [...]
+chr11 55579801 . T C 4602.895 REJECT NS=2;DP=285;DPB=326.0;AC=2;AN=4;AF=0.5;RO=158;AO=168;PRO=0.0;PAO=0.0;QR=5910;QA=6269;PQR=0.0;PQA=0.0;SRF=67;SRR=91;SAF=77;SAR=91;SRP=10.9266;SAP=5.54368;AB=0.515337;ABP=3.6764;RUN=1;RPP=3.47562;RPPR=3.50507;RPL=87.0;RPR=81.0;EPP=4.87156;EPPR=6.52863;DPRA=0.0;ODDS=249.732;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.881;MQMR=60.0;PAIRED=0.994048;PAIREDR=0.993671;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.881;Dels=0.0;FS=2.1735;Haplotype [...]
+chr11 57014669 . T G 4891.755 REJECT NS=2;DP=316;DPB=365.0;AC=2;AN=4;AF=0.5;RO=187;AO=178;PRO=0.0;PAO=0.0;QR=7161;QA=6845;PQR=0.0;PQA=0.0;SRF=97;SRR=90;SAF=108;SAR=70;SRP=3.5793;SAP=20.6261;AB=0.487671;ABP=3.49219;RUN=1;RPP=8.91475;RPPR=26.5249;RPL=78.0;RPR=100.0;EPP=20.6261;EPPR=20.6724;DPRA=0.0;ODDS=306.039;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989305;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.546;Dels=0.0;FS=6.1845;HaplotypeScore= [...]
+chr11 57014757 . A G 4991.66 REJECT NS=2;DP=299;DPB=346.0;AC=2;AN=4;AF=0.5;RO=167;AO=179;PRO=0.0;PAO=0.0;QR=6370;QA=6904;PQR=0.0;PQA=0.0;SRF=60;SRR=107;SAF=63;SAR=116;SRP=31.7335;SAP=37.0866;AB=0.517341;ABP=3.91403;RUN=1;RPP=17.8709;RPPR=27.0525;RPL=107.0;RPR=72.0;EPP=14.6683;EPPR=8.74455;DPRA=0.0;ODDS=284.38;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988024;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.109;Dels=0.0;FS=0.864;HaplotypeScore=5 [...]
+chr11 64572018 . T C 13893.75 REJECT NS=2;DP=369;DPB=427.0;AC=4;AN=4;AF=1.0;RO=0;AO=427;PRO=0.0;PAO=0.0;QR=0;QA=16318;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=168;SAR=259;SRP=0.0;SAP=45.1226;AB=0.0;ABP=0.0;RUN=1;RPP=3.25949;RPPR=0.0;RPL=217.0;RPR=210.0;EPP=3.62564;EPPR=0.0;DPRA=0.0;ODDS=76.6772;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997658;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8907;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.275;SOR= [...]
+chr11 64572557 . A G 12898.7 REJECT NS=2;DP=339;DPB=389.0;AC=4;AN=4;AF=1.0;RO=0;AO=389;PRO=0.0;PAO=0.0;QR=0;QA=14962;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=212;SAR=177;SRP=0.0;SAP=9.84848;AB=0.0;ABP=0.0;RUN=1;RPP=3.14985;RPPR=0.0;RPL=197.0;RPR=192.0;EPP=9.84848;EPPR=0.0;DPRA=0.0;ODDS=66.7329;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997429;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9329;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.535;SOR=0 [...]
+chr11 64573194 . T A 3009.7 PASS SOMATIC;NS=2;DP=464;DPB=464.0;AC=1;AN=3;AF=0.25;RO=348;AO=116;PRO=0.0;PAO=0.0;QR=13390;QA=4452;PQR=0.0;PQA=0.0;SRF=168;SRR=180;SAF=53;SAR=63;SRP=3.90884;SAP=4.88226;AB=0.33526;ABP=84.5723;RUN=1;RPP=3.08518;RPPR=24.0012;RPL=59.0;RPR=57.0;EPP=5.70592;EPPR=12.0207;DPRA=2.9322;ODDS=74.5314;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.958;Dels=0.0;FS=2.469;Haplo [...]
+chr11 65423082 . G A 12144.8 REJECT NS=2;DP=325;DPB=372.0;AC=4;AN=4;AF=1.0;RO=0;AO=371;PRO=0.0;PAO=0.0;QR=0;QA=14112;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=235;SAR=136;SRP=0.0;SAP=60.3758;AB=0.0;ABP=0.0;RUN=1;RPP=19.4514;RPPR=0.0;RPL=159.0;RPR=212.0;EPP=4.32723;EPPR=0.0;DPRA=0.0;ODDS=62.965;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997305;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=9.7031;MLEAC=2;MLEAF=1.0;MQ=59.985;QD=28.13;SOR=1 [...]
+chr11 65429936 . T C 2817.71 REJECT NS=2;DP=515;DPB=586.0;AC=2;AN=4;AF=0.5;RO=451;AO=135;PRO=0.0;PAO=0.0;QR=17292;QA=5143;PQR=0.0;PQA=0.0;SRF=222;SRR=229;SAF=63;SAR=72;SRP=3.24622;SAP=4.31318;AB=0.230375;ABP=373.035;RUN=1;RPP=4.31318;RPPR=7.05954;RPL=63.0;RPR=72.0;EPP=11.5193;EPPR=3.05363;DPRA=0.0;ODDS=168.093;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997783;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.665;Dels=0.0;FS=2.391;HaplotypeScore= [...]
+chr11 69462910 . G A 5055.71 REJECT NS=2;DP=314;DPB=358.0;AC=2;AN=4;AF=0.5;RO=175;AO=182;PRO=0.0;PAO=0.0;QR=6714;QA=6844;PQR=0.0;PQA=0.0;SRF=57;SRR=118;SAF=56;SAR=126;SRP=49.182;SAP=61.473;AB=0.50838;ABP=3.22866;RUN=1;RPP=15.2278;RPPR=18.2106;RPL=107.0;RPR=75.0;EPP=3.2012;EPPR=4.01538;DPRA=0.0;ODDS=272.36;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994286;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.206;Dels=0.0;FS=3.7305;HaplotypeScore=1.96 [...]
+chr11 76207633 . G A 13421.05 REJECT NS=2;DP=357;DPB=410.0;AC=4;AN=4;AF=1.0;RO=0;AO=410;PRO=0.0;PAO=0.0;QR=0;QA=15533;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=194;SAR=216;SRP=0.0;SAP=5.5737;AB=0.0;ABP=0.0;RUN=1;RPP=5.5737;RPPR=0.0;RPL=194.0;RPR=216.0;EPP=3.20097;EPPR=0.0;DPRA=0.0;ODDS=70.4248;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995122;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.935;SOR=0. [...]
+chr11 76227182 . G A 10425.099999999999 REJECT NS=2;DP=282;DPB=324.0;AC=4;AN=4;AF=1.0;RO=0;AO=323;PRO=0.0;PAO=0.0;QR=0;QA=12203;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=236;SAR=87;SRP=0.0;SAP=152.264;AB=0.0;ABP=0.0;RUN=1;RPP=49.3238;RPPR=0.0;RPL=120.0;RPR=203.0;EPP=3.01702;EPPR=0.0;DPRA=0.0;ODDS=56.0585;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996904;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.821;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29. [...]
+chr11 76936833 . C T 10851.0 REJECT NS=2;DP=380;DPB=432.0;AC=2;AN=4;AF=0.5;RO=79;AO=353;PRO=0.0;PAO=0.0;QR=2974;QA=13491;PQR=0.0;PQA=0.0;SRF=40;SRR=39;SAF=176;SAR=177;SRP=3.03779;SAP=3.01645;AB=0.81713;ABP=380.384;RUN=1;RPP=6.85497;RPPR=6.33623;RPL=189.0;RPR=164.0;EPP=49.5709;EPPR=5.23675;DPRA=0.0;ODDS=38.3262;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997167;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.166;Dels=0.0;FS=2.1425;HaplotypeScor [...]
+chr11 76938121 . G A 14748.15 REJECT NS=2;DP=389;DPB=438.0;AC=4;AN=4;AF=1.0;RO=0;AO=438;PRO=0.0;PAO=0.0;QR=0;QA=16758;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=201;SAR=237;SRP=0.0;SAP=9.43548;AB=0.0;ABP=0.0;RUN=1;RPP=19.688;RPPR=0.0;RPL=248.0;RPR=190.0;EPP=18.5576;EPPR=0.0;DPRA=0.0;ODDS=65.4815;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997717;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8793;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.135;SOR=1 [...]
+chr11 77051683 . G C 4006.795 REJECT NS=2;DP=267;DPB=311.0;AC=2;AN=4;AF=0.5;RO=161;AO=150;PRO=0.0;PAO=0.0;QR=6058;QA=5811;PQR=0.0;PQA=0.0;SRF=102;SRR=59;SAF=92;SAR=58;SRP=27.9485;SAP=19.7451;AB=0.482315;ABP=3.85515;RUN=1;RPP=14.3599;RPPR=27.9485;RPL=61.0;RPR=89.0;EPP=8.80089;EPPR=4.64228;DPRA=0.0;ODDS=240.837;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987578;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.8425;Dels=0.0;FS=1.2585;HaplotypeScore [...]
+chr11 77051820 . C T 2104.32 PASS SOMATIC;NS=2;DP=309;DPB=309.0;AC=1;AN=3;AF=0.25;RO=228;AO=81;PRO=0.0;PAO=0.0;QR=8762;QA=3138;PQR=0.0;PQA=0.0;SRF=86;SRR=142;SAF=31;SAR=50;SRP=32.8776;SAP=12.6881;AB=0.347639;ABP=49.9905;RUN=1;RPP=28.7731;RPPR=58.0209;RPL=56.0;RPR=25.0;EPP=4.32391;EPPR=3.61984;DPRA=3.06579;ODDS=48.4028;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.982456;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.565;Dels=0.0;FS=0.513; [...]
+chr11 77268460 . G A 1810.875 REJECT NS=2;DP=369;DPB=419.0;AC=2;AN=4;AF=0.5;RO=322;AO=97;PRO=0.0;PAO=0.0;QR=12196;QA=3682;PQR=0.0;PQA=0.0;SRF=153;SRR=169;SAF=44;SAR=53;SRP=4.73669;SAP=4.82359;AB=0.231504;ABP=265.375;RUN=1;RPP=27.389;RPPR=75.9502;RPL=65.0;RPR=32.0;EPP=12.8827;EPPR=7.56904;DPRA=0.0;ODDS=204.838;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.979381;PAIREDR=0.993789;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.909;Dels=0.0;FS=0.9735;Haplotype [...]
+chr11 77268856 . C T 2258.975 REJECT NS=2;DP=362;DPB=421.0;AC=2;AN=4;AF=0.5;RO=314;AO=107;PRO=0.0;PAO=0.0;QR=12049;QA=4021;PQR=0.0;PQA=0.0;SRF=155;SRR=159;SAF=52;SAR=55;SRP=3.12095;SAP=3.19295;AB=0.254157;ABP=224.021;RUN=1;RPP=3.19295;RPPR=3.25926;RPL=55.0;RPR=52.0;EPP=4.65412;EPPR=11.9728;DPRA=0.0;ODDS=151.6;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990654;PAIREDR=0.996815;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.774;Dels=0.0;FS=3.5775;Haplotype [...]
+chr11 79506686 . T C 4710.835 REJECT NS=2;DP=322;DPB=369.0;AC=2;AN=4;AF=0.5;RO=185;AO=184;PRO=0.0;PAO=0.0;QR=6979;QA=6855;PQR=0.0;PQA=0.0;SRF=116;SRR=69;SAF=119;SAR=65;SRP=28.9389;SAP=37.4234;AB=0.498645;ABP=3.01618;RUN=1;RPP=10.9881;RPPR=31.1925;RPL=79.0;RPR=105.0;EPP=15.095;EPPR=26.7791;DPRA=0.0;ODDS=207.955;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994565;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.315;Dels=0.0;FS=3.6205;HaplotypeScor [...]
+chr11 92086994 . C T 5137.285 REJECT NS=2;DP=335;DPB=386.0;AC=2;AN=4;AF=0.5;RO=198;AO=188;PRO=0.0;PAO=0.0;QR=7607;QA=7174;PQR=0.0;PQA=0.0;SRF=92;SRR=106;SAF=88;SAR=100;SRP=5.15984;SAP=4.67356;AB=0.487047;ABP=3.57286;RUN=1;RPP=8.60069;RPPR=4.107;RPL=105.0;RPR=83.0;EPP=5.27418;EPPR=10.424;DPRA=0.0;ODDS=325.873;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989362;PAIREDR=0.989899;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.402;Dels=0.0;FS=1.2645;HaplotypeSc [...]
+chr11 92088177 . C T 3854.46 REJECT NS=2;DP=300;DPB=340.0;AC=2;AN=4;AF=0.5;RO=193;AO=147;PRO=0.0;PAO=0.0;QR=7285;QA=5369;PQR=0.0;PQA=0.0;SRF=86;SRR=107;SAF=69;SAR=78;SRP=7.97206;SAP=4.20683;AB=0.432353;ABP=16.5245;RUN=1;RPP=3.02507;RPPR=3.29158;RPL=74.0;RPR=73.0;EPP=3.02507;EPPR=3.29158;DPRA=0.0;ODDS=186.631;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986395;PAIREDR=0.994819;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.564;Dels=0.0;FS=0.955;HaplotypeSc [...]
+chr11 92292532 . A C 1574.53 REJECT NS=1;DP=185;DPB=185.0;AC=1;AN=4;AF=0.5;RO=102;AO=77;PRO=0.0;PAO=0.0;QR=3408;QA=2606;PQR=0.0;PQA=0.0;SRF=33;SRR=69;SAF=21;SAR=56;SRP=30.6008;SAP=37.5565;AB=0.416216;ABP=14.2902;RUN=1;RPP=145.171;RPPR=132.532;RPL=74.0;RPR=3.0;EPP=33.7211;EPPR=37.0726;DPRA=0.0;ODDS=362.549;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=3.0;LEN=1;MQM=58.3896;MQMR=59.4804;PAIRED=0.935065;PAIREDR=0.990196;technology.ILLUMINA=1.0;BaseQRankSum=1.139;FS=5.737;MLEAC=1;MLEAF=0.5;MQ=60. [...]
+chr11 92292549 . C CT 106.323 REJECT NS=1;DP=39;DPB=94.68;AC=1;AN=4;AF=0.5;RO=14;AO=6;PRO=23.6333;PAO=24.6333;QR=478;QA=157;PQR=842.233;PQA=819.233;SRF=3;SRR=11;SAF=2;SAR=4;SRP=12.937;SAP=4.45795;AB=0.153846;ABP=43.6001;RUN=1;RPP=4.45795;RPPR=3.0103;RPL=4.0;RPR=2.0;EPP=4.45795;EPPR=8.59409;DPRA=0.0;ODDS=24.4819;GTI=0;TYPE=ins;CIGAR=1M1I24M;NUMALT=5;MEANALT=11.0;LEN=1;MQM=53.1667;MQMR=51.5714;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr11 92292549 . C CTT 106.323 REJECT NS=1;DP=39;DPB=94.68;AC=1;AN=3;AF=0.0;RO=14;AO=2;PRO=23.6333;PAO=20.6333;QR=478;QA=17;PQR=842.233;PQA=734.233;SRF=3;SRR=11;SAF=0;SAR=2;SRP=12.937;SAP=7.35324;AB=0.0512821;ABP=71.2168;RUN=1;RPP=3.0103;RPPR=3.0103;RPL=1.0;RPR=1.0;EPP=3.0103;EPPR=8.59409;DPRA=0.0;ODDS=24.4819;GTI=0;TYPE=ins;CIGAR=1M2I24M;NUMALT=5;MEANALT=11.0;LEN=2;MQM=50.0;MQMR=51.5714;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr11 92292549 . CT C 106.323 REJECT NS=1;DP=39;DPB=94.68;AC=1;AN=3;AF=0.0;RO=14;AO=7;PRO=23.6333;PAO=17.3;QR=478;QA=154;PQR=842.233;PQA=585.567;SRF=3;SRR=11;SAF=1;SAR=6;SRP=12.937;SAP=10.7656;AB=0.179487;ABP=37.8095;RUN=1;RPP=5.80219;RPPR=3.0103;RPL=5.0;RPR=2.0;EPP=10.7656;EPPR=8.59409;DPRA=0.0;ODDS=24.4819;GTI=0;TYPE=del;CIGAR=1M1D23M;NUMALT=5;MEANALT=11.0;LEN=1;MQM=55.2857;MQMR=51.5714;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr11 92292549 . CTT C 106.323 REJECT NS=1;DP=39;DPB=94.68;AC=1;AN=3;AF=0.0;RO=14;AO=2;PRO=23.6333;PAO=14.1;QR=478;QA=29;PQR=842.233;PQA=497.367;SRF=3;SRR=11;SAF=0;SAR=2;SRP=12.937;SAP=7.35324;AB=0.0512821;ABP=71.2168;RUN=1;RPP=3.0103;RPPR=3.0103;RPL=1.0;RPR=1.0;EPP=3.0103;EPPR=8.59409;DPRA=0.0;ODDS=24.4819;GTI=0;TYPE=del;CIGAR=1M2D22M;NUMALT=5;MEANALT=11.0;LEN=2;MQM=60.0;MQMR=51.5714;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr11 92292550 . T C 106.323 REJECT NS=1;DP=39;DPB=94.68;AC=1;AN=3;AF=0.0;RO=14;AO=2;PRO=23.6333;PAO=3.7;QR=478;QA=17;PQR=842.233;PQA=108.367;SRF=3;SRR=11;SAF=0;SAR=2;SRP=12.937;SAP=7.35324;AB=0.0512821;ABP=71.2168;RUN=1;RPP=7.35324;RPPR=3.0103;RPL=0.0;RPR=2.0;EPP=7.35324;EPPR=8.59409;DPRA=0.0;ODDS=24.4819;GTI=0;TYPE=snp;CIGAR=1M1X23M;NUMALT=5;MEANALT=11.0;LEN=1;MQM=60.0;MQMR=51.5714;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr11 92292618 . A G 391.706 REJECT NS=1;DP=65;DPB=65.0;AC=1;AN=4;AF=0.5;RO=39;AO=26;PRO=0.0;PAO=0.0;QR=1256;QA=793;PQR=0.0;PQA=0.0;SRF=2;SRR=37;SAF=0;SAR=26;SRP=71.2168;SAP=59.4686;AB=0.4;ABP=8.65613;RUN=1;RPP=4.34659;RPPR=3.06598;RPL=15.0;RPR=11.0;EPP=4.34659;EPPR=3.51141;DPRA=0.0;ODDS=90.1937;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=55.1538;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=0.594;FS=2.66;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.164;QD=8. [...]
+chr11 92495036 . T C 4588.33 REJECT NS=2;DP=287;DPB=329.0;AC=2;AN=4;AF=0.5;RO=162;AO=167;PRO=0.0;PAO=0.0;QR=6185;QA=6365;PQR=0.0;PQA=0.0;SRF=109;SRR=53;SAF=114;SAR=53;SRP=45.0457;SAP=51.3938;AB=0.507599;ABP=3.17531;RUN=1;RPP=7.70432;RPPR=4.35072;RPL=74.0;RPR=93.0;EPP=15.506;EPPR=6.44176;DPRA=0.0;ODDS=248.532;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988024;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.136;Dels=0.0;FS=0.435;HaplotypeScore=3. [...]
+chr11 92531356 . A G 11992.4 REJECT NS=2;DP=314;DPB=356.0;AC=4;AN=4;AF=1.0;RO=0;AO=356;PRO=0.0;PAO=0.0;QR=0;QA=13671;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=162;SAR=194;SRP=0.0;SAP=9.25633;AB=0.0;ABP=0.0;RUN=1;RPP=5.96253;RPPR=0.0;RPL=167.0;RPR=189.0;EPP=4.20583;EPPR=0.0;DPRA=0.0;ODDS=56.1012;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.9127;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.81;SOR=0.831 G [...]
+chr11 92532677 . T C 13503.25 REJECT NS=2;DP=358;DPB=413.0;AC=4;AN=4;AF=1.0;RO=0;AO=412;PRO=0.0;PAO=0.0;QR=0;QA=15687;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=199;SAR=213;SRP=0.0;SAP=4.04333;AB=0.0;ABP=0.0;RUN=1;RPP=9.10307;RPPR=0.0;RPL=223.0;RPR=189.0;EPP=6.04614;EPPR=0.0;DPRA=0.0;ODDS=71.6175;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.987864;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9243;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.89;SOR=0 [...]
+chr11 92534442 . A G 14281.75 REJECT NS=2;DP=380;DPB=444.0;AC=4;AN=4;AF=1.0;RO=1;AO=442;PRO=0.0;PAO=0.0;QR=40;QA=16955;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=211;SAR=231;SRP=5.18177;SAP=4.97543;AB=0.0;ABP=0.0;RUN=1;RPP=3.32472;RPPR=5.18177;RPL=217.0;RPR=225.0;EPP=15.2924;EPPR=5.18177;DPRA=0.0;ODDS=81.0793;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984163;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.213;Dels=0.0;FS=1.6125;HaplotypeScore=1.9574;MLE [...]
+chr11 92564767 . T G 5740.535 REJECT NS=2;DP=154;DPB=178.0;AC=4;AN=4;AF=1.0;RO=1;AO=177;PRO=0.0;PAO=0.0;QR=16;QA=6814;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=128;SAR=49;SRP=5.18177;SAP=79.5762;AB=0.0;ABP=0.0;RUN=1;RPP=75.7485;RPPR=5.18177;RPL=50.0;RPR=127.0;EPP=4.49475;EPPR=5.18177;DPRA=0.0;ODDS=33.7006;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.653;Dels=0.0;FS=0.0;HaplotypeScore=4.8325;MLEAC=2;MLEAF=1 [...]
+chr11 92570812 . TC AA 1449.275 REJECT NS=2;DP=227;DPB=259.5;AC=2;AN=4;AF=0.5;RO=192;AO=65;PRO=3.0;PAO=0.0;QR=7305;QA=2413;PQR=0.0;PQA=0.0;SRF=132;SRR=60;SAF=48;SAR=17;SRP=61.6401;SAP=35.1147;AB=0.251938;ABP=140.907;RUN=1;RPP=3.04371;RPPR=33.5919;RPL=33.0;RPR=32.0;EPP=15.0703;EPPR=5.9056;DPRA=0.0;ODDS=169.42;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=1;MEANALT=1.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989583;technology.ILLUMINA=1.0;MQ0=0;JOINED;BaseQRankSum=0.35;Dels=0.0;FS=0.958;HaplotypeSc [...]
+chr11 92573911 . G T 4540.155000000001 REJECT NS=2;DP=289;DPB=330.0;AC=2;AN=4;AF=0.5;RO=168;AO=161;PRO=0.0;PAO=0.0;QR=6464;QA=6235;PQR=0.0;PQA=0.0;SRF=44;SRR=124;SAF=51;SAR=110;SRP=85.7331;SAP=49.96;AB=0.487879;ABP=3.43143;RUN=1;RPP=25.6826;RPPR=3.83753;RPL=101.0;RPR=60.0;EPP=14.3532;EPPR=10.4553;DPRA=0.0;ODDS=256.701;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993789;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.274;Dels=0.0;FS=3.4145;Haplot [...]
+chr11 92590448 . A G 8807.18 REJECT NS=2;DP=377;DPB=433.0;AC=3;AN=4;AF=0.75;RO=120;AO=313;PRO=0.0;PAO=0.0;QR=4622;QA=12048;PQR=0.0;PQA=0.0;SRF=61;SRR=59;SAF=153;SAR=160;SRP=3.08268;SAP=3.35024;AB=0.628483;ABP=49.3238;RUN=1;RPP=3.01724;RPPR=3.08268;RPL=157.0;RPR=156.0;EPP=17.059;EPPR=10.2485;DPRA=0.0;ODDS=69.6237;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996805;PAIREDR=0.991667;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.611;Dels=0.0;FS=0.4435;Haploty [...]
+chr11 92623877 . G A 1541.565 REJECT NS=2;DP=341;DPB=382.0;AC=2;AN=4;AF=0.5;RO=297;AO=85;PRO=0.0;PAO=0.0;QR=11385;QA=3246;PQR=0.0;PQA=0.0;SRF=172;SRR=125;SAF=52;SAR=33;SRP=19.1611;SAP=12.2327;AB=0.222513;ABP=258.494;RUN=1;RPP=21.6339;RPPR=4.24592;RPL=29.0;RPR=56.0;EPP=5.07959;EPPR=3.89497;DPRA=0.0;ODDS=174.228;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.976471;PAIREDR=0.996633;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6805;Dels=0.0;FS=8.754;Haplotype [...]
+chr11 94197260 . A G 1796.8 PASS SOMATIC;NS=2;DP=288;DPB=288.0;AC=1;AN=3;AF=0.25;RO=213;AO=73;PRO=0.0;PAO=0.0;QR=8276;QA=2783;PQR=0.0;PQA=0.0;SRF=147;SRR=66;SAF=51;SAR=22;SRP=69.8978;SAP=28.0269;AB=0.341121;ABP=49.9303;RUN=1;RPP=53.0137;RPPR=51.5473;RPL=16.0;RPR=57.0;EPP=5.41974;EPPR=3.26517;DPRA=2.89189;ODDS=46.5771;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.981221;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.76;Dels=0.0;FS=0.0;Hap [...]
+chr11 94212048 . C T 2367.34 PASS SOMATIC;NS=2;DP=315;DPB=315.0;AC=1;AN=3;AF=0.25;RO=226;AO=89;PRO=0.0;PAO=0.0;QR=8706;QA=3462;PQR=0.0;PQA=0.0;SRF=60;SRR=166;SAF=23;SAR=66;SRP=110.969;SAP=48.1232;AB=0.383621;ABP=30.3035;RUN=1;RPP=23.5295;RPPR=28.9911;RPL=59.0;RPR=30.0;EPP=3.22989;EPPR=3.62523;DPRA=2.79518;ODDS=52.7942;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986726;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.586;Dels=0.0;FS=0.56;H [...]
+chr11 94212930 . T TA 341.053 REJECT NS=2;DP=248;DPB=291.529;AC=2;AN=3;AF=0.25;RO=188;AO=33;PRO=41.0;PAO=24.0;QR=7134;QA=1144;PQR=1510.67;PQA=874.667;SRF=38;SRR=150;SAF=7;SAR=26;SRP=147.898;SAP=26.7649;AB=0.133065;ABP=293.042;RUN=1;RPP=26.7649;RPPR=34.2425;RPL=26.0;RPR=7.0;EPP=4.65535;EPPR=3.19511;DPRA=0.0;ODDS=6.86127;GTI=0;TYPE=ins;CIGAR=1M1I16M;NUMALT=2;MEANALT=7.0;LEN=1;MQM=59.9394;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994681;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr11 94212930 . TA T 341.053 REJECT NS=2;DP=248;DPB=291.529;AC=2;AN=3;AF=0.25;RO=188;AO=16;PRO=41.0;PAO=19.0;QR=7134;QA=614;PQR=1510.67;PQA=687.667;SRF=38;SRR=150;SAF=4;SAR=12;SRP=147.898;SAP=11.6962;AB=0.0645161;ABP=411.527;RUN=1;RPP=7.89611;RPPR=34.2425;RPL=11.0;RPR=5.0;EPP=3.55317;EPPR=3.19511;DPRA=0.0;ODDS=6.86127;GTI=0;TYPE=del;CIGAR=1M1D15M;NUMALT=2;MEANALT=7.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994681;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr11 94225807 . C T 2533.07 PASS SOMATIC;NS=2;DP=428;DPB=428.0;AC=1;AN=3;AF=0.25;RO=325;AO=103;PRO=0.0;PAO=0.0;QR=12314;QA=3927;PQR=0.0;PQA=0.0;SRF=162;SRR=163;SAF=65;SAR=38;SRP=3.01698;SAP=18.3793;AB=0.30117;ABP=120.448;RUN=1;RPP=9.10307;RPPR=5.4223;RPL=43.0;RPR=60.0;EPP=3.03138;EPPR=23.2217;DPRA=3.97674;ODDS=54.633;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990291;PAIREDR=0.996923;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.142;Dels=0.0;FS= [...]
+chr11 94225920 . C T 2601.16 PASS SOMATIC;NS=2;DP=393;DPB=393.0;AC=1;AN=3;AF=0.25;RO=291;AO=102;PRO=0.0;PAO=0.0;QR=11142;QA=3823;PQR=0.0;PQA=0.0;SRF=153;SRR=138;SAF=53;SAR=49;SRP=4.68927;SAP=3.35092;AB=0.352941;ABP=57.2971;RUN=1;RPP=3.35092;RPPR=4.2714;RPL=53.0;RPR=49.0;EPP=5.13919;EPPR=3.01776;DPRA=2.77885;ODDS=65.8276;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996564;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.185;Dels=0.0;FS=0.0; [...]
+chr11 95724658 . C G 1556.46 PASS SOMATIC;NS=2;DP=219;DPB=219.0;AC=1;AN=3;AF=0.25;RO=155;AO=64;PRO=0.0;PAO=0.0;QR=5875;QA=2424;PQR=0.0;PQA=0.0;SRF=121;SRR=34;SAF=55;SAR=9;SRP=109.048;SAP=74.8046;AB=0.367816;ABP=29.4174;RUN=1;RPP=22.5536;RPPR=55.1396;RPL=20.0;RPR=44.0;EPP=9.66043;EPPR=7.05905;DPRA=3.86667;ODDS=29.0911;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984375;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.334;Dels=0.0;FS=12.311 [...]
+chr11 95825374 . TTGCTGCTGC T 5197.66 REJECT NS=2;DP=226;DPB=277.537;AC=3;AN=3;AF=1.0;RO=2;AO=193;PRO=123.0;PAO=117.0;QR=66;QA=6128;PQR=4446.0;PQA=4222.0;SRF=2;SRR=0;SAF=120;SAR=73;SRP=7.35324;SAP=27.8641;AB=0.0;ABP=0.0;RUN=1;RPP=3.56161;RPPR=3.0103;RPL=100.0;RPR=93.0;EPP=3.29158;EPPR=3.0103;DPRA=0.0;ODDS=13.7531;GTI=0;TYPE=del;CIGAR=1M9D31M;NUMALT=1;MEANALT=10.0;LEN=9;MQM=65.2176;MQMR=50.0;PAIRED=0.989637;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.276;FS= [...]
+chr11 95825374 . TTGCTGCTGCTGC T 12685.7 PASS SOMATIC;DP=253;AC=1;AN=3;AF=0.5;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.276;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=63.38;MQRankSum=1.496;QD=14.33;RPA=13;RU=TGC;ReadPosRankSum=-0.787;SOR=0.46;STR GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00409698 ./1:1,18:252:99.0:12723,6993,2147483647:18:10:176:.:1:.:.:.:.:-0.0101778
+chr11 95825797 . A G 6277.735000000001 REJECT NS=2;DP=268;DPB=301.0;AC=3;AN=4;AF=0.75;RO=85;AO=216;PRO=0.0;PAO=0.0;QR=3224;QA=8310;PQR=0.0;PQA=0.0;SRF=44;SRR=41;SAF=88;SAR=128;SRP=3.24022;SAP=19.0953;AB=0.638298;ABP=42.0506;RUN=1;RPP=3.05051;RPPR=12.2327;RPL=109.0;RPR=107.0;EPP=9.8062;EPPR=3.64897;DPRA=0.0;ODDS=42.1591;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99537;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.439;Dels=0.0;FS=4.3505;Haplot [...]
+chr11 102080325 . GA G 3184.8900000000003 REJECT NS=2;DP=169;DPB=216.69;AC=2;AN=2;AF=0.5;RO=8;AO=53;PRO=30.5833;PAO=43.5833;QR=302;QA=1639;PQR=1089.83;PQA=1459.83;SRF=0;SRR=8;SAF=11;SAR=42;SRP=20.3821;SAP=42.3836;AB=0.313609;ABP=54.0078;RUN=1;RPP=21.0786;RPPR=4.09604;RPL=37.0;RPR=16.0;EPP=3.37904;EPPR=4.09604;DPRA=0.0;ODDS=95.3717;GTI=0;TYPE=del;CIGAR=1M1D27M;NUMALT=3;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum= [...]
+chr11 102080325 . GAA G 3184.8900000000003 REJECT NS=2;DP=169;DPB=216.69;AC=2;AN=2;AF=0.5;RO=8;AO=73;PRO=30.5833;PAO=37.5833;QR=302;QA=2203;PQR=1089.83;PQA=1287.33;SRF=0;SRR=8;SAF=12;SAR=61;SRP=20.3821;SAP=74.4309;AB=0.431953;ABP=9.80739;RUN=1;RPP=13.7487;RPPR=4.09604;RPL=46.0;RPR=27.0;EPP=3.27802;EPPR=4.09604;DPRA=0.0;ODDS=95.3717;GTI=0;TYPE=del;CIGAR=1M2D26M;NUMALT=3;MEANALT=7.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum [...]
+chr11 102080325 . GAAA G 3341.05 REJECT NS=2;DP=169;DPB=216.69;AC=0;AN=4;AF=0.0;RO=8;AO=21;PRO=30.5833;PAO=23.25;QR=302;QA=684;PQR=1089.83;PQA=821.0;SRF=0;SRR=8;SAF=7;SAR=14;SRP=20.3821;SAP=8.07707;AB=0.12426;ABP=210.251;RUN=1;RPP=20.4855;RPPR=4.09604;RPL=17.0;RPR=4.0;EPP=3.94093;EPPR=4.09604;DPRA=0.0;ODDS=95.3717;GTI=0;TYPE=del;CIGAR=1M3D25M;NUMALT=3;MEANALT=7.5;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr11 108004798 . A C 6513.9400000000005 REJECT NS=2;DP=416;DPB=475.0;AC=2;AN=4;AF=0.5;RO=235;AO=240;PRO=0.0;PAO=0.0;QR=9001;QA=8943;PQR=0.0;PQA=0.0;SRF=123;SRR=112;SAF=123;SAR=117;SRP=4.12838;SAP=3.33602;AB=0.505263;ABP=3.12459;RUN=1;RPP=3.15506;RPPR=10.7814;RPL=122.0;RPR=118.0;EPP=3.04649;EPPR=21.7219;DPRA=0.0;ODDS=364.894;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995833;PAIREDR=0.995745;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4475;Dels=0.0;FS [...]
+chr11 108004927 . CT C 519.995 REJECT NS=2;DP=205;DPB=264.905;AC=2;AN=4;AF=0.5;RO=124;AO=35;PRO=59.5;PAO=38.5;QR=4538;QA=1061;PQR=2052.83;PQA=1299.83;SRF=47;SRR=77;SAF=12;SAR=23;SRP=18.771;SAP=10.5174;AB=0.170732;ABP=196.059;RUN=1;RPP=6.05036;RPPR=20.9425;RPL=21.0;RPR=14.0;EPP=3.07234;EPPR=4.76149;DPRA=0.0;ODDS=30.4167;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=2;MEANALT=13.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.983871;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=1.668;FS=1.3 [...]
+chr11 108004927 . CTT C 519.995 REJECT NS=2;DP=205;DPB=264.905;AC=2;AN=2;AF=0.0;RO=124;AO=10;PRO=59.5;PAO=31.0;QR=4538;QA=327;PQR=2052.83;PQA=1023.33;SRF=47;SRR=77;SAF=6;SAR=4;SRP=18.771;SAP=3.87889;AB=0.0487805;ABP=365.54;RUN=1;RPP=3.87889;RPPR=20.9425;RPL=6.0;RPR=4.0;EPP=3.87889;EPPR=4.76149;DPRA=0.0;ODDS=30.4167;GTI=0;TYPE=del;CIGAR=1M2D18M;NUMALT=2;MEANALT=13.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.983871;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr11 108150207 . CT C 5180.389999999999 REJECT NS=2;DP=295;DPB=324.556;AC=2;AN=4;AF=0.5;RO=148;AO=186;PRO=11.5;PAO=10.5;QR=5591;QA=6988;PQR=367.5;PQA=327.5;SRF=99;SRR=49;SAF=131;SAR=55;SRP=39.6906;SAP=70.4427;AB=0.555224;ABP=11.8842;RUN=1;RPP=25.6123;RPPR=28.8919;RPL=71.0;RPR=115.0;EPP=4.17776;EPPR=3.94932;DPRA=0.0;ODDS=191.63;GTI=0;TYPE=del;CIGAR=1M1D7M;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.97973;technology.ILLUMINA=1.0;MQ0=0;END=108150208;HOMLEN=1;HOMSEQ=T [...]
+chr11 108151707 . T TA 2470.835 REJECT NS=2;DP=206;DPB=272.4;AC=2;AN=4;AF=0.5;RO=128;AO=106;PRO=10.5;PAO=10.5;QR=4728;QA=3775;PQR=231.0;PQA=231.0;SRF=100;SRR=28;SAF=89;SAR=17;SRP=90.9549;SAP=109.208;AB=0.438017;ABP=11.086;RUN=1;RPP=21.4473;RPPR=38.9075;RPL=38.0;RPR=68.0;EPP=4.32138;EPPR=3.62103;DPRA=0.0;ODDS=203.962;GTI=0;TYPE=ins;CIGAR=1M1I4M;NUMALT=1;MEANALT=4.0;LEN=1;MQM=61.4151;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992188;technology.ILLUMINA=1.0;MQ0=0;END=108151707;HOMLEN=2;HOMSEQ=AA;SVLEN= [...]
+chr11 108163487 . C T 2825.75 PASS SOMATIC;NS=2;DP=438;DPB=438.0;AC=1;AN=3;AF=0.25;RO=326;AO=112;PRO=0.0;PAO=0.0;QR=12380;QA=4238;PQR=0.0;PQA=0.0;SRF=128;SRR=198;SAF=36;SAR=76;SRP=35.649;SAP=34.0313;AB=0.339394;ABP=76.9456;RUN=1;RPP=10.7656;RPPR=11.6429;RPL=66.0;RPR=46.0;EPP=4.25114;EPPR=6.84701;DPRA=3.05556;ODDS=68.3595;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.978528;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.98;Dels=0.0;FS=6.4 [...]
+chr11 108175394 . T C 3472.215 REJECT NS=2;DP=282;DPB=324.0;AC=2;AN=4;AF=0.5;RO=192;AO=132;PRO=0.0;PAO=0.0;QR=7423;QA=5048;PQR=0.0;PQA=0.0;SRF=134;SRR=58;SAF=86;SAR=46;SRP=68.3354;SAP=29.3312;AB=0.407407;ABP=27.1378;RUN=1;RPP=12.4858;RPPR=7.5342;RPL=54.0;RPR=78.0;EPP=9.59052;EPPR=7.5342;DPRA=0.0;ODDS=216.076;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992424;PAIREDR=0.994792;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.818;Dels=0.0;FS=4.1605;HaplotypeSc [...]
+chr11 108175462 . G A 4667.08 REJECT NS=2;DP=342;DPB=387.0;AC=2;AN=4;AF=0.5;RO=213;AO=173;PRO=0.0;PAO=0.0;QR=8236;QA=6420;PQR=0.0;PQA=0.0;SRF=107;SRR=106;SAF=90;SAR=83;SRP=3.02049;SAP=3.62534;AB=0.447028;ABP=12.4425;RUN=1;RPP=4.52908;RPPR=4.73321;RPL=81.0;RPR=92.0;EPP=4.52908;EPPR=14.1123;DPRA=0.0;ODDS=224.188;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99422;PAIREDR=0.995305;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.0505;Dels=0.0;FS=6.2005;Haplotyp [...]
+chr11 108183167 . A G 14236.599999999999 REJECT NS=2;DP=370;DPB=413.0;AC=4;AN=4;AF=1.0;RO=0;AO=413;PRO=0.0;PAO=0.0;QR=0;QA=15985;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=188;SAR=225;SRP=0.0;SAP=10.2082;AB=0.0;ABP=0.0;RUN=1;RPP=3.89887;RPPR=0.0;RPL=200.0;RPR=213.0;EPP=25.2245;EPPR=0.0;DPRA=0.0;ODDS=58.0225;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9516;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8325;MLEAC=2;MLEAF=1.0;MQ=59.975;QD= [...]
+chr11 108334321 . A G 6023.1 REJECT NS=2;DP=366;DPB=418.0;AC=2;AN=4;AF=0.5;RO=206;AO=212;PRO=0.0;PAO=0.0;QR=8000;QA=8145;PQR=0.0;PQA=0.0;SRF=97;SRR=109;SAF=105;SAR=107;SRP=4.52822;SAP=3.05127;AB=0.507177;ABP=3.19732;RUN=1;RPP=7.96781;RPPR=3.38978;RPL=95.0;RPR=117.0;EPP=5.63246;EPPR=4.52822;DPRA=0.0;ODDS=347.717;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995146;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0065;Dels=0.0;FS=1.714;HaplotypeSco [...]
+chr11 108336410 . G GT 6794.97 REJECT NS=2;DP=301;DPB=381.526;AC=2;AN=2;AF=0.25;RO=76;AO=38;PRO=47.3333;PAO=48.3333;QR=2875;QA=1304;PQR=1648.5;PQA=1690.0;SRF=24;SRR=52;SAF=11;SAR=27;SRP=25.4108;SAP=17.6392;AB=0.126246;ABP=368.229;RUN=1;RPP=30.668;RPPR=44.2683;RPL=30.0;RPR=8.0;EPP=3.9246;EPPR=3.12459;DPRA=0.0;ODDS=99.7959;GTI=0;TYPE=ins;CIGAR=1M1I18M;NUMALT=2;MEANALT=11.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986842;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.583;FS=1 [...]
+chr11 108336420 . A T 6122.870000000001 REJECT NS=2;DP=290;DPB=381.526;AC=2;AN=3;AF=0.5;RO=76;AO=149;PRO=47.3333;PAO=59.3333;QR=2875;QA=5455;PQR=1648.5;PQA=2108.5;SRF=24;SRR=52;SAF=50;SAR=99;SRP=25.4108;SAP=38.0016;AB=0.495017;ABP=3.07523;RUN=1;RPP=43.9477;RPPR=44.2683;RPL=101.0;RPR=48.0;EPP=8.27138;EPPR=3.12459;DPRA=0.0;ODDS=99.7959;GTI=0;TYPE=snp;CIGAR=10M1X8M;NUMALT=2;MEANALT=11.0;LEN=1;MQM=59.8658;MQMR=60.0;PAIRED=0.986577;PAIREDR=0.986842;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ [...]
+chr11 108336709 . TA T 537 REJECT NS=1;DP=47;DPB=87.9302;AC=1;AN=3;AF=0.0;RO=10;AO=4;PRO=31.5;PAO=24.5;QR=336;QA=102;PQR=1104.92;PQA=866.917;SRF=7;SRR=3;SAF=3;SAR=1;SRP=6.48466;SAP=5.18177;AB=0.0851064;ABP=73.2828;RUN=1;RPP=5.18177;RPPR=16.9077;RPL=1.0;RPR=3.0;EPP=3.0103;EPPR=10.8276;DPRA=0.0;ODDS=26.8108;GTI=0;TYPE=del;CIGAR=1M1D41M;NUMALT=3;MEANALT=26.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV [...]
+chr11 108336720 . AAAAAC A 537 REJECT NS=1;DP=47;DPB=87.9302;AC=1;AN=3;AF=0.0;RO=10;AO=3;PRO=31.5;PAO=21.0;QR=336;QA=91;PQR=1104.92;PQA=725.25;SRF=7;SRR=3;SAF=1;SAR=2;SRP=6.48466;SAP=3.73412;AB=0.0638298;ABP=80.6751;RUN=1;RPP=3.73412;RPPR=16.9077;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=10.8276;DPRA=0.0;ODDS=26.8108;GTI=0;TYPE=del;CIGAR=12M5D26M;NUMALT=3;MEANALT=26.0;LEN=5;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr11 108336721 . AAAAC A 537 REJECT NS=1;DP=47;DPB=87.9302;AC=1;AN=4;AF=0.5;RO=10;AO=7;PRO=31.5;PAO=22.0;QR=336;QA=227;PQR=1104.92;PQA=761.917;SRF=7;SRR=3;SAF=3;SAR=4;SRP=6.48466;SAP=3.32051;AB=0.148936;ABP=53.3238;RUN=1;RPP=18.2106;RPPR=16.9077;RPL=0.0;RPR=7.0;EPP=3.32051;EPPR=10.8276;DPRA=0.0;ODDS=26.8108;GTI=0;TYPE=del;CIGAR=13M4D26M;NUMALT=3;MEANALT=26.0;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr11 108337712 . A AAAC 4938.82 REJECT NS=2;DP=342;DPB=520.4;AC=2;AN=4;AF=0.5;RO=201;AO=175;PRO=19.5;PAO=27.5;QR=7590;QA=6459;PQR=688.5;PQA=962.5;SRF=89;SRR=112;SAF=71;SAR=104;SRP=8.72527;SAP=16.5231;AB=0.459318;ABP=8.48743;RUN=1;RPP=5.10732;RPPR=6.13247;RPL=94.0;RPR=81.0;EPP=6.59633;EPPR=9.76239;DPRA=0.0;ODDS=340.072;GTI=0;TYPE=ins;CIGAR=1M3I4M;NUMALT=1;MEANALT=3.0;LEN=3;MQM=60.2286;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995025;technology.ILLUMINA=1.0;MQ0=0;END=108337712;HOMLEN=3;HOMSEQ=AAC;SV [...]
+chr11 112504010 . C A 1427.875 REJECT NS=2;DP=279;DPB=321.0;AC=2;AN=4;AF=0.5;RO=245;AO=76;PRO=0.0;PAO=0.0;QR=9444;QA=2866;PQR=0.0;PQA=0.0;SRF=150;SRR=95;SAF=45;SAR=31;SRP=29.8213;SAP=8.61041;AB=0.23676;ABP=196.217;RUN=1;RPP=40.0396;RPPR=33.8629;RPL=20.0;RPR=56.0;EPP=4.03889;EPPR=22.589;DPRA=0.0;ODDS=134.278;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986842;PAIREDR=0.995918;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.216;Dels=0.0;FS=2.12;HaplotypeScore [...]
+chr11 118349476 . A AT 84.3097 REJECT NS=2;DP=184;DPB=219.875;AC=2;AN=2;AF=0.0;RO=151;AO=10;PRO=32.3333;PAO=24.3333;QR=5769;QA=381;PQR=1142.33;PQA=878.333;SRF=34;SRR=117;SAF=3;SAR=7;SRP=102.078;SAP=6.48466;AB=0.05;ABP=249.255;RUN=1;RPP=3.87889;RPPR=49.7329;RPL=6.0;RPR=4.0;EPP=6.48466;EPPR=4.17513;DPRA=0.0;ODDS=7.02614;GTI=0;TYPE=ins;CIGAR=1M1I15M;NUMALT=2;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=59.8675;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr11 118349476 . AT A 84.3097 REJECT NS=2;DP=184;DPB=219.875;AC=2;AN=3;AF=0.25;RO=151;AO=17;PRO=32.3333;PAO=24.3333;QR=5769;QA=594;PQR=1142.33;PQA=882.333;SRF=34;SRR=117;SAF=4;SAR=13;SRP=102.078;SAP=13.3567;AB=0.107143;ABP=190.688;RUN=1;RPP=18.4661;RPPR=49.7329;RPL=14.0;RPR=3.0;EPP=4.1599;EPPR=4.17513;DPRA=0.0;ODDS=7.02614;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=2;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=59.8675;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr11 118353037 . G GT 764.185 REJECT NS=2;DP=298;DPB=427.083;AC=2;AN=4;AF=0.5;RO=123;AO=39;PRO=68.8833;PAO=49.6333;QR=4374;QA=1206;PQR=2401.37;PQA=1681.62;SRF=46;SRR=77;SAF=23;SAR=16;SRP=19.976;SAP=5.73856;AB=0.130872;ABP=355.692;RUN=1;RPP=4.40227;RPPR=3.02795;RPL=22.0;RPR=17.0;EPP=4.40227;EPPR=4.44029;DPRA=0.0;ODDS=41.8121;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=5;MEANALT=22.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.414 [...]
+chr11 118353037 . G GTT 1011.64 PASS SOMATIC;NS=2;DP=298;DPB=427.083;AC=2;AN=2;AF=0.0;RO=123;AO=15;PRO=68.8833;PAO=46.6333;QR=4374;QA=368;PQR=2401.37;PQA=1592.62;SRF=46;SRR=77;SAF=5;SAR=10;SRP=19.976;SAP=6.62942;AB=0.0503356;ABP=526.379;RUN=1;RPP=6.62942;RPPR=3.02795;RPL=10.0;RPR=5.0;EPP=10.1038;EPPR=4.44029;DPRA=0.0;ODDS=41.8121;GTI=0;TYPE=ins;CIGAR=1M2I23M;NUMALT=5;MEANALT=22.0;LEN=2;MQM=59.8667;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:A [...]
+chr11 118353037 . GT G 1011.64 REJECT NS=2;DP=298;DPB=427.083;AC=2;AN=2;AF=0.0;RO=123;AO=24;PRO=68.8833;PAO=39.0833;QR=4374;QA=701;PQR=2401.37;PQA=1326.83;SRF=46;SRR=77;SAF=11;SAR=13;SRP=19.976;SAP=3.37221;AB=0.0805369;ABP=458.437;RUN=1;RPP=6.26751;RPPR=3.02795;RPL=9.0;RPR=15.0;EPP=3.0103;EPPR=4.44029;DPRA=0.0;ODDS=41.8121;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=5;MEANALT=22.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr11 118353054 . C T 1011.64 REJECT NS=2;DP=298;DPB=427.083;AC=2;AN=2;AF=0.0;RO=123;AO=25;PRO=68.8833;PAO=27.3833;QR=4374;QA=397;PQR=2401.37;PQA=908.783;SRF=46;SRR=77;SAF=25;SAR=0;SRP=19.976;SAP=57.2971;AB=0.0838926;ABP=451.179;RUN=1;RPP=3.79203;RPPR=3.02795;RPL=14.0;RPR=11.0;EPP=3.79203;EPPR=4.44029;DPRA=0.0;ODDS=41.8121;GTI=0;TYPE=snp;CIGAR=17M1X6M;NUMALT=5;MEANALT=22.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr11 118353054 . C TT 1011.64 REJECT NS=2;DP=298;DPB=427.083;AC=2;AN=2;AF=0.0;RO=123;AO=13;PRO=68.8833;PAO=25.3833;QR=4374;QA=231;PQR=2401.37;PQA=892.783;SRF=46;SRR=77;SAF=13;SAR=0;SRP=19.976;SAP=31.2394;AB=0.0436242;ABP=542.118;RUN=1;RPP=7.18621;RPPR=3.02795;RPL=9.0;RPR=4.0;EPP=7.18621;EPPR=4.44029;DPRA=0.0;ODDS=41.8121;GTI=0;TYPE=complex;CIGAR=1M1I16M1X6M;NUMALT=5;MEANALT=22.0;LEN=25;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO: [...]
+chr11 118353412 . G GCCAGCAGTTCAAGA 265.321 REJECT NS=2;DP=70;DPB=94.75;AC=2;AN=4;AF=0.5;RO=44;AO=20;PRO=9.0;PAO=9.0;QR=1591;QA=631;PQR=306.5;PQA=306.5;SRF=0;SRR=44;SAF=0;SAR=20;SRP=98.5551;SAP=46.4397;AB=0.285714;ABP=30.9292;RUN=1;RPP=18.6449;RPPR=31.4368;RPL=16.0;RPR=4.0;EPP=18.6449;EPPR=31.4368;DPRA=0.0;ODDS=6.98262;GTI=0;TYPE=ins;CIGAR=1M14I15M;NUMALT=1;MEANALT=4.0;LEN=14;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.977273;technology.ILLUMINA=1.0;BaseQRankSum=-0.978;FS=0.0;MLEAC=1;MLEAF=0 [...]
+chr11 118353467 . C A 23.733 REJECT NS=2;DP=22;DPB=31.1212;AC=2;AN=2;AF=0.0;RO=9;AO=2;PRO=6.1;PAO=2.6;QR=333;QA=48;PQR=211.2;PQA=72.2;SRF=0;SRR=9;SAF=0;SAR=2;SRP=22.5536;SAP=7.35324;AB=0.222222;ABP=9.04217;RUN=1;RPP=7.35324;RPPR=3.25157;RPL=0.0;RPR=2.0;EPP=7.35324;EPPR=3.25157;DPRA=0.0;ODDS=0.0876552;GTI=0;TYPE=snp;CIGAR=1X32M;NUMALT=4;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC: [...]
+chr11 118353467 . C CA 23.733 REJECT NS=2;DP=22;DPB=31.1212;AC=2;AN=3;AF=0.25;RO=9;AO=2;PRO=6.1;PAO=5.1;QR=333;QA=67;PQR=211.2;PQA=177.7;SRF=0;SRR=9;SAF=0;SAR=2;SRP=22.5536;SAP=7.35324;AB=0.153846;ABP=16.5402;RUN=1;RPP=7.35324;RPPR=3.25157;RPL=0.0;RPR=2.0;EPP=7.35324;EPPR=3.25157;DPRA=0.0;ODDS=0.0876552;GTI=0;TYPE=ins;CIGAR=1M1I32M;NUMALT=4;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:Ca [...]
+chr11 118353467 . CA C 23.733 REJECT NS=2;DP=22;DPB=31.1212;AC=2;AN=3;AF=0.25;RO=9;AO=3;PRO=6.1;PAO=5.1;QR=333;QA=78;PQR=211.2;PQA=165.7;SRF=0;SRR=9;SAF=0;SAR=3;SRP=22.5536;SAP=9.52472;AB=0.333333;ABP=5.18177;RUN=1;RPP=3.73412;RPPR=3.25157;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=3.25157;DPRA=0.0;ODDS=0.0876552;GTI=0;TYPE=del;CIGAR=1M1D31M;NUMALT=4;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:Ca [...]
+chr11 118353479 . AAAG A 23.733 REJECT NS=2;DP=22;DPB=31.1212;AC=2;AN=2;AF=0.0;RO=9;AO=2;PRO=6.1;PAO=5.1;QR=333;QA=78;PQR=211.2;PQA=173.2;SRF=0;SRR=9;SAF=0;SAR=2;SRP=22.5536;SAP=7.35324;AB=0.153846;ABP=16.5402;RUN=1;RPP=3.0103;RPPR=3.25157;RPL=1.0;RPR=1.0;EPP=3.0103;EPPR=3.25157;DPRA=0.0;ODDS=0.0876552;GTI=0;TYPE=del;CIGAR=13M3D17M;NUMALT=4;MEANALT=6.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:Ca [...]
+chr11 118353947 . CA C 29.3325 REJECT NS=2;DP=12;DPB=16.5652;AC=2;AN=4;AF=0.5;RO=5;AO=3;PRO=8.0;PAO=6.0;QR=167;QA=107;PQR=227.5;PQA=172.5;SRF=5;SRR=0;SAF=3;SAR=0;SRP=13.8677;SAP=9.52472;AB=0.25;ABP=9.52472;RUN=1;RPP=3.73412;RPPR=13.8677;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=13.8677;DPRA=0.0;ODDS=4.99;GTI=0;TYPE=del;CIGAR=1M1D21M;NUMALT=1;MEANALT=3.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI: [...]
+chr11 118354091 . CA C 2259.715 REJECT NS=2;DP=72;DPB=83.4167;AC=4;AN=4;AF=1.0;RO=0;AO=81;PRO=8.5;PAO=8.5;QR=0;QA=3008;PQR=300.0;PQA=300.0;SRF=0;SRR=0;SAF=81;SAR=0;SRP=0.0;SAP=178.9;AB=0.0;ABP=0.0;RUN=1;RPP=17.1919;RPPR=0.0;RPL=29.0;RPR=52.0;EPP=17.1919;EPPR=0.0;DPRA=0.0;ODDS=16.8462;GTI=0;TYPE=del;CIGAR=1M1D10M;NUMALT=1;MEANALT=1.5;LEN=1;MQM=52.8519;MQMR=0.0;PAIRED=0.975309;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.89;QD=31.035;RPA=7,6;RU=A;SOR=7.2355;STR [...]
+chr11 118357090 . G GT 4499.355 REJECT NS=2;DP=341;DPB=467.435;AC=2;AN=4;AF=0.5;RO=99;AO=175;PRO=67.6667;PAO=73.6667;QR=3602;QA=5744;PQR=2341.67;PQA=2569.67;SRF=46;SRR=53;SAF=82;SAR=93;SRP=4.08507;SAP=4.51172;AB=0.513196;ABP=3.5261;RUN=1;RPP=4.01538;RPPR=3.20771;RPL=83.0;RPR=92.0;EPP=3.12198;EPPR=6.71716;DPRA=0.0;ODDS=205.38;GTI=0;TYPE=ins;CIGAR=1M1I22M;NUMALT=3;MEANALT=13.5;LEN=1;MQM=60.1714;MQMR=59.798;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum= [...]
+chr11 118357090 . G GTT 5200.98 REJECT NS=2;DP=341;DPB=467.435;AC=2;AN=2;AF=0.0;RO=99;AO=22;PRO=67.6667;PAO=56.6667;QR=3602;QA=711;PQR=2341.67;PQA=1911.67;SRF=46;SRR=53;SAF=8;SAR=14;SRP=4.08507;SAP=6.56362;AB=0.0645161;ABP=564.721;RUN=1;RPP=4.58955;RPPR=3.20771;RPL=13.0;RPR=9.0;EPP=4.58955;EPPR=6.71716;DPRA=0.0;ODDS=205.38;GTI=0;TYPE=ins;CIGAR=1M2I22M;NUMALT=3;MEANALT=13.5;LEN=2;MQM=60.0;MQMR=59.798;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr11 118357090 . GT G 5200.98 REJECT NS=2;DP=341;DPB=467.435;AC=2;AN=2;AF=0.0;RO=99;AO=15;PRO=67.6667;PAO=46.0;QR=3602;QA=429;PQR=2341.67;PQA=1528.0;SRF=46;SRR=53;SAF=8;SAR=7;SRP=4.08507;SAP=3.15506;AB=0.0439883;ABP=618.925;RUN=1;RPP=3.15506;RPPR=3.20771;RPL=7.0;RPR=8.0;EPP=3.15506;EPPR=6.71716;DPRA=0.0;ODDS=205.38;GTI=0;TYPE=del;CIGAR=1M1D21M;NUMALT=3;MEANALT=13.5;LEN=1;MQM=60.0;MQMR=59.798;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr11 118357614 . T A 7212.61 REJECT NS=2;DP=274;DPB=319.0;AC=2;AN=4;AF=0.5;RO=74;AO=244;PRO=0.0;PAO=0.0;QR=2873;QA=9349;PQR=0.0;PQA=0.0;SRF=61;SRR=13;SAF=201;SAR=43;SRP=70.6194;SAP=225.177;AB=0.76489;ABP=197.429;RUN=1;RPP=35.0484;RPPR=36.9322;RPL=92.0;RPR=152.0;EPP=5.89373;EPPR=4.88833;DPRA=0.0;ODDS=75.7058;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983607;PAIREDR=0.972973;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4285;Dels=0.0;FS=7.427;HaplotypeSc [...]
+chr11 118358068 . T A 4360.56 PASS SOMATIC;NS=2;DP=535;DPB=535.0;AC=1;AN=3;AF=0.25;RO=375;AO=160;PRO=0.0;PAO=0.0;QR=14270;QA=6138;PQR=0.0;PQA=0.0;SRF=202;SRR=173;SAF=82;SAR=78;SRP=7.88019;SAP=3.22745;AB=0.395062;ABP=41.7483;RUN=1;RPP=10.8276;RPPR=15.8017;RPL=68.0;RPR=92.0;EPP=3.22745;EPPR=3.98891;DPRA=3.11538;ODDS=81.9866;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0625;MQMR=60.0;PAIRED=0.99375;PAIREDR=0.992;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.957;Dels=0.0;F [...]
+chr11 118359161 . G A 13836.6 REJECT NS=2;DP=523;DPB=592.0;AC=2;AN=4;AF=0.5;RO=124;AO=466;PRO=0.0;PAO=0.0;QR=4653;QA=17237;PQR=0.0;PQA=0.0;SRF=66;SRR=58;SAF=229;SAR=237;SRP=4.13106;SAP=3.30853;AB=0.787162;ABP=427.034;RUN=1;RPP=6.66359;RPPR=3.08035;RPL=247.0;RPR=219.0;EPP=3.17805;EPPR=3.08035;DPRA=0.0;ODDS=175.835;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997854;PAIREDR=0.975806;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4655;Dels=0.0;FS=2.7145;Hapl [...]
+chr11 118359946 . C AA 201.164 REJECT NS=2;DP=66;DPB=138.2;AC=2;AN=2;AF=0.0;RO=13;AO=4;PRO=34.0167;PAO=22.6;QR=454;QA=72;PQR=1173.15;PQA=775.4;SRF=7;SRR=6;SAF=0;SAR=4;SRP=3.17734;SAP=11.6962;AB=0.0851064;ABP=73.2828;RUN=1;RPP=5.18177;RPPR=16.5402;RPL=1.0;RPR=3.0;EPP=5.18177;EPPR=4.51363;DPRA=0.0;ODDS=3.92609;GTI=1;TYPE=complex;CIGAR=1X1I29M;NUMALT=4;MEANALT=19.0;LEN=31;MQM=70.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr11 118359946 . C CA 201.164 REJECT NS=2;DP=66;DPB=138.2;AC=2;AN=3;AF=0.25;RO=13;AO=13;PRO=34.0167;PAO=34.0167;QR=454;QA=362;PQR=1173.15;PQA=1173.15;SRF=7;SRR=6;SAF=10;SAR=3;SRP=3.17734;SAP=11.1951;AB=0.19697;ABP=55.6521;RUN=1;RPP=4.51363;RPPR=16.5402;RPL=5.0;RPR=8.0;EPP=4.51363;EPPR=4.51363;DPRA=0.0;ODDS=3.92609;GTI=1;TYPE=ins;CIGAR=1M1I29M;NUMALT=4;MEANALT=14.0;LEN=1;MQM=56.6154;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr11 118359946 . C CAA 201.164 REJECT NS=2;DP=66;DPB=138.2;AC=2;AN=3;AF=0.25;RO=13;AO=10;PRO=34.0167;PAO=34.0167;QR=454;QA=298;PQR=1173.15;PQA=1173.15;SRF=7;SRR=6;SAF=10;SAR=0;SRP=3.17734;SAP=24.725;AB=0.151515;ABP=72.629;RUN=1;RPP=10.8276;RPPR=16.5402;RPL=8.0;RPR=2.0;EPP=10.8276;EPPR=4.51363;DPRA=0.0;ODDS=3.92609;GTI=1;TYPE=ins;CIGAR=1M2I29M;NUMALT=4;MEANALT=14.0;LEN=2;MQM=52.4;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr11 118359946 . CA C 201.164 REJECT NS=2;DP=66;DPB=138.2;AC=2;AN=2;AF=0.0;RO=13;AO=4;PRO=34.0167;PAO=25.35;QR=454;QA=147;PQR=1173.15;PQA=873.15;SRF=7;SRR=6;SAF=4;SAR=0;SRP=3.17734;SAP=11.6962;AB=0.0606061;ABP=113.69;RUN=1;RPP=5.18177;RPPR=16.5402;RPL=1.0;RPR=3.0;EPP=5.18177;EPPR=4.51363;DPRA=0.0;ODDS=3.92609;GTI=1;TYPE=del;CIGAR=1M1D28M;NUMALT=4;MEANALT=14.0;LEN=1;MQM=57.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr11 118369265 . T TA 498.819 REJECT NS=2;DP=165;DPB=199.19;AC=2;AN=2;AF=0.0;RO=94;AO=13;PRO=31.1667;PAO=19.1667;QR=3498;QA=323;PQR=1117.42;PQA=685.417;SRF=29;SRR=65;SAF=2;SAR=11;SRP=32.9489;SAP=16.5402;AB=0.0787879;ABP=257.283;RUN=1;RPP=23.2217;RPPR=75.4543;RPL=12.0;RPR=1.0;EPP=11.1951;EPPR=5.32038;DPRA=0.0;ODDS=15.9448;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=3;MEANALT=10.0;LEN=1;MQM=58.4615;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr11 118369265 . TA T 498.819 REJECT NS=2;DP=165;DPB=199.19;AC=2;AN=4;AF=0.5;RO=94;AO=31;PRO=31.1667;PAO=16.5;QR=3498;QA=1131;PQR=1117.42;PQA=587.75;SRF=29;SRR=65;SAF=13;SAR=18;SRP=32.9489;SAP=4.76149;AB=0.187879;ABP=142.629;RUN=1;RPP=33.9012;RPPR=75.4543;RPL=26.0;RPR=5.0;EPP=3.08035;EPPR=5.32038;DPRA=0.0;ODDS=15.9448;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=3;MEANALT=10.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.304;FS=0.0;MLEA [...]
+chr11 118369281 . G A 498.819 REJECT NS=2;DP=165;DPB=199.19;AC=2;AN=2;AF=0.0;RO=94;AO=7;PRO=31.1667;PAO=19.1667;QR=3498;QA=111;PQR=1117.42;PQA=685.417;SRF=29;SRR=65;SAF=7;SAR=0;SRP=32.9489;SAP=18.2106;AB=0.0530303;ABP=232.068;RUN=1;RPP=18.2106;RPPR=75.4543;RPL=7.0;RPR=0.0;EPP=18.2106;EPPR=5.32038;DPRA=0.0;ODDS=15.9448;GTI=0;TYPE=snp;CIGAR=16M1X4M;NUMALT=3;MEANALT=16.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr11 119148573 . G T 8848.630000000001 REJECT NS=2;DP=235;DPB=273.0;AC=4;AN=4;AF=1.0;RO=0;AO=273;PRO=0.0;PAO=0.0;QR=0;QA=10517;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=67;SAR=206;SRP=0.0;SAP=156.692;AB=0.0;ABP=0.0;RUN=1;RPP=74.7962;RPPR=0.0;RPL=184.0;RPR=89.0;EPP=3.08189;EPPR=0.0;DPRA=0.0;ODDS=50.4885;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992674;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31. [...]
+chr11 125495839 . A T 2838.37 PASS SOMATIC;NS=2;DP=417;DPB=417.0;AC=1;AN=3;AF=0.25;RO=307;AO=110;PRO=0.0;PAO=0.0;QR=11654;QA=4188;PQR=0.0;PQA=0.0;SRF=137;SRR=170;SAF=46;SAR=64;SRP=10.713;SAP=9.40627;AB=0.342679;ABP=72.0171;RUN=1;RPP=3.08926;RPPR=13.7686;RPL=54.0;RPR=56.0;EPP=3.72096;EPPR=19.9931;DPRA=3.34375;ODDS=60.8854;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986971;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.649;Dels=0.0;FS=0.4 [...]
+chr11 125525195 . A G 12108.849999999999 REJECT NS=2;DP=322;DPB=370.0;AC=4;AN=4;AF=1.0;RO=0;AO=370;PRO=0.0;PAO=0.0;QR=0;QA=14093;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=172;SAR=198;SRP=0.0;SAP=6.97764;AB=0.0;ABP=0.0;RUN=1;RPP=12.4005;RPPR=0.0;RPL=205.0;RPR=165.0;EPP=61.6987;EPPR=0.0;DPRA=0.0;ODDS=62.7371;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991892;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.9326;MLEAC=2;MLEAF=1.0;MQ=60.0;QD= [...]
+chr11 128333503 . T C 3361.44 PASS SOMATIC;NS=2;DP=405;DPB=405.0;AC=1;AN=3;AF=0.25;RO=284;AO=121;PRO=0.0;PAO=0.0;QR=10926;QA=4676;PQR=0.0;PQA=0.0;SRF=101;SRR=183;SAF=54;SAR=67;SRP=54.4222;SAP=6.04318;AB=0.418685;ABP=19.6082;RUN=1;RPP=12.5038;RPPR=3.49965;RPL=72.0;RPR=49.0;EPP=3.02825;EPPR=11.8491;DPRA=2.49138;ODDS=73.3532;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983471;PAIREDR=0.996479;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.306;Dels=0.0; [...]
+chr11 130500152 . A T 12141.099999999999 REJECT NS=2;DP=330;DPB=381.0;AC=4;AN=4;AF=1.0;RO=1;AO=378;PRO=0.0;PAO=0.0;QR=16;QA=14332;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=112;SAR=266;SRP=5.18177;SAP=139.25;AB=0.0;ABP=0.0;RUN=1;RPP=180.956;RPPR=5.18177;RPL=277.0;RPR=101.0;EPP=6.31921;EPPR=5.18177;DPRA=0.0;ODDS=66.0423;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0794;MQMR=60.0;PAIRED=0.994709;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.645;Dels=0.0;FS=0.0;HaplotypeScore=1 [...]
+chr12 406292 . G A 3032.85 PASS SOMATIC;NS=2;DP=438;DPB=438.0;AC=1;AN=3;AF=0.25;RO=324;AO=113;PRO=0.0;PAO=0.0;QR=12451;QA=4423;PQR=0.0;PQA=0.0;SRF=186;SRR=138;SAF=53;SAR=60;SRP=18.4519;SAP=3.95191;AB=0.343465;ABP=73.032;RUN=1;RPP=3.18325;RPPR=14.8328;RPL=55.0;RPR=58.0;EPP=6.2579;EPPR=10.7579;DPRA=3.01835;ODDS=69.0063;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.882;Dels=0.0;FS=8.859;Haplot [...]
+chr12 427575 . A G 1951.84 PASS SOMATIC;NS=2;DP=394;DPB=394.0;AC=1;AN=3;AF=0.25;RO=311;AO=83;PRO=0.0;PAO=0.0;QR=12006;QA=3113;PQR=0.0;PQA=0.0;SRF=108;SRR=203;SAF=35;SAR=48;SRP=66.0249;SAP=7.43173;AB=0.285223;ABP=119.606;RUN=1;RPP=3.66436;RPPR=5.02816;RPL=44.0;RPR=39.0;EPP=7.43173;EPPR=12.569;DPRA=2.82524;ODDS=65.2646;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993569;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.322;Dels=0.0;FS=3.836; [...]
+chr12 496392 . C CA 882.326 REJECT NS=2;DP=263;DPB=326.842;AC=2;AN=2;AF=0.0;RO=125;AO=21;PRO=49.5;PAO=47.5;QR=4532;QA=610;PQR=1707.0;PQA=1600.0;SRF=87;SRR=38;SAF=10;SAR=11;SRP=44.7199;SAP=3.1137;AB=0.0798479;ABP=406.268;RUN=1;RPP=20.4855;RPPR=32.2123;RPL=4.0;RPR=17.0;EPP=11.386;EPPR=3.44459;DPRA=0.0;ODDS=82.4083;GTI=0;TYPE=ins;CIGAR=1M1I18M;NUMALT=2;MEANALT=16.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr12 496392 . CA C 639.528 REJECT NS=2;DP=248;DPB=326.842;AC=2;AN=4;AF=0.5;RO=125;AO=52;PRO=49.5;PAO=39.0;QR=4532;QA=1691;PQR=1707.0;PQA=1324.0;SRF=87;SRR=38;SAF=33;SAR=19;SRP=44.7199;SAP=11.1951;AB=0.197719;ABP=211.744;RUN=1;RPP=13.7006;RPPR=32.2123;RPL=18.0;RPR=34.0;EPP=3.17734;EPPR=3.44459;DPRA=0.0;ODDS=82.4083;GTI=0;TYPE=del;CIGAR=1M1D17M;NUMALT=2;MEANALT=16.5;LEN=1;MQM=60.1923;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.2475;FS=3. [...]
+chr12 496439 . A T 7936.885 REJECT NS=2;DP=388;DPB=439.0;AC=3;AN=4;AF=0.75;RO=129;AO=310;PRO=0.0;PAO=0.0;QR=4646;QA=10931;PQR=0.0;PQA=0.0;SRF=70;SRR=59;SAF=131;SAR=179;SRP=5.04711;SAP=19.1492;AB=0.629412;ABP=52.4688;RUN=1;RPP=21.9511;RPPR=9.08706;RPL=129.0;RPR=181.0;EPP=26.5743;EPPR=9.08706;DPRA=0.0;ODDS=52.7115;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9677;MQMR=59.9457;PAIRED=0.980645;PAIREDR=0.984496;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0165;Dels=0.0;FS=9.7925 [...]
+chr12 498247 . A C 60.568 REJECT NS=2;DP=237;DPB=261.286;AC=2;AN=2;AF=0.0;RO=154;AO=22;PRO=47.1667;PAO=2.16667;QR=5275;QA=285;PQR=1623.17;PQA=33.1667;SRF=58;SRR=96;SAF=0;SAR=22;SRP=23.3714;SAP=50.7827;AB=0.0526316;ABP=102.098;RUN=1;RPP=17.2236;RPPR=102.503;RPL=5.0;RPR=17.0;EPP=17.2236;EPPR=3.23591;DPRA=0.0;ODDS=5.64706;GTI=0;TYPE=snp;CIGAR=1X6M;NUMALT=4;MEANALT=8.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr12 498247 . ACG CCC 60.568 REJECT NS=2;DP=237;DPB=261.286;AC=2;AN=2;AF=0.0;RO=154;AO=17;PRO=47.1667;PAO=2.66667;QR=5275;QA=196;PQR=1623.17;PQA=20.6667;SRF=58;SRR=96;SAF=0;SAR=17;SRP=23.3714;SAP=39.9253;AB=0.0877193;ABP=87.1644;RUN=1;RPP=13.3567;RPPR=102.503;RPL=4.0;RPR=13.0;EPP=13.3567;EPPR=3.23591;DPRA=0.0;ODDS=5.64706;GTI=0;TYPE=complex;CIGAR=1X1M1X4M;NUMALT=4;MEANALT=8.5;LEN=7;MQM=61.7647;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:Q [...]
+chr12 498247 . ACGCCCG CCCCCCC 60.568 REJECT NS=2;DP=237;DPB=261.286;AC=2;AN=3;AF=0.25;RO=154;AO=15;PRO=47.1667;PAO=2.0;QR=5275;QA=212;PQR=1623.17;PQA=18.0;SRF=58;SRR=96;SAF=0;SAR=15;SRP=23.3714;SAP=35.5824;AB=0.105263;ABP=80.1547;RUN=1;RPP=10.1038;RPPR=102.503;RPL=4.0;RPR=11.0;EPP=10.1038;EPPR=3.23591;DPRA=0.0;ODDS=5.64706;GTI=0;TYPE=complex;CIGAR=1X1M1X3M1X;NUMALT=4;MEANALT=8.5;LEN=7;MQM=57.3333;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:A [...]
+chr12 498247 . ACGCCCG CCGCCCC 60.568 REJECT NS=2;DP=237;DPB=261.286;AC=2;AN=2;AF=0.0;RO=154;AO=11;PRO=47.1667;PAO=1.0;QR=5275;QA=132;PQR=1623.17;PQA=2.0;SRF=58;SRR=96;SAF=0;SAR=11;SRP=23.3714;SAP=26.8965;AB=0.0701754;ABP=94.4788;RUN=1;RPP=12.6832;RPPR=102.503;RPL=2.0;RPR=9.0;EPP=12.6832;EPPR=3.23591;DPRA=0.0;ODDS=5.64706;GTI=0;TYPE=complex;CIGAR=1X5M1X;NUMALT=4;MEANALT=8.5;LEN=7;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr12 498267 . CG C 621.148 REJECT NS=2;DP=131;DPB=138.913;AC=1;AN=3;AF=0.25;RO=5;AO=23;PRO=12.2333;PAO=13.2333;QR=184;QA=396;PQR=393.933;PQA=408.933;SRF=0;SRR=5;SAF=1;SAR=22;SRP=13.8677;SAP=44.6459;AB=0.175573;ABP=122.773;RUN=1;RPP=10.6577;RPPR=3.44459;RPL=16.0;RPR=7.0;EPP=7.63648;EPPR=3.44459;DPRA=0.0;ODDS=6.55357;GTI=0;TYPE=del;CIGAR=1M1D21M;NUMALT=4;MEANALT=10.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr12 498267 . CGG C 621.148 REJECT NS=2;DP=131;DPB=138.913;AC=2;AN=2;AF=0.5;RO=5;AO=47;PRO=12.2333;PAO=12.7333;QR=184;QA=751;PQR=393.933;PQA=397.933;SRF=0;SRR=5;SAF=2;SAR=45;SRP=13.8677;SAP=88.4369;AB=0.358779;ABP=25.703;RUN=1;RPP=5.27418;RPPR=3.44459;RPL=27.0;RPR=20.0;EPP=3.42611;EPPR=3.44459;DPRA=0.0;ODDS=6.55357;GTI=0;TYPE=del;CIGAR=1M2D20M;NUMALT=4;MEANALT=10.5;LEN=2;MQM=60.8511;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.117;FS=4. [...]
+chr12 498267 . CGGG C 621.148 REJECT SOMATIC;NS=2;DP=131;DPB=138.913;AC=1;AN=3;AF=0.25;RO=5;AO=25;PRO=12.2333;PAO=10.4;QR=184;QA=515;PQR=393.933;PQA=324.6;SRF=0;SRR=5;SAF=3;SAR=22;SRP=13.8677;SAP=34.3664;AB=0.19084;ABP=111.766;RUN=1;RPP=3.09716;RPPR=3.44459;RPL=13.0;RPR=12.0;EPP=5.18177;EPPR=3.44459;DPRA=0.0;ODDS=6.55357;GTI=0;TYPE=del;CIGAR=1M3D19M;NUMALT=4;MEANALT=10.5;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.025;FS= [...]
+chr12 498267 . CGGGG C 621.148 REJECT NS=2;DP=131;DPB=138.913;AC=0;AN=4;AF=0.0;RO=5;AO=15;PRO=12.2333;PAO=7.4;QR=184;QA=347;PQR=393.933;PQA=267.6;SRF=0;SRR=5;SAF=1;SAR=14;SRP=13.8677;SAP=27.4756;AB=0.114504;ABP=172.103;RUN=1;RPP=14.7363;RPPR=3.44459;RPL=12.0;RPR=3.0;EPP=10.1038;EPPR=3.44459;DPRA=0.0;ODDS=6.55357;GTI=0;TYPE=del;CIGAR=1M4D18M;NUMALT=4;MEANALT=10.5;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr12 3005685 . T C 1498.19 REJECT NS=2;DP=318;DPB=363.0;AC=2;AN=4;AF=0.5;RO=288;AO=74;PRO=0.0;PAO=0.0;QR=11047;QA=2827;PQR=0.0;PQA=0.0;SRF=124;SRR=164;SAF=30;SAR=44;SRP=15.074;SAP=8.76177;AB=0.203857;ABP=279.529;RUN=1;RPP=5.94472;RPPR=24.9965;RPL=42.0;RPR=32.0;EPP=5.94472;EPPR=13.8978;DPRA=0.0;ODDS=47.1313;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996528;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.231;Dels=0.0;FS=3.41;HaplotypeScore=6.7 [...]
+chr12 4286276 . C T 1436.75 REJECT NS=1;DP=106;DPB=106.0;AC=1;AN=4;AF=0.5;RO=54;AO=52;PRO=0.0;PAO=0.0;QR=2038;QA=2007;PQR=0.0;PQA=0.0;SRF=33;SRR=21;SAF=31;SAR=21;SRP=8.80089;SAP=7.18621;AB=0.490566;ABP=3.09224;RUN=1;RPP=3.67845;RPPR=26.1727;RPL=24.0;RPR=28.0;EPP=31.2394;EPPR=7.03155;DPRA=0.0;ODDS=330.823;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.980769;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.777;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=- [...]
+chr12 4290218 . CA C 4550.68 REJECT NS=2;DP=330;DPB=384.231;AC=2;AN=4;AF=0.5;RO=179;AO=170;PRO=54.5;PAO=45.5;QR=6790;QA=6503;PQR=1874.0;PQA=1534.0;SRF=75;SRR=104;SAF=76;SAR=94;SRP=13.2126;SAP=7.14887;AB=0.48433;ABP=3.75887;RUN=1;RPP=6.28028;RPPR=4.47817;RPL=93.0;RPR=77.0;EPP=3.21467;EPPR=3.02243;DPRA=0.0;ODDS=277.968;GTI=0;TYPE=del;CIGAR=1M1D11M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.1176;MQMR=60.0;PAIRED=0.994118;PAIREDR=0.988827;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.02;FS=1.4955;MLEA [...]
+chr12 4290249 . A G 6093.89 REJECT NS=2;DP=336;DPB=384.0;AC=2;AN=4;AF=0.5;RO=177;AO=207;PRO=0.0;PAO=0.0;QR=6718;QA=8013;PQR=0.0;PQA=0.0;SRF=69;SRR=108;SAF=83;SAR=124;SRP=21.6702;SAP=20.6443;AB=0.539062;ABP=8.09969;RUN=1;RPP=3.27256;RPPR=5.77065;RPL=106.0;RPR=101.0;EPP=3.10471;EPPR=8.42058;DPRA=0.0;ODDS=277.902;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.1695;PAIRED=0.980676;PAIREDR=0.99435;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.5785;Dels=0.0;FS=0.4215;Haplot [...]
+chr12 4292353 . A T 5493.29 REJECT NS=2;DP=372;DPB=421.0;AC=2;AN=4;AF=0.5;RO=225;AO=195;PRO=0.0;PAO=0.0;QR=8493;QA=7463;PQR=0.0;PQA=0.0;SRF=122;SRR=103;SAF=101;SAR=94;SRP=6.49431;SAP=3.55595;AB=0.463183;ABP=7.96703;RUN=1;RPP=6.22853;RPPR=3.4832;RPL=106.0;RPR=89.0;EPP=21.7295;EPPR=5.79944;DPRA=0.0;ODDS=209.863;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994872;PAIREDR=0.995556;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0825;Dels=0.0;FS=0.412;HaplotypeS [...]
+chr12 4388084 . C G 6628.9 REJECT NS=2;DP=259;DPB=298.0;AC=2;AN=4;AF=0.5;RO=73;AO=225;PRO=0.0;PAO=0.0;QR=2829;QA=8503;PQR=0.0;PQA=0.0;SRF=17;SRR=56;SAF=53;SAR=172;SRP=48.2543;SAP=139.678;AB=0.755034;ABP=171.365;RUN=1;RPP=11.1268;RPPR=11.607;RPL=127.0;RPR=98.0;EPP=4.64132;EPPR=3.27802;DPRA=0.0;ODDS=122.336;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4;Dels=0.0;FS=1.4505;HaplotypeScore=5.8743;MLE [...]
+chr12 4512480 . G A 2796.0150000000003 REJECT NS=2;DP=498;DPB=572.0;AC=2;AN=4;AF=0.5;RO=439;AO=133;PRO=0.0;PAO=0.0;QR=16802;QA=5123;PQR=0.0;PQA=0.0;SRF=202;SRR=237;SAF=58;SAR=75;SRP=9.06965;SAP=7.72876;AB=0.232517;ABP=358.479;RUN=1;RPP=8.9043;RPPR=9.06965;RPL=57.0;RPR=76.0;EPP=3.02663;EPPR=15.8759;DPRA=0.0;ODDS=156.226;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993166;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.48;Dels=0.0;FS=2.485;Haploty [...]
+chr12 4553332 . A G 2074.54 REJECT NS=2;DP=379;DPB=436.0;AC=2;AN=4;AF=0.5;RO=335;AO=100;PRO=0.0;PAO=0.0;QR=12778;QA=3752;PQR=0.0;PQA=0.0;SRF=179;SRR=156;SAF=37;SAR=63;SRP=6.43928;SAP=17.6895;AB=0.229358;ABP=280.401;RUN=1;RPP=3.79203;RPPR=10.9508;RPL=53.0;RPR=47.0;EPP=4.40004;EPPR=4.10576;DPRA=0.0;ODDS=108.837;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997015;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1655;Dels=0.0;FS=12.332;HaplotypeScor [...]
+chr12 4553383 . A G 1383.56 REJECT NS=2;DP=341;DPB=389.0;AC=2;AN=4;AF=0.5;RO=313;AO=73;PRO=0.0;PAO=0.0;QR=11803;QA=2795;PQR=0.0;PQA=0.0;SRF=128;SRR=185;SAF=23;SAR=50;SRP=25.5506;SAP=24.6953;AB=0.187661;ABP=332.633;RUN=1;RPP=13.7487;RPPR=23.9966;RPL=46.0;RPR=27.0;EPP=3.04005;EPPR=22.4981;DPRA=0.0;ODDS=58.672;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986301;PAIREDR=0.990415;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.474;Dels=0.0;FS=5.753;HaplotypeScor [...]
+chr12 4554548 . G C 14291.349999999999 REJECT NS=2;DP=376;DPB=433.0;AC=4;AN=4;AF=1.0;RO=0;AO=433;PRO=0.0;PAO=0.0;QR=0;QA=16524;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=217;SAR=216;SRP=0.0;SAP=3.01531;AB=0.0;ABP=0.0;RUN=1;RPP=20.4673;RPPR=0.0;RPL=246.0;RPR=187.0;EPP=3.61711;EPPR=0.0;DPRA=0.0;ODDS=73.5094;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993072;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8378;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31 [...]
+chr12 6711147 . C A 1032.075 REJECT NS=2;DP=302;DPB=347.0;AC=2;AN=4;AF=0.5;RO=274;AO=72;PRO=0.0;PAO=0.0;QR=10249;QA=2663;PQR=0.0;PQA=0.0;SRF=88;SRR=186;SAF=21;SAR=51;SRP=79.1228;SAP=30.1537;AB=0.207493;ABP=260.89;RUN=1;RPP=4.09604;RPPR=33.4743;RPL=39.0;RPR=33.0;EPP=4.9405;EPPR=5.57803;DPRA=0.0;ODDS=108.853;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=59.9854;PAIRED=1.0;PAIREDR=0.989051;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7375;Dels=0.03;FS=1.1655;HaplotypeScor [...]
+chr12 7502208 . G A 13008.05 REJECT NS=2;DP=347;DPB=401.0;AC=4;AN=4;AF=1.0;RO=0;AO=401;PRO=0.0;PAO=0.0;QR=0;QA=15264;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=197;SAR=204;SRP=0.0;SAP=3.27564;AB=0.0;ABP=0.0;RUN=1;RPP=3.66553;RPPR=0.0;RPL=206.0;RPR=195.0;EPP=13.0229;EPPR=0.0;DPRA=0.0;ODDS=70.4494;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.990025;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8463;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.89;SOR=0. [...]
+chr12 12007343 . G C 4603.64 REJECT NS=2;DP=286;DPB=324.0;AC=2;AN=4;AF=0.5;RO=159;AO=164;PRO=0.0;PAO=0.0;QR=6105;QA=6185;PQR=0.0;PQA=0.0;SRF=96;SRR=63;SAF=101;SAR=63;SRP=17.8828;SAP=22.1298;AB=0.506173;ABP=3.11753;RUN=1;RPP=8.30657;RPPR=7.9405;RPL=72.0;RPR=92.0;EPP=5.60547;EPPR=19.7402;DPRA=0.0;ODDS=223.955;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993902;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0385;Dels=0.0;FS=4.989;HaplotypeScore=11 [...]
+chr12 12007893 . C G 2358.0 PASS SOMATIC;NS=2;DP=362;DPB=362.0;AC=1;AN=3;AF=0.25;RO=270;AO=92;PRO=0.0;PAO=0.0;QR=10306;QA=3521;PQR=0.0;PQA=0.0;SRF=112;SRR=158;SAF=35;SAR=57;SRP=20.0282;SAP=14.4341;AB=0.335766;ABP=67.2035;RUN=1;RPP=3.0103;RPPR=6.2273;RPL=46.0;RPR=46.0;EPP=7.63648;EPPR=15.8783;DPRA=3.11364;ODDS=55.8671;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.956522;PAIREDR=0.981481;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.228;Dels=0.0;FS=0. [...]
+chr12 12008071 . T A 26.8715 REJECT NS=2;DP=55;DPB=58.6667;AC=2;AN=2;AF=0.0;RO=45;AO=3;PRO=2.0;PAO=0.0;QR=1434;QA=48;PQR=69.5;PQA=0.0;SRF=25;SRR=20;SAF=0;SAR=3;SRP=4.21667;SAP=9.52472;AB=0.0571429;ABP=62.6327;RUN=1;RPP=9.52472;RPPR=4.21667;RPL=3.0;RPR=0.0;EPP=9.52472;EPPR=8.84915;DPRA=0.0;ODDS=6.1826;GTI=0;TYPE=snp;CIGAR=1X2M;NUMALT=3;MEANALT=3.5;LEN=1;MQM=46.6667;MQMR=50.4444;PAIRED=1.0;PAIREDR=0.977778;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMIC [...]
+chr12 12008071 . TAC AAA 26.8715 REJECT NS=2;DP=55;DPB=58.6667;AC=2;AN=2;AF=0.0;RO=45;AO=3;PRO=2.0;PAO=1.5;QR=1434;QA=55;PQR=69.5;PQA=36.0;SRF=25;SRR=20;SAF=0;SAR=3;SRP=4.21667;SAP=9.52472;AB=0.0285714;ABP=70.5741;RUN=1;RPP=9.52472;RPPR=4.21667;RPL=3.0;RPR=0.0;EPP=9.52472;EPPR=8.84915;DPRA=0.0;ODDS=6.1826;GTI=0;TYPE=complex;CIGAR=1X1M1X;NUMALT=3;MEANALT=3.5;LEN=3;MQM=46.6667;MQMR=50.4444;PAIRED=1.0;PAIREDR=0.977778;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr12 12008073 . C A 26.8715 PASS SOMATIC;NS=2;DP=55;DPB=58.6667;AC=2;AN=3;AF=0.25;RO=45;AO=2;PRO=2.0;PAO=3.5;QR=1434;QA=28;PQR=69.5;PQA=105.5;SRF=25;SRR=20;SAF=0;SAR=2;SRP=4.21667;SAP=7.35324;AB=0.0571429;ABP=62.6327;RUN=1;RPP=3.0103;RPPR=4.21667;RPL=1.0;RPR=1.0;EPP=3.0103;EPPR=8.84915;DPRA=1.75;ODDS=6.1826;GTI=0;TYPE=snp;CIGAR=2M1X;NUMALT=3;MEANALT=5.0;LEN=1;MQM=53.0;MQMR=50.4444;PAIRED=1.0;PAIREDR=0.977778;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr12 12008073 . CA C 359.73 PASS SOMATIC;DP=87;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=2.448;FS=4.658;MLEAC=1;MLEAF=0.5;MQ=52.12;MQRankSum=-0.013;QD=4.13;RPA=17,16;RU=A;ReadPosRankSum=0.622;SOR=0.531;STR GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00757061 0/1:36,37:83:99.0:397,0,365:37:51:73:.:1:.:.:.:.:-0.0132393
+chr12 12008218 . C T 952.17 REJECT NS=2;DP=180;DPB=203.0;AC=2;AN=4;AF=0.5;RO=152;AO=51;PRO=0.0;PAO=0.0;QR=5753;QA=1939;PQR=0.0;PQA=0.0;SRF=114;SRR=38;SAF=33;SAR=18;SRP=85.5263;SAP=12.5903;AB=0.251232;ABP=112.129;RUN=1;RPP=4.07475;RPPR=19.5249;RPL=23.0;RPR=28.0;EPP=3.3935;EPPR=7.63896;DPRA=0.0;ODDS=120.095;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.960784;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.205;Dels=0.0;FS=3.1295;HaplotypeScore=2.8 [...]
+chr12 12008864 . G A 3592.59 PASS SOMATIC;NS=2;DP=547;DPB=547.0;AC=1;AN=3;AF=0.25;RO=408;AO=139;PRO=0.0;PAO=0.0;QR=15583;QA=5311;PQR=0.0;PQA=0.0;SRF=189;SRR=219;SAF=65;SAR=74;SRP=7.80031;SAP=4.27569;AB=0.336562;ABP=98.8337;RUN=1;RPP=11.2744;RPPR=3.54252;RPL=58.0;RPR=81.0;EPP=5.65044;EPPR=3.0103;DPRA=3.08209;ODDS=84.5536;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992647;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.371;Dels=0.0;FS=0.0 [...]
+chr12 12009529 . A G 5566.855 REJECT NS=2;DP=367;DPB=419.0;AC=2;AN=4;AF=0.5;RO=213;AO=205;PRO=0.0;PAO=0.0;QR=8318;QA=7838;PQR=0.0;PQA=0.0;SRF=123;SRR=90;SAF=102;SAR=103;SRP=14.1123;SAP=3.02089;AB=0.48926;ABP=3.43008;RUN=1;RPP=3.10563;RPPR=3.26517;RPL=101.0;RPR=104.0;EPP=3.02089;EPPR=4.73321;DPRA=0.0;ODDS=280.296;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995305;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.182;Dels=0.0;FS=6.7535;HaplotypeSco [...]
+chr12 12009874 . G A 3663.64 PASS SOMATIC;NS=2;DP=523;DPB=523.0;AC=1;AN=3;AF=0.25;RO=383;AO=140;PRO=0.0;PAO=0.0;QR=14714;QA=5336;PQR=0.0;PQA=0.0;SRF=198;SRR=185;SAF=70;SAR=70;SRP=3.96847;SAP=3.0103;AB=0.350877;ABP=80.0785;RUN=1;RPP=3.56868;RPPR=3.15204;RPL=67.0;RPR=73.0;EPP=3.56868;EPPR=3.46954;DPRA=3.21774;ODDS=78.3391;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994778;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.136;Dels=0.0;FS=2.22 [...]
+chr12 12010056 . G A 3113.27 PASS SOMATIC;NS=2;DP=480;DPB=480.0;AC=1;AN=3;AF=0.25;RO=361;AO=119;PRO=0.0;PAO=0.0;QR=13952;QA=4599;PQR=0.0;PQA=0.0;SRF=176;SRR=185;SAF=54;SAR=65;SRP=3.49753;SAP=5.21827;AB=0.333333;ABP=89.1454;RUN=1;RPP=3.90444;RPPR=6.76977;RPL=56.0;RPR=63.0;EPP=3.02855;EPPR=4.74868;DPRA=2.90244;ODDS=77.7337;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.97479;PAIREDR=0.99446;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.299;Dels=0.0;FS= [...]
+chr12 12010544 . G T 3609.73 PASS SOMATIC;NS=2;DP=539;DPB=539.0;AC=1;AN=3;AF=0.25;RO=399;AO=140;PRO=0.0;PAO=0.0;QR=15117;QA=5266;PQR=0.0;PQA=0.0;SRF=215;SRR=184;SAF=69;SAR=71;SRP=8.24034;SAP=3.07234;AB=0.35443;ABP=75.7134;RUN=1;RPP=6.05036;RPPR=3.05928;RPL=77.0;RPR=63.0;EPP=3.25847;EPPR=8.93695;DPRA=2.74306;ODDS=90.7708;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992857;PAIREDR=0.989975;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.405;Dels=0.0;F [...]
+chr12 12010736 . C T 17600.699999999997 REJECT NS=2;DP=468;DPB=538.0;AC=4;AN=4;AF=1.0;RO=0;AO=538;PRO=0.0;PAO=0.0;QR=0;QA=20468;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=271;SAR=267;SRP=0.0;SAP=3.07488;AB=0.0;ABP=0.0;RUN=1;RPP=26.3234;RPPR=0.0;RPL=307.0;RPR=231.0;EPP=3.80139;EPPR=0.0;DPRA=0.0;ODDS=91.6057;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994424;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9658;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=2 [...]
+chr12 12011325 . A AATAT 4307.73 PASS SOMATIC;DP=326;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-1.444;FS=5.929;MLEAC=1;MLEAF=0.5;MQ=59.88;MQRankSum=-1.724;QD=9.91;RPA=7,9;RU=AT;ReadPosRankSum=0.512;SOR=1.337;STR GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00757061 0/1:142,117:326:99.0:4345,0,7371:117:45:259:.:1:.:.:.:.:-0.0132393
+chr12 12011339 . T TA 814.73 PASS DP=94;AC=1;AN=4;AF=0.5;ALERT;BaseQRankSum=0.629;FS=4.259;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.864;QD=8.67;ReadPosRankSum=1.185;SOR=1.123;ClippingRankSum=1.384 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:59,30:89:99.0:852,0,3318:30:34:89:1:.:.:.:.:.:-0.00757061 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0132393
+chr12 12011340 . T A 5367.77 PASS SOMATIC;DP=299;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-0.788;Dels=0.0;FS=0.42;HaplotypeScore=26.5426;MLEAC=1;MLEAF=0.5;MQ=59.87;MQRankSum=-2.071;QD=17.95;ReadPosRankSum=1.479;SOR=0.73 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00757061 0/1:155,144:299:99.0:5396,0,5808:144:48:299:.:1:.:.:.:.:-0.0132393
+chr12 12011340 . T TA 1092.73 PASS DP=94;AC=1;AN=4;AF=0.5;ALERT;BaseQRankSum=0.415;FS=3.285;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.95;QD=11.62;ReadPosRankSum=1.979;SOR=1.005;ClippingRankSum=-0.635 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:58,36:94:99.0:1130,0,3240:36:38:94:1:.:.:.:.:.:-0.00757061 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0132393
+chr12 12011340 . T ATA 4278.16 REJECT NS=2;DP=275;DPB=400.0;AC=2;AN=4;AF=0.5;RO=120;AO=99;PRO=111.667;PAO=72.1667;QR=4541;QA=3539;PQR=4010.33;PQA=2544.33;SRF=55;SRR=65;SAF=50;SAR=49;SRP=4.81986;SAP=3.03223;AB=0.36;ABP=49.8272;RUN=1;RPP=7.94546;RPPR=3.08268;RPL=57.0;RPR=42.0;EPP=3.03223;EPPR=13.4334;DPRA=0.0;ODDS=156.972;GTI=0;TYPE=complex;CIGAR=1M2I14M1X12M;NUMALT=2;MEANALT=15.5;LEN=30;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:Q [...]
+chr12 12011340 . T ATATA 4278.16 REJECT NS=2;DP=275;DPB=400.0;AC=2;AN=2;AF=0.0;RO=120;AO=13;PRO=111.667;PAO=56.1667;QR=4541;QA=438;PQR=4010.33;PQA=1975.33;SRF=55;SRR=65;SAF=4;SAR=9;SRP=4.81986;SAP=7.18621;AB=0.0472727;ABP=492.587;RUN=1;RPP=4.51363;RPPR=3.08268;RPL=8.0;RPR=5.0;EPP=4.51363;EPPR=13.4334;DPRA=0.0;ODDS=156.972;GTI=0;TYPE=complex;CIGAR=1M4I14M1X12M;NUMALT=2;MEANALT=15.5;LEN=32;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO [...]
+chr12 12011520 . G A 5462.59 REJECT NS=2;DP=375;DPB=432.0;AC=2;AN=4;AF=0.5;RO=234;AO=198;PRO=0.0;PAO=0.0;QR=8756;QA=7599;PQR=0.0;PQA=0.0;SRF=116;SRR=118;SAF=96;SAR=102;SRP=3.04742;SAP=3.40511;AB=0.458333;ABP=9.52472;RUN=1;RPP=3.71219;RPPR=3.0103;RPL=95.0;RPR=103.0;EPP=4.58955;EPPR=3.60421;DPRA=0.0;ODDS=339.146;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989899;PAIREDR=0.995726;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.603;Dels=0.0;FS=2.7085;Haplotype [...]
+chr12 12011764 . TGAG T 5949.73 PASS DP=337;AC=2;AN=4;AF=0.5;MQ0=0;END=12011767;HOMLEN=3;HOMSEQ=GAG;SVLEN=-3;SVTYPE=DEL;BaseQRankSum=1.726;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.47;MQRankSum=0.325;QD=17.65;RPA=2,1;RU=GAG;ReadPosRankSum=0.495;SOR=0.672;STR GT:AD:GMIMUT:GMIMAF:GMICOV:DP:GQ:PL:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:51,80:80:61:131:.:.:.:.:.:.:1:.:.:-0.00757061 0/1:175,171:171:49:346:337:99.0:5987,0,9129:.:1:.:1:.:.:-0.0132393
+chr12 12011766 . AG A 2154.73 PASS DP=109;AC=1;AN=4;AF=0.5;BaseQRankSum=1.992;FS=1.548;MLEAC=1;MLEAF=0.5;MQ=60.3;MQRankSum=-0.658;QD=19.77;ReadPosRankSum=1.233;SOR=0.519;ClippingRankSum=0.724 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:53,56:109:99.0:2192,0,2543:56:51:109:1:.:.:.:.:.:-0.00757061 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0132393
+chr12 12011768 . GAGAA AG 5268.74 REJECT NS=2;DP=395;DPB=370.889;AC=2;AN=4;AF=0.5;RO=209;AO=181;PRO=49.0;PAO=27.0;QR=7913;QA=6585;PQR=1672.5;PQA=1009.5;SRF=85;SRR=124;SAF=80;SAR=101;SRP=18.8132;SAP=8.30101;AB=0.458228;ABP=8.99697;RUN=1;RPP=3.31023;RPPR=3.85188;RPL=88.0;RPR=93.0;EPP=3.11827;EPPR=4.26747;DPRA=0.0;ODDS=328.172;GTI=0;TYPE=complex;CIGAR=1M3D4M1X;NUMALT=1;MEANALT=3.5;LEN=6;MQM=60.663;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995215;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr12 12011770 . GAA G 2151.73 PASS DP=109;AC=1;AN=4;AF=0.5;BaseQRankSum=1.682;FS=2.499;MLEAC=1;MLEAF=0.5;MQ=60.3;MQRankSum=0.9;QD=19.74;ReadPosRankSum=1.165;SOR=0.461;ClippingRankSum=-0.252 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:53,56:109:99.0:2189,0,2579:56:51:109:1:.:.:.:.:.:-0.00757061 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0132393
+chr12 12011772 . A G 4963.77 PASS SOMATIC;DP=315;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=1.477;Dels=0.0;FS=0.418;HaplotypeScore=2.9328;MLEAC=1;MLEAF=0.5;MQ=60.37;MQRankSum=1.173;QD=15.76;ReadPosRankSum=0.892;SOR=0.642 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00757061 0/1:177,138:315:99.0:4992,0,6520:138:44:315:.:1:.:.:.:.:-0.0132393
+chr12 12012053 . G C 2271.24 REJECT NS=2;DP=88;DPB=99.0;AC=4;AN=4;AF=1.0;RO=9;AO=87;PRO=0.0;PAO=0.0;QR=110;QA=2959;PQR=0.0;PQA=0.0;SRF=0;SRR=9;SAF=20;SAR=67;SRP=22.5536;SAP=58.1457;AB=0.0;ABP=0.0;RUN=1;RPP=166.769;RPPR=14.8328;RPL=84.0;RPR=3.0;EPP=73.1214;EPPR=14.8328;DPRA=0.0;ODDS=19.6721;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=58.2299;MQMR=33.1111;PAIRED=0.988506;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.068;Dels=0.03;FS=0.0;HaplotypeScore=27.0526;MLEAC=2; [...]
+chr12 12012106 . T C 1076.67 REJECT NS=2;DP=64;DPB=64.0;AC=2;AN=4;AF=0.5;RO=14;AO=50;PRO=0.0;PAO=0.0;QR=489;QA=1494;PQR=0.0;PQA=0.0;SRF=5;SRR=9;SAF=14;SAR=36;SRP=5.49198;SAP=24.0302;AB=0.78125;ABP=46.9826;RUN=1;RPP=9.26414;RPPR=18.5208;RPL=19.0;RPR=31.0;EPP=9.26414;EPPR=3.0103;DPRA=0.0;ODDS=25.8519;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=47.76;MQMR=55.7143;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.75;Dels=0.0;FS=0.0;HaplotypeScore=15.425;MLEAC=1; [...]
+chr12 12012681 . T C 6481.365 REJECT NS=2;DP=397;DPB=449.0;AC=2;AN=4;AF=0.5;RO=221;AO=228;PRO=0.0;PAO=0.0;QR=8440;QA=8708;PQR=0.0;PQA=0.0;SRF=112;SRR=109;SAF=118;SAR=110;SRP=3.09873;SAP=3.61984;AB=0.507795;ABP=3.24728;RUN=1;RPP=4.38176;RPPR=5.84992;RPL=108.0;RPR=120.0;EPP=15.3534;EPPR=12.4528;DPRA=0.0;ODDS=341.97;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995614;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.013;Dels=0.0;FS=0.405;HaplotypeSc [...]
+chr12 12012801 . A G 14191.8 REJECT NS=2;DP=371;DPB=419.0;AC=4;AN=4;AF=1.0;RO=0;AO=419;PRO=0.0;PAO=0.0;QR=0;QA=16127;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=199;SAR=220;SRP=0.0;SAP=5.29579;AB=0.0;ABP=0.0;RUN=1;RPP=4.17637;RPPR=0.0;RPL=202.0;RPR=217.0;EPP=4.88119;EPPR=0.0;DPRA=0.0;ODDS=63.5852;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995227;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.7902;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.78;SOR=0. [...]
+chr12 12013189 . A G 6175.435 REJECT NS=2;DP=375;DPB=428.0;AC=2;AN=4;AF=0.5;RO=204;AO=224;PRO=0.0;PAO=0.0;QR=7463;QA=8511;PQR=0.0;PQA=0.0;SRF=101;SRR=103;SAF=119;SAR=105;SRP=3.05288;SAP=4.91034;AB=0.523364;ABP=5.03971;RUN=1;RPP=5.49198;RPPR=3.0103;RPL=120.0;RPR=104.0;EPP=20.1106;EPPR=10.206;DPRA=0.0;ODDS=246.37;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995536;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.1655;Dels=0.0;FS=2.72;HaplotypeScore [...]
+chr12 12013292 . G A 5743.285 REJECT NS=2;DP=336;DPB=384.0;AC=2;AN=4;AF=0.5;RO=177;AO=207;PRO=0.0;PAO=0.0;QR=6508;QA=7899;PQR=0.0;PQA=0.0;SRF=93;SRR=84;SAF=89;SAR=118;SRP=4.00402;SAP=11.8326;AB=0.539062;ABP=8.09969;RUN=1;RPP=5.3706;RPPR=3.31701;RPL=111.0;RPR=96.0;EPP=7.63648;EPPR=5.08363;DPRA=0.0;ODDS=233.212;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990338;PAIREDR=0.99435;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.01;Dels=0.0;FS=10.5135;HaplotypeSc [...]
+chr12 12013498 . C CA 1278.75 REJECT NS=2;DP=234;DPB=378.829;AC=2;AN=4;AF=0.5;RO=129;AO=56;PRO=106.333;PAO=72.3333;QR=4794;QA=1626;PQR=3790.25;PQA=2416.25;SRF=77;SRR=52;SAF=29;SAR=27;SRP=13.531;SAP=3.16541;AB=0.239316;ABP=141.131;RUN=1;RPP=12.937;RPPR=3.83512;RPL=20.0;RPR=36.0;EPP=3.16541;EPPR=9.08706;DPRA=0.0;ODDS=21.0727;GTI=0;TYPE=ins;CIGAR=1M1I34M;NUMALT=3;MEANALT=14.5;LEN=1;MQM=55.75;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-2.541 [...]
+chr12 12013498 . C CAA 1278.75 PASS SOMATIC;NS=2;DP=234;DPB=378.829;AC=2;AN=2;AF=0.0;RO=129;AO=12;PRO=106.333;PAO=62.3333;QR=4794;QA=366;PQR=3790.25;PQA=2161.25;SRF=77;SRR=52;SAF=7;SAR=5;SRP=13.531;SAP=3.73412;AB=0.0512821;ABP=412.249;RUN=1;RPP=14.5915;RPPR=3.83512;RPL=2.0;RPR=10.0;EPP=3.73412;EPPR=9.08706;DPRA=0.0;ODDS=21.0727;GTI=0;TYPE=ins;CIGAR=1M2I34M;NUMALT=3;MEANALT=14.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr12 12013498 . CA C 1278.75 REJECT NS=2;DP=234;DPB=378.829;AC=2;AN=2;AF=0.0;RO=129;AO=11;PRO=106.333;PAO=58.0;QR=4794;QA=322;PQR=3790.25;PQA=2003.25;SRF=77;SRR=52;SAF=6;SAR=5;SRP=13.531;SAP=3.20771;AB=0.0470085;ABP=420.081;RUN=1;RPP=12.6832;RPPR=3.83512;RPL=2.0;RPR=9.0;EPP=3.20771;EPPR=9.08706;DPRA=0.0;ODDS=21.0727;GTI=0;TYPE=del;CIGAR=1M1D33M;NUMALT=3;MEANALT=14.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr12 12013572 . G A 12049.6 REJECT NS=2;DP=441;DPB=491.0;AC=2;AN=4;AF=0.5;RO=98;AO=393;PRO=0.0;PAO=0.0;QR=3649;QA=15006;PQR=0.0;PQA=0.0;SRF=68;SRR=30;SAF=242;SAR=151;SRP=35.0063;SAP=48.7659;AB=0.800407;ABP=387.883;RUN=1;RPP=4.60713;RPPR=3.36483;RPL=188.0;RPR=205.0;EPP=9.02743;EPPR=3.0103;DPRA=0.0;ODDS=105.797;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0509;MQMR=60.0;PAIRED=0.992366;PAIREDR=0.989796;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.987;Dels=0.0;FS=2.9095;Haplot [...]
+chr12 12013612 . G A 6510.93 REJECT NS=2;DP=469;DPB=531.0;AC=2;AN=4;AF=0.5;RO=292;AO=239;PRO=0.0;PAO=0.0;QR=11295;QA=9118;PQR=0.0;PQA=0.0;SRF=161;SRR=131;SAF=135;SAR=104;SRP=9.70319;SAP=11.7416;AB=0.450094;ABP=14.4974;RUN=1;RPP=3.01939;RPPR=4.91406;RPL=119.0;RPR=120.0;EPP=23.0805;EPPR=13.7487;DPRA=0.0;ODDS=402.314;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8973;PAIRED=1.0;PAIREDR=0.986301;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3295;Dels=0.0;FS=3.1865;Haplo [...]
+chr12 12013985 . C A 9818.485 REJECT NS=2;DP=443;DPB=508.0;AC=3;AN=4;AF=0.75;RO=149;AO=357;PRO=0.0;PAO=0.0;QR=5691;QA=13471;PQR=0.0;PQA=0.0;SRF=74;SRR=75;SAF=163;SAR=194;SRP=3.02487;SAP=8.85564;AB=0.60686;ABP=40.6014;RUN=1;RPP=3.06504;RPPR=4.77371;RPL=180.0;RPR=177.0;EPP=6.22797;EPPR=5.47325;DPRA=0.0;ODDS=80.1593;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991597;PAIREDR=0.986577;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.387;Dels=0.0;FS=0.6265;Haplo [...]
+chr12 12014191 . G T 2769.335 REJECT NS=2;DP=394;DPB=458.0;AC=2;AN=4;AF=0.5;RO=336;AO=120;PRO=0.0;PAO=0.0;QR=12585;QA=4583;PQR=0.0;PQA=0.0;SRF=170;SRR=166;SAF=53;SAR=67;SRP=3.1137;SAP=6.55704;AB=0.262009;ABP=228.331;RUN=1;RPP=10.2485;RPPR=10.4812;RPL=70.0;RPR=50.0;EPP=6.55704;EPPR=6.13825;DPRA=0.0;ODDS=144.748;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0833;MQMR=60.0;PAIRED=0.991667;PAIREDR=0.991071;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9495;Dels=0.0;FS=4.0595;Haplo [...]
+chr12 12014424 . G A 5549.99 REJECT NS=2;DP=366;DPB=416.0;AC=2;AN=4;AF=0.5;RO=215;AO=201;PRO=0.0;PAO=0.0;QR=8367;QA=7608;PQR=0.0;PQA=0.0;SRF=104;SRR=111;SAF=108;SAR=93;SRP=3.50519;SAP=5.44105;AB=0.483173;ABP=4.0334;RUN=1;RPP=3.88537;RPPR=5.92916;RPL=96.0;RPR=105.0;EPP=3.53966;EPPR=4.23238;DPRA=0.0;ODDS=316.89;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99005;PAIREDR=0.995349;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.325;Dels=0.0;FS=3.4085;HaplotypeS [...]
+chr12 12014774 . T C 1682.54 REJECT NS=2;DP=409;DPB=468.0;AC=2;AN=4;AF=0.5;RO=380;AO=88;PRO=0.0;PAO=0.0;QR=14473;QA=3394;PQR=0.0;PQA=0.0;SRF=174;SRR=206;SAF=38;SAR=50;SRP=8.86185;SAP=6.56362;AB=0.188034;ABP=398.627;RUN=1;RPP=4.58955;RPPR=3.37602;RPL=40.0;RPR=48.0;EPP=4.58955;EPPR=3.10173;DPRA=0.0;ODDS=88.9314;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9658;PAIRED=1.0;PAIREDR=0.994737;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.414;Dels=0.0;FS=2.2985;HaplotypeSco [...]
+chr12 12014808 . T C 1902.6399999999999 REJECT NS=2;DP=396;DPB=452.0;AC=2;AN=4;AF=0.5;RO=357;AO=95;PRO=0.0;PAO=0.0;QR=13604;QA=3637;PQR=0.0;PQA=0.0;SRF=165;SRR=192;SAF=40;SAR=55;SRP=7.44448;SAP=8.15326;AB=0.210177;ABP=332.786;RUN=1;RPP=3.03316;RPPR=14.2569;RPL=48.0;RPR=47.0;EPP=6.87324;EPPR=25.6435;DPRA=0.0;ODDS=124.188;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9636;PAIRED=1.0;PAIREDR=0.991597;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.235;Dels=0.0;FS=3.653;Ha [...]
+chr12 12015401 . G A 7741.635 REJECT NS=2;DP=343;DPB=393.0;AC=3;AN=4;AF=0.75;RO=111;AO=282;PRO=0.0;PAO=0.0;QR=4267;QA=10609;PQR=0.0;PQA=0.0;SRF=61;SRR=50;SAF=131;SAR=151;SRP=5.3774;SAP=6.0904;AB=0.623729;ABP=42.2367;RUN=1;RPP=22.2609;RPPR=13.359;RPL=116.0;RPR=166.0;EPP=4.98157;EPPR=7.41193;DPRA=0.0;ODDS=62.0784;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989362;PAIREDR=0.990991;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.736;Dels=0.0;FS=4.222;Haplotyp [...]
+chr12 12015706 . G T 2708.94 PASS SOMATIC;NS=2;DP=382;DPB=382.0;AC=1;AN=3;AF=0.25;RO=277;AO=105;PRO=0.0;PAO=0.0;QR=10623;QA=3926;PQR=0.0;PQA=0.0;SRF=158;SRR=119;SAF=63;SAR=42;SRP=14.9338;SAP=12.1305;AB=0.373665;ABP=41.9654;RUN=1;RPP=3.52732;RPPR=7.90983;RPL=50.0;RPR=55.0;EPP=3.19643;EPPR=18.8848;DPRA=2.78218;ODDS=64.0174;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990476;PAIREDR=0.98917;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-2.544;Dels=0.0;F [...]
+chr12 12015905 . A G 3230.08 PASS SOMATIC;NS=2;DP=478;DPB=478.0;AC=1;AN=3;AF=0.25;RO=354;AO=123;PRO=0.0;PAO=0.0;QR=13589;QA=4747;PQR=0.0;PQA=0.0;SRF=190;SRR=164;SAF=60;SAR=63;SRP=7.15695;SAP=3.16919;AB=0.338843;ABP=84.8981;RUN=1;RPP=5.99387;RPPR=3.23113;RPL=55.0;RPR=68.0;EPP=3.02795;EPPR=4.21258;DPRA=3.15652;ODDS=72.0784;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.983051;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.356;Dels=0.0;FS=5.0 [...]
+chr12 12016008 . G A 11474.7 REJECT NS=2;DP=428;DPB=487.0;AC=2;AN=4;AF=0.5;RO=113;AO=374;PRO=0.0;PAO=0.0;QR=4406;QA=14303;PQR=0.0;PQA=0.0;SRF=60;SRR=53;SAF=197;SAR=177;SRP=3.95191;SAP=5.33273;AB=0.767967;ABP=306.753;RUN=1;RPP=4.14829;RPPR=3.18325;RPL=180.0;RPR=194.0;EPP=6.3546;EPPR=3.95191;DPRA=0.0;ODDS=124.179;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997326;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.006;Dels=0.0;FS=2.72;HaplotypeScore [...]
+chr12 12016045 . C T 7081.92 REJECT NS=2;DP=427;DPB=488.0;AC=2;AN=4;AF=0.5;RO=245;AO=243;PRO=0.0;PAO=0.0;QR=9379;QA=9421;PQR=0.0;PQA=0.0;SRF=124;SRR=121;SAF=117;SAR=126;SRP=3.09007;SAP=3.73412;AB=0.497951;ABP=3.0281;RUN=1;RPP=5.02092;RPPR=4.08274;RPL=129.0;RPR=114.0;EPP=4.09157;EPPR=3.23188;DPRA=0.0;ODDS=360.442;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995885;PAIREDR=0.995918;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.2395;Dels=0.0;FS=5.672;Haploty [...]
+chr12 12016183 . G T 8110.56 REJECT NS=2;DP=461;DPB=525.0;AC=2;AN=4;AF=0.5;RO=246;AO=279;PRO=0.0;PAO=0.0;QR=9375;QA=10778;PQR=0.0;PQA=0.0;SRF=126;SRR=120;SAF=136;SAR=143;SRP=3.32808;SAP=3.39167;AB=0.531429;ABP=7.51455;RUN=1;RPP=4.76149;RPPR=3.32808;RPL=147.0;RPR=132.0;EPP=7.12754;EPPR=7.28263;DPRA=0.0;ODDS=404.978;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987805;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0605;Dels=0.0;FS=0.5965;Haplotype [...]
+chr12 12017285 . T C 15057.0 REJECT NS=2;DP=401;DPB=459.0;AC=4;AN=4;AF=1.0;RO=2;AO=457;PRO=0.0;PAO=0.0;QR=54;QA=17448;PQR=0.0;PQA=0.0;SRF=0;SRR=2;SAF=226;SAR=231;SRP=7.35324;SAP=3.12909;AB=0.0;ABP=0.0;RUN=1;RPP=3.01505;RPPR=3.0103;RPL=228.0;RPR=229.0;EPP=4.07941;EPPR=3.0103;DPRA=0.0;ODDS=76.1064;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997812;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.682;Dels=0.0;FS=0.0;HaplotypeScore=5.8459;MLEAC=2;ML [...]
+chr12 12017687 . TA T 2162.84 REJECT NS=2;DP=385;DPB=457.625;AC=2;AN=4;AF=0.5;RO=241;AO=117;PRO=72.5;PAO=60.5;QR=9069;QA=4338;PQR=2539.5;PQA=2111.5;SRF=110;SRR=131;SAF=47;SAR=70;SRP=6.98382;SAP=12.8283;AB=0.291771;ABP=154.033;RUN=1;RPP=8.37402;RPPR=5.61426;RPL=67.0;RPR=50.0;EPP=31.2394;EPPR=4.10054;DPRA=0.0;ODDS=226.406;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=1;MEANALT=9.0;LEN=1;MQM=60.5128;MQMR=59.9336;PAIRED=1.0;PAIREDR=0.995851;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.051;FS=4.643;MLE [...]
+chr12 12017753 . A G 1997.34 REJECT NS=2;DP=402;DPB=466.0;AC=2;AN=4;AF=0.5;RO=366;AO=100;PRO=0.0;PAO=0.0;QR=13752;QA=3787;PQR=0.0;PQA=0.0;SRF=191;SRR=175;SAF=60;SAR=40;SRP=4.52914;SAP=11.6962;AB=0.214592;ABP=332.72;RUN=1;RPP=5.18177;RPPR=3.86465;RPL=45.0;RPR=55.0;EPP=3.09716;EPPR=3.03403;DPRA=0.0;ODDS=106.349;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.3;MQMR=60.082;PAIRED=0.99;PAIREDR=0.994536;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4005;Dels=0.0;FS=6.4385;HaplotypeSc [...]
+chr12 12018042 . A G 2503.87 REJECT NS=2;DP=74;DPB=92.0;AC=4;AN=4;AF=1.0;RO=0;AO=92;PRO=0.0;PAO=0.0;QR=0;QA=3238;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=39;SAR=53;SRP=0.0;SAP=7.63648;AB=0.0;ABP=0.0;RUN=1;RPP=4.52089;RPPR=0.0;RPL=42.0;RPR=50.0;EPP=18.9659;EPPR=0.0;DPRA=0.0;ODDS=26.0417;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=51.5326;MQMR=0.0;PAIRED=0.98913;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9304;MLEAC=2;MLEAF=1.0;MQ=53.075;QD=34.7;SOR=1.122 G [...]
+chr12 12018184 . C A 121.567 REJECT NS=2;DP=107;DPB=191.667;AC=2;AN=2;AF=0.0;RO=20;AO=7;PRO=34.8;PAO=16.5333;QR=710;QA=85;PQR=1238.25;PQA=558.783;SRF=15;SRR=5;SAF=0;SAR=7;SRP=13.8677;SAP=18.2106;AB=0.0654206;ABP=178.534;RUN=1;RPP=5.80219;RPPR=30.8051;RPL=2.0;RPR=5.0;EPP=5.80219;EPPR=13.8677;DPRA=0.0;ODDS=13.0566;GTI=0;TYPE=snp;CIGAR=1X26M;NUMALT=5;MEANALT=29.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr12 12018184 . C CA 121.567 REJECT NS=2;DP=107;DPB=191.667;AC=2;AN=3;AF=0.25;RO=20;AO=5;PRO=34.8;PAO=33.3;QR=710;QA=137;PQR=1238.25;PQA=1187.25;SRF=15;SRR=5;SAF=5;SAR=0;SRP=13.8677;SAP=13.8677;AB=0.046729;ABP=193.958;RUN=1;RPP=3.44459;RPPR=30.8051;RPL=2.0;RPR=3.0;EPP=3.44459;EPPR=13.8677;DPRA=0.0;ODDS=13.0566;GTI=0;TYPE=ins;CIGAR=1M1I26M;NUMALT=5;MEANALT=29.0;LEN=1;MQM=56.4;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr12 12018184 . CA C 121.567 REJECT NS=2;DP=107;DPB=191.667;AC=2;AN=3;AF=0.25;RO=20;AO=16;PRO=34.8;PAO=23.8;QR=710;QA=487;PQR=1238.25;PQA=834.25;SRF=15;SRR=5;SAF=13;SAR=3;SRP=13.8677;SAP=16.582;AB=0.149533;ABP=117.165;RUN=1;RPP=11.6962;RPPR=30.8051;RPL=4.0;RPR=12.0;EPP=3.55317;EPPR=13.8677;DPRA=0.0;ODDS=13.0566;GTI=0;TYPE=del;CIGAR=1M1D25M;NUMALT=5;MEANALT=29.0;LEN=1;MQM=59.4375;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.458;FS=0.0;MLEAC=1 [...]
+chr12 12018184 . CAA C 121.567 REJECT NS=2;DP=107;DPB=191.667;AC=2;AN=2;AF=0.0;RO=20;AO=4;PRO=34.8;PAO=20.3;QR=710;QA=128;PQR=1238.25;PQA=708.5;SRF=15;SRR=5;SAF=4;SAR=0;SRP=13.8677;SAP=11.6962;AB=0.0373832;ABP=201.913;RUN=1;RPP=11.6962;RPPR=30.8051;RPL=0.0;RPR=4.0;EPP=11.6962;EPPR=13.8677;DPRA=0.0;ODDS=13.0566;GTI=0;TYPE=del;CIGAR=1M2D24M;NUMALT=5;MEANALT=29.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr12 12018204 . T A 121.567 REJECT NS=2;DP=107;DPB=191.667;AC=2;AN=2;AF=0.0;RO=20;AO=3;PRO=34.8;PAO=25.2667;QR=710;QA=42;PQR=1238.25;PQA=840.967;SRF=15;SRR=5;SAF=3;SAR=0;SRP=13.8677;SAP=9.52472;AB=0.0857143;ABP=55.1877;RUN=1;RPP=9.52472;RPPR=30.8051;RPL=3.0;RPR=0.0;EPP=9.52472;EPPR=13.8677;DPRA=0.0;ODDS=13.0566;GTI=0;TYPE=snp;CIGAR=20M1X6M;NUMALT=5;MEANALT=21.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr12 12018349 . T C 1889.04 REJECT NS=2;DP=312;DPB=359.0;AC=2;AN=4;AF=0.5;RO=269;AO=90;PRO=0.0;PAO=0.0;QR=10398;QA=3484;PQR=0.0;PQA=0.0;SRF=133;SRR=136;SAF=39;SAR=51;SRP=3.08295;SAP=6.48466;AB=0.250696;ABP=196.816;RUN=1;RPP=3.10681;RPPR=5.34322;RPL=44.0;RPR=46.0;EPP=4.55446;EPPR=4.82659;DPRA=0.0;ODDS=139.653;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.981413;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.321;Dels=0.0;FS=2.8735;HaplotypeScore= [...]
+chr12 12019081 . G A 2219.665 REJECT NS=2;DP=457;DPB=518.0;AC=2;AN=4;AF=0.5;RO=401;AO=117;PRO=0.0;PAO=0.0;QR=15019;QA=4400;PQR=0.0;PQA=0.0;SRF=184;SRR=217;SAF=43;SAR=74;SRP=8.90739;SAP=20.8461;AB=0.225869;ABP=341.123;RUN=1;RPP=4.51363;RPPR=5.87491;RPL=63.0;RPR=54.0;EPP=3.91972;EPPR=3.66553;DPRA=0.0;ODDS=190.823;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0249;PAIRED=0.982906;PAIREDR=0.992519;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.95;Dels=0.0;FS=5.943;Haploty [...]
+chr12 12020114 . C T 9093.735 REJECT NS=2;DP=428;DPB=487.0;AC=3;AN=4;AF=0.75;RO=150;AO=337;PRO=0.0;PAO=0.0;QR=5734;QA=12509;PQR=0.0;PQA=0.0;SRF=81;SRR=69;SAF=187;SAR=150;SRP=5.09491;SAP=11.8315;AB=0.601078;ABP=35.9336;RUN=1;RPP=18.4812;RPPR=5.09491;RPL=144.0;RPR=193.0;EPP=3.53223;EPPR=3.06821;DPRA=0.0;ODDS=69.9066;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994065;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.633;Dels=0.0;FS=2.211;HaplotypeS [...]
+chr12 12020170 . C T 10559.685000000001 REJECT NS=2;DP=458;DPB=523.0;AC=3;AN=4;AF=0.75;RO=143;AO=379;PRO=0.0;PAO=0.0;QR=5483;QA=14405;PQR=0.0;PQA=0.0;SRF=75;SRR=68;SAF=191;SAR=188;SRP=3.75437;SAP=3.06187;AB=0.633588;ABP=63.9276;RUN=1;RPP=16.7668;RPPR=8.49213;RPL=214.0;RPR=165.0;EPP=12.6416;EPPR=4.8477;DPRA=0.0;ODDS=82.0541;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989446;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.738;Dels=0.0;FS=0.6205;H [...]
+chr12 12021372 . C T 111.77 PASS SOMATIC;DP=136;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-4.176;Dels=0.04;FS=36.516;HaplotypeScore=72.5575;MLEAC=1;MLEAF=0.5;MQ=58.0;MQRankSum=-2.195;QD=0.82;ReadPosRankSum=1.303;SOR=5.861 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00757061 0/1:105,24:131:99.0:140,0,3144:24:19:129:.:1:.:.:.:.:-0.0132393
+chr12 12021657 . T C 5331.0 REJECT NS=2;DP=336;DPB=384.0;AC=2;AN=4;AF=0.5;RO=181;AO=203;PRO=0.0;PAO=0.0;QR=6840;QA=7386;PQR=0.0;PQA=0.0;SRF=113;SRR=68;SAF=127;SAR=76;SRP=27.3044;SAP=30.833;AB=0.528646;ABP=5.74726;RUN=1;RPP=3.53445;RPPR=19.4343;RPL=98.0;RPR=105.0;EPP=12.0064;EPPR=10.5085;DPRA=0.0;ODDS=248.093;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990148;PAIREDR=0.994475;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.7145;Dels=0.0;FS=1.9365;Haplotype [...]
+chr12 12022013 . A T 358.687 REJECT NS=2;DP=102;DPB=114.0;AC=2;AN=4;AF=0.5;RO=92;AO=22;PRO=0.0;PAO=0.0;QR=3468;QA=824;PQR=0.0;PQA=0.0;SRF=31;SRR=61;SAF=9;SAR=13;SRP=24.253;SAP=4.58955;AB=0.192982;ABP=96.3455;RUN=1;RPP=3.40511;RPPR=3.10471;RPL=10.0;RPR=12.0;EPP=28.2783;EPPR=40.775;DPRA=0.0;ODDS=20.5724;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.2727;MQMR=60.0;PAIRED=0.954545;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.535;Dels=0.01;FS=2.6665;HaplotypeScore=1.96 [...]
+chr12 12022098 . A T 1330.79 REJECT NS=2;DP=113;DPB=131.0;AC=2;AN=4;AF=0.5;RO=76;AO=54;PRO=0.0;PAO=0.0;QR=2756;QA=1980;PQR=0.0;PQA=0.0;SRF=63;SRR=13;SAF=43;SAR=11;SRP=74.4403;SAP=44.1879;AB=0.412214;ABP=11.7791;RUN=1;RPP=3.0103;RPPR=3.46745;RPL=27.0;RPR=27.0;EPP=3.17115;EPPR=3.12459;DPRA=0.0;ODDS=73.3339;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=56.5741;MQMR=55.3684;PAIRED=1.0;PAIREDR=0.973684;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.229;Dels=0.0;FS=1.013;HaplotypeScore= [...]
+chr12 12022175 . G GA 1368.07 REJECT NS=2;DP=171;DPB=220.9;AC=2;AN=3;AF=0.5;RO=47;AO=46;PRO=31.0;PAO=33.0;QR=1702;QA=1532;PQR=999.75;PQA=1046.75;SRF=33;SRR=14;SAF=33;SAR=13;SRP=19.6891;SAP=21.8927;AB=0.269006;ABP=82.2627;RUN=1;RPP=30.2009;RPPR=8.60069;RPL=11.0;RPR=35.0;EPP=3.19912;EPPR=4.16534;DPRA=0.0;ODDS=7.54364;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=3;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.178;FS=0.0;ML [...]
+chr12 12022175 . GA G 1368.07 REJECT NS=2;DP=171;DPB=220.9;AC=2;AN=2;AF=0.25;RO=47;AO=41;PRO=31.0;PAO=26.5;QR=1702;QA=1410;PQR=999.75;PQA=849.75;SRF=33;SRR=14;SAF=35;SAR=6;SRP=19.6891;SAP=47.552;AB=0.239766;ABP=103.596;RUN=1;RPP=31.0276;RPPR=8.60069;RPL=9.0;RPR=32.0;EPP=22.1298;EPPR=4.16534;DPRA=0.0;ODDS=7.54364;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=3;MEANALT=11.5;LEN=1;MQM=59.3659;MQMR=60.0;PAIRED=0.97561;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=2.948;FS=13.295;M [...]
+chr12 12022175 . GAA G 1368.07 REJECT SOMATIC;NS=2;DP=171;DPB=220.9;AC=1;AN=3;AF=0.0;RO=47;AO=11;PRO=31.0;PAO=22.5;QR=1702;QA=376;PQR=999.75;PQA=707.75;SRF=33;SRR=14;SAF=6;SAR=5;SRP=19.6891;SAP=3.20771;AB=0.0643275;ABP=284.933;RUN=1;RPP=3.20771;RPPR=8.60069;RPL=5.0;RPR=6.0;EPP=7.94546;EPPR=4.16534;DPRA=0.0;ODDS=7.54364;GTI=0;TYPE=del;CIGAR=1M2D17M;NUMALT=3;MEANALT=11.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr12 12023023 . C G 7781.3 REJECT NS=2;DP=321;DPB=366.0;AC=3;AN=4;AF=0.75;RO=94;AO=272;PRO=0.0;PAO=0.0;QR=3568;QA=10425;PQR=0.0;PQA=0.0;SRF=49;SRR=45;SAF=138;SAR=134;SRP=3.37991;SAP=3.13803;AB=0.65942;ABP=63.9374;RUN=1;RPP=4.57504;RPPR=3.84193;RPL=129.0;RPR=143.0;EPP=12.2391;EPPR=6.33681;DPRA=0.0;ODDS=57.1119;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996324;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.32;Dels=0.0;FS=0.0;HaplotypeScore=7.7 [...]
+chr12 12023773 . C A 10358.685000000001 REJECT NS=2;DP=439;DPB=506.0;AC=3;AN=4;AF=0.75;RO=136;AO=370;PRO=0.0;PAO=0.0;QR=5231;QA=14192;PQR=0.0;PQA=0.0;SRF=71;SRR=65;SAF=192;SAR=178;SRP=3.5851;SAP=4.16059;AB=0.635389;ABP=62.3969;RUN=1;RPP=5.35784;RPPR=13.8038;RPL=175.0;RPR=195.0;EPP=3.85541;EPPR=3.0103;DPRA=0.0;ODDS=83.9993;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994595;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.428;Dels=0.0;FS=0.8885;Ha [...]
+chr12 12023843 . C A 2590.535 REJECT NS=2;DP=442;DPB=507.0;AC=2;AN=4;AF=0.5;RO=380;AO=127;PRO=0.0;PAO=0.0;QR=14523;QA=4841;PQR=0.0;PQA=0.0;SRF=191;SRR=189;SAF=64;SAR=63;SRP=3.03316;SAP=3.0274;AB=0.250493;ABP=277.16;RUN=1;RPP=10.5506;RPPR=3.10173;RPL=74.0;RPR=53.0;EPP=3.16418;EPPR=3.58174;DPRA=0.0;ODDS=217.366;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997368;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5085;Dels=0.0;FS=4.309;HaplotypeScore= [...]
+chr12 12023941 . C T 8704.36 REJECT NS=2;DP=386;DPB=447.0;AC=3;AN=4;AF=0.75;RO=127;AO=320;PRO=0.0;PAO=0.0;QR=4883;QA=12123;PQR=0.0;PQA=0.0;SRF=57;SRR=70;SAF=147;SAR=173;SRP=5.8999;SAP=7.59754;AB=0.611621;ABP=38.398;RUN=1;RPP=4.74748;RPPR=7.95168;RPL=168.0;RPR=152.0;EPP=3.03744;EPPR=3.43776;DPRA=0.0;ODDS=75.793;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990625;PAIREDR=0.984252;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.027;Dels=0.0;FS=1.5255;Haplotyp [...]
+chr12 12024131 . C CT 90.916 REJECT NS=2;DP=102;DPB=156.56;AC=2;AN=3;AF=0.25;RO=47;AO=9;PRO=39.1667;PAO=33.1667;QR=1614;QA=250;PQR=1382.83;PQA=1158.83;SRF=7;SRR=40;SAF=3;SAR=6;SRP=53.3238;SAP=5.18177;AB=0.0882353;ABP=153.225;RUN=1;RPP=9.04217;RPPR=4.16534;RPL=7.0;RPR=2.0;EPP=5.18177;EPPR=13.4056;DPRA=0.0;ODDS=2.18545;GTI=0;TYPE=ins;CIGAR=1M1I24M;NUMALT=3;MEANALT=10.5;LEN=1;MQM=59.2222;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr12 12024131 . CT C 90.916 REJECT NS=2;DP=102;DPB=156.56;AC=2;AN=3;AF=0.25;RO=47;AO=14;PRO=39.1667;PAO=30.6667;QR=1614;QA=273;PQR=1382.83;PQA=1038.83;SRF=7;SRR=40;SAF=5;SAR=9;SRP=53.3238;SAP=5.49198;AB=0.137255;ABP=119.589;RUN=1;RPP=5.49198;RPPR=4.16534;RPL=5.0;RPR=9.0;EPP=3.63072;EPPR=13.4056;DPRA=0.0;ODDS=2.18545;GTI=0;TYPE=del;CIGAR=1M1D23M;NUMALT=3;MEANALT=10.5;LEN=1;MQM=58.5714;MQMR=60.0;PAIRED=0.928571;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr12 12024131 . CTT C 90.916 REJECT NS=2;DP=102;DPB=156.56;AC=2;AN=2;AF=0.0;RO=47;AO=9;PRO=39.1667;PAO=27.0;QR=1614;QA=154;PQR=1382.83;PQA=946.5;SRF=7;SRR=40;SAF=1;SAR=8;SRP=53.3238;SAP=14.8328;AB=0.0882353;ABP=153.225;RUN=1;RPP=5.18177;RPPR=4.16534;RPL=3.0;RPR=6.0;EPP=9.04217;EPPR=13.4056;DPRA=0.0;ODDS=2.18545;GTI=0;TYPE=del;CIGAR=1M2D22M;NUMALT=3;MEANALT=10.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr12 12024284 . G A 1908.0 REJECT NS=2;DP=90;DPB=109.0;AC=3;AN=4;AF=0.75;RO=26;AO=83;PRO=0.0;PAO=0.0;QR=917;QA=2915;PQR=0.0;PQA=0.0;SRF=13;SRR=13;SAF=35;SAR=48;SRP=3.0103;SAP=7.43173;AB=0.633803;ABP=14.0512;RUN=1;RPP=3.24576;RPPR=4.34659;RPL=43.0;RPR=40.0;EPP=46.9892;EPPR=19.3799;DPRA=0.0;ODDS=24.7173;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.5422;MQMR=60.0;PAIRED=1.0;PAIREDR=0.961538;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.09;Dels=0.0;FS=0.0;HaplotypeScore=0.9998; [...]
+chr12 12025110 . A G 5968.700000000001 REJECT NS=2;DP=341;DPB=389.0;AC=2;AN=4;AF=0.5;RO=178;AO=211;PRO=0.0;PAO=0.0;QR=6914;QA=8056;PQR=0.0;PQA=0.0;SRF=99;SRR=79;SAF=105;SAR=106;SRP=7.89001;SAP=3.02059;AB=0.542416;ABP=9.08931;RUN=1;RPP=5.9845;RPPR=3.0591;RPL=114.0;RPR=97.0;EPP=17.0991;EPPR=31.1174;DPRA=0.0;ODDS=276.455;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995261;PAIREDR=0.988764;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.467;Dels=0.0;FS=3.307;Ha [...]
+chr12 12025363 . A C 3266.86 PASS SOMATIC;NS=2;DP=384;DPB=384.0;AC=1;AN=3;AF=0.25;RO=261;AO=122;PRO=0.0;PAO=0.0;QR=9323;QA=4629;PQR=0.0;PQA=0.0;SRF=76;SRR=185;SAF=41;SAR=81;SRP=101.858;SAP=31.4886;AB=0.398693;ABP=30.2885;RUN=1;RPP=5.57335;RPPR=13.2021;RPL=67.0;RPR=55.0;EPP=3.0815;EPPR=18.3936;DPRA=3.92308;ODDS=49.5796;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.1639;MQMR=59.9234;PAIRED=1.0;PAIREDR=0.97318;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.117;Dels=0.0;FS=4 [...]
+chr12 12025428 . C T 222.003 REJECT NS=2;DP=44;DPB=97.9643;AC=2;AN=2;AF=0.0;RO=6;AO=4;PRO=36.3333;PAO=5.58333;QR=215;QA=69;PQR=1313.95;PQA=192.5;SRF=2;SRR=4;SAF=0;SAR=4;SRP=4.45795;SAP=11.6962;AB=0.0571429;ABP=62.6327;RUN=1;RPP=5.18177;RPPR=8.80089;RPL=1.0;RPR=3.0;EPP=5.18177;EPPR=8.80089;DPRA=0.0;ODDS=3.94373;GTI=0;TYPE=snp;CIGAR=1X27M;NUMALT=5;MEANALT=6.0;LEN=1;MQM=55.0;MQMR=59.5;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMIC [...]
+chr12 12025428 . C CT 222.003 REJECT NS=2;DP=44;DPB=97.9643;AC=2;AN=2;AF=0.0;RO=6;AO=3;PRO=36.3333;PAO=35.3333;QR=215;QA=46;PQR=1313.95;PQA=1262.95;SRF=2;SRR=4;SAF=0;SAR=3;SRP=4.45795;SAP=9.52472;AB=0.0571429;ABP=62.6327;RUN=1;RPP=3.73412;RPPR=8.80089;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=8.80089;DPRA=0.0;ODDS=3.94373;GTI=0;TYPE=ins;CIGAR=1M1I27M;NUMALT=5;MEANALT=6.0;LEN=1;MQM=35.0;MQMR=59.5;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr12 12025428 . C CTTT 60.73 PASS DP=20;AC=1;AN=4;AF=0.5;BaseQRankSum=0.72;FS=3.979;MLEAC=1;MLEAF=0.5;MQ=58.12;MQRankSum=-0.72;QD=3.04;ReadPosRankSum=-1.38;SOR=1.414;ClippingRankSum=-0.72 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:2,4:6:62.0:98,0,62:4:67:6:1:.:.:.:.:.:-0.00757061 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0132393
+chr12 12025428 . CT C 222.003 REJECT NS=2;DP=44;DPB=97.9643;AC=2;AN=2;AF=0.0;RO=6;AO=5;PRO=36.3333;PAO=25.8333;QR=215;QA=100;PQR=1313.95;PQA=910.117;SRF=2;SRR=4;SAF=0;SAR=5;SRP=4.45795;SAP=13.8677;AB=0.114286;ABP=48.239;RUN=1;RPP=13.8677;RPPR=8.80089;RPL=5.0;RPR=0.0;EPP=13.8677;EPPR=8.80089;DPRA=0.0;ODDS=3.94373;GTI=0;TYPE=del;CIGAR=1M1D26M;NUMALT=5;MEANALT=6.0;LEN=1;MQM=52.0;MQMR=59.5;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr12 12025428 . CTTTTTTTTTTT C 222.003 PASS SOMATIC;NS=2;DP=44;DPB=97.9643;AC=2;AN=3;AF=0.25;RO=6;AO=20;PRO=36.3333;PAO=16.5833;QR=215;QA=631;PQR=1313.95;PQA=571.617;SRF=2;SRR=4;SAF=4;SAR=16;SRP=4.45795;SAP=18.6449;AB=0.571429;ABP=4.56135;RUN=1;RPP=3.44459;RPPR=8.80089;RPL=9.0;RPR=11.0;EPP=6.91895;EPPR=8.80089;DPRA=3.88889;ODDS=3.94373;GTI=0;TYPE=del;CIGAR=1M11D16M;NUMALT=5;MEANALT=6.0;LEN=11;MQM=60.0;MQMR=59.5;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQ [...]
+chr12 12025428 . CTTTTTTTTTTTT C 222.003 REJECT NS=2;DP=44;DPB=97.9643;AC=2;AN=2;AF=0.0;RO=6;AO=2;PRO=36.3333;PAO=10.3333;QR=215;QA=74;PQR=1313.95;PQA=365.867;SRF=2;SRR=4;SAF=1;SAR=1;SRP=4.45795;SAP=3.0103;AB=0.0571429;ABP=62.6327;RUN=1;RPP=7.35324;RPPR=8.80089;RPL=2.0;RPR=0.0;EPP=3.0103;EPPR=8.80089;DPRA=3.88889;ODDS=3.94373;GTI=0;TYPE=del;CIGAR=1M12D15M;NUMALT=5;MEANALT=6.0;LEN=12;MQM=60.0;MQMR=59.5;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr12 12026871 . A G 2069.5 REJECT NS=2;DP=282;DPB=340.0;AC=2;AN=4;AF=0.5;RO=246;AO=93;PRO=0.0;PAO=0.0;QR=9386;QA=3575;PQR=0.0;PQA=0.0;SRF=106;SRR=140;SAF=43;SAR=50;SRP=13.2145;SAP=4.15441;AB=0.273529;ABP=154.477;RUN=1;RPP=6.95631;RPPR=3.57524;RPL=53.0;RPR=40.0;EPP=3.03365;EPPR=17.1337;DPRA=0.0;ODDS=117.619;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.223;Dels=0.0;FS=4.684;HaplotypeScore=2.8995; [...]
+chr12 12027101 . G C 2193.87 REJECT NS=2;DP=98;DPB=116.0;AC=2;AN=4;AF=0.5;RO=34;AO=81;PRO=0.0;PAO=0.0;QR=1277;QA=3085;PQR=0.0;PQA=0.0;SRF=0;SRR=34;SAF=1;SAR=80;SRP=76.8404;SAP=170.321;AB=0.698276;ABP=42.621;RUN=1;RPP=5.18177;RPPR=12.2071;RPL=45.0;RPR=36.0;EPP=4.32391;EPPR=12.2071;DPRA=0.0;ODDS=72.2975;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.4691;MQMR=60.0;PAIRED=0.975309;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.439;Dels=0.0;FS=0.0;HaplotypeScore=0.9999;M [...]
+chr12 12027136 . C T 1674.02 REJECT NS=2;DP=71;DPB=87.0;AC=2;AN=4;AF=0.5;RO=24;AO=63;PRO=0.0;PAO=0.0;QR=886;QA=2426;PQR=0.0;PQA=0.0;SRF=0;SRR=24;SAF=0;SAR=63;SRP=55.1256;SAP=139.813;AB=0.724138;ABP=40.9736;RUN=1;RPP=24.5527;RPPR=16.0391;RPL=44.0;RPR=19.0;EPP=24.5527;EPPR=16.0391;DPRA=0.0;ODDS=25.3134;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.3175;MQMR=60.0;PAIRED=0.984127;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.479;Dels=0.0;FS=0.0;HaplotypeScore=0.9996;M [...]
+chr12 12027175 . G T 1661.15 REJECT NS=2;DP=63;DPB=72.0;AC=3;AN=4;AF=0.625;RO=12;AO=60;PRO=0.0;PAO=0.0;QR=465;QA=2284;PQR=0.0;PQA=0.0;SRF=0;SRR=12;SAF=1;SAR=59;SRP=29.068;SAP=124.758;AB=0.529412;ABP=3.13803;RUN=1;RPP=12.2752;RPPR=3.73412;RPL=22.0;RPR=38.0;EPP=10.1038;EPPR=3.73412;DPRA=0.0;ODDS=6.84252;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.0167;MQMR=60.0;PAIRED=0.583333;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1125;Dels=0.0;FS=0.0;HaplotypeScore=2.9633; [...]
+chr12 12027310 . CA C 228.73 PASS SOMATIC;DP=24;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.95;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.49;MQRankSum=-0.05;QD=9.53;RPA=14,13;RU=A;ReadPosRankSum=-1.25;SOR=0.352;STR GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.97948 0/1:4,15:22:41.0:266,0,41:15:79:19:.:1:.:.:.:.:-0.0132393
+chr12 12027342 . A G 69.7845 REJECT NS=2;DP=30;DPB=30.0;AC=2;AN=4;AF=0.5;RO=21;AO=9;PRO=0.0;PAO=0.0;QR=791;QA=219;PQR=0.0;PQA=0.0;SRF=1;SRR=20;SAF=6;SAR=3;SRP=40.3389;SAP=5.18177;AB=0.3;ABP=13.4334;RUN=1;RPP=3.25157;RPPR=8.07707;RPL=5.0;RPR=4.0;EPP=9.04217;EPPR=11.386;DPRA=0.0;ODDS=1.19624;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.2222;MQMR=58.1429;PAIRED=1.0;PAIREDR=0.380952;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI: [...]
+chr12 12027372 . GTA G 272.672 REJECT NS=2;DP=14;DPB=15.7692;AC=2;AN=4;AF=0.5;RO=2;AO=12;PRO=4.0;PAO=4.0;QR=77;QA=394;PQR=126.0;PQA=126.0;SRF=0;SRR=2;SAF=6;SAR=6;SRP=7.35324;SAP=3.0103;AB=0.857143;ABP=18.5208;RUN=1;RPP=3.73412;RPPR=3.0103;RPL=7.0;RPR=5.0;EPP=9.52472;EPPR=3.0103;DPRA=0.0;ODDS=0.0766886;GTI=1;TYPE=del;CIGAR=1M2D10M;NUMALT=1;MEANALT=1.0;LEN=2;MQM=54.8333;MQMR=60.0;PAIRED=0.583333;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.474;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.12 [...]
+chr12 12027405 . C T 385.77 PASS SOMATIC;DP=12;AC=2;AN=4;AF=1.0;MQ0=0;ALERT;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=50.33;QD=32.15;SOR=0.693 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.97948 1/1:0,12:12:30.0:414,30,0:12:100:12:.:1:.:.:.:.:-0.0132393
+chr12 12027405 . CAC TAT 316.161 REJECT NS=2;DP=12;DPB=13.0;AC=3;AN=4;AF=0.75;RO=1;AO=11;PRO=0.0;PAO=2.0;QR=39;QA=400;PQR=0.0;PQA=74.0;SRF=0;SRR=1;SAF=6;SAR=5;SRP=5.18177;SAP=3.20771;AB=0.5;ABP=3.0103;RUN=1;RPP=26.8965;RPPR=5.18177;RPL=11.0;RPR=0.0;EPP=3.20771;EPPR=5.18177;DPRA=0.0;ODDS=0.81053;GTI=0;TYPE=complex;CIGAR=1X1M1X;NUMALT=1;MEANALT=1.0;LEN=3;MQM=46.8182;MQMR=60.0;PAIRED=0.636364;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:Call [...]
+chr12 12027407 . C T 335.78 PASS SOMATIC;DP=10;AC=2;AN=4;AF=1.0;MQ0=0;ALERT;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=48.16;QD=33.58;SOR=0.693 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.97948 1/1:0,10:10:27.0:364,27,0:10:100:10:.:1:.:.:.:.:-0.0132393
+chr12 12027499 . C T 11.83 LowQual SOMATIC;DP=1;AC=2;AN=4;AF=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=11.83;SOR=1.609 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.97948 1/1:0,1:1:3.0:38,3,0:1:100:1:.:1:.:.:.:.:-0.0132393
+chr12 12027504 . G A 17.61 LowQual SOMATIC;DP=1;AC=2;AN=4;AF=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=17.61;SOR=1.609 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-3.97948 1/1:0,1:1:3.0:44,3,0:1:100:1:.:1:.:.:.:.:-0.0132393
+chr12 12027538 . ATG A 96.384 REJECT NS=2;DP=3;DPB=1.5;AC=4;AN=4;AF=1.0;RO=0;AO=3;PRO=0.0;PAO=0.0;QR=0;QA=113;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=2;SAR=1;SRP=0.0;SAP=3.73412;AB=0.0;ABP=0.0;RUN=1;RPP=3.73412;RPPR=0.0;RPL=1.0;RPR=2.0;EPP=3.73412;EPPR=0.0;DPRA=0.0;ODDS=5.01051;GTI=0;TYPE=del;CIGAR=1M2D1M;NUMALT=1;MEANALT=1.0;LEN=2;MQM=56.6667;MQMR=0.0;PAIRED=0.666667;PAIREDR=0.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/ [...]
+chr12 12027555 . CAT C 160.187 REJECT NS=2;DP=5;DPB=2.5;AC=4;AN=4;AF=1.0;RO=0;AO=5;PRO=0.0;PAO=0.0;QR=0;QA=189;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=3;SAR=2;SRP=0.0;SAP=3.44459;AB=0.0;ABP=0.0;RUN=1;RPP=3.44459;RPPR=0.0;RPL=3.0;RPR=2.0;EPP=3.44459;EPPR=0.0;DPRA=0.0;ODDS=5.63406;GTI=0;TYPE=del;CIGAR=1M2D1M;NUMALT=1;MEANALT=1.0;LEN=2;MQM=52.8;MQMR=0.0;PAIRED=0.8;PAIREDR=0.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:24.49 [...]
+chr12 12027564 . ATG A 182.885 REJECT NS=2;DP=6;DPB=5.07692;AC=4;AN=4;AF=1.0;RO=0;AO=6;PRO=0.0;PAO=0.0;QR=0;QA=216;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=4;SAR=2;SRP=0.0;SAP=4.45795;AB=0.0;ABP=0.0;RUN=1;RPP=3.0103;RPPR=0.0;RPL=3.0;RPR=3.0;EPP=3.0103;EPPR=0.0;DPRA=0.0;ODDS=6.25722;GTI=0;TYPE=del;CIGAR=1M2D10M;NUMALT=1;MEANALT=1.0;LEN=2;MQM=52.8333;MQMR=0.0;PAIRED=0.833333;PAIREDR=0.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:L [...]
+chr12 12027586 . A G 194.187 REJECT NS=2;DP=6;DPB=6.0;AC=4;AN=4;AF=1.0;RO=0;AO=6;PRO=0.0;PAO=0.0;QR=0;QA=231;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=4;SAR=2;SRP=0.0;SAP=4.45795;AB=0.0;ABP=0.0;RUN=1;RPP=4.45795;RPPR=0.0;RPL=2.0;RPR=4.0;EPP=4.45795;EPPR=0.0;DPRA=0.0;ODDS=6.25782;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=52.8333;MQMR=0.0;PAIRED=0.833333;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=52.01;QD=34.43;SOR=1.179 GT:GQ:DP:RO [...]
+chr12 12027596 . A G 126.034 REJECT NS=2;DP=12;DPB=12.0;AC=2;AN=4;AF=0.5;RO=5;AO=7;PRO=0.0;PAO=0.0;QR=191;QA=275;PQR=0.0;PQA=0.0;SRF=4;SRR=1;SAF=7;SAR=0;SRP=6.91895;SAP=18.2106;AB=0.583333;ABP=3.73412;RUN=1;RPP=18.2106;RPPR=6.91895;RPL=0.0;RPR=7.0;EPP=18.2106;EPPR=3.44459;DPRA=0.0;ODDS=2.94879;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=53.1429;MQMR=53.4;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.573;Dels=0.0;FS=4.771;HaplotypeScore=5.799;MLEAC=1;MLEA [...]
+chr12 12027600 . ATATATGTGTGTATATATG A 398.789 REJECT NS=2;DP=13;DPB=13.8;AC=2;AN=2;AF=0.5;RO=0;AO=4;PRO=0.5;PAO=0.0;QR=0;QA=121;PQR=19.0;PQA=0.0;SRF=0;SRR=0;SAF=3;SAR=1;SRP=0.0;SAP=5.18177;AB=0.307692;ABP=7.18621;RUN=1;RPP=3.0103;RPPR=0.0;RPL=2.0;RPR=2.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=4.2566;GTI=0;TYPE=del;CIGAR=1M18D1M;NUMALT=2;MEANALT=2.5;LEN=18;MQM=51.75;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:C [...]
+chr12 12027618 . G GTA 398.789 REJECT NS=2;DP=13;DPB=13.8;AC=2;AN=2;AF=0.5;RO=0;AO=8;PRO=0.5;PAO=5.5;QR=0;QA=312;PQR=19.0;PQA=211.0;SRF=0;SRR=0;SAF=8;SAR=0;SRP=0.0;SAP=20.3821;AB=0.615385;ABP=4.51363;RUN=1;RPP=20.3821;RPPR=0.0;RPL=0.0;RPR=8.0;EPP=20.3821;EPPR=0.0;DPRA=0.0;ODDS=4.2566;GTI=0;TYPE=ins;CIGAR=19M2I1M;NUMALT=2;MEANALT=2.5;LEN=2;MQM=54.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.23;QD=29.27;RPA=2,3;RU=TA;SOR=3 [...]
+chr12 12027885 . C T 477.8795 REJECT NS=2;DP=131;DPB=149.0;AC=2;AN=4;AF=0.5;RO=116;AO=33;PRO=0.0;PAO=0.0;QR=4306;QA=1231;PQR=0.0;PQA=0.0;SRF=104;SRR=12;SAF=31;SAR=2;SRP=161.453;SAP=58.3499;AB=0.221477;ABP=103.408;RUN=1;RPP=4.65535;RPPR=22.1792;RPL=14.0;RPR=19.0;EPP=4.65535;EPPR=22.1792;DPRA=0.0;ODDS=55.0039;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=42.0909;MQMR=44.4483;PAIRED=1.0;PAIREDR=0.991379;technology.ILLUMINA=1.0;MQ0=1;BaseQRankSum=-0.2665;Dels=0.0;FS=1.0035;Haplotype [...]
+chr12 12027980 . TA T 2895.135 REJECT NS=2;DP=231;DPB=297.25;AC=2;AN=4;AF=0.5;RO=118;AO=127;PRO=53.0;PAO=45.0;QR=4440;QA=4690;PQR=1937.5;PQA=1651.5;SRF=92;SRR=26;SAF=90;SAR=37;SRP=83.1708;SAP=51.0392;AB=0.496094;ABP=3.04423;RUN=1;RPP=13.6967;RPPR=19.5724;RPL=51.0;RPR=76.0;EPP=5.8999;EPPR=4.85053;DPRA=0.0;ODDS=212.783;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=1;MEANALT=5.5;LEN=1;MQM=58.4094;MQMR=59.6102;PAIRED=0.976378;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.588;FS=5.385;MLEAC= [...]
+chr12 12028142 . A C 2020.605 REJECT NS=2;DP=413;DPB=476.0;AC=2;AN=4;AF=0.5;RO=373;AO=103;PRO=0.0;PAO=0.0;QR=14300;QA=3866;PQR=0.0;PQA=0.0;SRF=197;SRR=176;SAF=53;SAR=50;SRP=5.57764;SAP=3.20004;AB=0.216387;ABP=335.574;RUN=1;RPP=3.53736;RPPR=5.57764;RPL=54.0;RPR=49.0;EPP=7.75381;EPPR=19.3633;DPRA=0.0;ODDS=143.396;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986595;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0175;Dels=0.0;FS=0.6285;HaplotypeSco [...]
+chr12 12028157 . G T 6057.42 REJECT NS=2;DP=411;DPB=473.0;AC=2;AN=4;AF=0.5;RO=247;AO=226;PRO=0.0;PAO=0.0;QR=9343;QA=8519;PQR=0.0;PQA=0.0;SRF=136;SRR=111;SAF=114;SAR=112;SRP=8.50492;SAP=3.04873;AB=0.477801;ABP=5.03487;RUN=1;RPP=4.89352;RPPR=6.18399;RPL=120.0;RPR=106.0;EPP=7.66071;EPPR=4.49604;DPRA=0.0;ODDS=364.944;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.977876;PAIREDR=0.995951;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.339;Dels=0.0;FS=2.73;Haploty [...]
+chr12 12029748 . G A 14874.599999999999 REJECT NS=2;DP=397;DPB=451.0;AC=4;AN=4;AF=1.0;RO=0;AO=451;PRO=0.0;PAO=0.0;QR=0;QA=17043;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=254;SAR=197;SRP=0.0;SAP=18.6536;AB=0.0;ABP=0.0;RUN=1;RPP=3.4003;RPPR=0.0;RPL=230.0;RPR=221.0;EPP=6.01955;EPPR=0.0;DPRA=0.0;ODDS=71.6658;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995565;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.8702;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28 [...]
+chr12 12030052 . A C 13643.75 REJECT NS=2;DP=361;DPB=423.0;AC=4;AN=4;AF=1.0;RO=0;AO=423;PRO=0.0;PAO=0.0;QR=0;QA=16167;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=206;SAR=217;SRP=0.0;SAP=3.63145;AB=0.0;ABP=0.0;RUN=1;RPP=7.9436;RPPR=0.0;RPL=227.0;RPR=196.0;EPP=3.0565;EPPR=0.0;DPRA=0.0;ODDS=80.3892;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995272;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9663;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.325;SOR=0. [...]
+chr12 12030117 . A G 12112.2 REJECT NS=2;DP=325;DPB=376.0;AC=4;AN=4;AF=1.0;RO=0;AO=376;PRO=0.0;PAO=0.0;QR=0;QA=14192;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=193;SAR=183;SRP=0.0;SAP=3.58782;AB=0.0;ABP=0.0;RUN=1;RPP=6.91433;RPPR=0.0;RPL=175.0;RPR=201.0;EPP=4.48875;EPPR=0.0;DPRA=0.0;ODDS=66.5866;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992021;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.655;SOR=0. [...]
+chr12 12030236 . C CT 821.618 REJECT NS=2;DP=232;DPB=333.821;AC=2;AN=2;AF=0.0;RO=108;AO=18;PRO=83.3333;PAO=54.3333;QR=3879;QA=517;PQR=2914.33;PQA=1842.33;SRF=44;SRR=64;SAF=11;SAR=7;SRP=11.0528;SAP=4.9405;AB=0.0775862;ABP=362.576;RUN=1;RPP=3.49285;RPPR=3.09072;RPL=8.0;RPR=10.0;EPP=4.9405;EPPR=3.73412;DPRA=0.0;ODDS=40.6266;GTI=0;TYPE=ins;CIGAR=1M1I27M;NUMALT=3;MEANALT=22.5;LEN=1;MQM=58.8889;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990741;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr12 12030236 . CT C 821.618 REJECT NS=2;DP=232;DPB=333.821;AC=2;AN=4;AF=0.5;RO=108;AO=36;PRO=83.3333;PAO=55.3333;QR=3879;QA=1134;PQR=2914.33;PQA=1905.83;SRF=44;SRR=64;SAF=21;SAR=15;SRP=11.0528;SAP=5.18177;AB=0.155172;ABP=242.621;RUN=1;RPP=6.8707;RPPR=3.09072;RPL=14.0;RPR=22.0;EPP=3.25157;EPPR=3.73412;DPRA=0.0;ODDS=40.6266;GTI=0;TYPE=del;CIGAR=1M1D26M;NUMALT=3;MEANALT=22.5;LEN=1;MQM=60.5556;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990741;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.05 [...]
+chr12 12030236 . CTT C 821.618 REJECT NS=2;DP=232;DPB=333.821;AC=2;AN=2;AF=0.0;RO=108;AO=16;PRO=83.3333;PAO=43.0;QR=3879;QA=493;PQR=2914.33;PQA=1484.5;SRF=44;SRR=64;SAF=7;SAR=9;SRP=11.0528;SAP=3.55317;AB=0.0689655;ABP=377.402;RUN=1;RPP=5.18177;RPPR=3.09072;RPL=10.0;RPR=6.0;EPP=7.89611;EPPR=3.73412;DPRA=0.0;ODDS=40.6266;GTI=0;TYPE=del;CIGAR=1M2D25M;NUMALT=3;MEANALT=22.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990741;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr12 12030306 . A G 11942.599999999999 REJECT NS=2;DP=332;DPB=383.0;AC=4;AN=4;AF=1.0;RO=1;AO=382;PRO=0.0;PAO=0.0;QR=36;QA=13957;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=215;SAR=167;SRP=5.18177;SAP=16.1073;AB=0.0;ABP=0.0;RUN=1;RPP=9.58156;RPPR=5.18177;RPL=174.0;RPR=208.0;EPP=3.37411;EPPR=5.18177;DPRA=0.0;ODDS=67.8279;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0262;MQMR=60.0;PAIRED=0.994764;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.857;Dels=0.0;FS=0.0;HaplotypeScore=1 [...]
+chr12 12031465 . A C 5601.77 REJECT NS=2;DP=350;DPB=398.0;AC=2;AN=4;AF=0.5;RO=198;AO=200;PRO=0.0;PAO=0.0;QR=7652;QA=7552;PQR=0.0;PQA=0.0;SRF=90;SRR=108;SAF=105;SAR=95;SRP=6.56362;SAP=4.09604;AB=0.502513;ABP=3.03212;RUN=1;RPP=4.57376;RPPR=10.424;RPL=94.0;RPR=106.0;EPP=5.13834;EPPR=3.40511;DPRA=0.0;ODDS=295.493;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995;PAIREDR=0.994949;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.6565;Dels=0.0;FS=6.2025;HaplotypeSc [...]
+chr12 12031761 . G GA 2669.73 PASS SOMATIC;DP=242;AC=1;AN=3;AF=0.5;SPLITMULTIALLELIC;MQ0=0;ALERT;BaseQRankSum=0.671;FS=2.64;MLEAC=1;MLEAF=0.5;MQ=58.98;MQRankSum=2.383;QD=11.03;ReadPosRankSum=0.21;SOR=1.012 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.000759707 ./1:35,43:242:88.0:2707,1572,2147483647:43:25:171:.:1:.:.:.:.:-0.0132393
+chr12 12031761 . G GAA 552.73 PASS DP=65;AC=1;AN=4;AF=0.5;ALERT;BaseQRankSum=-0.065;FS=6.368;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.457;QD=8.5;ReadPosRankSum=-1.763;SOR=0.053;ClippingRankSum=0.979 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:11,26:37:92.0:539,0,92:26:70:37:1:.:.:.:.:.:-0.000759707 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0132393
+chr12 12031761 . G GAAA 2669.73 PASS SOMATIC;DP=242;AC=1;AN=3;AF=0.5;SPLITMULTIALLELIC;MQ0=0;ALERT;BaseQRankSum=0.671;FS=2.64;MLEAC=1;MLEAF=0.5;MQ=58.98;MQRankSum=2.383;QD=11.03;ReadPosRankSum=0.21;SOR=1.012 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.000759707 ./1:35,93:242:88.0:2707,88,642:93:54:171:.:1:.:.:.:.:-0.0132393
+chr12 12031761 . GGA G 5842.58 REJECT NS=2;DP=279;DPB=339.75;AC=0;AN=4;AF=0.0;RO=19;AO=7;PRO=1.61905;PAO=2.08571;QR=610;QA=160;PQR=42.9286;PQA=50.4286;SRF=8;SRR=11;SAF=3;SAR=4;SRP=4.03889;SAP=3.32051;AB=0.0250896;ABP=549.575;RUN=1;RPP=18.2106;RPPR=5.8675;RPL=0.0;RPR=7.0;EPP=3.32051;EPPR=3.12459;DPRA=0.0;ODDS=16.4132;GTI=0;TYPE=del;CIGAR=1M2D1M;NUMALT=6;MEANALT=11.0;LEN=2;MQM=60.0;MQMR=57.1579;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr12 12031762 . G A 5842.58 REJECT NS=2;DP=258;DPB=339.75;AC=2;AN=2;AF=0.5;RO=19;AO=142;PRO=1.61905;PAO=4.26905;QR=610;QA=4748;PQR=42.9286;PQA=122.529;SRF=8;SRR=11;SAF=94;SAR=48;SRP=4.03889;SAP=35.3683;AB=0.508961;ABP=3.20488;RUN=1;RPP=116.11;RPPR=5.8675;RPL=114.0;RPR=28.0;EPP=54.4528;EPPR=3.12459;DPRA=0.0;ODDS=16.4132;GTI=0;TYPE=snp;CIGAR=1M1X2M;NUMALT=6;MEANALT=11.0;LEN=1;MQM=58.4789;MQMR=57.1579;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;ALERT;BaseQRankSum [...]
+chr12 12031762 . G AA 5842.58 REJECT NS=2;DP=279;DPB=339.75;AC=0;AN=4;AF=0.0;RO=19;AO=23;PRO=1.61905;PAO=4.26905;QR=610;QA=716;PQR=42.9286;PQA=122.529;SRF=8;SRR=11;SAF=10;SAR=13;SRP=4.03889;SAP=3.86001;AB=0.0824373;ABP=425.545;RUN=1;RPP=14.4341;RPPR=5.8675;RPL=17.0;RPR=6.0;EPP=3.86001;EPPR=3.12459;DPRA=0.0;ODDS=16.4132;GTI=0;TYPE=complex;CIGAR=1M1I1X2M;NUMALT=6;MEANALT=11.0;LEN=5;MQM=60.0;MQMR=57.1579;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr12 12031762 . G AAA 5842.58 REJECT NS=2;DP=279;DPB=339.75;AC=2;AN=2;AF=0.5;RO=19;AO=54;PRO=1.61905;PAO=4.26905;QR=610;QA=1592;PQR=42.9286;PQA=122.529;SRF=8;SRR=11;SAF=23;SAR=31;SRP=4.03889;SAP=5.5839;AB=0.193548;ABP=230.595;RUN=1;RPP=3.6537;RPPR=5.8675;RPL=25.0;RPR=29.0;EPP=7.03155;EPPR=3.12459;DPRA=0.0;ODDS=16.4132;GTI=0;TYPE=complex;CIGAR=1M2I1X2M;NUMALT=6;MEANALT=11.0;LEN=6;MQM=59.6296;MQMR=57.1579;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:Q [...]
+chr12 12031762 . G AAAA 5842.58 REJECT NS=2;DP=279;DPB=339.75;AC=0;AN=4;AF=0.0;RO=19;AO=9;PRO=1.61905;PAO=4.26905;QR=610;QA=220;PQR=42.9286;PQA=122.529;SRF=8;SRR=11;SAF=4;SAR=5;SRP=4.03889;SAP=3.25157;AB=0.0322581;ABP=533.2;RUN=1;RPP=3.25157;RPPR=5.8675;RPL=4.0;RPR=5.0;EPP=5.18177;EPPR=3.12459;DPRA=0.0;ODDS=16.4132;GTI=0;TYPE=complex;CIGAR=1M3I1X2M;NUMALT=6;MEANALT=11.0;LEN=7;MQM=56.4444;MQMR=57.1579;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr12 12031762 . G GAAA 5842.58 REJECT NS=2;DP=279;DPB=339.75;AC=0;AN=4;AF=0.0;RO=19;AO=8;PRO=1.61905;PAO=2.21905;QR=610;QA=161;PQR=42.9286;PQA=65.5286;SRF=8;SRR=11;SAF=0;SAR=8;SRP=4.03889;SAP=20.3821;AB=0.0286738;ABP=541.356;RUN=1;RPP=7.35324;RPPR=5.8675;RPL=2.0;RPR=6.0;EPP=7.35324;EPPR=3.12459;DPRA=0.0;ODDS=16.4132;GTI=0;TYPE=ins;CIGAR=2M3I2M;NUMALT=6;MEANALT=11.0;LEN=3;MQM=60.0;MQMR=57.1579;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr12 12031894 . G C 2584.14 PASS SOMATIC;NS=2;DP=396;DPB=396.0;AC=1;AN=3;AF=0.25;RO=297;AO=99;PRO=0.0;PAO=0.0;QR=11291;QA=3797;PQR=0.0;PQA=0.0;SRF=176;SRR=121;SAF=55;SAR=44;SRP=25.1271;SAP=5.66432;AB=0.346154;ABP=61.8071;RUN=1;RPP=4.78696;RPPR=5.6497;RPL=45.0;RPR=54.0;EPP=3.55865;EPPR=8.34028;DPRA=2.6;ODDS=69.5179;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989899;PAIREDR=0.976431;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.273;Dels=0.0;FS=2.13 [...]
+chr12 12032966 . T A 112.153 REJECT NS=2;DP=75;DPB=192.378;AC=2;AN=2;AF=0.0;RO=27;AO=2;PRO=59.4;PAO=29.5167;QR=1013;QA=16;PQR=2058.47;PQA=1014.67;SRF=5;SRR=22;SAF=0;SAR=2;SRP=26.2531;SAP=7.35324;AB=0.0952381;ABP=32.8939;RUN=1;RPP=7.35324;RPPR=3.73412;RPL=0.0;RPR=2.0;EPP=7.35324;EPPR=6.95112;DPRA=0.0;ODDS=6.2464;GTI=0;TYPE=snp;CIGAR=1X36M;NUMALT=5;MEANALT=7.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr12 12032966 . T TA 112.153 REJECT NS=2;DP=75;DPB=192.378;AC=2;AN=4;AF=0.5;RO=27;AO=9;PRO=59.4;PAO=51.4;QR=1013;QA=263;PQR=2058.47;PQA=1755.47;SRF=5;SRR=22;SAF=1;SAR=8;SRP=26.2531;SAP=14.8328;AB=0.12;ABP=97.0785;RUN=1;RPP=3.25157;RPPR=3.73412;RPL=4.0;RPR=5.0;EPP=3.25157;EPPR=6.95112;DPRA=0.0;ODDS=6.2464;GTI=0;TYPE=ins;CIGAR=1M1I36M;NUMALT=5;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV [...]
+chr12 12032966 . T TAA 112.153 REJECT NS=2;DP=75;DPB=192.378;AC=2;AN=2;AF=0.0;RO=27;AO=5;PRO=59.4;PAO=52.4;QR=1013;QA=113;PQR=2058.47;PQA=1781.47;SRF=5;SRR=22;SAF=0;SAR=5;SRP=26.2531;SAP=13.8677;AB=0.0925926;ABP=80.8616;RUN=1;RPP=13.8677;RPPR=3.73412;RPL=5.0;RPR=0.0;EPP=13.8677;EPPR=6.95112;DPRA=0.0;ODDS=6.2464;GTI=0;TYPE=ins;CIGAR=1M2I36M;NUMALT=5;MEANALT=19.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr12 12032966 . TA T 112.153 REJECT NS=2;DP=75;DPB=192.378;AC=2;AN=2;AF=0.0;RO=27;AO=8;PRO=59.4;PAO=41.8167;QR=1013;QA=244;PQR=2058.47;PQA=1424.97;SRF=5;SRR=22;SAF=3;SAR=5;SRP=26.2531;SAP=4.09604;AB=0.106667;ABP=103.796;RUN=1;RPP=3.0103;RPPR=3.73412;RPL=4.0;RPR=4.0;EPP=4.09604;EPPR=6.95112;DPRA=0.0;ODDS=6.2464;GTI=0;TYPE=del;CIGAR=1M1D35M;NUMALT=5;MEANALT=13.0;LEN=1;MQM=62.5;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr12 12032966 . TAAA T 112.153 REJECT NS=2;DP=75;DPB=192.378;AC=2;AN=2;AF=0.0;RO=27;AO=2;PRO=59.4;PAO=35.4667;QR=1013;QA=41;PQR=2058.47;PQA=1212.97;SRF=5;SRR=22;SAF=1;SAR=1;SRP=26.2531;SAP=3.0103;AB=0.0952381;ABP=32.8939;RUN=1;RPP=3.0103;RPPR=3.73412;RPL=1.0;RPR=1.0;EPP=7.35324;EPPR=6.95112;DPRA=0.0;ODDS=6.2464;GTI=0;TYPE=del;CIGAR=1M3D33M;NUMALT=5;MEANALT=7.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr12 12032986 . G A 33.77 PASS DP=49;AC=1;AN=4;AF=0.5;BaseQRankSum=-3.55;FS=17.281;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.594;QD=0.69;ReadPosRankSum=-2.159;SOR=4.011;ClippingRankSum=-0.362 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:38,8:46:62.0:62,0,1525:8:17:46:1:.:.:.:.:.:-0.000759707 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0132393
+chr12 12032987 . G A 33.77 PASS DP=51;AC=1;AN=4;AF=0.5;BaseQRankSum=-3.5;FS=17.41;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.373;QD=0.66;ReadPosRankSum=-2.227;SOR=4.03;ClippingRankSum=0.761 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:40,8:48:62.0:62,0,1525:8:17:48:1:.:.:.:.:.:-0.000759707 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0132393
+chr12 12033570 . C G 4546.05 PASS SOMATIC;NS=2;DP=490;DPB=490.0;AC=1;AN=3;AF=0.25;RO=327;AO=163;PRO=0.0;PAO=0.0;QR=12610;QA=6288;PQR=0.0;PQA=0.0;SRF=174;SRR=153;SAF=80;SAR=83;SRP=5.9388;SAP=3.1302;AB=0.420103;ABP=24.5235;RUN=1;RPP=3.66307;RPPR=5.9388;RPL=78.0;RPR=85.0;EPP=6.00773;EPPR=6.52317;DPRA=3.80392;ODDS=64.6447;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993865;PAIREDR=0.990826;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.906;Dels=0.0;FS=3 [...]
+chr12 12033871 . C T 2507.99 PASS SOMATIC;NS=2;DP=412;DPB=412.0;AC=1;AN=3;AF=0.25;RO=313;AO=99;PRO=0.0;PAO=0.0;QR=11994;QA=3750;PQR=0.0;PQA=0.0;SRF=139;SRR=174;SAF=48;SAR=51;SRP=11.5089;SAP=3.20771;AB=0.33;ABP=78.317;RUN=1;RPP=3.55865;RPPR=27.1601;RPL=52.0;RPR=47.0;EPP=3.03223;EPPR=5.51478;DPRA=2.67857;ODDS=70.8319;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.905;Dels=0.0;FS=0.936;Haplotyp [...]
+chr12 12033974 . C A 1473.75 PASS SOMATIC;NS=2;DP=240;DPB=240.0;AC=1;AN=3;AF=0.25;RO=180;AO=60;PRO=0.0;PAO=0.0;QR=6869;QA=2258;PQR=0.0;PQA=0.0;SRF=48;SRR=132;SAF=16;SAR=44;SRP=88.132;SAP=31.3842;AB=0.338983;ABP=42.8697;RUN=1;RPP=3.58936;RPPR=9.95901;RPL=28.0;RPR=32.0;EPP=3.58936;EPPR=6.09862;DPRA=2.80952;ODDS=40.3422;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8889;PAIRED=0.983333;PAIREDR=0.994444;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.435;Dels=0.0;FS [...]
+chr12 12035282 . C G 3138.24 PASS SOMATIC;NS=2;DP=472;DPB=472.0;AC=1;AN=3;AF=0.25;RO=350;AO=121;PRO=0.0;PAO=0.0;QR=13230;QA=4644;PQR=0.0;PQA=0.0;SRF=176;SRR=174;SAF=65;SAR=56;SRP=3.03512;SAP=4.46393;AB=0.333333;ABP=90.593;RUN=1;RPP=3.45895;RPPR=7.20434;RPL=58.0;RPR=63.0;EPP=3.88966;EPPR=6.01314;DPRA=3.33028;ODDS=68.3195;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997143;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.805;Dels=0.0;FS=0.0; [...]
+chr12 12035664 . A G 9669.835 REJECT NS=2;DP=395;DPB=457.0;AC=3;AN=4;AF=0.75;RO=112;AO=345;PRO=0.0;PAO=0.0;QR=4293;QA=13117;PQR=0.0;PQA=0.0;SRF=56;SRR=56;SAF=181;SAR=164;SRP=3.0103;SAP=4.8293;AB=0.664671;ABP=81.6774;RUN=1;RPP=3.06695;RPPR=6.81038;RPL=174.0;RPR=171.0;EPP=16.914;EPPR=3.08785;DPRA=0.0;ODDS=77.6284;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.2029;MQMR=60.0;PAIRED=0.991304;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.608;Dels=0.0;FS=0.209;HaplotypeSc [...]
+chr12 12035698 . T TC 8462.09 REJECT NS=2;DP=379;DPB=496.875;AC=3;AN=4;AF=0.75;RO=98;AO=317;PRO=32.0;PAO=39.0;QR=3660;QA=11558;PQR=1124.0;PQA=1342.0;SRF=51;SRR=47;SAF=155;SAR=162;SRP=3.36483;SAP=3.34595;AB=0.677316;ABP=88.4886;RUN=1;RPP=9.59322;RPPR=6.20103;RPL=174.0;RPR=143.0;EPP=3.83916;EPPR=3.09893;DPRA=0.0;ODDS=67.2418;GTI=0;TYPE=ins;CIGAR=1M1I7M;NUMALT=1;MEANALT=3.0;LEN=1;MQM=60.1577;MQMR=60.0;PAIRED=0.993691;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.071;FS=2.1945;MLE [...]
+chr12 12035714 . C T 9235.935000000001 REJECT NS=2;DP=383;DPB=439.0;AC=3;AN=4;AF=0.75;RO=110;AO=329;PRO=0.0;PAO=0.0;QR=4210;QA=12413;PQR=0.0;PQA=0.0;SRF=56;SRR=54;SAF=153;SAR=176;SRP=3.08926;SAP=6.50182;AB=0.666667;ABP=82.631;RUN=1;RPP=4.49535;RPPR=4.98437;RPL=172.0;RPR=157.0;EPP=3.17531;EPPR=3.08926;DPRA=0.0;ODDS=68.9137;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.2736;MQMR=60.0;PAIRED=0.99696;PAIREDR=0.990909;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.315;Dels=0.0;FS=2. [...]
+chr12 12036210 . C CTTCTTCT 5230.73 PASS SOMATIC;DP=114;AC=1;AN=3;AF=0.5;SPLITMULTIALLELIC;MQ0=0;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=65.57;QD=15.29;SOR=3.007 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.000759707 ./1:0,77:110:99.0:5268,882,909:77:90:86:.:1:.:.:.:.:-0.0132393
+chr12 12036210 . CTTTTTTTTTTT C 3145.7299999999996 PASS DP=71;AC=3;AN=3;AF=0.75;SPLITMULTIALLELIC;MQ0=0;FS=0.0;MLEAC=1;MLEAF=0.75;MQ=62.77;QD=23.74;SOR=2.655 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:0,26:26:82.0:1098,82,0:26:100:26:1:.:.:.:.:.:-0.000759707 ./1:0,9:110:99.0:5268,4363,2147483647:9:10:86:.:1:.:.:.:.:-0.0132393
+chr12 12036213 . TTTTTTTTTTTTT CTTC 3827.79 REJECT NS=2;DP=7;DPB=47.2979;AC=2;AN=2;AF=0.5;RO=0;AO=1;PRO=20.1;PAO=47.9333;QR=0;QA=15;PQR=662.85;PQA=1459.52;SRF=0;SRR=0;SAF=0;SAR=1;SRP=0.0;SAP=5.18177;AB=0.5;ABP=3.0103;RUN=1;RPP=5.18177;RPPR=0.0;RPL=1.0;RPR=0.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=0.522238;GTI=1;TYPE=complex;CIGAR=1M9D2M1X2M1X31M;NUMALT=4;MEANALT=2.0;LEN=38;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr12 12036213 . TTTTTTTTTTTTTTT CTTC 3827.79 REJECT NS=2;DP=7;DPB=47.2979;AC=2;AN=2;AF=0.5;RO=0;AO=4;PRO=20.1;PAO=45.9333;QR=0;QA=86;PQR=662.85;PQA=1384.52;SRF=0;SRR=0;SAF=1;SAR=3;SRP=0.0;SAP=5.18177;AB=0.571429;ABP=3.32051;RUN=1;RPP=3.0103;RPPR=0.0;RPL=2.0;RPR=2.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=0.522238;GTI=1;TYPE=complex;CIGAR=1M11D2M1X2M1X29M;NUMALT=4;MEANALT=2.5;LEN=36;MQM=58.5;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr12 12036213 . TTTTTTTTTTTTTTTT CTTTG 3827.79 REJECT NS=2;DP=7;DPB=47.2979;AC=0;AN=4;AF=0.0;RO=0;AO=1;PRO=20.1;PAO=11.9333;QR=0;QA=15;PQR=662.85;PQA=396.267;SRF=0;SRR=0;SAF=0;SAR=1;SRP=0.0;SAP=5.18177;AB=0.2;ABP=6.91895;RUN=1;RPP=5.18177;RPPR=0.0;RPL=1.0;RPR=0.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=0.522238;GTI=1;TYPE=complex;CIGAR=1M11D2M1X3M1X28M;NUMALT=4;MEANALT=3.0;LEN=36;MQM=40.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr12 12036216 . TTTTTTTTTTTT C 3827.79 REJECT NS=2;DP=7;DPB=47.2979;AC=0;AN=4;AF=0.0;RO=0;AO=1;PRO=20.1;PAO=11.1;QR=0;QA=15;PQR=662.85;PQA=345.85;SRF=0;SRR=0;SAF=0;SAR=1;SRP=0.0;SAP=5.18177;AB=0.2;ABP=6.91895;RUN=1;RPP=5.18177;RPPR=0.0;RPL=1.0;RPR=0.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=0.522238;GTI=1;TYPE=complex;CIGAR=1M11D5M1X29M;NUMALT=4;MEANALT=3.0;LEN=36;MQM=40.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:C [...]
+chr12 12036224 . T C 1113.77 PASS DP=28;AC=2;AN=4;AF=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.96;QD=34.54;SOR=2.147 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:0,28:28:84.0:1142,84,0:28:100:28:1:.:.:.:.:.:-0.000759707 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0132393
+chr12 12036227 . T C 998.77 PASS DP=24;AC=2;AN=4;AF=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.96;QD=33.64;SOR=1.802 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:0,24:24:75.0:1027,75,0:24:100:24:1:.:.:.:.:.:-0.000759707 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0132393
+chr12 12036301 . T C 1774.37 REJECT NS=2;DP=57;DPB=69.0;AC=4;AN=4;AF=1.0;RO=1;AO=68;PRO=0.0;PAO=0.0;QR=16;QA=2219;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=32;SAR=36;SRP=5.18177;SAP=3.52123;AB=0.0;ABP=0.0;RUN=1;RPP=3.13803;RPPR=5.18177;RPL=33.0;RPR=35.0;EPP=4.1599;EPPR=5.18177;DPRA=0.0;ODDS=18.6012;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.970588;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.496;Dels=0.0;FS=0.0;HaplotypeScore=3.866;MLEAC=2;MLEAF=1.0; [...]
+chr12 12036529 . A G 6329.345 REJECT NS=2;DP=259;DPB=299.0;AC=3;AN=4;AF=0.75;RO=72;AO=227;PRO=0.0;PAO=0.0;QR=2779;QA=8701;PQR=0.0;PQA=0.0;SRF=48;SRR=24;SAF=160;SAR=67;SRP=20.3821;SAP=85.7463;AB=0.672727;ABP=60.0213;RUN=1;RPP=72.1243;RPPR=15.074;RPL=71.0;RPR=156.0;EPP=3.78514;EPPR=10.7311;DPRA=0.0;ODDS=50.3197;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9119;MQMR=60.0;PAIRED=0.995595;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.506;Dels=0.0;FS=0.5955;HaplotypeSco [...]
+chr12 12037081 . G A 6374.34 REJECT NS=2;DP=432;DPB=481.0;AC=2;AN=4;AF=0.5;RO=256;AO=223;PRO=0.0;PAO=0.0;QR=9868;QA=8600;PQR=0.0;PQA=0.0;SRF=128;SRR=128;SAF=107;SAR=116;SRP=3.0103;SAP=3.79904;AB=0.463617;ABP=8.54056;RUN=1;RPP=5.20125;RPPR=9.66043;RPL=119.0;RPR=104.0;EPP=3.02004;EPPR=3.55317;DPRA=0.0;ODDS=276.722;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991031;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.729;Dels=0.0;FS=2.588;HaplotypeScor [...]
+chr12 12037132 . T C 3377.54 PASS SOMATIC;NS=2;DP=433;DPB=433.0;AC=1;AN=3;AF=0.25;RO=305;AO=127;PRO=0.0;PAO=0.0;QR=11472;QA=4822;PQR=0.0;PQA=0.0;SRF=155;SRR=150;SAF=58;SAR=69;SRP=3.18829;SAP=5.07918;AB=0.379104;ABP=45.5387;RUN=1;RPP=3.16418;RPPR=3.35916;RPL=62.0;RPR=65.0;EPP=3.0274;EPPR=3.35916;DPRA=3.41837;ODDS=62.0778;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996721;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.444;Dels=0.0;FS=3.01 [...]
+chr12 12037178 . G A 5286.835 REJECT NS=2;DP=360;DPB=414.0;AC=2;AN=4;AF=0.5;RO=223;AO=191;PRO=0.0;PAO=0.0;QR=8485;QA=7259;PQR=0.0;PQA=0.0;SRF=108;SRR=115;SAF=95;SAR=96;SRP=3.48744;SAP=3.02167;AB=0.461353;ABP=8.38128;RUN=1;RPP=3.56738;RPPR=5.20125;RPL=99.0;RPR=92.0;EPP=4.38594;EPPR=3.02004;DPRA=0.0;ODDS=280.053;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.979058;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.161;Dels=0.0;FS=0.434;HaplotypeScore [...]
+chr12 12037318 . C G 6195.360000000001 REJECT NS=2;DP=419;DPB=485.0;AC=2;AN=4;AF=0.5;RO=259;AO=226;PRO=0.0;PAO=0.0;QR=9902;QA=8632;PQR=0.0;PQA=0.0;SRF=111;SRR=148;SAF=123;SAR=103;SRP=14.4881;SAP=6.85361;AB=0.465979;ABP=7.88604;RUN=1;RPP=5.47002;RPPR=21.5307;RPL=121.0;RPR=105.0;EPP=3.04873;EPPR=10.0613;DPRA=0.0;ODDS=397.586;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99115;PAIREDR=0.992278;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.489;Dels=0.0;FS=10. [...]
+chr12 12044534 . G GA 274.307 REJECT NS=2;DP=297;DPB=333.067;AC=2;AN=2;AF=0.0;RO=236;AO=15;PRO=31.1667;PAO=22.1667;QR=8893;QA=506;PQR=1098.5;PQA=784.5;SRF=63;SRR=173;SAF=5;SAR=10;SRP=114.344;SAP=6.62942;AB=0.0505051;ABP=524.229;RUN=1;RPP=14.7363;RPPR=50.7091;RPL=12.0;RPR=3.0;EPP=3.15506;EPPR=9.23028;DPRA=0.0;ODDS=30.1364;GTI=0;TYPE=ins;CIGAR=1M1I14M;NUMALT=2;MEANALT=6.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995763;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr12 12044534 . GA G 274.307 REJECT NS=2;DP=297;DPB=333.067;AC=2;AN=4;AF=0.5;RO=236;AO=33;PRO=31.1667;PAO=20.6667;QR=8893;QA=1231;PQR=1098.5;PQA=723.0;SRF=63;SRR=173;SAF=8;SAR=25;SRP=114.344;SAP=22.0271;AB=0.111111;ABP=393.152;RUN=1;RPP=14.1309;RPPR=50.7091;RPL=23.0;RPR=10.0;EPP=4.65535;EPPR=9.23028;DPRA=0.0;ODDS=30.1364;GTI=0;TYPE=del;CIGAR=1M1D13M;NUMALT=2;MEANALT=6.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995763;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.091;FS=1 [...]
+chr12 12772733 . T C 4868.265 REJECT NS=2;DP=365;DPB=408.0;AC=2;AN=4;AF=0.5;RO=232;AO=176;PRO=0.0;PAO=0.0;QR=8977;QA=6779;PQR=0.0;PQA=0.0;SRF=107;SRR=125;SAF=92;SAR=84;SRP=6.04287;SAP=3.79993;AB=0.431373;ABP=19.7008;RUN=1;RPP=3.20771;RPPR=3.34725;RPL=86.0;RPR=90.0;EPP=53.5464;EPPR=32.3626;DPRA=0.0;ODDS=256.44;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99569;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.8745;Dels=0.0;FS=6.3895;HaplotypeScore= [...]
+chr12 12773521 . A G 5410.88 REJECT NS=2;DP=361;DPB=417.0;AC=2;AN=4;AF=0.5;RO=219;AO=197;PRO=0.0;PAO=0.0;QR=8426;QA=7661;PQR=0.0;PQA=0.0;SRF=106;SRR=113;SAF=104;SAR=93;SRP=3.49615;SAP=4.34405;AB=0.472422;ABP=5.765;RUN=1;RPP=3.02132;RPPR=3.81345;RPL=98.0;RPR=99.0;EPP=33.9731;EPPR=30.8627;DPRA=0.0;ODDS=353.16;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989848;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3145;Dels=0.0;FS=1.731;HaplotypeScore=6. [...]
+chr12 12775191 . G C 2598.98 PASS SOMATIC;NS=2;DP=411;DPB=411.0;AC=1;AN=3;AF=0.25;RO=310;AO=101;PRO=0.0;PAO=0.0;QR=11791;QA=3887;PQR=0.0;PQA=0.0;SRF=181;SRR=129;SAF=60;SAR=41;SRP=21.9511;SAP=10.7717;AB=0.333333;ABP=76.1165;RUN=1;RPP=6.64375;RPPR=7.04504;RPL=44.0;RPR=57.0;EPP=16.4476;EPPR=59.7488;DPRA=2.80556;ODDS=68.2626;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.970297;PAIREDR=0.996774;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.733;Dels=0.0;F [...]
+chr12 12871099 . T G 1725.6599999999999 REJECT NS=2;DP=370;DPB=418.0;AC=2;AN=4;AF=0.5;RO=327;AO=91;PRO=0.0;PAO=0.0;QR=12456;QA=3441;PQR=0.0;PQA=0.0;SRF=158;SRR=169;SAF=42;SAR=49;SRP=3.81381;SAP=4.17955;AB=0.217703;ABP=292.346;RUN=1;RPP=7.04303;RPPR=7.85129;RPL=52.0;RPR=39.0;EPP=3.03416;EPPR=3.17631;DPRA=0.0;ODDS=151.899;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0306;PAIRED=0.978022;PAIREDR=0.993884;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4155;Dels=0.0;FS=2. [...]
+chr12 16501995 . G A 4996.76 REJECT NS=2;DP=290;DPB=332.0;AC=2;AN=4;AF=0.5;RO=155;AO=177;PRO=0.0;PAO=0.0;QR=5982;QA=6707;PQR=0.0;PQA=0.0;SRF=92;SRR=63;SAF=111;SAR=66;SRP=14.7923;SAP=27.8534;AB=0.533133;ABP=6.17594;RUN=1;RPP=45.7159;RPPR=26.5603;RPL=59.0;RPR=118.0;EPP=13.3279;EPPR=14.7923;DPRA=0.0;ODDS=264.993;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988701;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.525;Dels=0.0;FS=0.8055;HaplotypeScore= [...]
+chr12 18008222 . T C 4374.72 REJECT NS=2;DP=198;DPB=225.0;AC=3;AN=4;AF=0.75;RO=65;AO=159;PRO=0.0;PAO=0.0;QR=2488;QA=6029;PQR=0.0;PQA=0.0;SRF=44;SRR=21;SAF=101;SAR=58;SRP=20.6827;SAP=28.2622;AB=0.616279;ABP=23.21;RUN=1;RPP=121.13;RPPR=59.1679;RPL=33.0;RPR=126.0;EPP=3.6795;EPPR=3.31097;DPRA=0.0;ODDS=34.0379;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987421;PAIREDR=0.969231;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.775;Dels=0.0;FS=1.9125;HaplotypeScore [...]
+chr12 22507319 . G A 2098.225 REJECT NS=2;DP=359;DPB=416.0;AC=2;AN=4;AF=0.5;RO=312;AO=104;PRO=0.0;PAO=0.0;QR=11819;QA=3865;PQR=0.0;PQA=0.0;SRF=148;SRR=164;SAF=46;SAR=58;SRP=4.79202;SAP=6.01695;AB=0.25;ABP=228.843;RUN=1;RPP=5.09825;RPPR=3.12166;RPL=57.0;RPR=47.0;EPP=3.09382;EPPR=19.0458;DPRA=0.0;ODDS=154.903;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.980769;PAIREDR=0.996795;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7685;Dels=0.0;FS=0.77;HaplotypeScor [...]
+chr12 25368462 . C T 13856.95 REJECT NS=2;DP=368;DPB=417.0;AC=4;AN=4;AF=1.0;RO=0;AO=417;PRO=0.0;PAO=0.0;QR=0;QA=15865;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=220;SAR=197;SRP=0.0;SAP=5.765;AB=0.0;ABP=0.0;RUN=1;RPP=5.30675;RPPR=0.0;RPL=219.0;RPR=198.0;EPP=16.5547;EPPR=0.0;DPRA=0.0;ODDS=64.836;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.990408;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8487;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.755;SOR=0.7 [...]
+chr12 25498629 . C T 14418.0 REJECT NS=2;DP=381;DPB=427.0;AC=4;AN=4;AF=1.0;RO=0;AO=427;PRO=0.0;PAO=0.0;QR=0;QA=16258;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=188;SAR=239;SRP=0.0;SAP=16.2375;AB=0.0;ABP=0.0;RUN=1;RPP=3.25949;RPPR=0.0;RPL=217.0;RPR=210.0;EPP=54.8866;EPPR=0.0;DPRA=0.0;ODDS=61.0505;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997658;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8487;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.245;SOR=1 [...]
+chr12 25499342 . T C 14105.9 REJECT NS=2;DP=371;DPB=419.0;AC=4;AN=4;AF=1.0;RO=2;AO=417;PRO=0.0;PAO=0.0;QR=80;QA=16147;PQR=0.0;PQA=0.0;SRF=1;SRR=1;SAF=204;SAR=213;SRP=3.0103;SAP=3.4321;AB=0.0;ABP=0.0;RUN=1;RPP=3.26546;RPPR=7.35324;RPL=205.0;RPR=212.0;EPP=4.18196;EPPR=3.0103;DPRA=0.0;ODDS=62.9714;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992806;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.437;Dels=0.0;FS=0.0;HaplotypeScore=3.8378;MLEAC=2;MLE [...]
+chr12 25501790 . T C 4109.57 REJECT NS=1;DP=130;DPB=130.0;AC=2;AN=4;AF=1.0;RO=0;AO=129;PRO=0.0;PAO=0.0;QR=0;QA=4651;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=77;SAR=52;SRP=0.0;SAP=13.531;AB=0.0;ABP=0.0;RUN=1;RPP=7.87507;RPPR=0.0;RPL=56.0;RPR=73.0;EPP=28.6135;EPPR=0.0;DPRA=0.0;ODDS=84.9341;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.984496;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.87;QD=32.94;SOR=1.071 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr12 39018673 . C T 2488.1 PASS SOMATIC;NS=2;DP=387;DPB=387.0;AC=1;AN=3;AF=0.25;RO=290;AO=97;PRO=0.0;PAO=0.0;QR=10966;QA=3723;PQR=0.0;PQA=0.0;SRF=172;SRR=118;SAF=56;SAR=41;SRP=24.8448;SAP=8.04722;AB=0.327703;ABP=79.3346;RUN=1;RPP=4.82359;RPPR=8.88076;RPL=44.0;RPR=53.0;EPP=3.56996;EPPR=4.08855;DPRA=3.25275;ODDS=57.7081;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989691;PAIREDR=0.986207;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=4.824;Dels=0.0;FS= [...]
+chr12 40619082 . G A 13160.3 REJECT NS=2;DP=346;DPB=398.0;AC=4;AN=4;AF=1.0;RO=0;AO=397;PRO=0.0;PAO=0.0;QR=0;QA=15266;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=155;SAR=242;SRP=0.0;SAP=44.4105;AB=0.0;ABP=0.0;RUN=1;RPP=42.5289;RPPR=0.0;RPL=241.0;RPR=156.0;EPP=6.42886;EPPR=0.0;DPRA=0.0;ODDS=66.6601;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.987406;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=7.7731;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.805;SOR=1 [...]
+chr12 40631791 . T C 6419.280000000001 REJECT NS=2;DP=299;DPB=337.0;AC=3;AN=4;AF=0.75;RO=107;AO=230;PRO=0.0;PAO=0.0;QR=4096;QA=8771;PQR=0.0;PQA=0.0;SRF=72;SRR=35;SAF=162;SAR=68;SRP=30.793;SAP=86.4326;AB=0.591603;ABP=22.106;RUN=1;RPP=6.06924;RPPR=6.44001;RPL=106.0;RPR=124.0;EPP=6.06924;EPPR=17.8047;DPRA=0.0;ODDS=47.7762;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.447;Dels=0.0;FS=1.162;HaplotypeSc [...]
+chr12 40645257 . C A 1323.595 REJECT NS=2;DP=354;DPB=407.0;AC=2;AN=4;AF=0.5;RO=331;AO=76;PRO=0.0;PAO=0.0;QR=12513;QA=2779;PQR=0.0;PQA=0.0;SRF=173;SRR=158;SAF=32;SAR=44;SRP=4.48638;SAP=7.12467;AB=0.186732;ABP=349.939;RUN=1;RPP=4.03889;RPPR=10.1545;RPL=35.0;RPR=41.0;EPP=3.12459;EPPR=4.48638;DPRA=0.0;ODDS=72.3044;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.19;Dels=0.0;FS=5.3795;HaplotypeScore=7.79 [...]
+chr12 40657700 . C G 4763.27 REJECT NS=2;DP=340;DPB=393.0;AC=2;AN=4;AF=0.5;RO=208;AO=185;PRO=0.0;PAO=0.0;QR=7764;QA=6975;PQR=0.0;PQA=0.0;SRF=82;SRR=126;SAF=66;SAR=119;SRP=23.2217;SAP=35.9815;AB=0.470738;ABP=5.93322;RUN=1;RPP=8.18662;RPPR=4.05428;RPL=103.0;RPR=82.0;EPP=10.3464;EPPR=4.05428;DPRA=0.0;ODDS=304.724;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995192;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.721;Dels=0.0;FS=2.8875;HaplotypeScore [...]
+chr12 40681352 . T TA 2329.77 REJECT NS=2;DP=252;DPB=296.714;AC=2;AN=4;AF=0.5;RO=144;AO=108;PRO=19.3333;PAO=19.3333;QR=5487;QA=3867;PQR=704.0;PQA=683.5;SRF=32;SRR=112;SAF=24;SAR=84;SRP=99.5202;SAP=75.3927;AB=0.409091;ABP=21.9613;RUN=1;RPP=21.1059;RPPR=68.6973;RPL=69.0;RPR=39.0;EPP=6.95112;EPPR=3.07062;DPRA=0.0;ODDS=159.783;GTI=0;TYPE=ins;CIGAR=1M1I13M;NUMALT=2;MEANALT=3.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990741;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-2. [...]
+chr12 40681352 . T TAA 2922.81 REJECT NS=2;DP=264;DPB=296.714;AC=2;AN=2;AF=0.0;RO=144;AO=9;PRO=19.3333;PAO=13.3333;QR=5487;QA=300;PQR=704.0;PQA=475.5;SRF=32;SRR=112;SAF=6;SAR=3;SRP=99.5202;SAP=5.18177;AB=0.0340909;ABP=500.771;RUN=1;RPP=14.8328;RPPR=68.6973;RPL=8.0;RPR=1.0;EPP=3.25157;EPPR=3.07062;DPRA=0.0;ODDS=159.783;GTI=0;TYPE=ins;CIGAR=1M2I13M;NUMALT=2;MEANALT=3.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr12 40702911 . G A 5749.085 REJECT NS=2;DP=340;DPB=388.0;AC=2;AN=4;AF=0.5;RO=178;AO=210;PRO=0.0;PAO=0.0;QR=6687;QA=7974;PQR=0.0;PQA=0.0;SRF=111;SRR=67;SAF=150;SAR=60;SRP=26.6281;SAP=86.7671;AB=0.541237;ABP=8.7412;RUN=1;RPP=30.9706;RPPR=15.5024;RPL=79.0;RPR=131.0;EPP=3.17575;EPPR=3.0591;DPRA=0.0;ODDS=224.259;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9905;MQMR=60.0;PAIRED=0.995238;PAIREDR=0.983146;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.8705;Dels=0.0;FS=6.7955;Haplot [...]
+chr12 40702987 . G A 6380.790000000001 REJECT NS=2;DP=367;DPB=425.0;AC=2;AN=4;AF=0.5;RO=198;AO=227;PRO=0.0;PAO=0.0;QR=7343;QA=8763;PQR=0.0;PQA=0.0;SRF=81;SRR=117;SAF=95;SAR=132;SRP=17.2236;SAP=16.1061;AB=0.534118;ABP=7.30726;RUN=1;RPP=8.07069;RPPR=5.15984;RPL=125.0;RPR=102.0;EPP=31.9473;EPPR=20.5576;DPRA=0.0;ODDS=307.386;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.982379;PAIREDR=0.989899;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.4685;Dels=0.0;FS=3.11 [...]
+chr12 40713834 . C A 12616.349999999999 REJECT NS=2;DP=337;DPB=388.0;AC=4;AN=4;AF=1.0;RO=0;AO=388;PRO=0.0;PAO=0.0;QR=0;QA=14707;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=219;SAR=169;SRP=0.0;SAP=17.0017;AB=0.0;ABP=0.0;RUN=1;RPP=5.71904;RPPR=0.0;RPL=183.0;RPR=205.0;EPP=7.39802;EPPR=0.0;DPRA=0.0;ODDS=67.3541;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.987113;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.866;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32 [...]
+chr12 40713873 . A G 5944.47 REJECT NS=2;DP=370;DPB=427.0;AC=2;AN=4;AF=0.5;RO=215;AO=211;PRO=0.0;PAO=0.0;QR=8214;QA=8164;PQR=0.0;PQA=0.0;SRF=117;SRR=98;SAF=109;SAR=102;SRP=6.65635;SAP=3.51458;AB=0.494145;ABP=3.13744;RUN=1;RPP=3.51458;RPPR=3.50519;RPL=102.0;RPR=109.0;EPP=3.51458;EPPR=6.65635;DPRA=0.0;ODDS=376.81;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995261;PAIREDR=0.990698;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5225;Dels=0.0;FS=4.25;Haplotype [...]
+chr12 40715013 . T A 3446.705 REJECT NS=2;DP=215;DPB=243.0;AC=2;AN=4;AF=0.5;RO=121;AO=122;PRO=0.0;PAO=0.0;QR=4643;QA=4765;PQR=0.0;PQA=0.0;SRF=43;SRR=78;SAF=47;SAR=75;SRP=24.9942;SAP=16.9647;AB=0.502058;ABP=3.01924;RUN=1;RPP=67.0865;RPPR=57.2971;RPL=91.0;RPR=31.0;EPP=4.7902;EPPR=3.02825;DPRA=0.0;ODDS=146.51;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.061;Dels=0.0;FS=5.3715;HaplotypeScore=5.8237;M [...]
+chr12 40716260 . T C 5451.575000000001 REJECT NS=2;DP=327;DPB=372.0;AC=2;AN=4;AF=0.5;RO=178;AO=194;PRO=0.0;PAO=0.0;QR=6915;QA=7403;PQR=0.0;PQA=0.0;SRF=68;SRR=110;SAF=79;SAR=115;SRP=24.5298;SAP=17.5166;AB=0.521505;ABP=4.50465;RUN=1;RPP=10.5769;RPPR=5.40136;RPL=110.0;RPR=84.0;EPP=4.62211;EPPR=6.96287;DPRA=0.0;ODDS=273.701;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989691;PAIREDR=0.994382;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.5375;Dels=0.0;FS=3.82 [...]
+chr12 40757330 . A G 6534.870000000001 REJECT NS=2;DP=409;DPB=463.0;AC=2;AN=4;AF=0.5;RO=229;AO=234;PRO=0.0;PAO=0.0;QR=8836;QA=8879;PQR=0.0;PQA=0.0;SRF=91;SRR=138;SAF=94;SAR=140;SRP=23.9569;SAP=22.6463;AB=0.5054;ABP=3.12755;RUN=1;RPP=26.2098;RPPR=20.5433;RPL=142.0;RPR=92.0;EPP=3.04742;EPPR=4.15767;DPRA=0.0;ODDS=321.478;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995726;PAIREDR=0.995633;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.621;Dels=0.0;FS=5.9065; [...]
+chr12 40758652 . T C 10782.849999999999 REJECT NS=2;DP=287;DPB=328.0;AC=4;AN=4;AF=1.0;RO=1;AO=327;PRO=0.0;PAO=0.0;QR=16;QA=12530;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=231;SAR=96;SRP=5.18177;SAP=124.035;AB=0.0;ABP=0.0;RUN=1;RPP=7.16067;RPPR=5.18177;RPL=151.0;RPR=176.0;EPP=15.2887;EPPR=5.18177;DPRA=0.0;ODDS=54.8759;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993884;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.662;Dels=0.0;FS=0.0;HaplotypeScore=6.831 [...]
+chr12 48013327 . T C 5533.64 REJECT NS=2;DP=317;DPB=372.0;AC=2;AN=4;AF=0.5;RO=171;AO=200;PRO=0.0;PAO=0.0;QR=6505;QA=7693;PQR=0.0;PQA=0.0;SRF=116;SRR=55;SAF=134;SAR=66;SRP=50.262;SAP=53.2147;AB=0.537634;ABP=7.58674;RUN=1;RPP=25.9845;RPPR=15.2137;RPL=77.0;RPR=123.0;EPP=22.1627;EPPR=9.7279;DPRA=0.0;ODDS=296.14;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995;PAIREDR=0.988304;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.9085;Dels=0.0;FS=2.857;HaplotypeScore= [...]
+chr12 48375568 . A G 6042.21 REJECT NS=2;DP=407;DPB=469.0;AC=2;AN=4;AF=0.5;RO=247;AO=222;PRO=0.0;PAO=0.0;QR=9497;QA=8447;PQR=0.0;PQA=0.0;SRF=111;SRR=136;SAF=105;SAR=117;SRP=8.50492;SAP=4.41882;AB=0.473348;ABP=5.90405;RUN=1;RPP=20.2647;RPPR=3.01909;RPL=132.0;RPR=90.0;EPP=8.64439;EPPR=24.1184;DPRA=0.0;ODDS=392.975;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995495;PAIREDR=0.987854;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.3535;Dels=0.0;FS=1.6615;Haplot [...]
+chr12 48375965 . C T 4297.765 REJECT NS=2;DP=277;DPB=317.0;AC=2;AN=4;AF=0.5;RO=162;AO=155;PRO=0.0;PAO=0.0;QR=6194;QA=5909;PQR=0.0;PQA=0.0;SRF=53;SRR=109;SAF=52;SAR=103;SRP=45.0457;SAP=39.449;AB=0.488959;ABP=3.34595;RUN=1;RPP=4.14507;RPPR=22.3659;RPL=82.0;RPR=73.0;EPP=10.4213;EPPR=3.22477;DPRA=0.0;ODDS=244.013;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987097;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6815;Dels=0.0;FS=0.445;HaplotypeScore= [...]
+chr12 48376291 . G A 7020.67 REJECT NS=2;DP=422;DPB=485.0;AC=2;AN=4;AF=0.5;RO=230;AO=255;PRO=0.0;PAO=0.0;QR=8698;QA=9650;PQR=0.0;PQA=0.0;SRF=127;SRR=103;SAF=138;SAR=117;SRP=8.44842;SAP=6.76567;AB=0.525773;ABP=5.80859;RUN=1;RPP=4.92631;RPPR=3.95442;RPL=120.0;RPR=135.0;EPP=7.51504;EPPR=3.16136;DPRA=0.0;ODDS=335.582;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996078;PAIREDR=0.986957;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6745;Dels=0.0;FS=1.1495;Haplo [...]
+chr12 48376969 . C A 4097.605 REJECT NS=2;DP=261;DPB=304.0;AC=2;AN=4;AF=0.5;RO=149;AO=155;PRO=0.0;PAO=0.0;QR=5650;QA=5663;PQR=0.0;PQA=0.0;SRF=79;SRR=70;SAF=75;SAR=80;SRP=4.19076;SAP=3.36054;AB=0.509868;ABP=3.26745;RUN=1;RPP=24.3187;RPPR=35.2035;RPL=97.0;RPR=58.0;EPP=14.7923;EPPR=4.77371;DPRA=0.0;ODDS=243.181;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.6345;Dels=0.0;FS=2.7765;HaplotypeScore=3.93 [...]
+chr12 48389023 . C T 5212.24 REJECT NS=2;DP=306;DPB=350.0;AC=2;AN=4;AF=0.5;RO=165;AO=184;PRO=0.0;PAO=0.0;QR=6216;QA=7086;PQR=0.0;PQA=0.0;SRF=107;SRR=58;SAF=117;SAR=67;SRP=34.6085;SAP=32.514;AB=0.525714;ABP=5.02046;RUN=1;RPP=32.514;RPPR=6.81367;RPL=67.0;RPR=117.0;EPP=12.2627;EPPR=12.6043;DPRA=0.0;ODDS=251.751;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4985;Dels=0.0;FS=0.403;HaplotypeScore=2.9662 [...]
+chr12 48389643 . A C 12819.2 REJECT NS=2;DP=335;DPB=380.0;AC=4;AN=4;AF=1.0;RO=0;AO=380;PRO=0.0;PAO=0.0;QR=0;QA=14673;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=182;SAR=198;SRP=0.0;SAP=4.47319;AB=0.0;ABP=0.0;RUN=1;RPP=3.58174;RPPR=0.0;RPL=195.0;RPR=185.0;EPP=11.2619;EPPR=0.0;DPRA=0.0;ODDS=60.4961;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.325;SOR=0.805 [...]
+chr12 48390435 . A T 1279.31 REJECT NS=2;DP=267;DPB=305.0;AC=2;AN=4;AF=0.5;RO=234;AO=70;PRO=0.0;PAO=0.0;QR=8908;QA=2617;PQR=0.0;PQA=0.0;SRF=62;SRR=172;SAF=26;SAR=44;SRP=115.296;SAP=13.0611;AB=0.229508;ABP=196.841;RUN=1;RPP=30.9292;RPPR=92.1335;RPL=50.0;RPR=20.0;EPP=4.12706;EPPR=4.82914;DPRA=0.0;ODDS=119.912;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991453;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.121;Dels=0.0;FS=4.394;HaplotypeScore=6.8 [...]
+chr12 48393781 . G A 2945.89 PASS SOMATIC;NS=2;DP=429;DPB=429.0;AC=1;AN=3;AF=0.25;RO=316;AO=112;PRO=0.0;PAO=0.0;QR=12183;QA=4343;PQR=0.0;PQA=0.0;SRF=160;SRR=156;SAF=51;SAR=61;SRP=3.12025;SAP=4.94911;AB=0.340426;ABP=75.7777;RUN=1;RPP=20.4596;RPPR=21.5915;RPL=71.0;RPR=41.0;EPP=3.32051;EPPR=18.8428;DPRA=3.29;ODDS=63.3533;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996835;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.226;Dels=0.0;FS=2.516; [...]
+chr12 48398002 . G C 2992.19 REJECT NS=1;DP=88;DPB=88.0;AC=2;AN=4;AF=1.0;RO=0;AO=88;PRO=0.0;PAO=0.0;QR=0;QA=3385;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=50;SAR=38;SRP=0.0;SAP=6.56362;AB=0.0;ABP=0.0;RUN=1;RPP=22.3561;RPPR=0.0;RPL=30.0;RPR=58.0;EPP=3.0103;EPPR=0.0;DPRA=0.0;ODDS=59.5278;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.49;SOR=1.03 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:AD: [...]
+chr12 48398080 . T A 3126.67 REJECT NS=1;DP=93;DPB=93.0;AC=2;AN=4;AF=1.0;RO=0;AO=93;PRO=0.0;PAO=0.0;QR=0;QA=3553;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=32;SAR=61;SRP=0.0;SAP=22.6469;AB=0.0;ABP=0.0;RUN=1;RPP=3.03365;RPPR=0.0;RPL=46.0;RPR=47.0;EPP=22.6469;EPPR=0.0;DPRA=0.0;ODDS=62.674;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.23;SOR=1.46 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:AD: [...]
+chr12 49416046 . TC T 2638.81 PASS SOMATIC;NS=2;DP=474;DPB=465.5;AC=1;AN=4;AF=0.25;RO=348;AO=117;PRO=15.5;PAO=8.5;QR=13094;QA=4086;PQR=427.0;PQA=190.0;SRF=121;SRR=227;SAF=40;SAR=77;SRP=73.1214;SAP=28.4184;AB=0.327731;ABP=95.0333;RUN=1;RPP=9.71031;RPPR=3.23494;RPL=49.0;RPR=68.0;EPP=5.25601;EPPR=3.11014;DPRA=3.05128;ODDS=75.8793;GTI=0;TYPE=del;CIGAR=1M1D4M;NUMALT=1;MEANALT=6.0;LEN=1;MQM=60.3419;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994253;technology.ILLUMINA=1.0;MQ0=0;END=49416047;HOMLEN=1;HOMSEQ [...]
+chr12 49425978 . T C 2719.22 PASS SOMATIC;NS=2;DP=450;DPB=450.0;AC=1;AN=3;AF=0.25;RO=343;AO=107;PRO=0.0;PAO=0.0;QR=13181;QA=4077;PQR=0.0;PQA=0.0;SRF=160;SRR=183;SAF=50;SAR=57;SRP=6.35931;SAP=4.00471;AB=0.32622;ABP=89.0483;RUN=1;RPP=3.51765;RPPR=18.2106;RPL=56.0;RPR=51.0;EPP=8.8753;EPPR=5.80219;DPRA=2.68852;ODDS=77.1103;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990654;PAIREDR=0.991254;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.294;Dels=0.0;FS= [...]
+chr12 49427108 . G A 3885.27 REJECT NS=2;DP=276;DPB=307.0;AC=2;AN=4;AF=0.5;RO=159;AO=147;PRO=0.0;PAO=0.0;QR=6002;QA=5313;PQR=0.0;PQA=0.0;SRF=87;SRR=72;SAF=84;SAR=63;SRP=6.08314;SAP=9.52472;AB=0.478827;ABP=4.20567;RUN=1;RPP=3.73412;RPPR=3.35173;RPL=70.0;RPR=77.0;EPP=4.20683;EPPR=3.35173;DPRA=0.0;ODDS=132.09;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993197;PAIREDR=0.993711;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.568;Dels=0.0;FS=7.151;HaplotypeScor [...]
+chr12 49427652 . C T 2357.43 PASS SOMATIC;NS=2;DP=316;DPB=316.0;AC=1;AN=3;AF=0.25;RO=226;AO=90;PRO=0.0;PAO=0.0;QR=8692;QA=3382;PQR=0.0;PQA=0.0;SRF=115;SRR=111;SAF=47;SAR=43;SRP=3.16403;SAP=3.39634;AB=0.384615;ABP=30.0702;RUN=1;RPP=5.42305;RPPR=4.89352;RPL=50.0;RPR=40.0;EPP=3.0103;EPPR=3.16403;DPRA=2.85366;ODDS=52.1928;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.5619;PAIRED=1.0;PAIREDR=0.995575;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.733;Dels=0.0;FS=0.0 [...]
+chr12 49434074 . C A 2475.19 PASS SOMATIC;NS=2;DP=400;DPB=400.0;AC=1;AN=3;AF=0.25;RO=298;AO=102;PRO=0.0;PAO=0.0;QR=11435;QA=3690;PQR=0.0;PQA=0.0;SRF=149;SRR=149;SAF=47;SAR=55;SRP=3.0103;SAP=4.37279;AB=0.350515;ABP=59.491;RUN=1;RPP=3.35092;RPPR=4.43852;RPL=53.0;RPR=49.0;EPP=9.90792;EPPR=4.0596;DPRA=2.66972;ODDS=69.0317;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-4.55;Dels=0.01;FS=0.948;Hapl [...]
+chr12 49439659 . C T 8184.595 REJECT NS=2;DP=217;DPB=246.0;AC=4;AN=4;AF=1.0;RO=0;AO=246;PRO=0.0;PAO=0.0;QR=0;QA=9413;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=166;SAR=80;SRP=0.0;SAP=68.2957;AB=0.0;ABP=0.0;RUN=1;RPP=91.2815;RPPR=0.0;RPL=73.0;RPR=173.0;EPP=3.57524;EPPR=0.0;DPRA=0.0;ODDS=39.8836;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.987805;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9129;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.015;SOR=1.5 [...]
+chr12 49442356 . C CA . PASS SOMATIC;AC=1;AN=4 GT:AD:DP:MM:MQS:NQSBQ:NQSMM:REnd:RStart:SC:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:8,0:8:0.125,0.0:60.0,0.0:35.75,0.0:0.0,0.0:0,0:0,0:7,1,0,0:0:0:8:.:.:.:.:0:.:-0.00355946 0/1:27,13:40:0.0740741,0.0:60.0,63.0769:36.1111,36.0583:0.0,0.0:94,2:5,2:22,5,12,1:13:33:40:.:.:.:.:1:.:-0.0302105
+chr12 49444545 . G A 2953.72 PASS SOMATIC;NS=2;DP=393;DPB=393.0;AC=1;AN=3;AF=0.25;RO=283;AO=110;PRO=0.0;PAO=0.0;QR=10428;QA=4225;PQR=0.0;PQA=0.0;SRF=114;SRR=169;SAF=42;SAR=68;SRP=26.2213;SAP=16.355;AB=0.381944;ABP=37.8745;RUN=1;RPP=4.2737;RPPR=7.80595;RPL=59.0;RPR=51.0;EPP=3.32615;EPPR=24.5639;DPRA=2.74286;ODDS=66.3636;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990909;PAIREDR=0.996466;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.132;Dels=0.0;FS= [...]
+chr12 51181970 . C T 118.724 REJECT NS=1;DP=66;DPB=90.6667;AC=1;AN=3;AF=0.0;RO=39;AO=5;PRO=16.4167;PAO=5.08333;QR=1437;QA=85;PQR=593.583;PQA=131.25;SRF=7;SRR=32;SAF=0;SAR=5;SRP=37.8095;SAP=13.8677;AB=0.0757576;ABP=106.188;RUN=1;RPP=6.91895;RPPR=19.1015;RPL=1.0;RPR=4.0;EPP=6.91895;EPPR=3.51141;DPRA=0.0;ODDS=9.74379;GTI=0;TYPE=snp;CIGAR=1X17M;NUMALT=3;MEANALT=6.0;LEN=1;MQM=56.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr12 51181970 . C CT 118.724 REJECT NS=1;DP=66;DPB=90.6667;AC=1;AN=3;AF=0.0;RO=39;AO=9;PRO=16.4167;PAO=15.4167;QR=1437;QA=262;PQR=593.583;PQA=518.583;SRF=7;SRR=32;SAF=2;SAR=7;SRP=37.8095;SAP=9.04217;AB=0.136364;ABP=78.8144;RUN=1;RPP=9.04217;RPPR=19.1015;RPL=7.0;RPR=2.0;EPP=3.25157;EPPR=3.51141;DPRA=0.0;ODDS=9.74379;GTI=0;TYPE=ins;CIGAR=1M1I17M;NUMALT=3;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr12 51181970 . CT C 118.724 REJECT NS=1;DP=66;DPB=90.6667;AC=1;AN=4;AF=0.5;RO=39;AO=9;PRO=16.4167;PAO=13.0833;QR=1437;QA=320;PQR=593.583;PQA=472.583;SRF=7;SRR=32;SAF=2;SAR=7;SRP=37.8095;SAP=9.04217;AB=0.136364;ABP=78.8144;RUN=1;RPP=3.25157;RPPR=19.1015;RPL=5.0;RPR=4.0;EPP=5.18177;EPPR=3.51141;DPRA=0.0;ODDS=9.74379;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=3;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr12 51203226 . GT G 8193.56 REJECT NS=2;DP=271;DPB=308.0;AC=4;AN=4;AF=1.0;RO=2;AO=302;PRO=14.5;PAO=15.5;QR=36;QA=10445;PQR=507.5;PQA=547.5;SRF=2;SRR=0;SAF=238;SAR=64;SRP=7.35324;SAP=220.704;AB=0.0;ABP=0.0;RUN=1;RPP=113.568;RPPR=7.35324;RPL=89.0;RPR=213.0;EPP=25.5591;EPPR=7.35324;DPRA=0.0;ODDS=58.8831;GTI=0;TYPE=del;CIGAR=1M1D10M;NUMALT=1;MEANALT=6.0;LEN=1;MQM=60.1656;MQMR=50.5;PAIRED=0.993377;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.2;QD=31.49;RPA=8,7;RU [...]
+chr12 51203602 . C CTGTTT 967.753 REJECT NS=2;DP=116;DPB=243.639;AC=2;AN=4;AF=0.5;RO=74;AO=40;PRO=117.0;PAO=118.0;QR=2779;QA=1456;PQR=4355.5;PQA=4392.5;SRF=19;SRR=55;SAF=8;SAR=32;SRP=41.0404;SAP=34.2795;AB=0.344828;ABP=27.2709;RUN=1;RPP=10.8276;RPPR=19.9126;RPL=26.0;RPR=14.0;EPP=3.0103;EPPR=5.94472;DPRA=0.0;ODDS=79.2076;GTI=0;TYPE=ins;CIGAR=1M5I35M;NUMALT=1;MEANALT=2.0;LEN=5;MQM=60.0;MQMR=60.0;PAIRED=0.975;PAIREDR=1.0;technology.ILLUMINA=1.0;END=51203602;HOMLEN=32;HOMSEQ=TGTTTTGTTTTGTTTT [...]
+chr12 51203688 . C G 1650.385 REJECT NS=2;DP=125;DPB=146.0;AC=2;AN=4;AF=0.5;RO=77;AO=69;PRO=0.0;PAO=0.0;QR=2967;QA=2525;PQR=0.0;PQA=0.0;SRF=5;SRR=72;SAF=9;SAR=60;SRP=129.604;SAP=84.8654;AB=0.472603;ABP=3.96218;RUN=1;RPP=3.79707;RPPR=3.71532;RPL=37.0;RPR=32.0;EPP=6.81824;EPPR=3.71532;DPRA=0.0;ODDS=118.29;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.7101;MQMR=60.0;PAIRED=0.971014;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.001;Dels=0.0;FS=3.184;HaplotypeScore=1.9 [...]
+chr12 51203953 . A G 1443.88 REJECT NS=2;DP=125;DPB=145.0;AC=2;AN=4;AF=0.5;RO=81;AO=62;PRO=0.0;PAO=0.0;QR=3053;QA=2263;PQR=0.0;PQA=0.0;SRF=46;SRR=35;SAF=40;SAR=22;SRP=6.2541;SAP=14.358;AB=0.427586;ABP=9.61457;RUN=1;RPP=19.9618;RPPR=3.68051;RPL=20.0;RPR=42.0;EPP=4.27115;EPPR=6.2541;DPRA=0.0;ODDS=93.2216;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.1613;MQMR=60.0;PAIRED=0.935484;PAIREDR=0.962963;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.572;Dels=0.0;FS=2.0;HaplotypeScore=1 [...]
+chr12 51204002 . C CT 164.392 REJECT NS=2;DP=34;DPB=70.4;AC=2;AN=4;AF=0.5;RO=13;AO=4;PRO=20.7667;PAO=20.7667;QR=441;QA=121;PQR=731.05;PQA=743.05;SRF=8;SRR=5;SAF=2;SAR=2;SRP=4.51363;SAP=3.0103;AB=0.117647;ABP=46.1843;RUN=1;RPP=5.18177;RPPR=16.5402;RPL=3.0;RPR=1.0;EPP=5.18177;EPPR=11.1951;DPRA=0.0;ODDS=15.6924;GTI=0;TYPE=ins;CIGAR=1M1I24M;NUMALT=4;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=58.4615;PAIRED=1.0;PAIREDR=0.923077;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.361;FS=0.0;MLEAC=1; [...]
+chr12 51204002 . CT C 164.392 REJECT NS=2;DP=34;DPB=70.4;AC=2;AN=2;AF=0.0;RO=13;AO=4;PRO=20.7667;PAO=11.7667;QR=441;QA=134;PQR=731.05;PQA=416.05;SRF=8;SRR=5;SAF=3;SAR=1;SRP=4.51363;SAP=5.18177;AB=0.117647;ABP=46.1843;RUN=1;RPP=11.6962;RPPR=16.5402;RPL=4.0;RPR=0.0;EPP=5.18177;EPPR=11.1951;DPRA=0.0;ODDS=15.6924;GTI=0;TYPE=del;CIGAR=1M1D23M;NUMALT=4;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=58.4615;PAIRED=1.0;PAIREDR=0.923077;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr12 51204002 . CTTT C 164.392 REJECT NS=2;DP=34;DPB=70.4;AC=2;AN=2;AF=0.0;RO=13;AO=3;PRO=20.7667;PAO=10.1;QR=441;QA=86;PQR=731.05;PQA=354.8;SRF=8;SRR=5;SAF=1;SAR=2;SRP=4.51363;SAP=3.73412;AB=0.0882353;ABP=53.0819;RUN=1;RPP=9.52472;RPPR=16.5402;RPL=3.0;RPR=0.0;EPP=3.73412;EPPR=11.1951;DPRA=0.0;ODDS=15.6924;GTI=0;TYPE=del;CIGAR=1M3D21M;NUMALT=4;MEANALT=7.5;LEN=3;MQM=60.0;MQMR=58.4615;PAIRED=1.0;PAIREDR=0.923077;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr12 51204018 . TG T 164.392 REJECT NS=2;DP=34;DPB=70.4;AC=2;AN=2;AF=0.0;RO=13;AO=2;PRO=20.7667;PAO=13.6;QR=441;QA=16;PQR=731.05;PQA=488.05;SRF=8;SRR=5;SAF=2;SAR=0;SRP=4.51363;SAP=7.35324;AB=0.08;ABP=41.3151;RUN=1;RPP=7.35324;RPPR=16.5402;RPL=2.0;RPR=0.0;EPP=7.35324;EPPR=11.1951;DPRA=0.0;ODDS=15.6924;GTI=0;TYPE=del;CIGAR=17M1D7M;NUMALT=4;MEANALT=9.0;LEN=1;MQM=60.0;MQMR=58.4615;PAIRED=0.5;PAIREDR=0.923077;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr12 51204149 . T C 2483.65 REJECT NS=2;DP=77;DPB=91.0;AC=4;AN=4;AF=1.0;RO=0;AO=91;PRO=0.0;PAO=0.0;QR=0;QA=3082;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=50;SAR=41;SRP=0.0;SAP=4.94315;AB=0.0;ABP=0.0;RUN=1;RPP=3.03416;RPPR=0.0;RPL=45.0;RPR=46.0;EPP=20.4059;EPPR=0.0;DPRA=0.0;ODDS=20.5085;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.2308;MQMR=0.0;PAIRED=0.956044;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=59.49;QD=33.045;SOR=1.013 GT [...]
+chr12 51204295 . C T 2989.275 REJECT NS=2;DP=175;DPB=201.0;AC=2;AN=4;AF=0.5;RO=94;AO=107;PRO=0.0;PAO=0.0;QR=3604;QA=4074;PQR=0.0;PQA=0.0;SRF=71;SRR=23;SAF=81;SAR=26;SRP=56.2345;SAP=64.4001;AB=0.532338;ABP=4.83607;RUN=1;RPP=5.46589;RPPR=18.6264;RPL=48.0;RPR=59.0;EPP=6.44001;EPPR=8.9241;DPRA=0.0;ODDS=156.132;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.4574;PAIRED=0.990654;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0285;Dels=0.0;FS=1.662;HaplotypeScore [...]
+chr12 51205066 . CA TT 6859.4 REJECT NS=2;DP=481;DPB=554.0;AC=2;AN=4;AF=0.5;RO=298;AO=252;PRO=2.0;PAO=4.0;QR=11429;QA=9571;PQR=76.0;PQA=149.0;SRF=156;SRR=142;SAF=116;SAR=136;SRP=4.43852;SAP=6.45708;AB=0.45735;ABP=11.7159;RUN=1;RPP=3.04477;RPPR=3.47666;RPL=125.0;RPR=127.0;EPP=5.80219;EPPR=3.0103;DPRA=0.0;ODDS=446.256;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=1;MEANALT=1.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989933;technology.ILLUMINA=1.0;MQ0=0;JOINED;BaseQRankSum=-0.7035;Dels=0.0;FS=4.9415 [...]
+chr12 51205306 . T C 6842.705 REJECT NS=2;DP=193;DPB=230.0;AC=4;AN=4;AF=1.0;RO=1;AO=229;PRO=0.0;PAO=0.0;QR=16;QA=8367;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=83;SAR=146;SRP=5.18177;SAP=40.646;AB=0.0;ABP=0.0;RUN=1;RPP=3.09564;RPPR=5.18177;RPL=116.0;RPR=113.0;EPP=10.985;EPPR=5.18177;DPRA=0.0;ODDS=48.9814;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995633;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.577;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEA [...]
+chr12 51205413 . G A 306.725 REJECT NS=2;DP=93;DPB=193.846;AC=2;AN=2;AF=0.0;RO=30;AO=11;PRO=60.25;PAO=23.25;QR=1006;QA=286;PQR=2149.93;PQA=788.1;SRF=24;SRR=6;SAF=1;SAR=10;SRP=26.4622;SAP=19.0002;AB=0.11828;ABP=120.713;RUN=1;RPP=3.20771;RPPR=10.2485;RPL=5.0;RPR=6.0;EPP=3.20771;EPPR=5.61607;DPRA=0.0;ODDS=0.230029;GTI=0;TYPE=snp;CIGAR=1X25M;NUMALT=4;MEANALT=12.0;LEN=1;MQM=56.9091;MQMR=59.3;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr12 51205413 . G GA 306.725 REJECT NS=2;DP=93;DPB=193.846;AC=2;AN=3;AF=0.25;RO=30;AO=17;PRO=60.25;PAO=56.25;QR=1006;QA=517;PQR=2149.93;PQA=2000.93;SRF=24;SRR=6;SAF=14;SAR=3;SRP=26.4622;SAP=18.4661;AB=0.182796;ABP=84.2887;RUN=1;RPP=3.13803;RPPR=10.2485;RPL=9.0;RPR=8.0;EPP=6.20364;EPPR=5.61607;DPRA=0.0;ODDS=0.230029;GTI=0;TYPE=ins;CIGAR=1M1I25M;NUMALT=4;MEANALT=12.0;LEN=1;MQM=55.4118;MQMR=59.3;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.467;FS=7 [...]
+chr12 51205413 . G AA 306.725 REJECT NS=2;DP=93;DPB=193.846;AC=2;AN=2;AF=0.0;RO=30;AO=4;PRO=60.25;PAO=23.25;QR=1006;QA=64;PQR=2149.93;PQA=788.1;SRF=24;SRR=6;SAF=0;SAR=4;SRP=26.4622;SAP=11.6962;AB=0.057971;ABP=120.112;RUN=1;RPP=5.18177;RPPR=10.2485;RPL=3.0;RPR=1.0;EPP=5.18177;EPPR=5.61607;DPRA=0.0;ODDS=0.230029;GTI=0;TYPE=complex;CIGAR=1X1I25M;NUMALT=4;MEANALT=16.0;LEN=27;MQM=70.0;MQMR=59.3;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr12 51205413 . GA G 306.725 REJECT NS=2;DP=93;DPB=193.846;AC=2;AN=3;AF=0.25;RO=30;AO=10;PRO=60.25;PAO=36.0;QR=1006;QA=324;PQR=2149.93;PQA=1266.93;SRF=24;SRR=6;SAF=8;SAR=2;SRP=26.4622;SAP=10.8276;AB=0.107527;ABP=127.438;RUN=1;RPP=3.87889;RPPR=10.2485;RPL=6.0;RPR=4.0;EPP=3.87889;EPPR=5.61607;DPRA=0.0;ODDS=0.230029;GTI=0;TYPE=del;CIGAR=1M1D24M;NUMALT=4;MEANALT=12.0;LEN=1;MQM=59.8;MQMR=59.3;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr12 51207414 . T C 1014.52 REJECT NS=2;DP=70;DPB=80.0;AC=2;AN=4;AF=0.5;RO=42;AO=38;PRO=0.0;PAO=0.0;QR=1576;QA=1455;PQR=0.0;PQA=0.0;SRF=22;SRR=20;SAF=13;SAR=25;SRP=3.21711;SAP=11.239;AB=0.475;ABP=3.44459;RUN=1;RPP=6.66752;RPPR=4.87156;RPL=23.0;RPR=15.0;EPP=21.525;EPPR=8.18047;DPRA=0.0;ODDS=54.5253;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.973684;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.425;Dels=0.0;FS=4.497;HaplotypeScore=0.9665;MLEAC [...]
+chr12 51207603 . GA G 4234.37 REJECT NS=2;DP=223;DPB=293.2;AC=2;AN=4;AF=0.5;RO=28;AO=178;PRO=36.5833;PAO=42.5833;QR=1039;QA=6029;PQR=1251.25;PQA=1457.25;SRF=18;SRR=10;SAF=145;SAR=33;SRP=7.97367;SAP=156.038;AB=0.754237;ABP=135.507;RUN=1;RPP=93.2362;RPPR=28.1373;RPL=46.0;RPR=132.0;EPP=10.0371;EPPR=3.32051;DPRA=0.0;ODDS=20.9675;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=3;MEANALT=9.5;LEN=1;MQM=60.2247;MQMR=60.0;PAIRED=0.994382;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQR [...]
+chr12 51207603 . GAA G 4765.01 REJECT NS=2;DP=236;DPB=293.2;AC=2;AN=2;AF=0.0;RO=28;AO=13;PRO=36.5833;PAO=35.0833;QR=1039;QA=496;PQR=1251.25;PQA=1201.75;SRF=18;SRR=10;SAF=9;SAR=4;SRP=7.97367;SAP=7.18621;AB=0.0550847;ABP=408.781;RUN=1;RPP=16.5402;RPPR=28.1373;RPL=2.0;RPR=11.0;EPP=3.17734;EPPR=3.32051;DPRA=0.0;ODDS=20.9675;GTI=0;TYPE=del;CIGAR=1M2D17M;NUMALT=3;MEANALT=9.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr12 51207603 . GAAA G 4765.01 REJECT NS=2;DP=236;DPB=293.2;AC=2;AN=2;AF=0.0;RO=28;AO=4;PRO=36.5833;PAO=28.75;QR=1039;QA=155;PQR=1251.25;PQA=963.75;SRF=18;SRR=10;SAF=3;SAR=1;SRP=7.97367;SAP=5.18177;AB=0.0169492;ABP=481.323;RUN=1;RPP=5.18177;RPPR=28.1373;RPL=1.0;RPR=3.0;EPP=3.0103;EPPR=3.32051;DPRA=0.0;ODDS=20.9675;GTI=0;TYPE=del;CIGAR=1M3D16M;NUMALT=3;MEANALT=9.5;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr12 51207704 . A G 7102.785 REJECT NS=2;DP=448;DPB=524.0;AC=2;AN=4;AF=0.5;RO=261;AO=262;PRO=0.0;PAO=0.0;QR=10067;QA=9879;PQR=0.0;PQA=0.0;SRF=136;SRR=125;SAF=149;SAR=113;SRP=4.017;SAP=13.7516;AB=0.5;ABP=3.0103;RUN=1;RPP=3.14291;RPPR=3.2183;RPL=129.0;RPR=133.0;EPP=64.3088;EPPR=28.1777;DPRA=0.0;ODDS=460.335;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992366;PAIREDR=0.992337;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.4255;Dels=0.0;FS=5.291;HaplotypeSco [...]
+chr12 51213433 . A G 2706.58 PASS SOMATIC;NS=2;DP=379;DPB=379.0;AC=1;AN=3;AF=0.25;RO=270;AO=109;PRO=0.0;PAO=0.0;QR=10092;QA=3942;PQR=0.0;PQA=0.0;SRF=191;SRR=79;SAF=70;SAR=39;SRP=103.895;SAP=22.1551;AB=0.396364;ABP=28.6653;RUN=1;RPP=24.7051;RPPR=24.7572;RPL=38.0;RPR=71.0;EPP=8.76769;EPPR=23.1165;DPRA=2.64423;ODDS=65.7867;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9407;PAIRED=0.990826;PAIREDR=0.996296;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.408;Dels=0. [...]
+chr12 53662624 . C A 9513.95 REJECT NS=2;DP=358;DPB=406.0;AC=2;AN=4;AF=0.5;RO=80;AO=326;PRO=0.0;PAO=0.0;QR=3103;QA=11898;PQR=0.0;PQA=0.0;SRF=50;SRR=30;SAF=161;SAR=165;SRP=13.8677;SAP=3.11688;AB=0.802956;ABP=326.677;RUN=1;RPP=17.1049;RPPR=3.0103;RPL=140.0;RPR=186.0;EPP=15.9059;EPPR=4.74748;DPRA=0.0;ODDS=95.658;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993865;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-3.021;Dels=0.0;FS=10.8185;HaplotypeScor [...]
+chr12 53662735 . C T 10319.9 REJECT NS=2;DP=386;DPB=437.0;AC=2;AN=4;AF=0.5;RO=100;AO=337;PRO=0.0;PAO=0.0;QR=3752;QA=12917;PQR=0.0;PQA=0.0;SRF=47;SRR=53;SAF=150;SAR=187;SRP=3.79203;SAP=11.8315;AB=0.771167;ABP=282.117;RUN=1;RPP=37.3479;RPPR=10.0459;RPL=205.0;RPR=132.0;EPP=11.8315;EPPR=3.35774;DPRA=0.0;ODDS=169.05;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7115;Dels=0.0;FS=2.4045;HaplotypeScore=2. [...]
+chr12 53664148 . G A 7045.59 REJECT NS=2;DP=270;DPB=305.0;AC=2;AN=4;AF=0.5;RO=60;AO=243;PRO=0.0;PAO=0.0;QR=2208;QA=8917;PQR=0.0;PQA=0.0;SRF=42;SRR=18;SAF=141;SAR=102;SRP=23.8564;SAP=16.6021;AB=0.796721;ABP=236.255;RUN=1;RPP=80.2986;RPPR=27.4756;RPL=75.0;RPR=168.0;EPP=6.23623;EPPR=4.31318;DPRA=0.0;ODDS=60.6093;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.579;Dels=0.0;FS=5.9435;HaplotypeScore=6.82 [...]
+chr12 53670545 . C A 10964.7 REJECT NS=2;DP=400;DPB=462.0;AC=2;AN=4;AF=0.5;RO=101;AO=360;PRO=0.0;PAO=0.0;QR=3823;QA=13657;PQR=0.0;PQA=0.0;SRF=43;SRR=58;SAF=164;SAR=196;SRP=7.84774;SAP=9.18693;AB=0.779221;ABP=315.872;RUN=1;RPP=4.55446;RPPR=3.0318;RPL=188.0;RPR=172.0;EPP=3.0103;EPPR=6.64375;DPRA=0.0;ODDS=145.926;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997222;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.178;Dels=0.0;FS=4.127;HaplotypeScore= [...]
+chr12 53681883 . A T 12327.9 REJECT NS=2;DP=326;DPB=372.0;AC=4;AN=4;AF=1.0;RO=0;AO=372;PRO=0.0;PAO=0.0;QR=0;QA=14186;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=205;SAR=167;SRP=0.0;SAP=11.4393;AB=0.0;ABP=0.0;RUN=1;RPP=20.0318;RPPR=0.0;RPL=159.0;RPR=213.0;EPP=3.0103;EPPR=0.0;DPRA=0.0;ODDS=61.7401;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8771;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.11;SOR=0.915 GT [...]
+chr12 53682267 . CAA C . PASS SOMATIC;AC=1;AN=4 GT:AD:DP:MM:MQS:NQSBQ:NQSMM:REnd:RStart:SC:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:41,0:41:0.195122,0.0:60.0,0.0:37.4827,0.0:0.0,0.0:0,0:0,0:24,17,0,0:0:0:41:.:.:.:.:0:.:-0.00355946 0/1:84,45:129:0.119048,0.933333:60.0,60.4444:37.4372,38.9368:0.0,0.0:73,10:27,10:48,36,28,17:45:35:129:.:.:.:.:1:.:-0.0302105
+chr12 53682326 . G A 2527.68 PASS SOMATIC;NS=2;DP=373;DPB=373.0;AC=1;AN=3;AF=0.25;RO=274;AO=98;PRO=0.0;PAO=0.0;QR=10350;QA=3705;PQR=0.0;PQA=0.0;SRF=174;SRR=100;SAF=61;SAR=37;SRP=46.408;SAP=15.7732;AB=0.357664;ABP=51.2265;RUN=1;RPP=4.4284;RPPR=3.80281;RPL=45.0;RPR=53.0;EPP=3.09893;EPPR=6.84604;DPRA=2.76768;ODDS=62.6985;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.2041;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992701;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.253;Dels=0.0;FS=1.0 [...]
+chr12 53682457 . G A 9285.235 REJECT NS=2;DP=382;DPB=434.0;AC=3;AN=4;AF=0.75;RO=106;AO=327;PRO=0.0;PAO=0.0;QR=4079;QA=12378;PQR=0.0;PQA=0.0;SRF=42;SRR=64;SAF=140;SAR=187;SRP=12.9253;SAP=17.6794;AB=0.679758;ABP=95.9113;RUN=1;RPP=7.85129;RPPR=14.81;RPL=150.0;RPR=177.0;EPP=20.2825;EPPR=19.071;DPRA=0.0;ODDS=64.641;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990826;PAIREDR=0.990566;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.15;Dels=0.0;FS=0.9975;Haplotype [...]
+chr12 53682986 . C T 6795.63 REJECT NS=2;DP=316;DPB=368.0;AC=3;AN=4;AF=0.75;RO=111;AO=257;PRO=0.0;PAO=0.0;QR=4213;QA=9687;PQR=0.0;PQA=0.0;SRF=55;SRR=56;SAF=99;SAR=158;SRP=3.02986;SAP=32.4223;AB=0.582707;ABP=18.8147;RUN=1;RPP=7.47998;RPPR=3.18637;RPL=140.0;RPR=117.0;EPP=3.22153;EPPR=3.02986;DPRA=0.0;ODDS=64.5849;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988327;PAIREDR=0.990991;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.435;Dels=0.0;FS=3.877;Haplotype [...]
+chr12 53684619 . A G 7345.7 REJECT NS=2;DP=301;DPB=353.0;AC=3;AN=4;AF=0.75;RO=87;AO=266;PRO=0.0;PAO=0.0;QR=3333;QA=10210;PQR=0.0;PQA=0.0;SRF=62;SRR=25;SAF=187;SAR=79;SRP=37.1798;SAP=98.2285;AB=0.656126;ABP=56.5761;RUN=1;RPP=14.7983;RPPR=4.23331;RPL=114.0;RPR=152.0;EPP=9.41043;EPPR=6.03039;DPRA=0.0;ODDS=63.2938;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.93609;PAIREDR=0.942529;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.897;Dels=0.0;FS=0.0;HaplotypeScor [...]
+chr12 53686703 . G A 15001.599999999999 REJECT NS=2;DP=397;DPB=458.0;AC=4;AN=4;AF=1.0;RO=0;AO=458;PRO=0.0;PAO=0.0;QR=0;QA=17388;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=225;SAR=233;SRP=0.0;SAP=3.31374;AB=0.0;ABP=0.0;RUN=1;RPP=3.48442;RPPR=0.0;RPL=224.0;RPR=234.0;EPP=6.72741;EPPR=0.0;DPRA=0.0;ODDS=78.4335;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.9869;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8902;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28. [...]
+chr12 56375881 . C T 1504.71 REJECT NS=1;DP=113;DPB=113.0;AC=1;AN=4;AF=0.5;RO=58;AO=55;PRO=0.0;PAO=0.0;QR=2142;QA=2119;PQR=0.0;PQA=0.0;SRF=33;SRR=25;SAF=34;SAR=21;SRP=5.40641;SAP=9.68264;AB=0.486726;ABP=3.18325;RUN=1;RPP=36.2141;RPPR=24.5753;RPL=13.0;RPR=42.0;EPP=9.68264;EPPR=15.1406;DPRA=0.0;ODDS=346.473;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=2.783;FS=1.536;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.52 [...]
+chr12 56477694 . A T 1665.175 REJECT NS=2;DP=265;DPB=307.0;AC=2;AN=4;AF=0.5;RO=227;AO=80;PRO=0.0;PAO=0.0;QR=8710;QA=3061;PQR=0.0;PQA=0.0;SRF=66;SRR=161;SAF=31;SAR=49;SRP=89.3431;SAP=11.8048;AB=0.260586;ABP=155.855;RUN=1;RPP=21.3592;RPPR=43.4265;RPL=53.0;RPR=27.0;EPP=6.91895;EPPR=3.01987;DPRA=0.0;ODDS=145.539;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995595;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8315;Dels=0.0;FS=4.108;HaplotypeScore=1 [...]
+chr12 56493822 . A C 7539.21 REJECT NS=2;DP=274;DPB=316.0;AC=2;AN=4;AF=0.5;RO=72;AO=244;PRO=0.0;PAO=0.0;QR=2769;QA=9443;PQR=0.0;PQA=0.0;SRF=33;SRR=39;SAF=106;SAR=138;SRP=4.09604;SAP=12.1234;AB=0.772152;ABP=206.304;RUN=1;RPP=30.9191;RPPR=3.0103;RPL=150.0;RPR=94.0;EPP=4.29182;EPPR=3.13094;DPRA=0.0;ODDS=143.493;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995902;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.441;Dels=0.0;FS=1.1535;HaplotypeScore=4 [...]
+chr12 56494991 . G A 9984.73 REJECT NS=2;DP=361;DPB=414.0;AC=2;AN=4;AF=0.5;RO=89;AO=325;PRO=0.0;PAO=0.0;QR=3413;QA=12420;PQR=0.0;PQA=0.0;SRF=39;SRR=50;SAF=173;SAR=152;SRP=5.96253;SAP=5.95682;AB=0.785024;ABP=295.142;RUN=1;RPP=3.07043;RPPR=8.49998;RPL=161.0;RPR=164.0;EPP=3.01698;EPPR=4.98658;DPRA=0.0;ODDS=142.33;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984615;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.159;Dels=0.0;FS=5.819;HaplotypeScore [...]
+chr12 57491672 . C CA 1038.42 PASS SOMATIC;NS=2;DP=227;DPB=321.125;AC=2;AN=3;AF=0.25;RO=136;AO=48;PRO=70.1667;PAO=63.1667;QR=5070;QA=1499;PQR=2503.83;PQA=2215.83;SRF=76;SRR=60;SAF=25;SAR=23;SRP=7.09778;SAP=3.19126;AB=0.269461;ABP=80.1041;RUN=1;RPP=5.9056;RPPR=28.557;RPL=28.0;RPR=20.0;EPP=7.5342;EPPR=3.26577;DPRA=0.0;ODDS=9.86917;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=2;MEANALT=10.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.970588;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRank [...]
+chr12 57491672 . CA C 1038.42 REJECT NS=2;DP=227;DPB=321.125;AC=2;AN=2;AF=0.0;RO=136;AO=19;PRO=70.1667;PAO=51.6667;QR=5070;QA=642;PQR=2503.83;PQA=1787.33;SRF=76;SRR=60;SAF=9;SAR=10;SRP=7.09778;SAP=3.12459;AB=0.0898204;ABP=247.06;RUN=1;RPP=3.12459;RPPR=28.557;RPL=10.0;RPR=9.0;EPP=3.12459;EPPR=3.26577;DPRA=0.0;ODDS=9.86917;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=2;MEANALT=10.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.970588;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr12 57491774 . G A 3668.97 PASS SOMATIC;NS=2;DP=523;DPB=523.0;AC=1;AN=3;AF=0.25;RO=383;AO=140;PRO=0.0;PAO=0.0;QR=14313;QA=5373;PQR=0.0;PQA=0.0;SRF=238;SRR=145;SAF=87;SAR=53;SRP=52.047;SAP=20.9405;AB=0.346535;ABP=85.6552;RUN=1;RPP=3.56868;RPPR=3.06133;RPL=73.0;RPR=67.0;EPP=4.00297;EPPR=22.7463;DPRA=3.39496;ODDS=75.1467;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.7714;MQMR=60.0;PAIRED=0.978571;PAIREDR=0.997389;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.144;Dels=0.0 [...]
+chr12 57491863 . G A 3770.56 PASS SOMATIC;NS=2;DP=532;DPB=532.0;AC=1;AN=3;AF=0.25;RO=388;AO=144;PRO=0.0;PAO=0.0;QR=14771;QA=5510;PQR=0.0;PQA=0.0;SRF=222;SRR=166;SAF=88;SAR=56;SRP=20.5612;SAP=18.4519;AB=0.350365;ABP=82.9427;RUN=1;RPP=5.18177;RPPR=6.23393;RPL=66.0;RPR=78.0;EPP=3.25157;EPPR=6.23393;DPRA=3.39669;ODDS=76.4226;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992268;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.107;Dels=0.0;FS=1.8 [...]
+chr12 57492745 . G A 4181.28 PASS SOMATIC;NS=2;DP=629;DPB=629.0;AC=1;AN=3;AF=0.25;RO=469;AO=160;PRO=0.0;PAO=0.0;QR=18004;QA=6112;PQR=0.0;PQA=0.0;SRF=230;SRR=239;SAF=80;SAR=80;SRP=3.38533;SAP=3.0103;AB=0.345572;ABP=98.9162;RUN=1;RPP=3.49888;RPPR=4.68173;RPL=77.0;RPR=83.0;EPP=9.579;EPPR=3.12605;DPRA=2.78916;ODDS=104.497;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.975;PAIREDR=0.991471;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.068;Dels=0.0;FS=0.0 [...]
+chr12 57492996 . G A 9003.365 REJECT NS=2;DP=540;DPB=629.0;AC=2;AN=4;AF=0.5;RO=302;AO=327;PRO=0.0;PAO=0.0;QR=11575;QA=12489;PQR=0.0;PQA=0.0;SRF=145;SRR=157;SAF=169;SAR=158;SRP=4.0457;SAP=3.81381;AB=0.519873;ABP=5.16796;RUN=1;RPP=14.1731;RPPR=3.0103;RPL=184.0;RPR=143.0;EPP=3.33569;EPPR=11.3223;DPRA=0.0;ODDS=536.952;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996942;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.2055;Dels=0.0;FS=1.8055;Haplotype [...]
+chr12 57494360 . T G 1644.79 REJECT NS=2;DP=418;DPB=475.0;AC=2;AN=4;AF=0.5;RO=374;AO=97;PRO=0.0;PAO=0.0;QR=14165;QA=3609;PQR=0.0;PQA=0.0;SRF=140;SRR=234;SAF=34;SAR=63;SRP=54.3128;SAP=21.8372;AB=0.204211;ABP=363.982;RUN=1;RPP=37.0599;RPPR=12.3;RPL=68.0;RPR=29.0;EPP=6.79359;EPPR=3.1032;DPRA=0.0;ODDS=159.881;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.6417;PAIRED=0.948454;PAIREDR=0.994652;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.199;Dels=0.0;FS=1.853;HaplotypeSco [...]
+chr12 57494407 . G GAGAGAA . PASS SOMATIC;AC=1;AN=4;END=57494407;HOMLEN=21;HOMSEQ=AGAGAAAGAGAAAGAGAAAGA;SVLEN=6;SVTYPE=INS GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:-0.00355946 0/1:124,48:48:28:172:.:.:.:1:.:.:-0.0302105
+chr12 57494421 . GAGAAAGAAAGAA G . PASS AC=2;AN=4;END=57494433;HOMLEN=51;HOMSEQ=AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA;SVLEN=-12;SVTYPE=DEL GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:32,29:29:48:61:.:.:.:1:.:.:-0.00355946 0/1:71,65:65:48:136:.:.:.:1:.:.:-0.0302105
+chr12 57494427 . GAAAGAA G 6458.73 PASS SOMATIC;DP=228;AC=1;AN=4;AF=0.5;MQ0=0;END=57494433;HOMLEN=1;HOMSEQ=A;SVLEN=-6;SVTYPE=DEL;BaseQRankSum=1.406;FS=38.08;MLEAC=1;MLEAF=0.5;MQ=55.49;MQRankSum=-0.671;QD=14.16;ReadPosRankSum=-0.719;SOR=0.634 GT:AD:GMIMUT:GMIMAF:GMICOV:DP:GQ:PL:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00355946 0/1:75,88:88:54:163:217:99.0:6496,0,3735:.:1:.:1:.:.:-0.0302105
+chr12 57494481 . AAG A 5266.73 PASS SOMATIC;DP=242;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=1.508;FS=6.838;MLEAC=1;MLEAF=0.5;MQ=48.8;MQRankSum=5.112;QD=21.76;RPA=2,1;RU=AG;ReadPosRankSum=-4.53;SOR=0.399;STR GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00355946 0/1:83,128:233:99.0:5304,0,1114:128:61:211:.:1:.:.:.:.:-0.0302105
+chr12 57494483 . G GAGAAAGAAAGAA . PASS AC=1;AN=4;END=57494483;HOMLEN=49;HOMSEQ=AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA;SVLEN=12;SVTYPE=INS GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:7,22:22:76:29:.:.:.:1:.:.:-0.00355946 0/0:.:.:.:.:.:.:.:.:.:.:-0.0302105
+chr12 57494483 . GAGAAAGAAAGAAAGAA G . PASS AC=2;AN=4;END=57494499;HOMLEN=33;HOMSEQ=AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA;SVLEN=-16;SVTYPE=DEL GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:18,39:39:68:57:.:.:.:1:.:.:-0.00355946 0/1:45,94:94:68:139:.:.:.:1:.:.:-0.0302105
+chr12 57494483 . GAGAAAGAAAGAAAGAAAGAAAGAA G . PASS SOMATIC;AC=1;AN=4;END=57494507;HOMLEN=25;HOMSEQ=AGAAAGAAAGAAAGAAAGAAAGAAA;SVLEN=-24;SVTYPE=DEL GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:-0.00355946 0/1:64,103:103:62:167:.:.:.:1:.:.:-0.0302105
+chr12 57494880 . C CT 114.513 REJECT NS=2;DP=255;DPB=329.5;AC=2;AN=4;AF=0.5;RO=190;AO=27;PRO=60.8333;PAO=45.8333;QR=7068;QA=866;PQR=2116.17;PQA=1571.17;SRF=30;SRR=160;SAF=8;SAR=19;SRP=196.157;SAP=12.7417;AB=0.105882;ABP=347.048;RUN=1;RPP=26.2531;RPPR=41.4568;RPL=22.0;RPR=5.0;EPP=3.09072;EPPR=3.05602;DPRA=0.0;ODDS=3.84743;GTI=0;TYPE=ins;CIGAR=1M1I15M;NUMALT=2;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.978947;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.212;FS=3. [...]
+chr12 57494880 . CT C 114.513 REJECT NS=2;DP=255;DPB=329.5;AC=2;AN=2;AF=0.0;RO=190;AO=23;PRO=60.8333;PAO=42.3333;QR=7068;QA=793;PQR=2116.17;PQA=1462.67;SRF=30;SRR=160;SAF=3;SAR=20;SRP=196.157;SAP=30.2953;AB=0.0901961;ABP=374.979;RUN=1;RPP=3.10471;RPPR=41.4568;RPL=11.0;RPR=12.0;EPP=7.63648;EPPR=3.05602;DPRA=0.0;ODDS=3.84743;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=2;MEANALT=7.5;LEN=1;MQM=60.4348;MQMR=60.0;PAIRED=1.0;PAIREDR=0.978947;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:Q [...]
+chr12 57497005 . T C 99.648 REJECT NS=2;DP=9;DPB=9.0;AC=3;AN=4;AF=0.75;RO=3;AO=6;PRO=0.0;PAO=0.0;QR=93;QA=183;PQR=0.0;PQA=0.0;SRF=0;SRR=3;SAF=0;SAR=6;SRP=9.52472;SAP=16.0391;AB=0.625;ABP=4.09604;RUN=1;RPP=4.45795;RPPR=3.73412;RPL=2.0;RPR=4.0;EPP=4.45795;EPPR=3.73412;DPRA=0.0;ODDS=1.67385;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.1667;MQMR=56.3333;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.322;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=1;MLEAF=0.5;MQ [...]
+chr12 57497970 . G A 5239.63 PASS SOMATIC;NS=2;DP=641;DPB=641.0;AC=1;AN=3;AF=0.25;RO=448;AO=193;PRO=0.0;PAO=0.0;QR=17177;QA=7332;PQR=0.0;PQA=0.0;SRF=215;SRR=233;SAF=87;SAR=106;SRP=4.58074;SAP=7.07197;AB=0.403766;ABP=41.4608;RUN=1;RPP=3.11156;RPPR=6.2869;RPL=98.0;RPR=95.0;EPP=3.02155;EPPR=3.32051;DPRA=2.93252;ODDS=102.653;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994819;PAIREDR=0.993304;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.047;Dels=0.0;F [...]
+chr12 57502182 . C T 7489.540000000001 REJECT NS=2;DP=460;DPB=535.0;AC=2;AN=4;AF=0.5;RO=265;AO=270;PRO=0.0;PAO=0.0;QR=10004;QA=10478;PQR=0.0;PQA=0.0;SRF=142;SRR=123;SAF=118;SAR=152;SRP=5.96842;SAP=12.3074;AB=0.504673;ABP=3.11177;RUN=1;RPP=4.16842;RPPR=13.0482;RPL=141.0;RPR=129.0;EPP=13.4334;EPPR=3.67403;DPRA=0.0;ODDS=451.979;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988679;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.306;Dels=0.0;FS=9.5105 [...]
+chr12 57502309 . T TGGGGAGGCAA 2466.07 PASS SOMATIC;NS=2;DP=445;DPB=611.583;AC=1;AN=4;AF=0.25;RO=353;AO=81;PRO=55.5;PAO=86.5;QR=13350;QA=2762;PQR=1845.5;PQA=2931.5;SRF=207;SRR=146;SAF=39;SAR=42;SRP=25.9;SAP=3.25157;AB=0.248466;ABP=182.163;RUN=1;RPP=3.25157;RPPR=3.16409;RPL=42.0;RPR=39.0;EPP=3.03711;EPPR=3.01645;DPRA=2.7395;ODDS=73.3753;GTI=0;TYPE=ins;CIGAR=1M10I11M;NUMALT=1;MEANALT=9.0;LEN=10;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997167;technology.ILLUMINA=1.0;MQ0=0;END=57502309;HOMLEN [...]
+chr12 57502981 . C T 5928.72 REJECT NS=2;DP=232;DPB=267.0;AC=2;AN=4;AF=0.5;RO=61;AO=206;PRO=0.0;PAO=0.0;QR=2261;QA=7602;PQR=0.0;PQA=0.0;SRF=49;SRR=12;SAF=152;SAR=54;SRP=51.7438;SAP=104.247;AB=0.771536;ABP=174.004;RUN=1;RPP=21.6049;RPPR=25.259;RPL=82.0;RPR=124.0;EPP=3.38978;EPPR=3.90025;DPRA=0.0;ODDS=67.2318;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.7573;MQMR=60.0;PAIRED=0.990291;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.7665;Dels=0.0;FS=3.1505;HaplotypeSco [...]
+chr12 57503775 . C T 8460.595000000001 REJECT NS=2;DP=505;DPB=577.0;AC=2;AN=4;AF=0.5;RO=277;AO=300;PRO=0.0;PAO=0.0;QR=10647;QA=11444;PQR=0.0;PQA=0.0;SRF=130;SRR=147;SAF=140;SAR=160;SRP=5.27584;SAP=5.9056;AB=0.519931;ABP=5.00113;RUN=1;RPP=3.12611;RPPR=4.77413;RPL=152.0;RPR=148.0;EPP=3.47355;EPPR=3.20628;DPRA=0.0;ODDS=439.595;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993333;PAIREDR=0.99278;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.327;Dels=0.0;FS=0. [...]
+chr12 57504197 . G T 4166.05 PASS SOMATIC;NS=2;DP=589;DPB=589.0;AC=1;AN=3;AF=0.25;RO=431;AO=158;PRO=0.0;PAO=0.0;QR=16305;QA=6035;PQR=0.0;PQA=0.0;SRF=204;SRR=227;SAF=72;SAR=86;SRP=5.67552;SAP=5.70403;AB=0.355856;ABP=83.1396;RUN=1;RPP=7.46319;RPPR=3.25717;RPL=70.0;RPR=88.0;EPP=4.38465;EPPR=3.13626;DPRA=3.06207;ODDS=91.3156;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993671;PAIREDR=0.99768;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.811;Dels=0.0;FS [...]
+chr12 57504529 . T C 4512.64 PASS SOMATIC;NS=2;DP=540;DPB=540.0;AC=1;AN=3;AF=0.25;RO=376;AO=164;PRO=0.0;PAO=0.0;QR=14584;QA=6307;PQR=0.0;PQA=0.0;SRF=191;SRR=185;SAF=81;SAR=83;SRP=3.21821;SAP=3.06326;AB=0.403941;ABP=35.5503;RUN=1;RPP=7.30028;RPPR=8.9241;RPL=91.0;RPR=73.0;EPP=3.8577;EPPR=3.0334;DPRA=3.02985;ODDS=84.6011;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.231;Dels=0.0;FS=0.0;Haplot [...]
+chr12 57859431 . G A 2176.535 REJECT NS=2;DP=352;DPB=408.0;AC=2;AN=4;AF=0.5;RO=305;AO=102;PRO=0.0;PAO=0.0;QR=11551;QA=3865;PQR=0.0;PQA=0.0;SRF=190;SRR=115;SAF=68;SAR=34;SRP=43.0579;SAP=27.6203;AB=0.25;ABP=224.5;RUN=1;RPP=3.35092;RPPR=16.1744;RPL=49.0;RPR=53.0;EPP=8.46027;EPPR=8.20047;DPRA=0.0;ODDS=133.388;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996721;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4605;Dels=0.0;FS=1.9235;HaplotypeScore=14. [...]
+chr12 57865321 . G A 1809.325 REJECT NS=2;DP=353;DPB=403.0;AC=2;AN=4;AF=0.5;RO=311;AO=92;PRO=0.0;PAO=0.0;QR=11754;QA=3495;PQR=0.0;PQA=0.0;SRF=150;SRR=161;SAF=49;SAR=43;SRP=3.85515;SAP=3.86001;AB=0.228288;ABP=261.437;RUN=1;RPP=4.52089;RPPR=5.53088;RPL=50.0;RPR=42.0;EPP=5.3706;EPPR=3.35243;DPRA=0.0;ODDS=151.248;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996785;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.076;Dels=0.0;FS=2.41;HaplotypeScore=4 [...]
+chr12 57865821 . G C 1437.87 REJECT NS=2;DP=286;DPB=332.0;AC=2;AN=4;AF=0.5;RO=254;AO=77;PRO=0.0;PAO=0.0;QR=9768;QA=2896;PQR=0.0;PQA=0.0;SRF=101;SRR=153;SAF=32;SAR=45;SRP=26.1271;SAP=7.77626;AB=0.231928;ABP=210.242;RUN=1;RPP=5.29458;RPPR=5.19887;RPL=43.0;RPR=34.0;EPP=4.39215;EPPR=18.0909;DPRA=0.0;ODDS=128.22;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987013;PAIREDR=0.996063;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.356;Dels=0.0;FS=0.0;HaplotypeScore= [...]
+chr12 57911160 . G A 2237.32 PASS SOMATIC;NS=2;DP=391;DPB=391.0;AC=1;AN=3;AF=0.25;RO=302;AO=88;PRO=0.0;PAO=0.0;QR=11516;QA=3398;PQR=0.0;PQA=0.0;SRF=127;SRR=175;SAF=32;SAR=56;SRP=19.5768;SAP=17.2236;AB=0.315412;ABP=85.5807;RUN=1;RPP=3.109;RPPR=16.9307;RPL=45.0;RPR=43.0;EPP=3.89863;EPPR=3.72933;DPRA=2.49107;ODDS=70.8361;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996689;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.924;Dels=0.0;FS=4.429; [...]
+chr12 57911468 . A G 3073.36 PASS SOMATIC;NS=2;DP=441;DPB=441.0;AC=1;AN=3;AF=0.25;RO=323;AO=117;PRO=0.0;PAO=0.0;QR=12206;QA=4445;PQR=0.0;PQA=0.0;SRF=164;SRR=159;SAF=60;SAR=57;SRP=3.17837;SAP=3.17734;AB=0.364486;ABP=54.2124;RUN=1;RPP=6.14687;RPPR=4.14646;RPL=52.0;RPR=65.0;EPP=5.25601;EPPR=3.07081;DPRA=2.675;ODDS=75.7934;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.974359;PAIREDR=0.990712;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.357;Dels=0.0;FS= [...]
+chr12 57911615 . C CT 275.439 REJECT NS=2;DP=142;DPB=192.833;AC=2;AN=3;AF=0.25;RO=77;AO=23;PRO=24.8;PAO=22.8;QR=2736;QA=665;PQR=870.65;PQA=803.65;SRF=17;SRR=60;SAF=6;SAR=17;SRP=55.1538;SAP=14.4341;AB=0.161972;ABP=143.942;RUN=1;RPP=3.86001;RPPR=9.35551;RPL=10.0;RPR=13.0;EPP=3.86001;EPPR=5.29458;DPRA=0.0;ODDS=2.86684;GTI=0;TYPE=ins;CIGAR=1M1I17M;NUMALT=4;MEANALT=7.0;LEN=1;MQM=60.0;MQMR=59.7403;PAIRED=1.0;PAIREDR=0.974026;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.968;F [...]
+chr12 57911615 . C CTT 275.439 REJECT NS=2;DP=142;DPB=192.833;AC=2;AN=2;AF=0.0;RO=77;AO=6;PRO=24.8;PAO=22.8;QR=2736;QA=181;PQR=870.65;PQA=803.65;SRF=17;SRR=60;SAF=2;SAR=4;SRP=55.1538;SAP=4.45795;AB=0.0594059;ABP=173.31;RUN=1;RPP=4.45795;RPPR=9.35551;RPL=4.0;RPR=2.0;EPP=4.45795;EPPR=5.29458;DPRA=0.0;ODDS=2.86684;GTI=0;TYPE=ins;CIGAR=1M2I17M;NUMALT=4;MEANALT=9.0;LEN=2;MQM=60.0;MQMR=59.7403;PAIRED=1.0;PAIREDR=0.974026;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr12 57911615 . CT C 275.439 REJECT NS=2;DP=142;DPB=192.833;AC=2;AN=3;AF=0.25;RO=77;AO=19;PRO=24.8;PAO=21.8;QR=2736;QA=560;PQR=870.65;PQA=764.65;SRF=17;SRR=60;SAF=4;SAR=15;SRP=55.1538;SAP=16.8392;AB=0.133803;ABP=168.409;RUN=1;RPP=8.61041;RPPR=9.35551;RPL=13.0;RPR=6.0;EPP=4.03889;EPPR=5.29458;DPRA=0.0;ODDS=2.86684;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=4;MEANALT=7.0;LEN=1;MQM=60.0;MQMR=59.7403;PAIRED=0.947368;PAIREDR=0.974026;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr12 57911615 . CTT C 275.439 REJECT NS=2;DP=142;DPB=192.833;AC=2;AN=2;AF=0.0;RO=77;AO=7;PRO=24.8;PAO=18.8;QR=2736;QA=169;PQR=870.65;PQA=654.4;SRF=17;SRR=60;SAF=2;SAR=5;SRP=55.1538;SAP=5.80219;AB=0.0492958;ABP=253.555;RUN=1;RPP=3.32051;RPPR=9.35551;RPL=4.0;RPR=3.0;EPP=5.80219;EPPR=5.29458;DPRA=0.0;ODDS=2.86684;GTI=0;TYPE=del;CIGAR=1M2D15M;NUMALT=4;MEANALT=7.0;LEN=2;MQM=60.0;MQMR=59.7403;PAIRED=1.0;PAIREDR=0.974026;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr12 57912556 . T C 978.885 PASS SOMATIC;NS=2;DP=145;DPB=145.0;AC=1;AN=3;AF=0.25;RO=105;AO=40;PRO=0.0;PAO=0.0;QR=4038;QA=1520;PQR=0.0;PQA=0.0;SRF=30;SRR=75;SAF=8;SAR=32;SRP=44.8887;SAP=34.2795;AB=0.357143;ABP=22.8638;RUN=1;RPP=4.96463;RPPR=3.52732;RPL=23.0;RPR=17.0;EPP=8.43898;EPPR=20.4028;DPRA=3.39394;ODDS=21.6094;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.980952;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.908;Dels=0.0;FS=4.32;Ha [...]
+chr12 58053029 . T C 5493.295 REJECT NS=2;DP=372;DPB=432.0;AC=2;AN=4;AF=0.5;RO=229;AO=203;PRO=0.0;PAO=0.0;QR=8787;QA=7614;PQR=0.0;PQA=0.0;SRF=95;SRR=134;SAF=88;SAR=115;SRP=17.433;SAP=10.8083;AB=0.469907;ABP=6.40825;RUN=1;RPP=3.021;RPPR=17.433;RPL=102.0;RPR=101.0;EPP=5.4171;EPPR=3.47494;DPRA=0.0;ODDS=322.658;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995074;PAIREDR=0.9869;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.456;Dels=0.0;FS=1.4575;HaplotypeScor [...]
+chr12 58056701 . T G 1191.33 REJECT NS=1;DP=86;DPB=86.0;AC=1;AN=4;AF=0.5;RO=41;AO=45;PRO=0.0;PAO=0.0;QR=1561;QA=1674;PQR=0.0;PQA=0.0;SRF=23;SRR=18;SAF=29;SAR=16;SRP=4.33437;SAP=11.1654;AB=0.523256;ABP=3.41429;RUN=1;RPP=11.1654;RPPR=5.60547;RPL=16.0;RPR=29.0;EPP=20.4303;EPPR=11.961;DPRA=0.0;ODDS=256.112;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.7778;MQMR=59.7317;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-1.363;FS=2.957;MLEAC=1;MLEAF=0.5;MQ=59.27;MQRankSum [...]
+chr12 58056763 . C T 1594.88 REJECT NS=1;DP=115;DPB=115.0;AC=1;AN=4;AF=0.5;RO=59;AO=56;PRO=0.0;PAO=0.0;QR=2271;QA=2199;PQR=0.0;PQA=0.0;SRF=21;SRR=38;SAF=16;SAR=40;SRP=13.6468;SAP=25.3454;AB=0.486957;ABP=3.18024;RUN=1;RPP=3.0103;RPPR=9.23028;RPL=28.0;RPR=28.0;EPP=3.63072;EPPR=4.81373;DPRA=0.0;ODDS=367.235;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.982143;PAIREDR=0.983051;technology.ILLUMINA=1.0;BaseQRankSum=1.189;FS=3.74;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRank [...]
+chr12 58061580 . C T 480.937 REJECT NS=2;DP=152;DPB=201.143;AC=2;AN=2;AF=0.0;RO=70;AO=9;PRO=35.0;PAO=0.0;QR=2537;QA=117;PQR=1247.92;PQA=0.0;SRF=21;SRR=49;SAF=0;SAR=9;SRP=27.3308;SAP=22.5536;AB=0.0592105;ABP=259.53;RUN=1;RPP=5.18177;RPPR=63.067;RPL=6.0;RPR=3.0;EPP=5.18177;EPPR=6.1124;DPRA=0.0;ODDS=16.8846;GTI=0;TYPE=snp;CIGAR=1X20M;NUMALT=4;MEANALT=12.5;LEN=1;MQM=57.7778;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV [...]
+chr12 58061580 . C CT 480.937 REJECT NS=2;DP=152;DPB=201.143;AC=2;AN=2;AF=0.0;RO=70;AO=12;PRO=35.0;PAO=26.0;QR=2537;QA=317;PQR=1247.92;PQA=906.917;SRF=21;SRR=49;SAF=3;SAR=9;SRP=27.3308;SAP=9.52472;AB=0.0789474;ABP=237.072;RUN=1;RPP=14.5915;RPPR=63.067;RPL=10.0;RPR=2.0;EPP=3.73412;EPPR=6.1124;DPRA=0.0;ODDS=16.8846;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=4;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr12 58061580 . CT C 480.937 REJECT NS=2;DP=152;DPB=201.143;AC=2;AN=4;AF=0.5;RO=70;AO=32;PRO=35.0;PAO=21.0;QR=2537;QA=938;PQR=1247.92;PQA=759.917;SRF=21;SRR=49;SAF=11;SAR=21;SRP=27.3308;SAP=9.79615;AB=0.210526;ABP=113.641;RUN=1;RPP=20.3821;RPPR=63.067;RPL=24.0;RPR=8.0;EPP=3.28173;EPPR=6.1124;DPRA=0.0;ODDS=16.8846;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=4;MEANALT=12.5;LEN=1;MQM=59.9375;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.966;FS=9.7;MLEAC [...]
+chr12 58061580 . CTT C 480.937 REJECT NS=2;DP=152;DPB=201.143;AC=2;AN=2;AF=0.0;RO=70;AO=8;PRO=35.0;PAO=16.0;QR=2537;QA=196;PQR=1247.92;PQA=575.25;SRF=21;SRR=49;SAF=1;SAR=7;SRP=27.3308;SAP=12.7819;AB=0.0526316;ABP=267.244;RUN=1;RPP=7.35324;RPPR=63.067;RPL=6.0;RPR=2.0;EPP=4.09604;EPPR=6.1124;DPRA=0.0;ODDS=16.8846;GTI=0;TYPE=del;CIGAR=1M2D18M;NUMALT=4;MEANALT=12.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr12 58064737 . A C 5522.88 REJECT NS=2;DP=379;DPB=425.0;AC=2;AN=4;AF=0.5;RO=224;AO=201;PRO=0.0;PAO=0.0;QR=8690;QA=7545;PQR=0.0;PQA=0.0;SRF=94;SRR=130;SAF=95;SAR=106;SRP=15.5738;SAP=4.3175;AB=0.472941;ABP=5.71314;RUN=1;RPP=22.9857;RPPR=4.40625;RPL=122.0;RPR=79.0;EPP=8.72527;EPPR=10.6105;DPRA=0.0;ODDS=300.403;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995536;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.195;Dels=0.0;FS=4.005;HaplotypeScore= [...]
+chr12 58242545 . T G 6491.885 REJECT NS=2;DP=390;DPB=443.0;AC=2;AN=4;AF=0.5;RO=209;AO=233;PRO=0.0;PAO=0.0;QR=8022;QA=8868;PQR=0.0;PQA=0.0;SRF=100;SRR=109;SAF=132;SAR=101;SRP=3.85188;SAP=11.9665;AB=0.525959;ABP=5.60332;RUN=1;RPP=3.01962;RPPR=3.5194;RPL=117.0;RPR=116.0;EPP=7.12025;EPPR=3.5194;DPRA=0.0;ODDS=261.365;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.985646;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1035;Dels=0.0;FS=8.497;HaplotypeSco [...]
+chr12 58242849 . T C 6164.42 REJECT NS=2;DP=382;DPB=434.0;AC=2;AN=4;AF=0.5;RO=213;AO=221;PRO=0.0;PAO=0.0;QR=8080;QA=8450;PQR=0.0;PQA=0.0;SRF=104;SRR=109;SAF=116;SAR=105;SRP=3.26517;SAP=4.19921;AB=0.509217;ABP=3.33052;RUN=1;RPP=3.49176;RPPR=10.4422;RPL=107.0;RPR=114.0;EPP=47.1177;EPPR=27.4878;DPRA=0.0;ODDS=290.867;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995305;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.666;Dels=0.0;FS=6.5465;HaplotypeSc [...]
+chr12 58244630 . C T 5337.475 REJECT NS=2;DP=329;DPB=376.0;AC=2;AN=4;AF=0.5;RO=182;AO=194;PRO=0.0;PAO=0.0;QR=6771;QA=7422;PQR=0.0;PQA=0.0;SRF=89;SRR=93;SAF=94;SAR=100;SRP=3.2012;SAP=3.41325;AB=0.515957;ABP=3.84193;RUN=1;RPP=14.4721;RPPR=4.72839;RPL=81.0;RPR=113.0;EPP=7.48756;EPPR=6.876;DPRA=0.0;ODDS=219.223;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989691;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.962;Dels=0.0;FS=1.578;HaplotypeScore=5.8 [...]
+chr12 66232383 . T TG . PASS SOMATIC;AC=1;AN=4 GT:AD:DP:MM:MQS:NQSBQ:NQSMM:REnd:RStart:SC:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:81,0:81:0.160494,0.0:60.0,0.0:38.6333,0.0:0.0,0.0:0,0:0,0:21,60,0,0:0:0:81:.:.:.:.:0:.:-0.00355946 0/1:136,83:219:0.125,0.0843373:60.0,57.8313:38.9485,38.8224:0.0,0.0:36,19:63,19:32,104,21,59:83:38:219:.:.:.:.:1:.:-0.0302105
+chr12 66308644 . A G 444.102 REJECT NS=1;DP=36;DPB=36.0;AC=1;AN=4;AF=0.5;RO=16;AO=20;PRO=0.0;PAO=0.0;QR=599;QA=743;PQR=0.0;PQA=0.0;SRF=16;SRR=0;SAF=20;SAR=0;SRP=37.7539;SAP=46.4397;AB=0.555556;ABP=3.9754;RUN=1;RPP=6.91895;RPPR=16.582;RPL=7.0;RPR=13.0;EPP=6.91895;EPPR=16.582;DPRA=0.0;ODDS=76.1368;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=44.75;MQMR=57.5;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.783;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=50.94;MQRankSum=-3.75;QD=19.7 [...]
+chr12 66308656 . T C 529.895 REJECT NS=1;DP=42;DPB=42.0;AC=1;AN=4;AF=0.5;RO=19;AO=23;PRO=0.0;PAO=0.0;QR=716;QA=867;PQR=0.0;PQA=0.0;SRF=19;SRR=0;SAF=23;SAR=0;SRP=44.2683;SAP=52.9542;AB=0.547619;ABP=3.83753;RUN=1;RPP=5.3706;RPPR=22.325;RPL=9.0;RPR=14.0;EPP=5.3706;EPPR=22.325;DPRA=0.0;ODDS=90.8007;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=48.087;MQMR=56.8421;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=0.25;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=52.64;MQRankSum=-1.852;QD=20 [...]
+chr12 69108909 . T C 2063.29 REJECT NS=2;DP=390;DPB=439.0;AC=2;AN=4;AF=0.5;RO=333;AO=105;PRO=0.0;PAO=0.0;QR=12918;QA=4017;PQR=0.0;PQA=0.0;SRF=135;SRR=198;SAF=42;SAR=63;SRP=28.8919;SAP=12.1305;AB=0.23918;ABP=262.405;RUN=1;RPP=7.66346;RPPR=10.9984;RPL=45.0;RPR=60.0;EPP=22.8844;EPPR=18.6671;DPRA=0.0;ODDS=173.593;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.961905;PAIREDR=0.996997;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5585;Dels=0.0;FS=1.8265;Haplotype [...]
+chr12 69115255 . A G 5569.025 REJECT NS=2;DP=369;DPB=432.0;AC=2;AN=4;AF=0.5;RO=228;AO=204;PRO=0.0;PAO=0.0;QR=8924;QA=7725;PQR=0.0;PQA=0.0;SRF=117;SRR=111;SAF=109;SAR=95;SRP=3.35316;SAP=5.09662;AB=0.472222;ABP=5.9056;RUN=1;RPP=3.3935;RPPR=7.61992;RPL=105.0;RPR=99.0;EPP=11.3556;EPPR=18.2487;DPRA=0.0;ODDS=326.317;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990196;PAIREDR=0.995614;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.449;Dels=0.0;FS=0.9365;Haplotyp [...]
+chr12 69119617 . G T 177.029 REJECT NS=1;DP=19;DPB=43.4348;AC=0;AN=4;AF=0.0;RO=0;AO=6;PRO=19.5;PAO=4.5;QR=0;QA=174;PQR=690.667;PQA=127.667;SRF=0;SRR=0;SAF=0;SAR=6;SRP=0.0;SAP=16.0391;AB=0.0;ABP=0.0;RUN=1;RPP=16.0391;RPPR=0.0;RPL=6.0;RPR=0.0;EPP=16.0391;EPPR=0.0;DPRA=0.0;ODDS=9.50877;GTI=0;TYPE=snp;CIGAR=1X22M;NUMALT=2;MEANALT=10.0;LEN=1;MQM=47.5;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:Call [...]
+chr12 69119617 . G GTT 177.029 REJECT NS=1;DP=19;DPB=43.4348;AC=1;AN=3;AF=1.0;RO=0;AO=5;PRO=19.5;PAO=21.0;QR=0;QA=123;PQR=690.667;PQA=739.667;SRF=0;SRR=0;SAF=2;SAR=3;SRP=0.0;SAP=3.44459;AB=0.0;ABP=0.0;RUN=1;RPP=6.91895;RPPR=0.0;RPL=4.0;RPR=1.0;EPP=3.44459;EPPR=0.0;DPRA=0.0;ODDS=9.50877;GTI=0;TYPE=ins;CIGAR=1M2I22M;NUMALT=2;MEANALT=10.0;LEN=2;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=64.34;QD=19.83;SOR=1.04 GT:GQ:DP:RO:Q [...]
+chr12 69119617 . G GGTTT 1288.73 PASS DP=65;AC=1;AN=3;AF=0.5;SPLITMULTIALLELIC;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=64.34;QD=19.83;SOR=1.04 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR ./1:0,31:39:99.0:1326,201,677:31:79:39:1:.:.:.:.:.:-0.00355946 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0302105
+chr12 69202326 . C T 7105.77 REJECT NS=2;DP=270;DPB=306.0;AC=2;AN=4;AF=0.5;RO=68;AO=238;PRO=0.0;PAO=0.0;QR=2578;QA=9052;PQR=0.0;PQA=0.0;SRF=30;SRR=38;SAF=69;SAR=169;SRP=5.05404;SAP=94.2486;AB=0.777778;ABP=208.094;RUN=1;RPP=55.7096;RPPR=13.3567;RPL=157.0;RPR=81.0;EPP=3.92268;EPPR=6.20364;DPRA=0.0;ODDS=112.358;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987395;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8895;Dels=0.0;FS=12.449;HaplotypeScore= [...]
+chr12 69214081 . A AT 439.205 REJECT NS=2;DP=235;DPB=299.2;AC=2;AN=3;AF=0.25;RO=152;AO=30;PRO=55.5;PAO=44.5;QR=5521;QA=1061;PQR=1932.17;PQA=1509.17;SRF=112;SRR=40;SAF=24;SAR=6;SRP=77.0689;SAP=26.4622;AB=0.12766;ABP=285.995;RUN=1;RPP=4.16842;RPPR=41.6397;RPL=13.0;RPR=17.0;EPP=4.16842;EPPR=8.7247;DPRA=0.0;ODDS=12.6985;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=2;MEANALT=10.5;LEN=1;MQM=60.0;MQMR=59.8684;PAIRED=1.0;PAIREDR=0.980263;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr12 69214081 . AT A 439.205 REJECT NS=2;DP=235;DPB=299.2;AC=2;AN=3;AF=0.25;RO=152;AO=32;PRO=55.5;PAO=41.0;QR=5521;QA=1103;PQR=1932.17;PQA=1399.67;SRF=112;SRR=40;SAF=24;SAR=8;SRP=77.0689;SAP=20.3821;AB=0.13617;ABP=273.206;RUN=1;RPP=35.8538;RPPR=41.6397;RPL=5.0;RPR=27.0;EPP=5.45321;EPPR=8.7247;DPRA=0.0;ODDS=12.6985;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=2;MEANALT=10.5;LEN=1;MQM=60.0;MQMR=59.8684;PAIRED=0.96875;PAIREDR=0.980263;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr12 69967862 . G A 6273.24 REJECT NS=2;DP=282;DPB=320.0;AC=3;AN=4;AF=0.75;RO=94;AO=225;PRO=0.0;PAO=0.0;QR=3538;QA=8551;PQR=0.0;PQA=0.0;SRF=54;SRR=40;SAF=149;SAR=76;SRP=7.53805;SAP=54.4404;AB=0.614754;ABP=30.9191;RUN=1;RPP=3.79203;RPPR=4.48875;RPL=108.0;RPR=117.0;EPP=4.17807;EPPR=8.9241;DPRA=0.0;ODDS=47.7535;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991111;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.745;Dels=0.0;FS=2.312;HaplotypeScore=3 [...]
+chr12 70915347 . A G 9541.985 REJECT NS=2;DP=258;DPB=296.0;AC=4;AN=4;AF=1.0;RO=0;AO=296;PRO=0.0;PAO=0.0;QR=0;QA=11184;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=88;SAR=208;SRP=0.0;SAP=108.649;AB=0.0;ABP=0.0;RUN=1;RPP=119.478;RPPR=0.0;RPL=211.0;RPR=85.0;EPP=3.2744;EPPR=0.0;DPRA=0.0;ODDS=51.6731;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993243;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.965;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=24.98;SOR=1.962 [...]
+chr12 70928616 . G A 2544.565 REJECT NS=2;DP=363;DPB=416.0;AC=2;AN=4;AF=0.5;RO=296;AO=120;PRO=0.0;PAO=0.0;QR=11294;QA=4565;PQR=0.0;PQA=0.0;SRF=169;SRR=127;SAF=67;SAR=53;SRP=15.9511;SAP=6.55704;AB=0.288462;ABP=164.701;RUN=1;RPP=11.7686;RPPR=3.12768;RPL=71.0;RPR=49.0;EPP=13.4334;EPPR=3.03964;DPRA=0.0;ODDS=261.816;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.172;Dels=0.0;FS=1.0665;HaplotypeScore=3. [...]
+chr12 70928724 . A G 10189.885 REJECT NS=2;DP=274;DPB=315.0;AC=4;AN=4;AF=1.0;RO=0;AO=315;PRO=0.0;PAO=0.0;QR=0;QA=11953;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=75;SAR=240;SRP=0.0;SAP=190.688;AB=0.0;ABP=0.0;RUN=1;RPP=25.4075;RPPR=0.0;RPL=186.0;RPR=129.0;EPP=5.00254;EPPR=0.0;DPRA=0.0;ODDS=53.6341;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.987302;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9644;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.475;SOR= [...]
+chr12 70933687 . A G 10448.5 REJECT NS=2;DP=373;DPB=430.0;AC=2;AN=4;AF=0.5;RO=94;AO=334;PRO=0.0;PAO=0.0;QR=3635;QA=12979;PQR=0.0;PQA=0.0;SRF=34;SRR=60;SAF=160;SAR=174;SRP=18.6264;SAP=4.28458;AB=0.776744;ABP=289.059;RUN=1;RPP=5.11676;RPPR=3.37991;RPL=158.0;RPR=176.0;EPP=3.03631;EPPR=4.48875;DPRA=0.0;ODDS=173.459;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991018;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0695;Dels=0.0;FS=9.8815;HaplotypeSco [...]
+chr12 70938279 . AGAG A . PASS SOMATIC;AC=1;AN=4 GT:AD:DP:MM:MQS:NQSBQ:NQSMM:REnd:RStart:SC:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:35,0:35:0.2,0.0:60.0,0.0:37.7914,0.0:0.0,0.0:0,0:0,0:23,12,0,0:0:0:35:.:.:.:.:0:.:-0.00355946 0/1:76,38:114:0.105263,0.157895:60.0,60.2632:38.1473,38.2686:0.0,0.0:81,8:19,8:58,18,31,7:38:33:114:.:.:.:.:1:.:-0.0302105
+chr12 70949085 . G A 2029.78 PASS SOMATIC;NS=2;DP=321;DPB=321.0;AC=1;AN=3;AF=0.25;RO=239;AO=82;PRO=0.0;PAO=0.0;QR=8947;QA=3063;PQR=0.0;PQA=0.0;SRF=74;SRR=165;SAF=30;SAR=52;SRP=78.2486;SAP=15.8273;AB=0.347458;ABP=50.7091;RUN=1;RPP=3.11623;RPPR=30.4944;RPL=42.0;RPR=40.0;EPP=26.8435;EPPR=3.23744;DPRA=2.77647;ODDS=54.057;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.983264;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.978;Dels=0.0;FS=4.172; [...]
+chr12 70953277 . T C 6566.725 REJECT NS=2;DP=409;DPB=461.0;AC=2;AN=4;AF=0.5;RO=229;AO=232;PRO=0.0;PAO=0.0;QR=8800;QA=8769;PQR=0.0;PQA=0.0;SRF=117;SRR=112;SAF=124;SAR=108;SRP=3.24736;SAP=5.40641;AB=0.503254;ABP=3.05269;RUN=1;RPP=3.34725;RPPR=6.43345;RPL=119.0;RPR=113.0;EPP=3.04774;EPPR=8.93681;DPRA=0.0;ODDS=335.308;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.45;Dels=0.0;FS=0.6275;HaplotypeScore= [...]
+chr12 70983895 . A C 2212.35 REJECT NS=2;DP=363;DPB=422.0;AC=2;AN=4;AF=0.5;RO=321;AO=101;PRO=0.0;PAO=0.0;QR=12243;QA=3863;PQR=0.0;PQA=0.0;SRF=175;SRR=146;SAF=55;SAR=46;SRP=8.69942;SAP=4.75178;AB=0.239336;ABP=252.061;RUN=1;RPP=7.84774;RPPR=10.3771;RPL=58.0;RPR=43.0;EPP=3.2038;EPPR=10.3771;DPRA=0.0;ODDS=125.607;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990099;PAIREDR=0.996885;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.787;Dels=0.0;FS=5.5885;HaplotypeS [...]
+chr12 70984019 . C T 1517.75 REJECT NS=2;DP=300;DPB=343.0;AC=2;AN=4;AF=0.5;RO=264;AO=78;PRO=0.0;PAO=0.0;QR=10103;QA=2872;PQR=0.0;PQA=0.0;SRF=59;SRR=205;SAF=17;SAR=61;SRP=178.34;SAP=56.9074;AB=0.227405;ABP=224.393;RUN=1;RPP=31.5178;RPPR=53.0529;RPL=55.0;RPR=23.0;EPP=4.01252;EPPR=3.0103;DPRA=0.0;ODDS=59.0796;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996212;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3455;Dels=0.0;FS=2.208;HaplotypeScore=11. [...]
+chr12 70988287 . A G 2002.41 REJECT NS=2;DP=344;DPB=402.0;AC=2;AN=4;AF=0.5;RO=309;AO=91;PRO=0.0;PAO=0.0;QR=11878;QA=3527;PQR=0.0;PQA=0.0;SRF=177;SRR=132;SAF=55;SAR=36;SRP=17.2408;SAP=11.6246;AB=0.226368;ABP=264.451;RUN=1;RPP=3.60686;RPPR=4.19793;RPL=43.0;RPR=48.0;EPP=25.942;EPPR=34.5564;DPRA=0.0;ODDS=29.0858;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993528;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9335;Dels=0.0;FS=6.4165;HaplotypeScore= [...]
+chr12 70989977 . T C 2568.48 PASS SOMATIC;NS=2;DP=429;DPB=429.0;AC=1;AN=4;AF=0.25;RO=323;AO=106;PRO=0.0;PAO=0.0;QR=12177;QA=3939;PQR=0.0;PQA=0.0;SRF=149;SRR=174;SAF=47;SAR=59;SRP=7.21207;SAP=5.96022;AB=0.322981;ABP=90.6515;RUN=1;RPP=5.05886;RPPR=12.2138;RPL=58.0;RPR=48.0;EPP=5.96022;EPPR=7.91124;DPRA=0.0;ODDS=57.8237;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990712;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.033;Dels=0.0;FS=0.0;Haplotype [...]
+chr12 70990054 . T C 6651.200000000001 REJECT NS=2;DP=283;DPB=331.0;AC=3;AN=4;AF=0.75;RO=72;AO=258;PRO=0.0;PAO=0.0;QR=2606;QA=9189;PQR=0.0;PQA=0.0;SRF=31;SRR=41;SAF=98;SAR=160;SRP=6.02623;SAP=35.3636;AB=0.690678;ABP=77.5396;RUN=1;RPP=3.3133;RPPR=4.09604;RPL=126.0;RPR=132.0;EPP=3.85196;EPPR=3.49285;DPRA=0.0;ODDS=60.0919;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996124;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.745;Dels=0.0;FS=3.111;Haplot [...]
+chr12 70990120 . T TAC 2332.46 REJECT NS=2;DP=139;DPB=179.964;AC=2;AN=2;AF=0.25;RO=20;AO=23;PRO=22.75;PAO=22.0833;QR=672;QA=474;PQR=807.25;PQA=751.25;SRF=4;SRR=16;SAF=0;SAR=23;SRP=18.6449;SAP=52.9542;AB=0.165468;ABP=138.126;RUN=1;RPP=24.253;RPPR=18.6449;RPL=19.0;RPR=4.0;EPP=24.253;EPPR=4.74748;DPRA=0.0;ODDS=4.32147;GTI=0;TYPE=ins;CIGAR=1M2I27M;NUMALT=3;MEANALT=21.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=0.956522;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-1.704;FS=4.313; [...]
+chr12 70990135 . A AC 2332.46 REJECT NS=2;DP=139;DPB=179.964;AC=2;AN=3;AF=0.5;RO=20;AO=40;PRO=22.75;PAO=22.0833;QR=672;QA=1147;PQR=807.25;PQA=751.25;SRF=4;SRR=16;SAF=10;SAR=30;SRP=18.6449;SAP=24.725;AB=0.28777;ABP=57.3908;RUN=1;RPP=16.9077;RPPR=18.6449;RPL=28.0;RPR=12.0;EPP=3.0103;EPPR=4.74748;DPRA=0.0;ODDS=4.32147;GTI=0;TYPE=ins;CIGAR=16M1I12M;NUMALT=3;MEANALT=21.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr12 70990136 . A C 2332.46 REJECT SOMATIC;NS=2;DP=139;DPB=179.964;AC=1;AN=3;AF=0.0;RO=20;AO=9;PRO=22.75;PAO=22.0833;QR=672;QA=330;PQR=807.25;PQA=751.25;SRF=4;SRR=16;SAF=1;SAR=8;SRP=18.6449;SAP=14.8328;AB=0.0647482;ABP=231.734;RUN=1;RPP=14.8328;RPPR=18.6449;RPL=8.0;RPR=1.0;EPP=9.04217;EPPR=4.74748;DPRA=0.0;ODDS=4.32147;GTI=0;TYPE=snp;CIGAR=16M1X11M;NUMALT=3;MEANALT=21.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr12 71002865 . T A 10549.9 REJECT NS=2;DP=280;DPB=321.0;AC=4;AN=4;AF=1.0;RO=1;AO=319;PRO=0.0;PAO=0.0;QR=16;QA=12206;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=181;SAR=138;SRP=5.18177;SAP=15.5967;AB=0.0;ABP=0.0;RUN=1;RPP=3.56168;RPPR=5.18177;RPL=155.0;RPR=164.0;EPP=7.97269;EPPR=5.18177;DPRA=0.0;ODDS=54.8321;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990596;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.688;Dels=0.0;FS=0.0;HaplotypeScore=3.866;MLEAC=2;M [...]
+chr12 71002893 . C T 12460.349999999999 REJECT NS=2;DP=331;DPB=379.0;AC=4;AN=4;AF=1.0;RO=0;AO=378;PRO=0.0;PAO=0.0;QR=0;QA=14402;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=202;SAR=176;SRP=0.0;SAP=6.89367;AB=0.0;ABP=0.0;RUN=1;RPP=11.3056;RPPR=0.0;RPL=170.0;RPR=208.0;EPP=4.13625;EPPR=0.0;DPRA=0.0;ODDS=62.9646;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.986772;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.866;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31 [...]
+chr12 78007092 . T C 2697.01 PASS SOMATIC;NS=2;DP=421;DPB=421.0;AC=1;AN=3;AF=0.25;RO=318;AO=103;PRO=0.0;PAO=0.0;QR=12372;QA=3986;PQR=0.0;PQA=0.0;SRF=193;SRR=125;SAF=50;SAR=53;SRP=34.5854;SAP=3.20004;AB=0.339934;ABP=70.4406;RUN=1;RPP=12.3076;RPPR=3.11956;RPL=41.0;RPR=62.0;EPP=9.10307;EPPR=5.22274;DPRA=2.5678;ODDS=74.617;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990291;PAIREDR=0.996855;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.047;Dels=0.0;FS= [...]
+chr12 78225374 . A G 14648.05 REJECT NS=2;DP=386;DPB=453.0;AC=4;AN=4;AF=1.0;RO=1;AO=452;PRO=0.0;PAO=0.0;QR=39;QA=17452;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=218;SAR=234;SRP=5.18177;SAP=4.24016;AB=0.0;ABP=0.0;RUN=1;RPP=4.56684;RPPR=5.18177;RPL=217.0;RPR=235.0;EPP=3.18325;EPPR=5.18177;DPRA=0.0;ODDS=86.6912;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995575;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.779;Dels=0.0;FS=0.0;HaplotypeScore=5.9322;MLEAC=2 [...]
+chr12 78334194 . A G 10033.8 REJECT NS=2;DP=374;DPB=422.0;AC=2;AN=4;AF=0.5;RO=97;AO=325;PRO=0.0;PAO=0.0;QR=3712;QA=12498;PQR=0.0;PQA=0.0;SRF=47;SRR=50;SAF=164;SAR=161;SRP=3.21178;SAP=3.07043;AB=0.770142;ABP=270.503;RUN=1;RPP=7.88108;RPPR=8.04722;RPL=149.0;RPR=176.0;EPP=3.81876;EPPR=4.82359;DPRA=0.0;ODDS=168.037;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993846;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1315;Dels=0.0;FS=2.6135;HaplotypeSc [...]
+chr12 78530979 . G A 9826.21 REJECT NS=2;DP=380;DPB=432.0;AC=2;AN=4;AF=0.5;RO=106;AO=325;PRO=0.0;PAO=0.0;QR=4086;QA=12328;PQR=0.0;PQA=0.0;SRF=59;SRR=47;SAF=182;SAR=143;SRP=5.96022;SAP=13.1728;AB=0.752315;ABP=241.892;RUN=1;RPP=11.1951;RPPR=3.09224;RPL=180.0;RPR=145.0;EPP=16.5402;EPPR=3.33807;DPRA=0.0;ODDS=142.713;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.097;Dels=0.0;FS=17.457;HaplotypeScore=4 [...]
+chr12 78537016 . A T 2448.885 REJECT NS=2;DP=366;DPB=426.0;AC=2;AN=4;AF=0.5;RO=313;AO=113;PRO=0.0;PAO=0.0;QR=12097;QA=4352;PQR=0.0;PQA=0.0;SRF=185;SRR=128;SAF=82;SAR=31;SRP=25.5506;SAP=52.9926;AB=0.265258;ABP=206.904;RUN=1;RPP=56.9896;RPPR=161.195;RPL=30.0;RPR=83.0;EPP=9.94748;EPPR=6.06979;DPRA=0.0;ODDS=163.439;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99115;PAIREDR=0.996805;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.236;Dels=0.0;FS=8.757;HaplotypeS [...]
+chr12 78537138 . C CGGT 1551.37 REJECT NS=2;DP=343;DPB=402.0;AC=2;AN=4;AF=0.5;RO=264;AO=75;PRO=27.5;PAO=29.5;QR=9925;QA=2773;PQR=856.0;PQA=931.0;SRF=84;SRR=180;SAF=21;SAR=54;SRP=78.8144;SAP=34.5401;AB=0.218659;ABP=238.827;RUN=1;RPP=3.73412;RPPR=30.6801;RPL=40.0;RPR=35.0;EPP=3.73412;EPPR=34.6283;DPRA=0.0;ODDS=94.5009;GTI=0;TYPE=ins;CIGAR=1M3I6M;NUMALT=1;MEANALT=3.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992424;technology.ILLUMINA=1.0;END=78537138;HOMLEN=5;HOMSEQ=GGTGG;SVLEN=3;SVTYP [...]
+chr12 78540174 . TA T 8109.255 REJECT NS=2;DP=283;DPB=323.5;AC=4;AN=4;AF=1.0;RO=7;AO=279;PRO=37.5;PAO=55.5;QR=261;QA=10517;PQR=1344.0;PQA=2023.0;SRF=2;SRR=5;SAF=68;SAR=211;SRP=5.80219;SAP=162.166;AB=0.0;ABP=0.0;RUN=1;RPP=113.226;RPPR=3.32051;RPL=199.0;RPR=80.0;EPP=7.12754;EPPR=5.80219;DPRA=0.0;ODDS=35.367;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=1;MEANALT=4.0;LEN=1;MQM=60.0717;MQMR=60.0;PAIRED=0.992832;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.406;FS=1.0745;MLEAC=2;MLEAF=1.0;M [...]
+chr12 78542594 . T G 967.098 REJECT NS=2;DP=241;DPB=265.0;AC=2;AN=4;AF=0.5;RO=212;AO=53;PRO=0.0;PAO=0.0;QR=8044;QA=2003;PQR=0.0;PQA=0.0;SRF=143;SRR=69;SAF=40;SAR=13;SRP=59.0998;SAP=32.8783;AB=0.2;ABP=210.169;RUN=1;RPP=37.4671;RPPR=82.3305;RPL=12.0;RPR=41.0;EPP=3.37904;EPPR=14.851;DPRA=0.0;ODDS=61.1961;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.1887;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4535;Dels=0.0;FS=2.6755;HaplotypeScore=34.7887;M [...]
+chr12 78542602 . A AT 1165.57 REJECT NS=2;DP=298;DPB=332.308;AC=2;AN=4;AF=0.5;RO=231;AO=61;PRO=32.5;PAO=29.5;QR=8850;QA=2250;PQR=1144.5;PQA=1025.5;SRF=147;SRR=84;SAF=43;SAR=18;SRP=40.3201;SAP=25.259;AB=0.204698;ABP=228.727;RUN=1;RPP=9.02635;RPPR=27.4605;RPL=24.0;RPR=37.0;EPP=11.0198;EPPR=37.9889;DPRA=0.0;ODDS=80.2302;GTI=0;TYPE=ins;CIGAR=1M1I12M;NUMALT=1;MEANALT=4.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=0.129;FS=3.992;MLEAC=1;MLEAF=0.5;MQ=60 [...]
+chr12 78542699 . T C 1380.6599999999999 REJECT NS=2;DP=321;DPB=365.0;AC=2;AN=4;AF=0.5;RO=293;AO=72;PRO=0.0;PAO=0.0;QR=11040;QA=2804;PQR=0.0;PQA=0.0;SRF=89;SRR=204;SAF=28;SAR=44;SRP=101.023;SAP=10.7311;AB=0.19726;ABP=293.577;RUN=1;RPP=20.3821;RPPR=54.0658;RPL=48.0;RPR=24.0;EPP=7.35324;EPPR=3.37345;DPRA=0.0;ODDS=86.041;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986111;PAIREDR=0.989761;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.664;Dels=0.0;FS=3.1895;Ha [...]
+chr12 78569059 . G A 1837.38 REJECT NS=1;DP=56;DPB=56.0;AC=2;AN=4;AF=1.0;RO=0;AO=56;PRO=0.0;PAO=0.0;QR=0;QA=2172;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=42;SAR=14;SRP=0.0;SAP=33.4109;AB=0.0;ABP=0.0;RUN=1;RPP=53.2644;RPPR=0.0;RPL=10.0;RPR=46.0;EPP=8.59409;EPPR=0.0;DPRA=0.0;ODDS=39.5737;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.14;SOR=2.221 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:A [...]
+chr12 78570914 . G C 1575.52 REJECT NS=2;DP=308;DPB=356.0;AC=2;AN=4;AF=0.5;RO=276;AO=80;PRO=0.0;PAO=0.0;QR=10509;QA=3073;PQR=0.0;PQA=0.0;SRF=199;SRR=77;SAF=53;SAR=27;SRP=120.112;SAP=21.3592;AB=0.224719;ABP=237.334;RUN=1;RPP=16.1477;RPPR=35.2362;RPL=29.0;RPR=51.0;EPP=6.91895;EPPR=3.04177;DPRA=0.0;ODDS=117.32;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.9875;PAIREDR=0.996377;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.219;Dels=0.0;FS=4.7895;HaplotypeScore [...]
+chr12 78582566 . A G 10478.085 REJECT NS=2;DP=282;DPB=333.0;AC=4;AN=4;AF=1.0;RO=0;AO=333;PRO=0.0;PAO=0.0;QR=0;QA=12723;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=93;SAR=240;SRP=0.0;SAP=143.921;AB=0.0;ABP=0.0;RUN=1;RPP=140.113;RPPR=0.0;RPL=239.0;RPR=94.0;EPP=10.9984;EPPR=0.0;DPRA=0.0;ODDS=66.7319;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996997;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.035;SOR=2 [...]
+chr12 78592992 . ATGGGAACATTATTAC A 5155.41 REJECT NS=2;DP=269;DPB=109.0;AC=2;AN=4;AF=0.5;RO=66;AO=203;PRO=55.5;PAO=38.5;QR=2476;QA=6671;PQR=2087.5;PQA=1453.5;SRF=25;SRR=41;SAF=92;SAR=111;SRP=11.433;SAP=6.87188;AB=0.751852;ABP=151.764;RUN=1;RPP=10.8083;RPPR=28.8048;RPL=115.0;RPR=88.0;EPP=3.87675;EPPR=6.30041;DPRA=0.0;ODDS=128.35;GTI=0;TYPE=del;CIGAR=1M15D1M;NUMALT=1;MEANALT=1.5;LEN=15;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=78593007;HOMLEN=1;HOMSEQ=T;S [...]
+chr12 78594396 . AT A 2700.46 REJECT NS=2;DP=118;DPB=141.105;AC=2;AN=2;AF=0.0;RO=33;AO=7;PRO=11.0;PAO=18.5;QR=1229;QA=202;PQR=385.5;PQA=645.5;SRF=8;SRR=25;SAF=3;SAR=4;SRP=22.0271;SAP=3.32051;AB=0.059322;ABP=202.05;RUN=1;RPP=18.2106;RPPR=17.8158;RPL=7.0;RPR=0.0;EPP=3.32051;EPPR=3.60252;DPRA=0.0;ODDS=67.2822;GTI=0;TYPE=del;CIGAR=1M1D17M;NUMALT=3;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV [...]
+chr12 78594405 . T A 2700.46 REJECT NS=2;DP=118;DPB=141.105;AC=2;AN=4;AF=0.5;RO=33;AO=64;PRO=11.0;PAO=18.5;QR=1229;QA=2292;PQR=385.5;PQA=645.5;SRF=8;SRR=25;SAF=18;SAR=46;SRP=22.0271;SAP=29.6108;AB=0.542373;ABP=4.85053;RUN=1;RPP=42.2325;RPPR=17.8158;RPL=49.0;RPR=15.0;EPP=3.14602;EPPR=3.60252;DPRA=0.0;ODDS=67.2822;GTI=0;TYPE=snp;CIGAR=9M1X9M;NUMALT=3;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr12 78594405 . TA T 2700.46 REJECT NS=2;DP=118;DPB=141.105;AC=2;AN=2;AF=0.0;RO=33;AO=6;PRO=11.0;PAO=11.0;QR=1229;QA=214;PQR=385.5;PQA=385.5;SRF=8;SRR=25;SAF=1;SAR=5;SRP=22.0271;SAP=8.80089;AB=0.0508475;ABP=209.779;RUN=1;RPP=16.0391;RPPR=17.8158;RPL=6.0;RPR=0.0;EPP=8.80089;EPPR=3.60252;DPRA=0.0;ODDS=67.2822;GTI=0;TYPE=del;CIGAR=10M1D8M;NUMALT=3;MEANALT=6.0;LEN=1;MQM=56.3333;MQMR=60.0;PAIRED=0.833333;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr12 78598891 . G A 8346.55 REJECT NS=2;DP=333;DPB=380.0;AC=2;AN=4;AF=0.5;RO=107;AO=273;PRO=0.0;PAO=0.0;QR=3994;QA=10504;PQR=0.0;PQA=0.0;SRF=47;SRR=60;SAF=121;SAR=152;SRP=6.44001;SAP=10.6542;AB=0.718421;ABP=160.476;RUN=1;RPP=3.08189;RPPR=6.44001;RPL=135.0;RPR=138.0;EPP=6.51806;EPPR=3.51765;DPRA=0.0;ODDS=222.75;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.2345;Dels=0.0;FS=1.3645;HaplotypeScore=10 [...]
+chr12 89743223 . G A 13402.25 REJECT NS=2;DP=353;DPB=406.0;AC=4;AN=4;AF=1.0;RO=0;AO=406;PRO=0.0;PAO=0.0;QR=0;QA=15586;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=174;SAR=232;SRP=0.0;SAP=21.0025;AB=0.0;ABP=0.0;RUN=1;RPP=3.0103;RPPR=0.0;RPL=203.0;RPR=203.0;EPP=8.48712;EPPR=0.0;DPRA=0.0;ODDS=70.4501;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992611;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.4;SOR=1.1 [...]
+chr12 89745477 . C A 2903.31 REJECT NS=1;DP=86;DPB=86.0;AC=2;AN=4;AF=1.0;RO=0;AO=86;PRO=0.0;PAO=0.0;QR=0;QA=3269;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=49;SAR=37;SRP=0.0;SAP=6.64625;AB=0.0;ABP=0.0;RUN=1;RPP=4.62628;RPPR=0.0;RPL=47.0;RPR=39.0;EPP=5.53527;EPPR=0.0;DPRA=0.0;ODDS=58.2642;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=38.97;SOR=0.961 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:A [...]
+chr12 105003006 . T G 10353.3 REJECT NS=2;DP=385;DPB=436.0;AC=2;AN=4;AF=0.5;RO=100;AO=336;PRO=0.0;PAO=0.0;QR=3865;QA=12897;PQR=0.0;PQA=0.0;SRF=60;SRR=40;SAF=174;SAR=162;SRP=11.6962;SAP=3.94093;AB=0.770642;ABP=280.401;RUN=1;RPP=3.42391;RPPR=17.6895;RPL=164.0;RPR=172.0;EPP=4.66476;EPPR=3.09716;DPRA=0.0;ODDS=169.069;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988095;PAIREDR=0.98;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.075;Dels=0.0;FS=5.9845;Haplotype [...]
+chr12 111884608 . T C 5037.245000000001 REJECT NS=2;DP=337;DPB=385.0;AC=2;AN=4;AF=0.5;RO=201;AO=184;PRO=0.0;PAO=0.0;QR=7605;QA=6893;PQR=0.0;PQA=0.0;SRF=117;SRR=84;SAF=107;SAR=77;SRP=14.7751;SAP=13.6316;AB=0.477922;ABP=4.64031;RUN=1;RPP=4.19045;RPPR=3.53966;RPL=97.0;RPR=87.0;EPP=6.03148;EPPR=7.77458;DPRA=0.0;ODDS=274.318;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1915;Dels=0.0;FS=0.386;Haplotype [...]
+chr12 111885351 . ATGGGG A 753.16 REJECT NS=2;DP=195;DPB=230.786;AC=2;AN=4;AF=0.5;RO=84;AO=45;PRO=53.5;PAO=42.5;QR=2999;QA=1302;PQR=1896.5;PQA=1471.5;SRF=58;SRR=26;SAF=27;SAR=18;SRP=29.4816;SAP=6.91895;AB=0.230769;ABP=125.782;RUN=1;RPP=16.956;RPPR=8.07707;RPL=31.0;RPR=14.0;EPP=4.21667;EPPR=5.59539;DPRA=0.0;ODDS=39.6723;GTI=0;TYPE=del;CIGAR=1M5D22M;NUMALT=2;MEANALT=19.0;LEN=5;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988095;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;END=111885356;HOMLEN=20;H [...]
+chr12 111885352 . TGGGGT G 753.16 REJECT NS=2;DP=195;DPB=230.786;AC=2;AN=2;AF=0.0;RO=84;AO=5;PRO=53.5;PAO=1.0;QR=2999;QA=70;PQR=1896.5;PQA=35.0;SRF=58;SRR=26;SAF=0;SAR=5;SRP=29.4816;SAP=13.8677;AB=0.025641;ABP=384.132;RUN=1;RPP=3.44459;RPPR=8.07707;RPL=2.0;RPR=3.0;EPP=3.44459;EPPR=5.59539;DPRA=0.0;ODDS=39.6723;GTI=0;TYPE=complex;CIGAR=1M5D1X21M;NUMALT=2;MEANALT=19.0;LEN=23;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988095;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr12 111984851 . T C 2020.285 REJECT NS=2;DP=329;DPB=382.0;AC=2;AN=4;AF=0.5;RO=292;AO=90;PRO=0.0;PAO=0.0;QR=11298;QA=3551;PQR=0.0;PQA=0.0;SRF=116;SRR=176;SAF=35;SAR=55;SRP=29.7819;SAP=12.6613;AB=0.235602;ABP=234.96;RUN=1;RPP=7.73928;RPPR=17.4075;RPL=52.0;RPR=38.0;EPP=4.55446;EPPR=3.48624;DPRA=0.0;ODDS=121.761;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989726;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.2275;Dels=0.0;FS=2.998;HaplotypeScore [...]
+chr12 111989099 . C CA 97.6299 REJECT NS=1;DP=69;DPB=90.5926;AC=1;AN=4;AF=0.5;RO=26;AO=8;PRO=16.8333;PAO=14.8333;QR=930;QA=286;PQR=544.833;PQA=479.833;SRF=16;SRR=10;SAF=6;SAR=2;SRP=6.01695;SAP=7.35324;AB=0.115942;ABP=91.4113;RUN=1;RPP=20.3821;RPPR=11.3621;RPL=0.0;RPR=8.0;EPP=7.35324;EPPR=3.34437;DPRA=0.0;ODDS=1.32047;GTI=0;TYPE=ins;CIGAR=1M1I26M;NUMALT=3;MEANALT=18.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr12 111989099 . CA C 97.6299 REJECT NS=1;DP=69;DPB=90.5926;AC=1;AN=3;AF=0.0;RO=26;AO=10;PRO=16.8333;PAO=13.8333;QR=930;QA=295;PQR=544.833;PQA=445.5;SRF=16;SRR=10;SAF=6;SAR=4;SRP=6.01695;SAP=3.87889;AB=0.144928;ABP=78.5712;RUN=1;RPP=3.87889;RPPR=11.3621;RPL=4.0;RPR=6.0;EPP=10.8276;EPPR=3.34437;DPRA=0.0;ODDS=1.32047;GTI=0;TYPE=del;CIGAR=1M1D25M;NUMALT=3;MEANALT=18.0;LEN=1;MQM=61.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.228;FS=1.756;MLEAC [...]
+chr12 111989117 . G A 97.6299 REJECT NS=1;DP=69;DPB=90.5926;AC=1;AN=3;AF=0.0;RO=26;AO=4;PRO=16.8333;PAO=11.5;QR=930;QA=56;PQR=544.833;PQA=328.833;SRF=16;SRR=10;SAF=4;SAR=0;SRP=6.01695;SAP=11.6962;AB=0.057971;ABP=120.112;RUN=1;RPP=5.18177;RPPR=11.3621;RPL=3.0;RPR=1.0;EPP=5.18177;EPPR=3.34437;DPRA=0.0;ODDS=1.32047;GTI=0;TYPE=snp;CIGAR=18M1X8M;NUMALT=3;MEANALT=18.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr12 115117337 . G A 1943.995 REJECT NS=2;DP=356;DPB=409.0;AC=2;AN=4;AF=0.5;RO=309;AO=100;PRO=0.0;PAO=0.0;QR=11813;QA=3869;PQR=0.0;PQA=0.0;SRF=175;SRR=134;SAF=61;SAR=39;SRP=14.8234;SAP=13.5202;AB=0.244499;ABP=234.922;RUN=1;RPP=10.0459;RPPR=3.86062;RPL=41.0;RPR=59.0;EPP=6.13722;EPPR=4.59147;DPRA=0.0;ODDS=183.993;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990291;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.518;Dels=0.0;FS=1.8705;HaplotypeSc [...]
+chr12 121416622 . C G 4493.05 REJECT NS=2;DP=321;DPB=364.0;AC=2;AN=4;AF=0.5;RO=203;AO=160;PRO=0.0;PAO=0.0;QR=7753;QA=6160;PQR=0.0;PQA=0.0;SRF=111;SRR=92;SAF=71;SAR=89;SRP=6.87188;SAP=7.40753;AB=0.43956;ABP=14.5597;RUN=1;RPP=3.87889;RPPR=3.27772;RPL=76.0;RPR=84.0;EPP=4.36747;EPPR=3.021;DPRA=0.0;ODDS=220.609;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99375;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.5475;Dels=0.0;FS=6.7345;HaplotypeScore=7.9 [...]
+chr12 121432117 . G C 5826.25 REJECT NS=2;DP=379;DPB=433.0;AC=2;AN=4;AF=0.5;RO=215;AO=218;PRO=0.0;PAO=0.0;QR=7919;QA=8144;PQR=0.0;PQA=0.0;SRF=96;SRR=119;SAF=97;SAR=121;SRP=8.35313;SAP=8.74777;AB=0.503464;ABP=3.05543;RUN=1;RPP=6.23763;RPPR=6.65635;RPL=118.0;RPR=100.0;EPP=15.9196;EPPR=3.82839;DPRA=0.0;ODDS=294.038;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995349;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.147;Dels=0.0;FS=4.2065;HaplotypeSco [...]
+chr12 121434630 . C CTCATTCAT 6631.81 REJECT NS=2;DP=197;DPB=406.056;AC=4;AN=4;AF=1.0;RO=2;AO=186;PRO=87.5;PAO=108.5;QR=75;QA=6759;PQR=3049.0;PQA=3773.0;SRF=2;SRR=0;SAF=104;SAR=82;SRP=7.35324;SAP=8.6608;AB=0.0;ABP=0.0;RUN=1;RPP=3.43058;RPPR=3.0103;RPL=96.0;RPR=90.0;EPP=5.29852;EPPR=3.0103;DPRA=0.0;ODDS=33.251;GTI=0;TYPE=ins;CIGAR=1M8I17M;NUMALT=1;MEANALT=4.0;LEN=8;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=121434630;HOMLEN=16;HOMSEQ=TCATTCATTCATTCAT;SVLEN [...]
+chr12 121435475 . G A 6168.845 REJECT NS=2;DP=402;DPB=468.0;AC=2;AN=4;AF=0.5;RO=246;AO=222;PRO=0.0;PAO=0.0;QR=9286;QA=8472;PQR=0.0;PQA=0.0;SRF=144;SRR=102;SAF=137;SAR=85;SRP=18.5813;SAP=29.4592;AB=0.474359;ABP=5.68288;RUN=1;RPP=33.6848;RPPR=6.54115;RPL=83.0;RPR=139.0;EPP=4.92746;EPPR=8.09472;DPRA=0.0;ODDS=344.701;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995495;PAIREDR=0.995935;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.3545;Dels=0.0;FS=3.667;Haplot [...]
+chr12 121435536 . A G 8198.880000000001 REJECT NS=2;DP=490;DPB=573.0;AC=2;AN=4;AF=0.5;RO=279;AO=294;PRO=0.0;PAO=0.0;QR=10502;QA=11046;PQR=0.0;PQA=0.0;SRF=151;SRR=128;SAF=148;SAR=146;SRP=7.12754;SAP=3.03984;AB=0.513089;ABP=3.86297;RUN=1;RPP=3.03984;RPPR=3.64073;RPL=146.0;RPR=148.0;EPP=11.5485;EPPR=3.08035;DPRA=0.0;ODDS=452.287;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993197;PAIREDR=0.996416;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7325;Dels=0.0;FS [...]
+chr12 121435587 . G T 7495.505 REJECT NS=2;DP=487;DPB=567.0;AC=2;AN=4;AF=0.5;RO=296;AO=271;PRO=0.0;PAO=0.0;QR=11347;QA=10254;PQR=0.0;PQA=0.0;SRF=140;SRR=156;SAF=114;SAR=157;SRP=4.88833;SAP=17.826;AB=0.477954;ABP=5.4039;RUN=1;RPP=8.85164;RPPR=3.74391;RPL=149.0;RPR=122.0;EPP=5.326;EPPR=15.9511;DPRA=0.0;ODDS=418.74;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9932;PAIRED=0.99631;PAIREDR=0.989865;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3375;Dels=0.0;FS=2.669;Hapl [...]
+chr12 121437114 . G A 2875.92 PASS SOMATIC;NS=2;DP=393;DPB=393.0;AC=1;AN=3;AF=0.25;RO=282;AO=111;PRO=0.0;PAO=0.0;QR=10680;QA=4218;PQR=0.0;PQA=0.0;SRF=176;SRR=106;SAF=72;SAR=39;SRP=40.7416;SAP=24.3142;AB=0.356913;ABP=58.3165;RUN=1;RPP=4.59489;RPPR=32.6101;RPL=51.0;RPR=60.0;EPP=3.49937;EPPR=14.1295;DPRA=3.79268;ODDS=51.2652;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.882;Dels=0.0;FS=5.588;H [...]
+chr12 121437221 . T C 14211.15 REJECT NS=2;DP=377;DPB=435.0;AC=4;AN=4;AF=1.0;RO=0;AO=435;PRO=0.0;PAO=0.0;QR=0;QA=16594;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=186;SAR=249;SRP=0.0;SAP=22.8231;AB=0.0;ABP=0.0;RUN=1;RPP=4.13348;RPPR=0.0;RPL=225.0;RPR=210.0;EPP=17.0325;EPPR=0.0;DPRA=0.0;ODDS=75.4646;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993103;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=10.7279;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.02;SOR [...]
+chr12 121437382 . A G 8887.494999999999 REJECT NS=2;DP=243;DPB=281.0;AC=4;AN=4;AF=1.0;RO=1;AO=280;PRO=0.0;PAO=0.0;QR=16;QA=10510;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=73;SAR=207;SRP=5.18177;SAP=142.264;AB=0.0;ABP=0.0;RUN=1;RPP=5.523;RPPR=5.18177;RPL=149.0;RPR=131.0;EPP=43.2136;EPPR=5.18177;DPRA=0.0;ODDS=51.0429;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.648;Dels=0.0;FS=0.0;HaplotypeScore=8.8598;MLEAC [...]
+chr12 121438844 . T C 2787.81 REJECT NS=2;DP=191;DPB=224.0;AC=2;AN=4;AF=0.5;RO=119;AO=105;PRO=0.0;PAO=0.0;QR=4569;QA=3937;PQR=0.0;PQA=0.0;SRF=86;SRR=33;SAF=83;SAR=22;SRP=54.268;SAP=79.9631;AB=0.46875;ABP=4.91034;RUN=1;RPP=13.9504;RPPR=39.9618;RPL=41.0;RPR=64.0;EPP=3.03098;EPPR=5.21827;DPRA=0.0;ODDS=149.56;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.54;Dels=0.0;FS=2.942;HaplotypeScore=1.9664;MLEA [...]
+chr12 121506154 . G A 2640.2 PASS SOMATIC;NS=2;DP=404;DPB=404.0;AC=1;AN=3;AF=0.25;RO=302;AO=102;PRO=0.0;PAO=0.0;QR=11688;QA=3941;PQR=0.0;PQA=0.0;SRF=162;SRR=140;SAF=61;SAR=41;SRP=6.49041;SAP=11.5259;AB=0.329032;ABP=81.7157;RUN=1;RPP=3.35092;RPPR=8.6475;RPL=53.0;RPR=49.0;EPP=7.18293;EPPR=7.15192;DPRA=3.29787;ODDS=59.6778;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990066;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.535;Dels=0.0;FS=4.79 [...]
+chr12 133202215 . G A 1114.99 REJECT NS=2;DP=260;DPB=297.0;AC=2;AN=4;AF=0.5;RO=240;AO=57;PRO=0.0;PAO=0.0;QR=9233;QA=2233;PQR=0.0;PQA=0.0;SRF=144;SRR=96;SAF=32;SAR=25;SRP=23.8564;SAP=4.877;AB=0.191919;ABP=247.86;RUN=1;RPP=39.6206;RPPR=63.8477;RPL=13.0;RPR=44.0;EPP=4.877;EPPR=52.5561;DPRA=0.0;ODDS=41.0786;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.982456;PAIREDR=0.995833;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.585;Dels=0.0;FS=1.482;HaplotypeScore=1. [...]
+chr12 133208886 . C T 4803.845 REJECT NS=2;DP=202;DPB=232.0;AC=3;AN=4;AF=0.75;RO=58;AO=174;PRO=0.0;PAO=0.0;QR=2229;QA=6617;PQR=0.0;PQA=0.0;SRF=44;SRR=14;SAF=137;SAR=37;SRP=36.7056;SAP=127.808;AB=0.666667;ABP=44.9921;RUN=1;RPP=75.0932;RPPR=12.5947;RPL=49.0;RPR=125.0;EPP=9.05049;EPPR=3.60933;DPRA=0.0;ODDS=37.1639;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994253;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.121;Dels=0.0;FS=0.0;HaplotypeScore=0 [...]
+chr12 133208979 . T C 9163.685000000001 REJECT NS=2;DP=373;DPB=447.0;AC=3;AN=4;AF=0.75;RO=105;AO=342;PRO=0.0;PAO=0.0;QR=4045;QA=13136;PQR=0.0;PQA=0.0;SRF=52;SRR=53;SAF=167;SAR=175;SRP=3.03098;SAP=3.41666;AB=0.651163;ABP=62.751;RUN=1;RPP=9.51202;RPPR=3.03098;RPL=155.0;RPR=187.0;EPP=7.30245;EPPR=8.98702;DPRA=0.0;ODDS=92.0208;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991228;PAIREDR=0.990476;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.29;Dels=0.0;FS=1.65 [...]
+chr12 133210985 . C T 5078.31 REJECT NS=2;DP=211;DPB=237.0;AC=3;AN=4;AF=0.75;RO=59;AO=178;PRO=0.0;PAO=0.0;QR=2237;QA=6797;PQR=0.0;PQA=0.0;SRF=13;SRR=46;SAF=35;SAR=143;SRP=43.0905;SAP=145.303;AB=0.682796;ABP=56.9936;RUN=1;RPP=89.0884;RPPR=13.6468;RPL=131.0;RPR=47.0;EPP=17.1127;EPPR=3.93042;DPRA=0.0;ODDS=32.826;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.983051;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.168;Dels=0.0;FS=0.0;HaplotypeScore=1. [...]
+chr12 133219831 . T C 7002.725 REJECT NS=2;DP=306;DPB=348.0;AC=3;AN=4;AF=0.75;RO=93;AO=255;PRO=0.0;PAO=0.0;QR=3508;QA=9545;PQR=0.0;PQA=0.0;SRF=67;SRR=26;SAF=154;SAR=101;SRP=42.2602;SAP=26.9306;AB=0.647727;ABP=53.0529;RUN=1;RPP=18.7556;RPPR=20.0318;RPL=106.0;RPR=149.0;EPP=9.21816;EPPR=3.22044;DPRA=0.0;ODDS=53.3398;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996078;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.636;Dels=0.0;FS=6.114;HaplotypeSco [...]
+chr12 133220526 . T C 6641.59 REJECT NS=2;DP=409;DPB=466.0;AC=2;AN=4;AF=0.5;RO=231;AO=235;PRO=0.0;PAO=0.0;QR=8729;QA=8956;PQR=0.0;PQA=0.0;SRF=119;SRR=112;SAF=122;SAR=113;SRP=3.47092;SAP=3.75876;AB=0.504292;ABP=3.08486;RUN=1;RPP=3.01954;RPPR=6.40381;RPL=118.0;RPR=117.0;EPP=9.74648;EPPR=12.044;DPRA=0.0;ODDS=358.286;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991489;PAIREDR=0.974026;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.798;Dels=0.0;FS=0.771;Haploty [...]
+chr12 133233705 . T C 8500.99 REJECT NS=2;DP=228;DPB=259.0;AC=4;AN=4;AF=1.0;RO=1;AO=258;PRO=0.0;PAO=0.0;QR=27;QA=9945;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=202;SAR=56;SRP=5.18177;SAP=182.418;AB=0.0;ABP=0.0;RUN=1;RPP=112.392;RPPR=5.18177;RPL=72.0;RPR=186.0;EPP=24.0517;EPPR=5.18177;DPRA=0.0;ODDS=41.7574;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992248;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.662;Dels=0.0;FS=3.44;HaplotypeScore=0.9973;MLEAC=2;M [...]
+chr12 133236000 . C T 9603.635 REJECT NS=2;DP=405;DPB=462.0;AC=3;AN=4;AF=0.75;RO=122;AO=340;PRO=0.0;PAO=0.0;QR=4721;QA=12963;PQR=0.0;PQA=0.0;SRF=59;SRR=63;SAF=154;SAR=186;SRP=3.29508;SAP=9.55026;AB=0.651429;ABP=72.7208;RUN=1;RPP=3.11249;RPPR=4.14943;RPL=172.0;RPR=168.0;EPP=3.41905;EPPR=4.7902;DPRA=0.0;ODDS=70.9008;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997059;PAIREDR=0.991803;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.014;Dels=0.0;FS=0.9245;Hapl [...]
+chr12 133252796 . C G 6364.5 REJECT NS=2;DP=259;DPB=294.0;AC=2;AN=4;AF=0.5;RO=80;AO=214;PRO=0.0;PAO=0.0;QR=2983;QA=8072;PQR=0.0;PQA=0.0;SRF=26;SRR=54;SAF=90;SAR=124;SRP=24.2907;SAP=14.7403;AB=0.727891;ABP=135.633;RUN=1;RPP=17.6627;RPPR=8.33041;RPL=126.0;RPR=88.0;EPP=17.6627;EPPR=8.33041;DPRA=0.0;ODDS=169.522;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990654;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6365;Dels=0.0;FS=3.827;HaplotypeScore=5 [...]
+chr12 133257837 . C A 1345.5349999999999 REJECT NS=2;DP=305;DPB=351.0;AC=2;AN=4;AF=0.5;RO=279;AO=71;PRO=0.0;PAO=0.0;QR=10441;QA=2677;PQR=0.0;PQA=0.0;SRF=75;SRR=204;SAF=21;SAR=50;SRP=132.528;SAP=28.7315;AB=0.202279;ABP=273.244;RUN=1;RPP=6.71098;RPPR=3.20488;RPL=41.0;RPR=30.0;EPP=19.1893;EPPR=61.9202;DPRA=0.0;ODDS=67.5366;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985915;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8255;Dels=0.0;FS=0.864;Hapl [...]
+chr13 19526947 . T C 8997.17 REJECT NS=2;DP=340;DPB=389.0;AC=2;AN=4;AF=0.5;RO=93;AO=295;PRO=0.0;PAO=0.0;QR=3514;QA=11315;PQR=0.0;PQA=0.0;SRF=47;SRR=46;SAF=127;SAR=168;SRP=3.03365;SAP=15.384;AB=0.758355;ABP=228.536;RUN=1;RPP=12.0274;RPPR=9.75821;RPL=165.0;RPR=130.0;EPP=48.9498;EPPR=4.90158;DPRA=0.0;ODDS=158.729;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99322;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0675;Dels=0.0;FS=4.9435;HaplotypeScore [...]
+chr13 19675226 . T A 2711.86 PASS SOMATIC;NS=2;DP=418;DPB=418.0;AC=1;AN=3;AF=0.25;RO=312;AO=106;PRO=0.0;PAO=0.0;QR=11914;QA=4047;PQR=0.0;PQA=0.0;SRF=145;SRR=167;SAF=39;SAR=67;SRP=6.37887;SAP=19.071;AB=0.336508;ABP=76.1441;RUN=1;RPP=5.96022;RPPR=3.26085;RPL=59.0;RPR=47.0;EPP=7.02548;EPPR=19.0458;DPRA=3.05825;ODDS=65.1787;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990566;PAIREDR=0.996795;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.094;Dels=0.0;FS [...]
+chr13 19812530 . T G 13212.5 REJECT NS=2;DP=358;DPB=407.0;AC=4;AN=4;AF=1.0;RO=0;AO=407;PRO=0.0;PAO=0.0;QR=0;QA=15177;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=185;SAR=222;SRP=0.0;SAP=10.3143;AB=0.0;ABP=0.0;RUN=1;RPP=26.9605;RPPR=0.0;RPL=237.0;RPR=170.0;EPP=24.1862;EPPR=0.0;DPRA=0.0;ODDS=64.1075;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.990172;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.7533;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.055;SOR=0 [...]
+chr13 19831333 . A G 7732.11 REJECT NS=2;DP=288;DPB=330.0;AC=2;AN=4;AF=0.5;RO=75;AO=255;PRO=0.0;PAO=0.0;QR=2920;QA=9776;PQR=0.0;PQA=0.0;SRF=53;SRR=22;SAF=160;SAR=95;SRP=30.8341;SAP=38.9886;AB=0.772727;ABP=216.209;RUN=1;RPP=25.1593;RPPR=13.4623;RPL=102.0;RPR=153.0;EPP=50.9104;EPPR=15.7786;DPRA=0.0;ODDS=143.598;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.723;Dels=0.0;FS=2.8815;HaplotypeScore=5.78 [...]
+chr13 19843834 . A G 10376.75 REJECT NS=2;DP=277;DPB=316.0;AC=4;AN=4;AF=1.0;RO=0;AO=316;PRO=0.0;PAO=0.0;QR=0;QA=12121;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=71;SAR=245;SRP=0.0;SAP=211.059;AB=0.0;ABP=0.0;RUN=1;RPP=10.047;RPPR=0.0;RPL=174.0;RPR=142.0;EPP=49.2159;EPPR=0.0;DPRA=0.0;ODDS=52.1372;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993671;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9662;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.57;SOR=2.4 [...]
+chr13 19869324 . A G 2572.25 PASS SOMATIC;NS=2;DP=385;DPB=385.0;AC=1;AN=3;AF=0.25;RO=285;AO=100;PRO=0.0;PAO=0.0;QR=11154;QA=3811;PQR=0.0;PQA=0.0;SRF=183;SRR=102;SAF=60;SAR=40;SRP=52.9999;SAP=11.6962;AB=0.34965;ABP=59.1649;RUN=1;RPP=22.5536;RPPR=33.2509;RPL=35.0;RPR=65.0;EPP=3.79203;EPPR=15.8182;DPRA=2.88889;ODDS=62.7959;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992982;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.583;Dels=0.0;FS=2.8 [...]
+chr13 19873459 . T C 9180.59 REJECT NS=2;DP=340;DPB=398.0;AC=2;AN=4;AF=0.5;RO=99;AO=298;PRO=0.0;PAO=0.0;QR=3774;QA=11541;PQR=0.0;PQA=0.0;SRF=61;SRR=38;SAF=168;SAR=130;SRP=14.6134;SAP=13.5325;AB=0.748744;ABP=216.906;RUN=1;RPP=11.4339;RPPR=3.20771;RPL=132.0;RPR=166.0;EPP=11.4339;EPPR=16.7191;DPRA=0.0;ODDS=84.1198;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=58.0067;MQMR=58.2727;PAIRED=0.996644;PAIREDR=0.979798;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.188;Dels=0.0;FS=3.0535;Ha [...]
+chr13 19873542 . T C 8031.92 REJECT NS=2;DP=319;DPB=364.0;AC=2;AN=4;AF=0.5;RO=97;AO=267;PRO=0.0;PAO=0.0;QR=3712;QA=10283;PQR=0.0;PQA=0.0;SRF=22;SRR=75;SAF=80;SAR=187;SRP=65.8935;SAP=96.1234;AB=0.733516;ABP=175.416;RUN=1;RPP=76.4093;RPPR=3.56996;RPL=181.0;RPR=86.0;EPP=3.01843;EPPR=5.71904;DPRA=0.0;ODDS=157.991;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8557;PAIRED=0.996255;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.8335;Dels=0.0;FS=4.0515;HaplotypeS [...]
+chr13 19877501 . T TA 4960.754999999999 REJECT NS=2;DP=231;DPB=308.0;AC=2;AN=4;AF=0.5;RO=66;AO=191;PRO=26.0;PAO=28.0;QR=2517;QA=7036;PQR=876.5;PQA=942.5;SRF=50;SRR=16;SAF=141;SAR=50;SRP=41.044;SAP=97.1567;AB=0.723485;ABP=117.539;RUN=1;RPP=39.9481;RPPR=28.8048;RPL=67.0;RPR=124.0;EPP=5.56832;EPPR=11.433;DPRA=0.0;ODDS=113.465;GTI=0;TYPE=ins;CIGAR=1M1I11M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.2304;MQMR=60.0;PAIRED=0.979058;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6565;FS=5.2725;M [...]
+chr13 19877547 . G A 9774.09 REJECT NS=2;DP=362;DPB=416.0;AC=2;AN=4;AF=0.5;RO=102;AO=314;PRO=0.0;PAO=0.0;QR=3784;QA=12235;PQR=0.0;PQA=0.0;SRF=62;SRR=40;SAF=189;SAR=125;SRP=13.3141;SAP=31.3363;AB=0.754808;ABP=237.613;RUN=1;RPP=9.23427;RPPR=6.07591;RPL=142.0;RPR=172.0;EPP=10.0918;EPPR=24.8102;DPRA=0.0;ODDS=176.731;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.2229;MQMR=60.0;PAIRED=0.990446;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6595;Dels=0.0;FS=0.0;HaplotypeSc [...]
+chr13 19960133 . T C 12807.7 REJECT NS=2;DP=357;DPB=407.0;AC=4;AN=4;AF=1.0;RO=0;AO=407;PRO=0.0;PAO=0.0;QR=0;QA=14920;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=229;SAR=178;SRP=0.0;SAP=16.8874;AB=0.0;ABP=0.0;RUN=1;RPP=29.9056;RPPR=0.0;RPL=168.0;RPR=239.0;EPP=61.8321;EPPR=0.0;DPRA=0.0;ODDS=66.7188;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8526;MQMR=0.0;PAIRED=0.995086;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=7.7677;MLEAC=2;MLEAF=1.0;MQ=59.745;QD=29.48;S [...]
+chr13 19960226 . T C 8971.33 REJECT NS=2;DP=244;DPB=271.0;AC=4;AN=4;AF=1.0;RO=0;AO=271;PRO=0.0;PAO=0.0;QR=0;QA=10368;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=95;SAR=176;SRP=0.0;SAP=55.5824;AB=0.0;ABP=0.0;RUN=1;RPP=226.48;RPPR=0.0;RPL=219.0;RPR=52.0;EPP=3.08242;EPPR=0.0;DPRA=0.0;ODDS=37.4401;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.5867;MQMR=0.0;PAIRED=0.99262;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=58.61;QD=28.615;SOR=1. [...]
+chr13 28531385 . C T 14118.65 REJECT NS=2;DP=371;DPB=429.0;AC=4;AN=4;AF=1.0;RO=0;AO=429;PRO=0.0;PAO=0.0;QR=0;QA=16495;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=198;SAR=231;SRP=0.0;SAP=8.5225;AB=0.0;ABP=0.0;RUN=1;RPP=6.70028;RPPR=0.0;RPL=228.0;RPR=201.0;EPP=50.6359;EPPR=0.0;DPRA=0.0;ODDS=75.418;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993007;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=12.6092;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.24;SOR=0. [...]
+chr13 28589267 . C T 1069.1599999999999 REJECT NS=2;DP=188;DPB=217.0;AC=2;AN=4;AF=0.5;RO=163;AO=54;PRO=0.0;PAO=0.0;QR=6244;QA=2050;PQR=0.0;PQA=0.0;SRF=121;SRR=42;SAF=42;SAR=12;SRP=86.1524;SAP=39.2015;AB=0.248848;ABP=121.901;RUN=1;RPP=67.3502;RPPR=118.232;RPL=7.0;RPR=47.0;EPP=13.3047;EPPR=17.5179;DPRA=0.0;ODDS=88.016;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993865;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.038;Dels=0.0;FS=0.0;HaplotypeSc [...]
+chr13 28609825 . A G 5647.45 REJECT NS=2;DP=229;DPB=280.067;AC=2;AN=4;AF=0.5;RO=46;AO=178;PRO=23.5;PAO=30.5;QR=1737;QA=6798;PQR=841.0;PQA=1044.0;SRF=19;SRR=27;SAF=71;SAR=107;SRP=6.03148;SAP=18.8206;AB=0.712;ABP=100.605;RUN=1;RPP=7.89001;RPPR=3.0103;RPL=99.0;RPR=79.0;EPP=3.44947;EPPR=3.19912;DPRA=0.0;ODDS=88.042;GTI=0;TYPE=snp;CIGAR=12M1X2M;NUMALT=1;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994382;PAIREDR=0.956522;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.48;Dels=0.0;FS=1.3795;Hap [...]
+chr13 28609846 . A T 4185.2 REJECT NS=2;DP=166;DPB=184.0;AC=2;AN=4;AF=0.5;RO=40;AO=144;PRO=0.0;PAO=0.0;QR=1452;QA=5479;PQR=0.0;PQA=0.0;SRF=14;SRR=26;SAF=57;SAR=87;SRP=10.8276;SAP=16.582;AB=0.782609;ABP=130.655;RUN=1;RPP=159.899;RPPR=45.5712;RPL=123.0;RPR=21.0;EPP=6.8707;EPPR=6.48466;DPRA=0.0;ODDS=68.2601;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.95;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.742;Dels=0.0;FS=2.2005;HaplotypeScore=0.0;MLEAC [...]
+chr13 28610183 . A G 7323.17 REJECT NS=2;DP=273;DPB=305.0;AC=2;AN=4;AF=0.5;RO=64;AO=240;PRO=0.0;PAO=0.0;QR=2497;QA=9215;PQR=0.0;PQA=0.0;SRF=14;SRR=50;SAF=85;SAR=155;SRP=46.9826;SAP=47.3445;AB=0.786885;ABP=221.047;RUN=1;RPP=40.0701;RPPR=5.18177;RPL=152.0;RPR=88.0;EPP=3.04649;EPPR=7.89611;DPRA=0.0;ODDS=155.847;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995833;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5015;Dels=0.0;FS=6.6185;HaplotypeScore= [...]
+chr13 28611382 . T G 1956.16 REJECT NS=2;DP=355;DPB=411.0;AC=2;AN=4;AF=0.5;RO=314;AO=97;PRO=0.0;PAO=0.0;QR=12183;QA=3691;PQR=0.0;PQA=0.0;SRF=140;SRR=174;SAF=40;SAR=57;SRP=11.0046;SAP=9.47994;AB=0.23601;ABP=251.8;RUN=1;RPP=3.21178;RPPR=20.2991;RPL=50.0;RPR=47.0;EPP=12.8827;EPPR=20.2991;DPRA=0.0;ODDS=155.11;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996815;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.416;Dels=0.0;FS=2.73;HaplotypeScore=10.714 [...]
+chr13 28623699 . G T 6207.41 REJECT NS=2;DP=375;DPB=426.0;AC=2;AN=4;AF=0.5;RO=207;AO=219;PRO=0.0;PAO=0.0;QR=7920;QA=8331;PQR=0.0;PQA=0.0;SRF=95;SRR=112;SAF=102;SAR=117;SRP=6.04197;SAP=5.24126;AB=0.514085;ABP=3.74432;RUN=1;RPP=5.87585;RPPR=4.27961;RPL=118.0;RPR=101.0;EPP=4.686;EPPR=10.6577;DPRA=0.0;ODDS=331.27;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.980676;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.873;Dels=0.0;FS=3.428;HaplotypeScore=1 [...]
+chr13 28623759 . C T 6037.620000000001 REJECT NS=2;DP=378;DPB=432.0;AC=2;AN=4;AF=0.5;RO=210;AO=222;PRO=0.0;PAO=0.0;QR=8063;QA=8267;PQR=0.0;PQA=0.0;SRF=116;SRR=94;SAF=120;SAR=102;SRP=8.01503;SAP=6.17948;AB=0.513889;ABP=3.73412;RUN=1;RPP=3.04943;RPPR=4.49931;RPL=110.0;RPR=112.0;EPP=3.36243;EPPR=3.17575;DPRA=0.0;ODDS=338.764;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990991;PAIREDR=0.980952;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.2885;Dels=0.0;FS=2. [...]
+chr13 28624294 . G A 3103.89 PASS SOMATIC;NS=2;DP=427;DPB=427.0;AC=1;AN=3;AF=0.25;RO=309;AO=117;PRO=0.0;PAO=0.0;QR=11946;QA=4534;PQR=0.0;PQA=0.0;SRF=164;SRR=145;SAF=57;SAR=60;SRP=5.5472;SAP=3.17734;AB=0.35474;ABP=62.9416;RUN=1;RPP=5.25601;RPPR=9.76365;RPL=64.0;RPR=53.0;EPP=3.47429;EPPR=10.6632;DPRA=0.0;ODDS=55.2068;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990291;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.411;Dels=0.0;FS=3.143;Hap [...]
+chr13 28636084 . G A 13909.65 REJECT NS=2;DP=363;DPB=410.0;AC=4;AN=4;AF=1.0;RO=0;AO=410;PRO=0.0;PAO=0.0;QR=0;QA=15779;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=197;SAR=213;SRP=0.0;SAP=4.36615;AB=0.0;ABP=0.0;RUN=1;RPP=3.0103;RPPR=0.0;RPL=205.0;RPR=205.0;EPP=18.4542;EPPR=0.0;DPRA=0.0;ODDS=61.765;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995122;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8906;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.875;SOR=0. [...]
+chr13 28882948 . G A 3262.83 REJECT NS=2;DP=220;DPB=253.0;AC=2;AN=4;AF=0.5;RO=130;AO=123;PRO=0.0;PAO=0.0;QR=4905;QA=4610;PQR=0.0;PQA=0.0;SRF=80;SRR=50;SAF=69;SAR=54;SRP=18.0436;SAP=6.98251;AB=0.486166;ABP=3.43086;RUN=1;RPP=45.3981;RPPR=41.4955;RPL=37.0;RPR=86.0;EPP=6.98251;EPPR=7.28643;DPRA=0.0;ODDS=201.681;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992308;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4705;Dels=0.0;FS=1.7665;HaplotypeScore= [...]
+chr13 28883061 . G A 4984.040000000001 REJECT NS=2;DP=286;DPB=333.0;AC=2;AN=4;AF=0.5;RO=157;AO=176;PRO=0.0;PAO=0.0;QR=6058;QA=6788;PQR=0.0;PQA=0.0;SRF=52;SRR=105;SAF=54;SAR=122;SRP=41.8617;SAP=60.0608;AB=0.528529;ABP=5.36436;RUN=1;RPP=47.4268;RPPR=31.0181;RPL=118.0;RPR=58.0;EPP=3.79993;EPPR=3.68802;DPRA=0.0;ODDS=294.525;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993631;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3285;Dels=0.0;FS=0.5435;Ha [...]
+chr13 28886113 . A G 9455.44 REJECT NS=2;DP=264;DPB=310.0;AC=4;AN=4;AF=1.0;RO=0;AO=310;PRO=0.0;PAO=0.0;QR=0;QA=11321;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=211;SAR=99;SRP=0.0;SAP=90.8779;AB=0.0;ABP=0.0;RUN=1;RPP=64.9043;RPPR=0.0;RPL=108.0;RPR=202.0;EPP=3.12238;EPPR=0.0;DPRA=0.0;ODDS=60.8772;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0516;MQMR=0.0;PAIRED=0.996774;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.799;MLEAC=2;MLEAF=1.0;MQ=60.025;QD=29.545;SO [...]
+chr13 28893642 . A G 9062.31 REJECT NS=2;DP=356;DPB=404.0;AC=2;AN=4;AF=0.5;RO=108;AO=296;PRO=0.0;PAO=0.0;QR=4183;QA=11402;PQR=0.0;PQA=0.0;SRF=52;SRR=56;SAF=132;SAR=164;SRP=3.332;SAP=10.5224;AB=0.732673;ABP=192.982;RUN=1;RPP=10.5224;RPPR=3.09072;RPL=164.0;RPR=132.0;EPP=22.847;EPPR=12.7417;DPRA=0.0;ODDS=239.373;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8581;MQMR=60.0;PAIRED=0.993243;PAIREDR=0.990741;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.418;Dels=0.0;FS=0.5855;Haplot [...]
+chr13 28942840 . C CT 167.226 REJECT NS=2;DP=110;DPB=176.542;AC=2;AN=2;AF=0.0;RO=42;AO=11;PRO=48.6667;PAO=33.6667;QR=1506;QA=348;PQR=1758.5;PQA=1172.5;SRF=19;SRR=23;SAF=7;SAR=4;SRP=3.83753;SAP=4.78696;AB=0.1;ABP=155.882;RUN=1;RPP=19.0002;RPPR=94.2121;RPL=10.0;RPR=1.0;EPP=3.20771;EPPR=3.83753;DPRA=0.0;ODDS=0.247534;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=3;MEANALT=17.0;LEN=1;MQM=59.4545;MQMR=59.7619;PAIRED=1.0;PAIREDR=0.952381;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr13 28942840 . CT C 167.226 REJECT NS=2;DP=110;DPB=176.542;AC=2;AN=3;AF=0.25;RO=42;AO=14;PRO=48.6667;PAO=30.1667;QR=1506;QA=382;PQR=1758.5;PQA=1053.5;SRF=19;SRR=23;SAF=5;SAR=9;SRP=3.83753;SAP=5.49198;AB=0.127273;ABP=135.746;RUN=1;RPP=33.4109;RPPR=94.2121;RPL=14.0;RPR=0.0;EPP=5.49198;EPPR=3.83753;DPRA=0.0;ODDS=0.247534;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=3;MEANALT=17.0;LEN=1;MQM=60.0;MQMR=59.7619;PAIRED=1.0;PAIREDR=0.952381;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr13 28942840 . CTT C 167.226 REJECT NS=2;DP=110;DPB=176.542;AC=2;AN=3;AF=0.25;RO=42;AO=9;PRO=48.6667;PAO=24.5;QR=1506;QA=290;PQR=1758.5;PQA=876.5;SRF=19;SRR=23;SAF=5;SAR=4;SRP=3.83753;SAP=3.25157;AB=0.0818182;ABP=170.095;RUN=1;RPP=22.5536;RPPR=94.2121;RPL=9.0;RPR=0.0;EPP=3.25157;EPPR=3.83753;DPRA=0.0;ODDS=0.247534;GTI=0;TYPE=del;CIGAR=1M2D21M;NUMALT=3;MEANALT=17.0;LEN=2;MQM=60.0;MQMR=59.7619;PAIRED=1.0;PAIREDR=0.952381;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr13 28980036 . T TA 855.919 PASS SOMATIC;NS=2;DP=202;DPB=226.067;AC=2;AN=3;AF=0.25;RO=139;AO=43;PRO=22.1667;PAO=17.1667;QR=5281;QA=1491;PQR=803.0;PQA=624.0;SRF=19;SRR=120;SAF=7;SAR=36;SRP=162.371;SAP=45.4803;AB=0.212871;ABP=147.66;RUN=1;RPP=14.3727;RPPR=12.7741;RPL=29.0;RPR=14.0;EPP=4.27278;EPPR=5.65044;DPRA=0.0;ODDS=7.36968;GTI=0;TYPE=ins;CIGAR=1M1I14M;NUMALT=2;MEANALT=3.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.84 [...]
+chr13 28980036 . TA T 855.919 REJECT NS=2;DP=202;DPB=226.067;AC=2;AN=3;AF=0.25;RO=139;AO=13;PRO=22.1667;PAO=15.6667;QR=5281;QA=477;PQR=803.0;PQA=568.0;SRF=19;SRR=120;SAF=2;SAR=11;SRP=162.371;SAP=16.5402;AB=0.0643564;ABP=335.998;RUN=1;RPP=3.17734;RPPR=12.7741;RPL=6.0;RPR=7.0;EPP=7.18621;EPPR=5.65044;DPRA=0.0;ODDS=7.36968;GTI=0;TYPE=del;CIGAR=1M1D13M;NUMALT=2;MEANALT=3.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr13 29041007 . A T 2745.82 PASS SOMATIC;NS=2;DP=405;DPB=405.0;AC=1;AN=3;AF=0.25;RO=299;AO=105;PRO=0.0;PAO=0.0;QR=11535;QA=4016;PQR=0.0;PQA=0.0;SRF=151;SRR=148;SAF=53;SAR=52;SRP=3.07566;SAP=3.03098;AB=0.351171;ABP=60.5362;RUN=1;RPP=4.02365;RPPR=5.63204;RPL=56.0;RPR=49.0;EPP=6.50534;EPPR=7.54933;DPRA=2.82075;ODDS=66.5129;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9833;PAIRED=0.990476;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.221;Dels=0.0;FS= [...]
+chr13 32790641 . A G 7792.610000000001 REJECT NS=2;DP=328;DPB=379.0;AC=3;AN=4;AF=0.75;RO=94;AO=284;PRO=0.0;PAO=0.0;QR=3655;QA=10691;PQR=0.0;PQA=0.0;SRF=59;SRR=35;SAF=173;SAR=111;SRP=16.3163;SAP=32.4016;AB=0.658273;ABP=63.4991;RUN=1;RPP=11.8491;RPPR=3.37991;RPL=125.0;RPR=159.0;EPP=4.96768;EPPR=7.53805;DPRA=0.0;ODDS=63.0092;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9366;MQMR=60.0;PAIRED=0.989437;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.41;Dels=0.0;FS=0.0;Hap [...]
+chr13 32790998 . G A 2237.7650000000003 REJECT NS=2;DP=389;DPB=444.0;AC=2;AN=4;AF=0.5;RO=334;AO=110;PRO=0.0;PAO=0.0;QR=12786;QA=4075;PQR=0.0;PQA=0.0;SRF=161;SRR=173;SAF=52;SAR=58;SRP=3.9465;SAP=3.72096;AB=0.247748;ABP=248.406;RUN=1;RPP=9.40627;RPPR=6.15698;RPL=46.0;RPR=64.0;EPP=20.7769;EPPR=8.10741;DPRA=0.0;ODDS=164.363;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990909;PAIREDR=0.997006;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.721;Dels=0.0;FS=1.524; [...]
+chr13 32791053 . G T 6081.085 REJECT NS=2;DP=387;DPB=443.0;AC=2;AN=4;AF=0.5;RO=224;AO=218;PRO=0.0;PAO=0.0;QR=8646;QA=8268;PQR=0.0;PQA=0.0;SRF=101;SRR=123;SAF=102;SAR=116;SRP=7.70223;SAP=4.96263;AB=0.492099;ABP=3.25049;RUN=1;RPP=3.05014;RPPR=3.35929;RPL=110.0;RPR=108.0;EPP=4.96263;EPPR=3.16541;DPRA=0.0;ODDS=330.896;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990826;PAIREDR=0.995536;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0285;Dels=0.0;FS=1.788;Hapl [...]
+chr13 32890572 . G A 1485.98 REJECT NS=2;DP=285;DPB=327.0;AC=2;AN=4;AF=0.5;RO=253;AO=74;PRO=0.0;PAO=0.0;QR=9655;QA=2813;PQR=0.0;PQA=0.0;SRF=147;SRR=106;SAF=44;SAR=30;SRP=17.4381;SAP=8.76177;AB=0.2263;ABP=215.781;RUN=1;RPP=19.9126;RPPR=67.9742;RPL=25.0;RPR=49.0;EPP=7.23587;EPPR=4.46081;DPRA=0.0;ODDS=102.9;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986486;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.683;Dels=0.0;FS=3.8365;HaplotypeScore=4.863 [...]
+chr13 32911888 . A G 2295.15 REJECT NS=2;DP=326;DPB=383.0;AC=2;AN=4;AF=0.5;RO=276;AO=107;PRO=0.0;PAO=0.0;QR=10538;QA=4083;PQR=0.0;PQA=0.0;SRF=141;SRR=135;SAF=53;SAR=54;SRP=3.29354;SAP=3.03059;AB=0.279373;ABP=164.941;RUN=1;RPP=4.65412;RPPR=3.51383;RPL=58.0;RPR=49.0;EPP=4.65412;EPPR=3.04177;DPRA=0.0;ODDS=181.078;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996377;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.124;Dels=0.0;FS=2.395;HaplotypeScore= [...]
+chr13 32912299 . T C 3070.45 PASS SOMATIC;NS=2;DP=397;DPB=397.0;AC=1;AN=3;AF=0.25;RO=280;AO=117;PRO=0.0;PAO=0.0;QR=10776;QA=4392;PQR=0.0;PQA=0.0;SRF=130;SRR=150;SAF=53;SAR=64;SRP=6.1124;SAP=5.25601;AB=0.384868;ABP=38.011;RUN=1;RPP=3.91972;RPPR=4.12706;RPL=55.0;RPR=62.0;EPP=3.91972;EPPR=6.1124;DPRA=3.26882;ODDS=58.9508;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991453;PAIREDR=0.996429;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.542;Dels=0.0;FS= [...]
+chr13 32913055 . A G 14207.65 REJECT NS=2;DP=374;DPB=426.0;AC=4;AN=4;AF=1.0;RO=0;AO=426;PRO=0.0;PAO=0.0;QR=0;QA=16304;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=187;SAR=239;SRP=0.0;SAP=16.7935;AB=0.0;ABP=0.0;RUN=1;RPP=5.47742;RPPR=0.0;RPL=224.0;RPR=202.0;EPP=5.04924;EPPR=0.0;DPRA=0.0;ODDS=68.5465;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99061;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.7983;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.18;SOR=0. [...]
+chr13 32915005 . G C 13525.15 REJECT NS=2;DP=360;DPB=417.0;AC=4;AN=4;AF=1.0;RO=0;AO=417;PRO=0.0;PAO=0.0;QR=0;QA=15864;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=201;SAR=216;SRP=0.0;SAP=4.18196;AB=0.0;ABP=0.0;RUN=1;RPP=5.30675;RPPR=0.0;RPL=198.0;RPR=219.0;EPP=8.01458;EPPR=0.0;DPRA=0.0;ODDS=74.1913;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992806;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8905;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.755;SOR= [...]
+chr13 32929232 . A G 1826.71 REJECT NS=2;DP=393;DPB=448.0;AC=2;AN=4;AF=0.5;RO=352;AO=96;PRO=0.0;PAO=0.0;QR=13430;QA=3632;PQR=0.0;PQA=0.0;SRF=160;SRR=192;SAF=47;SAR=49;SRP=9.32731;SAP=3.10078;AB=0.214286;ABP=320.666;RUN=1;RPP=3.8246;RPPR=7.84676;RPL=45.0;RPR=51.0;EPP=4.45795;EPPR=7.84676;DPRA=0.0;ODDS=149.591;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997159;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4685;Dels=0.0;FS=0.987;HaplotypeScore=1 [...]
+chr13 32929387 . T C 11824.3 REJECT NS=2;DP=312;DPB=362.0;AC=4;AN=4;AF=1.0;RO=0;AO=362;PRO=0.0;PAO=0.0;QR=0;QA=13921;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=167;SAR=195;SRP=0.0;SAP=7.71316;AB=0.0;ABP=0.0;RUN=1;RPP=4.95383;RPPR=0.0;RPL=190.0;RPR=172.0;EPP=12.608;EPPR=0.0;DPRA=0.0;ODDS=66.754;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9663;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.805;SOR=0.858 GT [...]
+chr13 32936646 . T C 5376.295 REJECT NS=2;DP=257;DPB=292.0;AC=3;AN=4;AF=0.75;RO=95;AO=197;PRO=0.0;PAO=0.0;QR=3693;QA=7462;PQR=0.0;PQA=0.0;SRF=58;SRR=37;SAF=135;SAR=62;SRP=13.0905;SAP=61.7503;AB=0.575893;ABP=14.2166;RUN=1;RPP=61.7503;RPPR=27.9022;RPL=62.0;RPR=135.0;EPP=3.90314;EPPR=4.86177;DPRA=0.0;ODDS=43.4103;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.979695;PAIREDR=0.989474;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.686;Dels=0.0;FS=0.537;Haplotype [...]
+chr13 32970031 . T C 3544.4 REJECT NS=1;DP=265;DPB=265.0;AC=1;AN=4;AF=0.5;RO=136;AO=129;PRO=0.0;PAO=0.0;QR=5153;QA=4839;PQR=0.0;PQA=0.0;SRF=46;SRR=90;SAF=44;SAR=85;SRP=33.9218;SAP=31.3068;AB=0.486792;ABP=3.41182;RUN=1;RPP=6.79775;RPPR=3.5851;RPL=57.0;RPR=72.0;EPP=6.79775;EPPR=8.18351;DPRA=0.0;ODDS=816.127;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8603;PAIRED=0.906977;PAIREDR=0.897059;technology.ILLUMINA=1.0;BaseQRankSum=1.645;FS=0.537;MLEAC=1;MLEAF=0.5;MQ=60.0;M [...]
+chr13 33055620 . T C 14032.849999999999 REJECT NS=2;DP=369;DPB=425.0;AC=4;AN=4;AF=1.0;RO=1;AO=424;PRO=0.0;PAO=0.0;QR=16;QA=16293;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=204;SAR=220;SRP=5.18177;SAP=4.32138;AB=0.0;ABP=0.0;RUN=1;RPP=3.0103;RPPR=5.18177;RPL=212.0;RPR=212.0;EPP=58.4033;EPPR=5.18177;DPRA=0.0;ODDS=71.001;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988208;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.71;Dels=0.0;FS=0.0;HaplotypeScore=2.932;M [...]
+chr13 33063902 . G A 1249.11 REJECT SOMATIC;NS=2;DP=202;DPB=279.81;AC=1;AN=3;AF=0.0;RO=30;AO=11;PRO=27.7857;PAO=12.8524;QR=1110;QA=146;PQR=998.083;PQA=457.1;SRF=11;SRR=19;SAF=0;SAR=11;SRP=7.64277;SAP=26.8965;AB=0.0544554;ABP=351.306;RUN=1;RPP=7.94546;RPPR=3.0103;RPL=3.0;RPR=8.0;EPP=7.94546;EPPR=3.29983;DPRA=0.0;ODDS=0.988727;GTI=1;TYPE=snp;CIGAR=1X20M;NUMALT=6;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr13 33063902 . G GA 1249.11 REJECT NS=2;DP=202;DPB=279.81;AC=2;AN=2;AF=0.25;RO=30;AO=40;PRO=27.7857;PAO=27.7857;QR=1110;QA=910;PQR=998.083;PQA=988.083;SRF=11;SRR=19;SAF=11;SAR=29;SRP=7.64277;SAP=20.5992;AB=0.19802;ABP=163.011;RUN=1;RPP=3.22745;RPPR=3.0103;RPL=21.0;RPR=19.0;EPP=10.8276;EPPR=3.29983;DPRA=0.0;ODDS=0.988727;GTI=1;TYPE=ins;CIGAR=1M1I20M;NUMALT=6;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-1.04;FS [...]
+chr13 33063902 . G GAA 1249.11 REJECT SOMATIC;NS=2;DP=202;DPB=279.81;AC=1;AN=3;AF=0.0;RO=30;AO=19;PRO=27.7857;PAO=26.7857;QR=1110;QA=476;PQR=998.083;PQA=961.083;SRF=11;SRR=19;SAF=6;SAR=13;SRP=7.64277;SAP=8.61041;AB=0.0940594;ABP=292.139;RUN=1;RPP=8.61041;RPPR=3.0103;RPL=13.0;RPR=6.0;EPP=8.61041;EPPR=3.29983;DPRA=0.0;ODDS=0.988727;GTI=1;TYPE=ins;CIGAR=1M2I20M;NUMALT=6;MEANALT=11.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:Q [...]
+chr13 33063902 . G GAAA 1249.11 REJECT SOMATIC;NS=2;DP=202;DPB=279.81;AC=1;AN=3;AF=0.0;RO=30;AO=8;PRO=27.7857;PAO=26.7857;QR=1110;QA=180;PQR=998.083;PQA=961.083;SRF=11;SRR=19;SAF=2;SAR=6;SRP=7.64277;SAP=7.35324;AB=0.039604;ABP=374.913;RUN=1;RPP=4.09604;RPPR=3.0103;RPL=5.0;RPR=3.0;EPP=4.09604;EPPR=3.29983;DPRA=0.0;ODDS=0.988727;GTI=1;TYPE=ins;CIGAR=1M3I20M;NUMALT=6;MEANALT=11.5;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr13 33063902 . GA G 1249.11 REJECT NS=2;DP=202;DPB=279.81;AC=2;AN=3;AF=0.5;RO=30;AO=64;PRO=27.7857;PAO=24.3857;QR=1110;QA=1957;PQR=998.083;PQA=871.733;SRF=11;SRR=19;SAF=16;SAR=48;SRP=7.64277;SAP=37.7539;AB=0.316832;ABP=61.8766;RUN=1;RPP=11.6962;RPPR=3.0103;RPL=40.0;RPR=24.0;EPP=7.89611;EPPR=3.29983;DPRA=0.0;ODDS=0.988727;GTI=1;TYPE=del;CIGAR=1M1D19M;NUMALT=6;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-1.004;FS=2.9 [...]
+chr13 33063902 . GAA G 1249.11 REJECT SOMATIC;NS=2;DP=202;DPB=279.81;AC=1;AN=3;AF=0.0;RO=30;AO=15;PRO=27.7857;PAO=21.619;QR=1110;QA=374;PQR=998.083;PQA=750.833;SRF=11;SRR=19;SAF=4;SAR=11;SRP=7.64277;SAP=10.1038;AB=0.0742574;ABP=321.034;RUN=1;RPP=3.15506;RPPR=3.0103;RPL=7.0;RPR=8.0;EPP=3.15506;EPPR=3.29983;DPRA=0.0;ODDS=0.988727;GTI=1;TYPE=del;CIGAR=1M2D18M;NUMALT=6;MEANALT=11.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr13 33065137 . C CA 4256.805 REJECT NS=2;DP=288;DPB=393.864;AC=2;AN=2;AF=0.5;RO=32;AO=84;PRO=36.7;PAO=41.3667;QR=1186;QA=2676;PQR=1251.1;PQA=1405.6;SRF=15;SRR=17;SAF=45;SAR=39;SRP=3.28173;SAP=3.94093;AB=0.291667;ABP=111.584;RUN=1;RPP=20.4855;RPPR=3.28173;RPL=55.0;RPR=29.0;EPP=4.66476;EPPR=4.09604;DPRA=0.0;ODDS=11.2533;GTI=0;TYPE=ins;CIGAR=1M1I21M;NUMALT=4;MEANALT=18.0;LEN=1;MQM=60.0;MQMR=59.375;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.327;FS [...]
+chr13 33065152 . TACTTTT ATACTTTC 6256.88 REJECT NS=2;DP=288;DPB=393.864;AC=0;AN=4;AF=0.0;RO=32;AO=40;PRO=36.7;PAO=35.3667;QR=1186;QA=1081;PQR=1251.1;PQA=1282.77;SRF=15;SRR=17;SAF=23;SAR=17;SRP=3.28173;SAP=4.96463;AB=0.138889;ABP=329.214;RUN=1;RPP=3.87889;RPPR=3.28173;RPL=22.0;RPR=18.0;EPP=8.43898;EPPR=4.09604;DPRA=0.0;ODDS=11.2533;GTI=0;TYPE=complex;CIGAR=1M1I20M1X;NUMALT=4;MEANALT=18.0;LEN=23;MQM=60.0;MQMR=59.375;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP [...]
+chr13 33065152 . TACTTTT AATACTTTC 6256.88 REJECT NS=2;DP=288;DPB=393.864;AC=0;AN=4;AF=0.0;RO=32;AO=33;PRO=36.7;PAO=35.3667;QR=1186;QA=860;PQR=1251.1;PQA=1193.77;SRF=15;SRR=17;SAF=14;SAR=19;SRP=3.28173;SAP=4.65535;AB=0.114583;ABP=374.604;RUN=1;RPP=17.8158;RPPR=3.28173;RPL=24.0;RPR=9.0;EPP=3.60252;EPPR=4.09604;DPRA=0.0;ODDS=11.2533;GTI=0;TYPE=complex;CIGAR=1M2I20M1X;NUMALT=4;MEANALT=18.0;LEN=24;MQM=60.0;MQMR=59.375;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP: [...]
+chr13 33065158 . T C 5103.825 REJECT NS=2;DP=283;DPB=393.864;AC=2;AN=2;AF=0.5;RO=32;AO=30;PRO=36.7;PAO=31.2;QR=1186;QA=1062;PQR=1251.1;PQA=1142.77;SRF=15;SRR=17;SAF=14;SAR=16;SRP=3.28173;SAP=3.29983;AB=0.104167;ABP=394.961;RUN=1;RPP=3.0103;RPPR=3.28173;RPL=15.0;RPR=15.0;EPP=13.4334;EPPR=4.09604;DPRA=0.0;ODDS=11.2533;GTI=0;TYPE=snp;CIGAR=21M1X;NUMALT=4;MEANALT=18.0;LEN=1;MQM=60.0;MQMR=59.375;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-1.759;Dels=0. [...]
+chr13 34509735 . G A 12925.849999999999 REJECT NS=2;DP=342;DPB=392.0;AC=4;AN=4;AF=1.0;RO=0;AO=392;PRO=0.0;PAO=0.0;QR=0;QA=15015;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=147;SAR=245;SRP=0.0;SAP=56.2114;AB=0.0;ABP=0.0;RUN=1;RPP=49.8964;RPPR=0.0;RPL=242.0;RPR=150.0;EPP=65.2518;EPPR=0.0;DPRA=0.0;ODDS=66.6852;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9325;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.23; [...]
+chr13 35252882 . T C 2766.37 PASS SOMATIC;NS=2;DP=425;DPB=425.0;AC=1;AN=3;AF=0.25;RO=320;AO=105;PRO=0.0;PAO=0.0;QR=12303;QA=4096;PQR=0.0;PQA=0.0;SRF=136;SRR=184;SAF=49;SAR=56;SRP=18.6449;SAP=4.02365;AB=0.33123;ABP=81.4368;RUN=1;RPP=3.19643;RPPR=3.03744;RPL=51.0;RPR=54.0;EPP=8.98702;EPPR=3.25459;DPRA=2.93519;ODDS=68.3339;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990625;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.182;Dels=0.0;FS=1.42 [...]
+chr13 40501283 . A G 12979.55 REJECT NS=2;DP=346;DPB=398.0;AC=4;AN=4;AF=1.0;RO=0;AO=398;PRO=0.0;PAO=0.0;QR=0;QA=15107;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=262;SAR=136;SRP=0.0;SAP=89.6291;AB=0.0;ABP=0.0;RUN=1;RPP=55.4093;RPPR=0.0;RPL=150.0;RPR=248.0;EPP=14.5551;EPPR=0.0;DPRA=0.0;ODDS=67.8859;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997487;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.8995;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.31;SOR=1 [...]
+chr13 41135488 . C CA 934.26 REJECT NS=2;DP=97;DPB=182.828;AC=2;AN=2;AF=0.5;RO=12;AO=22;PRO=41.3214;PAO=38.3214;QR=405;QA=700;PQR=1370.21;PQA=1263.21;SRF=10;SRR=2;SAF=17;SAR=5;SRP=14.5915;SAP=17.2236;AB=0.226804;ABP=65.8935;RUN=1;RPP=4.58955;RPPR=5.9056;RPL=9.0;RPR=13.0;EPP=12.8806;EPPR=5.9056;DPRA=0.0;ODDS=0.349831;GTI=1;TYPE=ins;CIGAR=1M1I28M;NUMALT=6;MEANALT=18.5;LEN=1;MQM=59.0909;MQMR=60.0;PAIRED=0.954545;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.4225 [...]
+chr13 41135488 . C CAA 1384.79 REJECT NS=2;DP=97;DPB=182.828;AC=0;AN=4;AF=0.0;RO=12;AO=4;PRO=41.3214;PAO=38.3214;QR=405;QA=145;PQR=1370.21;PQA=1263.21;SRF=10;SRR=2;SAF=4;SAR=0;SRP=14.5915;SAP=11.6962;AB=0.0412371;ABP=180.332;RUN=1;RPP=5.18177;RPPR=5.9056;RPL=1.0;RPR=3.0;EPP=5.18177;EPPR=5.9056;DPRA=0.0;ODDS=0.349831;GTI=1;TYPE=ins;CIGAR=1M2I28M;NUMALT=6;MEANALT=18.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr13 41135488 . CA C 1384.79 REJECT NS=2;DP=97;DPB=182.828;AC=0;AN=4;AF=0.0;RO=12;AO=11;PRO=41.3214;PAO=35.8214;QR=405;QA=320;PQR=1370.21;PQA=1173.21;SRF=10;SRR=2;SAF=8;SAR=3;SRP=14.5915;SAP=7.94546;AB=0.113402;ABP=128.933;RUN=1;RPP=3.20771;RPPR=5.9056;RPL=5.0;RPR=6.0;EPP=7.94546;EPPR=5.9056;DPRA=0.0;ODDS=0.349831;GTI=1;TYPE=del;CIGAR=1M1D27M;NUMALT=6;MEANALT=18.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr13 41135508 . TTCTATATC ATTCTATATT 1384.79 REJECT NS=2;DP=97;DPB=182.828;AC=2;AN=2;AF=0.5;RO=12;AO=7;PRO=41.3214;PAO=10.2381;QR=405;QA=112;PQR=1370.21;PQA=320.381;SRF=10;SRR=2;SAF=7;SAR=0;SRP=14.5915;SAP=18.2106;AB=0.0721649;ABP=157.23;RUN=1;RPP=5.80219;RPPR=5.9056;RPL=5.0;RPR=2.0;EPP=5.80219;EPPR=5.9056;DPRA=0.0;ODDS=0.349831;GTI=1;TYPE=complex;CIGAR=1M1I27M1X;NUMALT=6;MEANALT=18.5;LEN=30;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO: [...]
+chr13 41135508 . TTCTATATC ATTTTATATT 1384.79 REJECT NS=2;DP=97;DPB=182.828;AC=0;AN=4;AF=0.0;RO=12;AO=6;PRO=41.3214;PAO=10.7381;QR=405;QA=96;PQR=1370.21;PQA=328.381;SRF=10;SRR=2;SAF=6;SAR=0;SRP=14.5915;SAP=16.0391;AB=0.0618557;ABP=164.751;RUN=1;RPP=8.80089;RPPR=5.9056;RPL=5.0;RPR=1.0;EPP=8.80089;EPPR=5.9056;DPRA=0.0;ODDS=0.349831;GTI=1;TYPE=complex;CIGAR=1M1I21M1X5M1X;NUMALT=6;MEANALT=18.5;LEN=30;MQM=52.3333;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ [...]
+chr13 41135508 . TTCTATATC AATTCTATATT 1384.79 REJECT NS=2;DP=97;DPB=182.828;AC=0;AN=4;AF=0.0;RO=12;AO=3;PRO=41.3214;PAO=10.2381;QR=405;QA=48;PQR=1370.21;PQA=320.381;SRF=10;SRR=2;SAF=3;SAR=0;SRP=14.5915;SAP=9.52472;AB=0.0309278;ABP=188.391;RUN=1;RPP=3.73412;RPPR=5.9056;RPL=1.0;RPR=2.0;EPP=3.73412;EPPR=5.9056;DPRA=0.0;ODDS=0.349831;GTI=1;TYPE=complex;CIGAR=1M2I27M1X;NUMALT=6;MEANALT=18.5;LEN=31;MQM=53.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO [...]
+chr13 41136080 . C A 12.522 REJECT NS=2;DP=82;DPB=177.385;AC=2;AN=2;AF=0.0;RO=16;AO=6;PRO=68.8333;PAO=40.6667;QR=590;QA=118;PQR=2439.0;PQA=1431.83;SRF=4;SRR=12;SAF=3;SAR=3;SRP=11.6962;SAP=3.0103;AB=0.0677966;ABP=98.7391;RUN=1;RPP=16.0391;RPPR=37.7539;RPL=0.0;RPR=6.0;EPP=3.0103;EPPR=11.6962;DPRA=0.0;ODDS=1.82234;GTI=0;TYPE=snp;CIGAR=1X38M;NUMALT=3;MEANALT=24.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr13 41136080 . C CA 12.522 REJECT NS=2;DP=82;DPB=177.385;AC=2;AN=3;AF=0.25;RO=16;AO=6;PRO=68.8333;PAO=64.8333;QR=590;QA=116;PQR=2439.0;PQA=2263.0;SRF=4;SRR=12;SAF=1;SAR=5;SRP=11.6962;SAP=8.80089;AB=0.101695;ABP=84.3117;RUN=1;RPP=4.45795;RPPR=37.7539;RPL=2.0;RPR=4.0;EPP=3.0103;EPPR=11.6962;DPRA=2.56522;ODDS=1.82234;GTI=0;TYPE=ins;CIGAR=1M1I38M;NUMALT=3;MEANALT=30.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.833333;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr13 41136080 . CA C 12.522 REJECT NS=2;DP=82;DPB=177.385;AC=2;AN=2;AF=0.0;RO=16;AO=5;PRO=68.8333;PAO=50.6667;QR=590;QA=100;PQR=2439.0;PQA=1742.17;SRF=4;SRR=12;SAF=1;SAR=4;SRP=11.6962;SAP=6.91895;AB=0.0847458;ABP=91.3782;RUN=1;RPP=13.8677;RPPR=37.7539;RPL=0.0;RPR=5.0;EPP=6.91895;EPPR=11.6962;DPRA=2.56522;ODDS=1.82234;GTI=0;TYPE=del;CIGAR=1M1D37M;NUMALT=3;MEANALT=30.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.867;FS=7.3 [...]
+chr13 41137804 . A C 9121.485 REJECT NS=2;DP=408;DPB=478.0;AC=3;AN=4;AF=0.75;RO=135;AO=343;PRO=0.0;PAO=0.0;QR=5191;QA=13037;PQR=0.0;PQA=0.0;SRF=62;SRR=73;SAF=162;SAR=181;SRP=4.95658;SAP=5.29573;AB=0.602941;ABP=34.305;RUN=1;RPP=3.16857;RPPR=3.41242;RPL=174.0;RPR=169.0;EPP=4.08021;EPPR=6.62942;DPRA=0.0;ODDS=87.0648;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991254;PAIREDR=0.992593;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.267;Dels=0.0;FS=0.9125;Haplo [...]
+chr13 41138389 . C T 8146.16 REJECT NS=2;DP=381;DPB=430.0;AC=3;AN=4;AF=0.75;RO=123;AO=307;PRO=0.0;PAO=0.0;QR=4469;QA=11050;PQR=0.0;PQA=0.0;SRF=64;SRR=59;SAF=158;SAR=149;SRP=3.45166;SAP=3.58323;AB=0.631737;ABP=53.3573;RUN=1;RPP=3.01737;RPPR=5.14646;RPL=154.0;RPR=153.0;EPP=3.18713;EPPR=6.98251;DPRA=0.0;ODDS=60.8163;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996743;PAIREDR=0.98374;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.719;Dels=0.0;FS=0.2115;Haploty [...]
+chr13 41138419 . TA T 822.012 REJECT NS=2;DP=322;DPB=403.95;AC=2;AN=4;AF=0.5;RO=201;AO=50;PRO=104.5;PAO=72.5;QR=7219;QA=1730;PQR=3626.5;PQA=2558.5;SRF=99;SRR=102;SAF=28;SAR=22;SRP=3.10753;SAP=4.57376;AB=0.15528;ABP=335.367;RUN=1;RPP=3.18402;RPPR=3.88537;RPL=24.0;RPR=26.0;EPP=3.18402;EPPR=3.10753;DPRA=0.0;ODDS=45.8465;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=1;MEANALT=19.0;LEN=1;MQM=60.6;MQMR=60.0;PAIRED=1.0;PAIREDR=0.985075;technology.ILLUMINA=1.0;BaseQRankSum=0.032;FS=1.142;MLEAC=1;MLEAF=0.5 [...]
+chr13 41139082 . G GAGTCGGGGAACCCCGACATGGTGT 1240.73 PASS DP=101;AC=2;AN=4;AF=0.5;END=41139082;HOMLEN=29;HOMSEQ=AGTCGGGGAACCCCGACATGGTGTAGTCGGGGAACCCCGACATGGTGTA;SVLEN=24;SVTYPE=INS;BaseQRankSum=1.22;FS=5.324;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.043;QD=12.28;ReadPosRankSum=0.493;SOR=0.86;ClippingRankSum=1.93 GT:AD:GMIMUT:GMIMAF:GMICOV:DP:GQ:PL:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:53,37:37:43:90:54:99.0:1278,0,1067:1:.:.:1:.:.:-0.0017966 0/1:280,32:32:10:312:.:.:.:.:.:.:1:.: [...]
+chr13 41139712 . T C 9896.835 REJECT NS=2;DP=399;DPB=460.0;AC=3;AN=4;AF=0.75;RO=108;AO=352;PRO=0.0;PAO=0.0;QR=4187;QA=13391;PQR=0.0;PQA=0.0;SRF=61;SRR=47;SAF=189;SAR=163;SRP=6.95112;SAP=7.18051;AB=0.681416;ABP=99.9195;RUN=1;RPP=7.84676;RPPR=3.73412;RPL=190.0;RPR=162.0;EPP=5.00904;EPPR=5.9056;DPRA=0.0;ODDS=76.4898;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994318;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.874;Dels=0.0;FS=0.701;HaplotypeSc [...]
+chr13 41140516 . A AT 250.309 REJECT NS=2;DP=122;DPB=178.783;AC=2;AN=3;AF=0.25;RO=60;AO=17;PRO=39.05;PAO=20.55;QR=2203;QA=372;PQR=1399.32;PQA=720.817;SRF=5;SRR=55;SAF=2;SAR=15;SRP=93.4883;SAP=24.5973;AB=0.139344;ABP=140.845;RUN=1;RPP=13.3567;RPPR=12.2752;RPL=13.0;RPR=4.0;EPP=6.20364;EPPR=6.62942;DPRA=0.0;ODDS=13.0456;GTI=0;TYPE=ins;CIGAR=1M1I22M;NUMALT=4;MEANALT=9.0;LEN=1;MQM=60.0;MQMR=59.5;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr13 41140516 . AT A 250.309 REJECT NS=2;DP=122;DPB=178.783;AC=2;AN=3;AF=0.25;RO=60;AO=21;PRO=39.05;PAO=21.05;QR=2203;QA=523;PQR=1399.32;PQA=749.65;SRF=5;SRR=55;SAF=3;SAR=18;SRP=93.4883;SAP=26.2761;AB=0.172131;ABP=116.924;RUN=1;RPP=11.386;RPPR=12.2752;RPL=15.0;RPR=6.0;EPP=8.07707;EPPR=6.62942;DPRA=0.0;ODDS=13.0456;GTI=0;TYPE=del;CIGAR=1M1D21M;NUMALT=4;MEANALT=9.0;LEN=1;MQM=60.4762;MQMR=59.5;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.428;FS=1.30 [...]
+chr13 41140516 . ATT A 250.309 REJECT NS=2;DP=122;DPB=178.783;AC=2;AN=2;AF=0.0;RO=60;AO=7;PRO=39.05;PAO=17.05;QR=2203;QA=183;PQR=1399.32;PQA=595.4;SRF=5;SRR=55;SAF=2;SAR=5;SRP=93.4883;SAP=5.80219;AB=0.0752688;ABP=148.732;RUN=1;RPP=10.7656;RPPR=12.2752;RPL=6.0;RPR=1.0;EPP=10.7656;EPPR=6.62942;DPRA=0.0;ODDS=13.0456;GTI=0;TYPE=del;CIGAR=1M2D20M;NUMALT=4;MEANALT=13.0;LEN=2;MQM=60.0;MQMR=59.5;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr13 41140533 . A T 250.309 REJECT NS=2;DP=122;DPB=178.783;AC=2;AN=2;AF=0.0;RO=60;AO=5;PRO=39.05;PAO=18.3;QR=2203;QA=192;PQR=1399.32;PQA=642.817;SRF=5;SRR=55;SAF=1;SAR=4;SRP=93.4883;SAP=6.91895;AB=0.0409836;ABP=226.28;RUN=1;RPP=3.44459;RPPR=12.2752;RPL=3.0;RPR=2.0;EPP=3.44459;EPPR=6.62942;DPRA=0.0;ODDS=13.0456;GTI=0;TYPE=snp;CIGAR=17M1X5M;NUMALT=4;MEANALT=9.0;LEN=1;MQM=56.0;MQMR=59.5;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr13 41140619 . G A 487.767 PASS SOMATIC;NS=2;DP=90;DPB=90.0;AC=1;AN=3;AF=0.25;RO=68;AO=22;PRO=0.0;PAO=0.0;QR=2364;QA=835;PQR=0.0;PQA=0.0;SRF=18;SRR=50;SAF=2;SAR=20;SRP=35.7101;SAP=34.9902;AB=0.34375;ABP=16.582;RUN=1;RPP=12.8806;RPPR=9.26925;RPL=6.0;RPR=16.0;EPP=6.56362;EPPR=9.26925;DPRA=2.46154;ODDS=17.2169;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=57.4091;MQMR=57.5441;PAIRED=1.0;PAIREDR=0.985294;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.0;Dels=0.0;FS=7.226;Haplo [...]
+chr13 41141232 . T C 8333.619999999999 REJECT NS=2;DP=353;DPB=404.0;AC=3;AN=4;AF=0.75;RO=113;AO=291;PRO=0.0;PAO=0.0;QR=4390;QA=11314;PQR=0.0;PQA=0.0;SRF=64;SRR=49;SAF=161;SAR=130;SRP=7.33403;SAP=10.1814;AB=0.628289;ABP=46.4683;RUN=1;RPP=7.67412;RPPR=3.49071;RPL=133.0;RPR=158.0;EPP=3.91321;EPPR=3.49071;DPRA=0.0;ODDS=63.3605;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996564;PAIREDR=0.99115;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.765;Dels=0.0;FS=1.28 [...]
+chr13 41141282 . C G 9504.935000000001 REJECT NS=2;DP=412;DPB=473.0;AC=3;AN=4;AF=0.75;RO=132;AO=341;PRO=0.0;PAO=0.0;QR=5103;QA=13035;PQR=0.0;PQA=0.0;SRF=59;SRR=73;SAF=182;SAR=159;SRP=6.23461;SAP=6.37895;AB=0.625;ABP=50.7827;RUN=1;RPP=6.99027;RPPR=6.23461;RPL=158.0;RPR=183.0;EPP=3.06761;EPPR=12.4858;DPRA=0.0;ODDS=76.4498;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994135;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.177;Dels=0.0;FS=2.864;Hapl [...]
+chr13 41141886 . C G 2861.55 REJECT NS=2;DP=120;DPB=140.0;AC=3;AN=4;AF=0.75;RO=31;AO=109;PRO=0.0;PAO=0.0;QR=1164;QA=4093;PQR=0.0;PQA=0.0;SRF=5;SRR=26;SAF=14;SAR=95;SRP=33.9012;SAP=133.717;AB=0.696078;ABP=37.0726;RUN=1;RPP=10.2021;RPPR=4.76149;RPL=64.0;RPR=45.0;EPP=5.42083;EPPR=6.44263;DPRA=0.0;ODDS=24.7271;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8532;MQMR=60.0;PAIRED=0.981651;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.715;Dels=0.0;FS=2.551;HaplotypeScore= [...]
+chr13 41141998 . G A 2543.17 REJECT NS=2;DP=105;DPB=121.0;AC=3;AN=4;AF=0.75;RO=28;AO=93;PRO=0.0;PAO=0.0;QR=1033;QA=3511;PQR=0.0;PQA=0.0;SRF=17;SRR=11;SAF=53;SAR=40;SRP=5.80219;SAP=6.95631;AB=0.685393;ABP=29.5803;RUN=1;RPP=3.03365;RPPR=5.80219;RPL=46.0;RPR=47.0;EPP=4.90158;EPPR=4.25114;DPRA=0.0;ODDS=21.0082;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.6022;MQMR=60.0;PAIRED=0.989247;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.384;Dels=0.0;FS=0.442;HaplotypeScore= [...]
+chr13 41142092 . A G 2830.815 REJECT NS=2;DP=131;DPB=147.0;AC=3;AN=4;AF=0.75;RO=44;AO=102;PRO=0.0;PAO=0.0;QR=1659;QA=3833;PQR=0.0;PQA=0.0;SRF=31;SRR=13;SAF=81;SAR=21;SRP=19.0002;SAP=79.6505;AB=0.612069;ABP=15.6647;RUN=1;RPP=3.35092;RPPR=15.6443;RPL=49.0;RPR=53.0;EPP=3.7767;EPPR=12.6832;DPRA=0.0;ODDS=20.3366;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0882;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.206;Dels=0.0;FS=5.0425;HaplotypeScore=4.85 [...]
+chr13 41142104 . T TA 1796.18 REJECT NS=2;DP=153;DPB=189.65;AC=2;AN=2;AF=0.0;RO=58;AO=11;PRO=23.25;PAO=21.25;QR=2162;QA=370;PQR=820.583;PQA=744.583;SRF=42;SRR=16;SAF=9;SAR=2;SRP=28.3192;SAP=12.6832;AB=0.0718954;ABP=246.57;RUN=1;RPP=7.94546;RPPR=10.3484;RPL=8.0;RPR=3.0;EPP=3.20771;EPPR=3.16006;DPRA=0.0;ODDS=53.7303;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=3;MEANALT=5.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr13 41142104 . TA T 1564.955 REJECT NS=2;DP=144;DPB=189.65;AC=2;AN=4;AF=0.5;RO=58;AO=72;PRO=23.25;PAO=23.75;QR=2162;QA=2514;PQR=820.583;PQA=825.583;SRF=42;SRR=16;SAF=61;SAR=11;SRP=28.3192;SAP=78.4086;AB=0.470588;ABP=4.1599;RUN=1;RPP=42.0968;RPPR=10.3484;RPL=18.0;RPR=54.0;EPP=12.7819;EPPR=3.16006;DPRA=0.0;ODDS=53.7303;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=3;MEANALT=5.5;LEN=1;MQM=60.8333;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.404;FS= [...]
+chr13 41142104 . TAA T 1796.18 REJECT NS=2;DP=153;DPB=189.65;AC=2;AN=2;AF=0.0;RO=58;AO=7;PRO=23.25;PAO=19.75;QR=2162;QA=241;PQR=820.583;PQA=687.25;SRF=42;SRR=16;SAF=5;SAR=2;SRP=28.3192;SAP=5.80219;AB=0.0457516;ABP=277.226;RUN=1;RPP=10.7656;RPPR=10.3484;RPL=1.0;RPR=6.0;EPP=3.32051;EPPR=3.16006;DPRA=0.0;ODDS=53.7303;GTI=0;TYPE=del;CIGAR=1M2D17M;NUMALT=3;MEANALT=5.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr13 41142223 . C T 8152.775000000001 REJECT NS=2;DP=350;DPB=391.0;AC=3;AN=4;AF=0.75;RO=115;AO=276;PRO=0.0;PAO=0.0;QR=4420;QA=10763;PQR=0.0;PQA=0.0;SRF=72;SRR=43;SAF=167;SAR=109;SRP=18.8904;SAP=29.4771;AB=0.629032;ABP=47.8407;RUN=1;RPP=3.04177;RPPR=3.18024;RPL=139.0;RPR=137.0;EPP=21.1374;EPPR=5.29507;DPRA=0.0;ODDS=51.5703;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996377;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.229;Dels=0.0;FS=1.628;Ha [...]
+chr13 41143148 . T C 2547.73 REJECT NS=2;DP=461;DPB=529.0;AC=2;AN=4;AF=0.5;RO=405;AO=123;PRO=0.0;PAO=0.0;QR=14902;QA=4567;PQR=0.0;PQA=0.0;SRF=210;SRR=195;SAF=58;SAR=65;SRP=4.21667;SAP=3.87536;AB=0.232514;ABP=331.765;RUN=1;RPP=3.45166;RPPR=6.36134;RPL=59.0;RPR=64.0;EPP=3.16919;EPPR=8.16286;DPRA=0.0;ODDS=137.706;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99187;PAIREDR=0.992593;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.553;Dels=0.0;FS=2.4315;HaplotypeS [...]
+chr13 41143720 . C T 10213.035 REJECT NS=2;DP=423;DPB=484.0;AC=3;AN=4;AF=0.75;RO=128;AO=355;PRO=0.0;PAO=0.0;QR=4790;QA=13753;PQR=0.0;PQA=0.0;SRF=67;SRR=61;SAF=160;SAR=195;SRP=3.62103;SAP=10.5034;AB=0.647383;ABP=71.4984;RUN=1;RPP=6.83331;RPPR=4.09604;RPL=165.0;RPR=190.0;EPP=6.83331;EPPR=3.62103;DPRA=0.0;ODDS=75.8909;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994366;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.083;Dels=0.0;FS=4.549;HaplotypeS [...]
+chr13 41143881 . C A 8502.935000000001 REJECT NS=2;DP=393;DPB=447.0;AC=3;AN=4;AF=0.75;RO=132;AO=315;PRO=0.0;PAO=0.0;QR=4975;QA=11779;PQR=0.0;PQA=0.0;SRF=48;SRR=84;SAF=96;SAR=219;SRP=24.3302;SAP=107.303;AB=0.611765;ABP=39.8998;RUN=1;RPP=16.9698;RPPR=17.8158;RPL=180.0;RPR=135.0;EPP=3.34808;EPPR=6.23461;DPRA=0.0;ODDS=67.6644;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990476;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.654;Dels=0.0;FS=0.708;Ha [...]
+chr13 41144454 . A T 5860.605 REJECT NS=2;DP=268;DPB=302.0;AC=3;AN=4;AF=0.75;RO=88;AO=213;PRO=0.0;PAO=0.0;QR=3385;QA=7979;PQR=0.0;PQA=0.0;SRF=64;SRR=24;SAF=168;SAR=45;SRP=42.4916;SAP=157.246;AB=0.627119;ABP=36.1345;RUN=1;RPP=38.4981;RPPR=7.84676;RPL=77.0;RPR=136.0;EPP=3.50984;EPPR=19.6912;DPRA=0.0;ODDS=41.5629;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=59.8864;PAIRED=0.981221;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.064;Dels=0.0;FS=2.9025;HaplotypeS [...]
+chr13 41144507 . G A 9662.885 REJECT NS=2;DP=429;DPB=484.0;AC=3;AN=4;AF=0.75;RO=140;AO=343;PRO=0.0;PAO=0.0;QR=5197;QA=13007;PQR=0.0;PQA=0.0;SRF=84;SRR=56;SAF=223;SAR=120;SRP=15.1705;SAP=70.174;AB=0.625995;ABP=54.9932;RUN=1;RPP=15.8302;RPPR=9.21451;RPL=149.0;RPR=194.0;EPP=5.29573;EPPR=3.0103;DPRA=0.0;ODDS=67.7597;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.982507;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.628;Dels=0.0;FS=2.121;HaplotypeScor [...]
+chr13 41144919 . G A 9724.535 REJECT NS=2;DP=422;DPB=490.0;AC=3;AN=4;AF=0.75;RO=138;AO=352;PRO=0.0;PAO=0.0;QR=5295;QA=13538;PQR=0.0;PQA=0.0;SRF=74;SRR=64;SAF=179;SAR=173;SRP=4.58383;SAP=3.23238;AB=0.611268;ABP=41.1854;RUN=1;RPP=8.56236;RPPR=3.0103;RPL=161.0;RPR=191.0;EPP=3.40511;EPPR=5.27618;DPRA=0.0;ODDS=85.2395;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988636;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.266;Dels=0.0;FS=3.181;HaplotypeSco [...]
+chr13 41145330 . A T 5351.175 REJECT NS=2;DP=275;DPB=314.0;AC=3;AN=4;AF=0.75;RO=88;AO=220;PRO=0.0;PAO=0.0;QR=2918;QA=7447;PQR=0.0;PQA=0.0;SRF=27;SRR=61;SAF=76;SAR=144;SRP=31.5356;SAP=48.6507;AB=0.616034;ABP=30.7264;RUN=1;RPP=3.04978;RPPR=4.58955;RPL=109.0;RPR=111.0;EPP=7.78754;EPPR=11.0053;DPRA=0.0;ODDS=46.8386;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=59.8045;MQMR=59.7727;PAIRED=0.981818;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.15;Dels=0.0;FS=0.0;HaplotypeSc [...]
+chr13 41146301 . T C 9883.185000000001 REJECT NS=2;DP=431;DPB=500.0;AC=3;AN=4;AF=0.75;RO=141;AO=359;PRO=0.0;PAO=0.0;QR=5423;QA=13753;PQR=0.0;PQA=0.0;SRF=87;SRR=54;SAF=177;SAR=182;SRP=19.7815;SAP=3.16152;AB=0.61157;ABP=42.2583;RUN=1;RPP=8.09723;RPPR=7.46105;RPL=194.0;RPR=165.0;EPP=20.001;EPPR=11.1572;DPRA=0.0;ODDS=86.4256;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991643;PAIREDR=0.992908;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.011;Dels=0.0;FS=6.98 [...]
+chr13 41146547 . T TCTC 8427.46 REJECT NS=2;DP=373;DPB=742.333;AC=3;AN=4;AF=0.75;RO=140;AO=291;PRO=9.0;PAO=12.0;QR=5222;QA=10629;PQR=246.5;PQA=349.5;SRF=73;SRR=67;SAF=159;SAR=132;SRP=3.56868;SAP=8.45017;AB=0.570033;ABP=16.0886;RUN=1;RPP=3.61473;RPPR=10.5174;RPL=150.0;RPR=141.0;EPP=20.9268;EPPR=3.25847;DPRA=0.0;ODDS=7.7448;GTI=0;TYPE=ins;CIGAR=1M3I2M;NUMALT=1;MEANALT=2.0;LEN=3;MQM=60.1031;MQMR=59.7071;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=41146547;HOMLEN=2;HOMSEQ=CT;SVL [...]
+chr13 41147158 . T C 9783.835 REJECT NS=2;DP=386;DPB=445.0;AC=3;AN=4;AF=0.75;RO=98;AO=347;PRO=0.0;PAO=0.0;QR=3732;QA=13085;PQR=0.0;PQA=0.0;SRF=49;SRR=49;SAF=176;SAR=171;SRP=3.0103;SAP=3.16675;AB=0.70303;ABP=121.165;RUN=1;RPP=13.5297;RPPR=5.22609;RPL=153.0;RPR=194.0;EPP=3.06662;EPPR=3.36483;DPRA=0.0;ODDS=72.7012;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988473;PAIREDR=0.989796;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.003;Dels=0.0;FS=0.0;HaplotypeSc [...]
+chr13 41147493 . C A 6117.765 REJECT NS=2;DP=347;DPB=400.0;AC=2;AN=4;AF=0.5;RO=188;AO=212;PRO=0.0;PAO=0.0;QR=7145;QA=8129;PQR=0.0;PQA=0.0;SRF=91;SRR=97;SAF=134;SAR=78;SRP=3.42611;SAP=35.1317;AB=0.53;ABP=6.13722;RUN=1;RPP=3.66584;RPPR=4.16534;RPL=102.0;RPR=110.0;EPP=3.0103;EPPR=3.19511;DPRA=0.0;ODDS=316.584;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994681;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.576;Dels=0.0;FS=11.716;HaplotypeScore=5.8 [...]
+chr13 41148353 . T C 9650.985 REJECT NS=2;DP=408;DPB=475.0;AC=3;AN=4;AF=0.75;RO=120;AO=355;PRO=0.0;PAO=0.0;QR=4651;QA=13415;PQR=0.0;PQA=0.0;SRF=57;SRR=63;SAF=199;SAR=156;SRP=3.66174;SAP=14.3203;AB=0.650146;ABP=70.174;RUN=1;RPP=6.2461;RPPR=3.0103;RPL=189.0;RPR=166.0;EPP=3.01642;EPPR=4.81986;DPRA=0.0;ODDS=83.3474;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994366;PAIREDR=0.983333;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.746;Dels=0.0;FS=1.533;Haplotyp [...]
+chr13 41149311 . T TA 364.323 REJECT NS=2;DP=107;DPB=143.292;AC=2;AN=2;AF=0.0;RO=61;AO=11;PRO=24.6667;PAO=16.6667;QR=2252;QA=356;PQR=885.167;PQA=585.167;SRF=30;SRR=31;SAF=5;SAR=6;SRP=3.0459;SAP=3.20771;AB=0.102804;ABP=149.635;RUN=1;RPP=3.20771;RPPR=3.0459;RPL=6.0;RPR=5.0;EPP=12.6832;EPPR=32.9481;DPRA=0.0;ODDS=26.5181;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=3;MEANALT=10.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr13 41149311 . TA T 231.5265 REJECT NS=2;DP=106;DPB=143.292;AC=2;AN=4;AF=0.5;RO=61;AO=17;PRO=24.6667;PAO=18.1667;QR=2252;QA=643;PQR=885.167;PQA=636.167;SRF=30;SRR=31;SAF=7;SAR=10;SRP=3.0459;SAP=4.1599;AB=0.158879;ABP=111.158;RUN=1;RPP=13.3567;RPPR=3.0459;RPL=4.0;RPR=13.0;EPP=6.20364;EPPR=32.9481;DPRA=0.0;ODDS=26.5181;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=3;MEANALT=10.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.1035;FS=1 [...]
+chr13 41149311 . TAA T 364.323 REJECT NS=2;DP=107;DPB=143.292;AC=2;AN=2;AF=0.0;RO=61;AO=4;PRO=24.6667;PAO=14.5;QR=2252;QA=145;PQR=885.167;PQA=507.5;SRF=30;SRR=31;SAF=2;SAR=2;SRP=3.0459;SAP=3.0103;AB=0.0373832;ABP=201.913;RUN=1;RPP=3.0103;RPPR=3.0459;RPL=2.0;RPR=2.0;EPP=11.6962;EPPR=32.9481;DPRA=0.0;ODDS=26.5181;GTI=0;TYPE=del;CIGAR=1M2D21M;NUMALT=3;MEANALT=10.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr13 41149345 . T G 3008.385 REJECT NS=2;DP=133;DPB=157.0;AC=3;AN=4;AF=0.75;RO=33;AO=122;PRO=0.0;PAO=0.0;QR=1136;QA=4277;PQR=0.0;PQA=0.0;SRF=26;SRR=7;SAF=89;SAR=33;SRP=26.7649;SAP=58.8278;AB=0.690909;ABP=37.8328;RUN=1;RPP=31.4886;RPPR=4.65535;RPL=41.0;RPR=81.0;EPP=71.4295;EPPR=10.9724;DPRA=0.0;ODDS=26.3034;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991803;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.515;Dels=0.0;FS=0.4675;HaplotypeScore=16 [...]
+chr13 41150505 . A C 9256.485 REJECT NS=2;DP=417;DPB=469.0;AC=3;AN=4;AF=0.75;RO=141;AO=328;PRO=0.0;PAO=0.0;QR=5407;QA=12463;PQR=0.0;PQA=0.0;SRF=68;SRR=73;SAF=155;SAR=173;SRP=3.39531;SAP=5.15529;AB=0.617486;ABP=46.8907;RUN=1;RPP=8.96861;RPPR=9.80193;RPL=149.0;RPR=179.0;EPP=6.82362;EPPR=9.80193;DPRA=0.0;ODDS=57.3023;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.978659;PAIREDR=0.992908;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6585;Dels=0.0;FS=1.746;Haplo [...]
+chr13 41151134 . A G 2778.15 PASS SOMATIC;NS=2;DP=480;DPB=480.0;AC=1;AN=3;AF=0.25;RO=370;AO=110;PRO=0.0;PAO=0.0;QR=14345;QA=4192;PQR=0.0;PQA=0.0;SRF=188;SRR=182;SAF=68;SAR=42;SRP=3.22158;SAP=16.355;AB=0.321637;ABP=97.5138;RUN=1;RPP=3.0103;RPPR=4.16059;RPL=55.0;RPR=55.0;EPP=3.32615;EPPR=4.16059;DPRA=2.47826;ODDS=87.1199;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990909;PAIREDR=0.986486;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.99;Dels=0.0;FS=1 [...]
+chr13 41151292 . A C 599.77 PASS DP=82;AC=1;AN=4;AF=0.5;BaseQRankSum=-2.351;FS=176.619;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.634;QD=7.31;ReadPosRankSum=-2.154;SOR=6.182;ClippingRankSum=-0.241 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:61,21:82:99.0:628,0,3214:21:26:82:1:.:.:.:.:.:-0.0017966 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0152891
+chr13 41151296 . A C 584.77 PASS DP=81;AC=1;AN=4;AF=0.5;BaseQRankSum=-3.772;FS=145.221;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.25;QD=7.22;ReadPosRankSum=-3.206;SOR=6.089;ClippingRankSum=0.828 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:60,20:80:99.0:613,0,3456:20:25:80:1:.:.:.:.:.:-0.0017966 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0152891
+chr13 41151300 . A C 527.77 PASS DP=86;AC=1;AN=4;AF=0.5;BaseQRankSum=-2.544;FS=123.996;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.328;QD=6.14;ReadPosRankSum=-2.501;SOR=5.889;ClippingRankSum=-0.221 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:67,18:85:99.0:556,0,3625:18:21:85:1:.:.:.:.:.:-0.0017966 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0152891
+chr13 41151305 . T C 501.77 PASS DP=90;AC=1;AN=4;AF=0.5;ALERT;BaseQRankSum=-0.715;FS=101.645;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-1.289;QD=5.58;ReadPosRankSum=-4.138;SOR=5.781;ClippingRankSum=-0.485 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:72,17:89:99.0:530,0,3754:17:19:89:1:.:.:.:.:.:-0.0017966 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0152891
+chr13 41151307 . CTCCTCAATGTGAAAGGCATGATTA C 381.73 PASS DP=114;AC=1;AN=4;AF=0.5;ALERT;BaseQRankSum=-0.536;FS=84.02;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-1.534;QD=3.35;ReadPosRankSum=-5.112;SOR=5.667;ClippingRankSum=0.121 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:96,16:112:99.0:419,0,4708:16:14:112:1:.:.:.:.:.:-0.0017966 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0152891
+chr13 41151338 . G C 67.77 PASS DP=82;AC=1;AN=4;AF=0.5;BaseQRankSum=-0.878;FS=9.878;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=1.741;QD=0.83;SOR=2.22;ClippingRankSum=-0.046 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:78,2:80:96.0:96,0,3969:2:3:80:1:.:.:.:.:.:-0.0017966 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0152891
+chr13 41153225 . C T 11632.599999999999 REJECT NS=2;DP=497;DPB=565.0;AC=3;AN=4;AF=0.75;RO=158;AO=407;PRO=0.0;PAO=0.0;QR=6013;QA=15654;PQR=0.0;PQA=0.0;SRF=75;SRR=83;SAF=197;SAR=210;SRP=3.88988;SAP=3.91197;AB=0.632558;ABP=68.6393;RUN=1;RPP=6.34487;RPPR=6.52863;RPL=191.0;RPR=216.0;EPP=4.21075;EPPR=3.06527;DPRA=0.0;ODDS=85.1587;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997543;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.438;Dels=0.0;FS=0.2715; [...]
+chr13 41155776 . C G 9255.985 REJECT NS=2;DP=396;DPB=457.0;AC=3;AN=4;AF=0.75;RO=121;AO=336;PRO=0.0;PAO=0.0;QR=4619;QA=12758;PQR=0.0;PQA=0.0;SRF=62;SRR=59;SAF=175;SAR=161;SRP=3.17181;SAP=4.27699;AB=0.639881;ABP=60.1149;RUN=1;RPP=3.03615;RPPR=3.88966;RPL=167.0;RPR=169.0;EPP=11.386;EPPR=3.88966;DPRA=0.0;ODDS=76.4659;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988095;PAIREDR=0.991736;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.58;Dels=0.0;FS=0.0;HaplotypeS [...]
+chr13 41156188 . T C 9194.35 REJECT NS=2;DP=383;DPB=429.0;AC=3;AN=4;AF=0.75;RO=113;AO=316;PRO=0.0;PAO=0.0;QR=4321;QA=11971;PQR=0.0;PQA=0.0;SRF=62;SRR=51;SAF=152;SAR=164;SRP=5.3355;SAP=3.99983;AB=0.666667;ABP=84.8024;RUN=1;RPP=3.12025;RPPR=3.95191;RPL=156.0;RPR=160.0;EPP=6.96843;EPPR=3.02952;DPRA=0.0;ODDS=56.9978;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990506;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.571;Dels=0.0;FS=2.241;HaplotypeSco [...]
+chr13 41156708 . C T 4050.1049999999996 REJECT NS=2;DP=172;DPB=190.0;AC=3;AN=4;AF=0.75;RO=50;AO=140;PRO=0.0;PAO=0.0;QR=1921;QA=5302;PQR=0.0;PQA=0.0;SRF=22;SRR=28;SAF=51;SAR=89;SRP=4.57376;SAP=25.4075;AB=0.677419;ABP=45.389;RUN=1;RPP=30.3709;RPPR=3.70517;RPL=91.0;RPR=49.0;EPP=15.1705;EPPR=14.1282;DPRA=0.0;ODDS=22.857;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.971429;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.635;Dels=0.0;FS=2.18;HaplotypeS [...]
+chr13 41156938 . G A 4566.58 REJECT NS=2;DP=194;DPB=223.0;AC=3;AN=4;AF=0.75;RO=56;AO=166;PRO=0.0;PAO=0.0;QR=2127;QA=6223;PQR=0.0;PQA=0.0;SRF=30;SRR=26;SAF=93;SAR=73;SRP=3.63072;SAP=8.24276;AB=0.660606;ABP=39.978;RUN=1;RPP=3.2196;RPPR=8.59409;RPL=81.0;RPR=85.0;EPP=14.7833;EPPR=5.49198;DPRA=0.0;ODDS=36.5499;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993976;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.614;Dels=0.0;FS=0.305;HaplotypeScore=5.770 [...]
+chr13 41157372 . G A 4726.445 REJECT NS=2;DP=206;DPB=236.0;AC=3;AN=4;AF=0.75;RO=63;AO=173;PRO=0.0;PAO=0.0;QR=2382;QA=6452;PQR=0.0;PQA=0.0;SRF=34;SRR=29;SAF=67;SAR=106;SRP=3.872;SAP=22.1017;AB=0.642045;ABP=33.8551;RUN=1;RPP=6.63779;RPPR=3.32051;RPL=95.0;RPR=78.0;EPP=3.3241;EPPR=3.32051;DPRA=0.0;ODDS=38.3727;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99422;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.83;Dels=0.0;FS=4.709;HaplotypeScore=3.8994 [...]
+chr13 41158390 . C T 7807.76 REJECT NS=2;DP=352;DPB=402.0;AC=3;AN=4;AF=0.75;RO=112;AO=289;PRO=0.0;PAO=0.0;QR=4251;QA=10626;PQR=0.0;PQA=0.0;SRF=42;SRR=70;SAF=124;SAR=165;SRP=18.2106;SAP=15.6409;AB=0.630719;ABP=48.4267;RUN=1;RPP=3.07792;RPPR=4.25114;RPL=146.0;RPR=143.0;EPP=9.32936;EPPR=3.0103;DPRA=0.0;ODDS=60.7532;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99308;PAIREDR=0.982143;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.66;Dels=0.0;FS=1.6705;Haplotyp [...]
+chr13 41158593 . TCCAC CCCAA 8.80382 REJECT NS=2;DP=79;DPB=85.0;AC=1;AN=4;AF=0.25;RO=70;AO=5;PRO=11.0;PAO=0.0;QR=2448;QA=46;PQR=340.0;PQA=0.0;SRF=10;SRR=60;SAF=0;SAR=5;SRP=80.5629;SAP=13.8677;AB=0.0909091;ABP=34.9902;RUN=1;RPP=6.91895;RPPR=93.4676;RPL=4.0;RPR=1.0;EPP=6.91895;EPPR=93.4676;DPRA=0.0;ODDS=1.88593;GTI=0;TYPE=complex;CIGAR=1X3M1X;NUMALT=1;MEANALT=3.0;LEN=5;MQM=48.4;MQMR=59.0714;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:C [...]
+chr13 41158638 . A C 821.077 REJECT SOMATIC;NS=2;DP=59;DPB=107.5;AC=1;AN=3;AF=0.0;RO=20;AO=2;PRO=8.08333;PAO=4.75;QR=659;QA=76;PQR=191.417;PQA=110.917;SRF=16;SRR=4;SAF=0;SAR=2;SRP=18.6449;SAP=7.35324;AB=0.0454545;ABP=81.9729;RUN=1;RPP=7.35324;RPPR=24.2907;RPL=2.0;RPR=0.0;EPP=7.35324;EPPR=24.2907;DPRA=0.0;ODDS=1.87918;GTI=0;TYPE=snp;CIGAR=1X3M;NUMALT=3;MEANALT=7.0;LEN=1;MQM=50.0;MQMR=56.9;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr13 41158638 . A AGC 821.077 REJECT NS=2;DP=59;DPB=107.5;AC=2;AN=3;AF=0.5;RO=20;AO=17;PRO=8.08333;PAO=9.08333;QR=659;QA=558;PQR=191.417;PQA=219.083;SRF=16;SRR=4;SAF=10;SAR=7;SRP=18.6449;SAP=4.1599;AB=0.386364;ABP=7.94546;RUN=1;RPP=18.4661;RPPR=24.2907;RPL=3.0;RPR=14.0;EPP=13.3567;EPPR=24.2907;DPRA=0.0;ODDS=1.87918;GTI=0;TYPE=ins;CIGAR=1M2I3M;NUMALT=3;MEANALT=7.0;LEN=2;MQM=63.0;MQMR=56.9;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;END=41158638;HOMLEN=2;HOMSEQ= [...]
+chr13 41158638 . A AAAAAGC 821.077 REJECT NS=2;DP=59;DPB=107.5;AC=2;AN=2;AF=0.25;RO=20;AO=14;PRO=8.08333;PAO=7.08333;QR=659;QA=390;PQR=191.417;PQA=170.583;SRF=16;SRR=4;SAF=10;SAR=4;SRP=18.6449;SAP=8.59409;AB=0.933333;ABP=27.4756;RUN=1;RPP=12.937;RPPR=24.2907;RPL=3.0;RPR=11.0;EPP=25.3454;EPPR=24.2907;DPRA=0.0;ODDS=1.87918;GTI=0;TYPE=ins;CIGAR=1M6I3M;NUMALT=3;MEANALT=2.0;LEN=6;MQM=66.2143;MQMR=56.9;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr13 41159480 . G GCACA 2157.06 REJECT SOMATIC;NS=2;DP=242;DPB=397.531;AC=1;AN=3;AF=0.0;RO=56;AO=15;PRO=49.0;PAO=49.6667;QR=2067;QA=559;PQR=1765.6;PQA=1790.27;SRF=25;SRR=31;SAF=9;SAR=6;SRP=4.40625;SAP=4.31318;AB=0.0619835;ABP=406.294;RUN=1;RPP=4.31318;RPPR=3.16541;RPL=6.0;RPR=9.0;EPP=3.15506;EPPR=3.63072;DPRA=0.0;ODDS=46.9907;GTI=0;TYPE=ins;CIGAR=1M4I31M;NUMALT=4;MEANALT=13.5;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO [...]
+chr13 41159480 . G GCACACA 2341.395 REJECT NS=2;DP=242;DPB=397.531;AC=2;AN=2;AF=0.375;RO=56;AO=59;PRO=49.0;PAO=49.6667;QR=2067;QA=1963;PQR=1765.6;PQA=1790.27;SRF=25;SRR=31;SAF=29;SAR=30;SRP=4.40625;SAP=3.0471;AB=0.243802;ABP=140.98;RUN=1;RPP=3.34154;RPPR=3.16541;RPL=28.0;RPR=31.0;EPP=3.93042;EPPR=3.63072;DPRA=0.0;ODDS=46.9907;GTI=0;TYPE=ins;CIGAR=1M6I31M;NUMALT=4;MEANALT=13.5;LEN=6;MQM=59.9831;MQMR=60.0;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRank [...]
+chr13 41159480 . G GCACACACA 2157.06 REJECT NS=2;DP=242;DPB=397.531;AC=2;AN=3;AF=0.5;RO=56;AO=57;PRO=49.0;PAO=49.6667;QR=2067;QA=1783;PQR=1765.6;PQA=1790.27;SRF=25;SRR=31;SAF=20;SAR=37;SRP=4.40625;SAP=14.02;AB=0.235537;ABP=150.024;RUN=1;RPP=7.61992;RPPR=3.16541;RPL=23.0;RPR=34.0;EPP=3.0484;EPPR=3.63072;DPRA=0.0;ODDS=46.9907;GTI=0;TYPE=ins;CIGAR=1M8I31M;NUMALT=4;MEANALT=13.5;LEN=8;MQM=59.9298;MQMR=60.0;PAIRED=0.982456;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum [...]
+chr13 41159480 . GCA G 2157.06 REJECT SOMATIC;NS=2;DP=242;DPB=397.531;AC=1;AN=3;AF=0.0;RO=56;AO=11;PRO=49.0;PAO=36.0;QR=2067;QA=366;PQR=1765.6;PQA=1287.6;SRF=25;SRR=31;SAF=4;SAR=7;SRP=4.40625;SAP=4.78696;AB=0.0614525;ABP=302.031;RUN=1;RPP=3.20771;RPPR=3.16541;RPL=6.0;RPR=5.0;EPP=3.20771;EPPR=3.63072;DPRA=0.0;ODDS=46.9907;GTI=0;TYPE=del;CIGAR=1M2D29M;NUMALT=4;MEANALT=17.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr13 41161403 . T A 221.056 REJECT NS=2;DP=110;DPB=241.607;AC=2;AN=2;AF=0.0;RO=20;AO=8;PRO=87.45;PAO=27.0333;QR=752;QA=122;PQR=3101.73;PQA=922.233;SRF=3;SRR=17;SAF=0;SAR=8;SRP=24.2907;SAP=20.3821;AB=0.0727273;ABP=177.439;RUN=1;RPP=7.35324;RPPR=3.44459;RPL=2.0;RPR=6.0;EPP=7.35324;EPPR=4.74748;DPRA=0.0;ODDS=20.3108;GTI=0;TYPE=snp;CIGAR=1X27M;NUMALT=4;MEANALT=22.5;LEN=1;MQM=57.5;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr13 41161403 . T TA 181.893 REJECT NS=2;DP=110;DPB=241.607;AC=2;AN=4;AF=0.5;RO=20;AO=17;PRO=87.45;PAO=78.45;QR=752;QA=315;PQR=3101.73;PQA=2765.23;SRF=3;SRR=17;SAF=2;SAR=15;SRP=24.2907;SAP=24.5973;AB=0.154545;ABP=117.032;RUN=1;RPP=4.1599;RPPR=3.44459;RPL=7.0;RPR=10.0;EPP=3.13803;EPPR=4.74748;DPRA=0.0;ODDS=20.3108;GTI=0;TYPE=ins;CIGAR=1M1I27M;NUMALT=4;MEANALT=22.5;LEN=1;MQM=59.6471;MQMR=60.0;PAIRED=0.941176;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.6405; [...]
+chr13 41161403 . TA T 221.056 REJECT NS=2;DP=110;DPB=241.607;AC=2;AN=2;AF=0.0;RO=20;AO=8;PRO=87.45;PAO=42.6167;QR=752;QA=196;PQR=3101.73;PQA=1460.4;SRF=3;SRR=17;SAF=3;SAR=5;SRP=24.2907;SAP=4.09604;AB=0.0727273;ABP=177.439;RUN=1;RPP=3.0103;RPPR=3.44459;RPL=4.0;RPR=4.0;EPP=12.7819;EPPR=4.74748;DPRA=0.0;ODDS=20.3108;GTI=0;TYPE=del;CIGAR=1M1D26M;NUMALT=4;MEANALT=22.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr13 41161403 . TAA T 221.056 REJECT NS=2;DP=110;DPB=241.607;AC=2;AN=2;AF=0.0;RO=20;AO=8;PRO=87.45;PAO=39.45;QR=752;QA=157;PQR=3101.73;PQA=1345.4;SRF=3;SRR=17;SAF=0;SAR=8;SRP=24.2907;SAP=20.3821;AB=0.0727273;ABP=177.439;RUN=1;RPP=7.35324;RPPR=3.44459;RPL=2.0;RPR=6.0;EPP=7.35324;EPPR=4.74748;DPRA=0.0;ODDS=20.3108;GTI=0;TYPE=del;CIGAR=1M2D25M;NUMALT=4;MEANALT=22.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr13 41161770 . G A 3828.23 PASS SOMATIC;NS=2;DP=493;DPB=493.0;AC=1;AN=3;AF=0.25;RO=351;AO=142;PRO=0.0;PAO=0.0;QR=13469;QA=5478;PQR=0.0;PQA=0.0;SRF=175;SRR=176;SAF=62;SAR=80;SRP=3.01649;SAP=7.96493;AB=0.37467;ABP=54.7188;RUN=1;RPP=14.9993;RPPR=5.73856;RPL=85.0;RPR=57.0;EPP=3.98899;EPPR=5.73856;DPRA=3.32456;ODDS=72.0253;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985915;PAIREDR=0.985755;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.309;Dels=0.0;FS [...]
+chr13 41161979 . C G 3906.05 PASS SOMATIC;NS=2;DP=544;DPB=544.0;AC=1;AN=3;AF=0.25;RO=396;AO=148;PRO=0.0;PAO=0.0;QR=15088;QA=5676;PQR=0.0;PQA=0.0;SRF=224;SRR=172;SAF=85;SAR=63;SRP=17.8377;SAP=10.1116;AB=0.352381;ABP=82.5069;RUN=1;RPP=3.0103;RPPR=3.79993;RPL=74.0;RPR=74.0;EPP=3.06899;EPPR=11.7839;DPRA=3.3871;ODDS=78.3771;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997475;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.362;Dels=0.0;FS=0.0;H [...]
+chr13 41162225 . C T 10013.335 REJECT NS=2;DP=415;DPB=472.0;AC=3;AN=4;AF=0.75;RO=125;AO=347;PRO=0.0;PAO=0.0;QR=4796;QA=13384;PQR=0.0;PQA=0.0;SRF=62;SRR=63;SAF=162;SAR=185;SRP=3.02767;SAP=6.3207;AB=0.651811;ABP=74.8745;RUN=1;RPP=3.51719;RPPR=5.11229;RPL=169.0;RPR=178.0;EPP=9.02409;EPPR=3.44459;DPRA=0.0;ODDS=71.4722;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.354;Dels=0.0;FS=0.416;HaplotypeScore=2 [...]
+chr13 41162632 . T A 9685.635 REJECT NS=2;DP=416;DPB=470.0;AC=3;AN=4;AF=0.75;RO=127;AO=342;PRO=0.0;PAO=0.0;QR=4779;QA=12893;PQR=0.0;PQA=0.0;SRF=70;SRR=57;SAF=166;SAR=176;SRP=5.8999;SAP=3.64523;AB=0.651099;ABP=75.1939;RUN=1;RPP=21.525;RPPR=5.8999;RPL=198.0;RPR=144.0;EPP=3.23888;EPPR=3.16418;DPRA=0.0;ODDS=66.4869;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997076;PAIREDR=0.992126;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.702;Dels=0.0;FS=3.6925;Haplotyp [...]
+chr13 41163323 . A G 7128.16 REJECT NS=2;DP=310;DPB=357.0;AC=3;AN=4;AF=0.75;RO=97;AO=258;PRO=0.0;PAO=0.0;QR=3689;QA=9860;PQR=0.0;PQA=0.0;SRF=70;SRR=27;SAF=177;SAR=81;SRP=44.4026;SAP=80.5773;AB=0.625;ABP=38.8396;RUN=1;RPP=6.37692;RPPR=4.10723;RPL=139.0;RPR=119.0;EPP=39.6728;EPPR=21.8372;DPRA=0.0;ODDS=58.982;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=59.9884;MQMR=60.0;PAIRED=0.984496;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.814;Dels=0.0;FS=1.194;HaplotypeScore=6 [...]
+chr13 41163373 . A G 7457.42 REJECT NS=2;DP=325;DPB=374.0;AC=3;AN=4;AF=0.75;RO=107;AO=267;PRO=0.0;PAO=0.0;QR=4139;QA=10302;PQR=0.0;PQA=0.0;SRF=60;SRR=47;SAF=149;SAR=118;SRP=6.44001;SAP=10.826;AB=0.615108;ABP=35.0044;RUN=1;RPP=8.93915;RPPR=7.57648;RPL=120.0;RPR=147.0;EPP=3.0835;EPPR=3.19295;DPRA=0.0;ODDS=60.926;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.981273;PAIREDR=0.990654;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.016;Dels=0.0;FS=0.228;HaplotypeS [...]
+chr13 41169625 . A G 10007.935000000001 REJECT NS=2;DP=417;DPB=480.0;AC=3;AN=4;AF=0.75;RO=120;AO=357;PRO=0.0;PAO=0.0;QR=4584;QA=13486;PQR=0.0;PQA=0.0;SRF=59;SRR=61;SAF=170;SAR=187;SRP=3.08268;SAP=4.76816;AB=0.658263;ABP=80.6785;RUN=1;RPP=4.76816;RPPR=4.16842;RPL=170.0;RPR=187.0;EPP=3.01638;EPPR=4.81986;DPRA=0.0;ODDS=77.0199;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988796;PAIREDR=0.975;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.012;Dels=0.0;FS=0.203 [...]
+chr13 41170075 . A AT 725.664 REJECT NS=2;DP=194;DPB=305.222;AC=2;AN=2;AF=0.0;RO=59;AO=11;PRO=54.7;PAO=46.7;QR=2121;QA=269;PQR=1923.72;PQA=1639.72;SRF=21;SRR=38;SAF=5;SAR=6;SRP=13.6468;SAP=3.20771;AB=0.056701;ABP=334.149;RUN=1;RPP=3.20771;RPPR=22.4799;RPL=5.0;RPR=6.0;EPP=3.20771;EPPR=3.0471;DPRA=0.0;ODDS=19.9977;GTI=0;TYPE=ins;CIGAR=1M1I26M;NUMALT=5;MEANALT=19.0;LEN=1;MQM=60.0;MQMR=59.4915;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr13 41170075 . AT A 725.664 REJECT NS=2;DP=194;DPB=305.222;AC=2;AN=4;AF=0.5;RO=59;AO=41;PRO=54.7;PAO=49.0333;QR=2121;QA=1106;PQR=1923.72;PQA=1706.88;SRF=21;SRR=38;SAF=17;SAR=24;SRP=13.6468;SAP=5.60547;AB=0.21134;ABP=143.417;RUN=1;RPP=4.33437;RPPR=22.4799;RPL=18.0;RPR=23.0;EPP=3.48696;EPPR=3.0471;DPRA=0.0;ODDS=19.9977;GTI=0;TYPE=del;CIGAR=1M1D25M;NUMALT=5;MEANALT=19.0;LEN=1;MQM=59.7805;MQMR=59.4915;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr13 41170075 . ATT A 725.664 REJECT NS=2;DP=194;DPB=305.222;AC=2;AN=2;AF=0.0;RO=59;AO=11;PRO=54.7;PAO=40.2;QR=2121;QA=291;PQR=1923.72;PQA=1376.13;SRF=21;SRR=38;SAF=3;SAR=8;SRP=13.6468;SAP=7.94546;AB=0.056701;ABP=334.149;RUN=1;RPP=3.20771;RPPR=22.4799;RPL=6.0;RPR=5.0;EPP=3.20771;EPPR=3.0471;DPRA=0.0;ODDS=19.9977;GTI=0;TYPE=del;CIGAR=1M2D24M;NUMALT=5;MEANALT=19.0;LEN=2;MQM=58.4545;MQMR=59.4915;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.05;FS=0. [...]
+chr13 41170075 . ATTT A 725.664 REJECT NS=2;DP=194;DPB=305.222;AC=2;AN=2;AF=0.0;RO=59;AO=14;PRO=54.7;PAO=37.2;QR=2121;QA=451;PQR=1923.72;PQA=1286.93;SRF=21;SRR=38;SAF=9;SAR=5;SRP=13.6468;SAP=5.49198;AB=0.0721649;ABP=311.449;RUN=1;RPP=3.63072;RPPR=22.4799;RPL=6.0;RPR=8.0;EPP=3.0103;EPPR=3.0471;DPRA=0.0;ODDS=19.9977;GTI=0;TYPE=del;CIGAR=1M3D23M;NUMALT=5;MEANALT=19.0;LEN=3;MQM=60.0;MQMR=59.4915;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr13 41170097 . C G 725.664 REJECT NS=2;DP=194;DPB=305.222;AC=2;AN=2;AF=0.0;RO=59;AO=7;PRO=54.7;PAO=35.1667;QR=2121;QA=74;PQR=1923.72;PQA=1185.62;SRF=21;SRR=38;SAF=7;SAR=0;SRP=13.6468;SAP=18.2106;AB=0.0360825;ABP=365.669;RUN=1;RPP=3.32051;RPPR=22.4799;RPL=4.0;RPR=3.0;EPP=3.32051;EPPR=3.0471;DPRA=0.0;ODDS=19.9977;GTI=0;TYPE=snp;CIGAR=22M1X4M;NUMALT=5;MEANALT=19.0;LEN=1;MQM=57.8571;MQMR=59.4915;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr13 41170134 . T A 7368.43 REJECT NS=2;DP=353;DPB=401.0;AC=3;AN=4;AF=0.75;RO=109;AO=292;PRO=0.0;PAO=0.0;QR=3958;QA=10077;PQR=0.0;PQA=0.0;SRF=58;SRR=51;SAF=157;SAR=135;SRP=3.98647;SAP=6.60959;AB=0.643791;ABP=57.9642;RUN=1;RPP=41.5614;RPPR=19.7645;RPL=110.0;RPR=182.0;EPP=21.6017;EPPR=17.5333;DPRA=0.0;ODDS=60.0599;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0514;MQMR=59.8165;PAIRED=0.986301;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.576;Dels=0.0;FS=0.0;Haploty [...]
+chr13 41170140 . C T 7779.030000000001 REJECT NS=2;DP=364;DPB=415.0;AC=3;AN=4;AF=0.75;RO=113;AO=296;PRO=0.0;PAO=0.0;QR=4099;QA=10660;PQR=0.0;PQA=0.0;SRF=62;SRR=51;SAF=160;SAR=136;SRP=5.3355;SAP=7.23587;AB=0.629747;ABP=49.2159;RUN=1;RPP=43.1825;RPPR=23.9371;RPL=111.0;RPR=185.0;EPP=18.5334;EPPR=26.5506;DPRA=0.0;ODDS=61.3258;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0169;MQMR=60.0;PAIRED=0.983108;PAIREDR=0.99115;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.975;Dels=0.0;FS=0. [...]
+chr13 41170685 . C G 15038.349999999999 REJECT NS=2;DP=398;DPB=451.0;AC=4;AN=4;AF=1.0;RO=0;AO=451;PRO=0.0;PAO=0.0;QR=0;QA=17218;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=220;SAR=231;SRP=0.0;SAP=3.59289;AB=0.0;ABP=0.0;RUN=1;RPP=12.7603;RPPR=0.0;RPL=248.0;RPR=203.0;EPP=20.9262;EPPR=0.0;DPRA=0.0;ODDS=69.2279;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995565;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=9.6959;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=3 [...]
+chr13 41171330 . CT C 9917.965 REJECT NS=2;DP=432;DPB=471.0;AC=3;AN=4;AF=0.75;RO=126;AO=348;PRO=33.0;PAO=38.0;QR=4784;QA=13006;PQR=1133.5;PQA=1300.5;SRF=55;SRR=71;SAF=168;SAR=180;SRP=7.42218;SAP=3.90884;AB=0.65;ABP=73.366;RUN=1;RPP=6.60446;RPPR=7.42218;RPL=186.0;RPR=162.0;EPP=3.0103;EPPR=8.59409;DPRA=0.0;ODDS=73.9106;GTI=0;TYPE=del;CIGAR=1M1D7M;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0287;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=41171331;HOMLEN=2;HOMSEQ=TT;SVLEN=-1;SV [...]
+chr13 41173267 . G GA 5558.11 REJECT NS=2;DP=332;DPB=408.3;AC=2;AN=2;AF=0.0;RO=70;AO=15;PRO=52.4167;PAO=42.4167;QR=2593;QA=479;PQR=1807.08;PQA=1446.08;SRF=33;SRR=37;SAF=9;SAR=6;SRP=3.50664;SAP=4.31318;AB=0.0451807;ABP=599.537;RUN=1;RPP=6.62942;RPPR=9.09042;RPL=5.0;RPR=10.0;EPP=4.31318;EPPR=20.8784;DPRA=0.0;ODDS=48.0193;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=3;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr13 41173267 . GA G 4414.92 REJECT NS=2;DP=316;DPB=408.3;AC=2;AN=4;AF=0.5;RO=70;AO=199;PRO=52.4167;PAO=55.4167;QR=2593;QA=6647;PQR=1807.08;PQA=1848.58;SRF=33;SRR=37;SAF=88;SAR=111;SRP=3.50664;SAP=8.78271;AB=0.599398;ABP=31.5011;RUN=1;RPP=3.89417;RPPR=9.09042;RPL=95.0;RPR=104.0;EPP=8.78271;EPPR=20.8784;DPRA=0.0;ODDS=48.0193;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=3;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.974874;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum= [...]
+chr13 41173267 . GAA G 5558.11 REJECT NS=2;DP=332;DPB=408.3;AC=2;AN=2;AF=0.0;RO=70;AO=18;PRO=52.4167;PAO=34.75;QR=2593;QA=598;PQR=1807.08;PQA=1162.25;SRF=33;SRR=37;SAF=5;SAR=13;SRP=3.50664;SAP=10.7311;AB=0.0542169;ABP=576.07;RUN=1;RPP=3.0103;RPPR=9.09042;RPL=9.0;RPR=9.0;EPP=3.49285;EPPR=20.8784;DPRA=0.0;ODDS=48.0193;GTI=0;TYPE=del;CIGAR=1M2D17M;NUMALT=3;MEANALT=12.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr13 41173354 . G GA 2795.415 REJECT NS=2;DP=325;DPB=421.444;AC=2;AN=4;AF=0.5;RO=109;AO=145;PRO=34.65;PAO=36.65;QR=4023;QA=4639;PQR=1208.15;PQA=1296.15;SRF=52;SRR=57;SAF=62;SAR=83;SRP=3.50834;SAP=9.61457;AB=0.435435;ABP=15.0675;RUN=1;RPP=3.74411;RPPR=3.98647;RPL=69.0;RPR=76.0;EPP=3.38469;EPPR=3.1896;DPRA=0.0;ODDS=113.515;GTI=0;TYPE=ins;CIGAR=1M1I17M;NUMALT=4;MEANALT=13.0;LEN=1;MQM=59.8621;MQMR=59.9817;PAIRED=0.993103;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankS [...]
+chr13 41173354 . G GAA 3572.1 REJECT NS=2;DP=333;DPB=421.444;AC=2;AN=2;AF=0.0;RO=109;AO=20;PRO=34.65;PAO=31.65;QR=4023;QA=562;PQR=1208.15;PQA=1103.15;SRF=52;SRR=57;SAF=5;SAR=15;SRP=3.50834;SAP=13.8677;AB=0.0600601;ABP=562.826;RUN=1;RPP=6.91895;RPPR=3.98647;RPL=13.0;RPR=7.0;EPP=4.74748;EPPR=3.1896;DPRA=0.0;ODDS=113.515;GTI=0;TYPE=ins;CIGAR=1M2I17M;NUMALT=4;MEANALT=13.0;LEN=2;MQM=60.0;MQMR=59.9817;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr13 41173354 . G GAAA 3572.1 REJECT NS=2;DP=333;DPB=421.444;AC=2;AN=2;AF=0.0;RO=109;AO=5;PRO=34.65;PAO=31.65;QR=4023;QA=122;PQR=1208.15;PQA=1103.15;SRF=52;SRR=57;SAF=1;SAR=4;SRP=3.50834;SAP=6.91895;AB=0.015015;ABP=683.333;RUN=1;RPP=3.44459;RPPR=3.98647;RPL=3.0;RPR=2.0;EPP=3.44459;EPPR=3.1896;DPRA=0.0;ODDS=113.515;GTI=0;TYPE=ins;CIGAR=1M3I17M;NUMALT=4;MEANALT=13.0;LEN=3;MQM=60.0;MQMR=59.9817;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr13 41173354 . GA G 3572.1 REJECT NS=2;DP=333;DPB=421.444;AC=2;AN=2;AF=0.0;RO=109;AO=24;PRO=34.65;PAO=23.4;QR=4023;QA=783;PQR=1208.15;PQA=796.4;SRF=52;SRR=57;SAF=16;SAR=8;SRP=3.50834;SAP=8.80089;AB=0.0720721;ABP=532.674;RUN=1;RPP=3.0103;RPPR=3.98647;RPL=12.0;RPR=12.0;EPP=4.45795;EPPR=3.1896;DPRA=0.0;ODDS=113.515;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=4;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=59.9817;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr13 41173433 . A G 8856.875 REJECT NS=2;DP=376;DPB=429.0;AC=3;AN=4;AF=0.75;RO=116;AO=313;PRO=0.0;PAO=0.0;QR=4436;QA=11957;PQR=0.0;PQA=0.0;SRF=62;SRR=54;SAF=144;SAR=169;SRP=4.20835;SAP=7.34631;AB=0.641975;ABP=59.7367;RUN=1;RPP=3.84975;RPPR=3.30981;RPL=151.0;RPR=162.0;EPP=3.84975;EPPR=7.80251;DPRA=0.0;ODDS=66.4367;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996805;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.789;Dels=0.0;FS=2.6195;HaplotypeS [...]
+chr13 41174224 . G A 9425.485 REJECT NS=2;DP=395;DPB=451.0;AC=3;AN=4;AF=0.75;RO=118;AO=333;PRO=0.0;PAO=0.0;QR=4500;QA=12704;PQR=0.0;PQA=0.0;SRF=59;SRR=59;SAF=153;SAR=180;SRP=3.0103;SAP=7.76406;AB=0.651917;ABP=70.9665;RUN=1;RPP=7.76406;RPPR=8.97265;RPL=180.0;RPR=153.0;EPP=10.9984;EPPR=3.30474;DPRA=0.0;ODDS=70.877;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993994;PAIREDR=0.991525;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.305;Dels=0.0;FS=0.94;Haplotyp [...]
+chr13 41174231 . A G 9198.935000000001 REJECT NS=2;DP=394;DPB=449.0;AC=3;AN=4;AF=0.75;RO=123;AO=326;PRO=0.0;PAO=0.0;QR=4685;QA=12450;PQR=0.0;PQA=0.0;SRF=63;SRR=60;SAF=152;SAR=174;SRP=3.16919;SAP=6.2342;AB=0.637168;ABP=58.4117;RUN=1;RPP=9.83112;RPPR=6.98251;RPL=179.0;RPR=147.0;EPP=3.96948;EPPR=8.11238;DPRA=0.0;ODDS=69.6027;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996933;PAIREDR=0.99187;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.899;Dels=0.0;FS=0.677 [...]
+chr13 41174437 . C T 8724.93 REJECT NS=2;DP=369;DPB=425.0;AC=3;AN=4;AF=0.75;RO=117;AO=307;PRO=0.0;PAO=0.0;QR=4459;QA=11922;PQR=0.0;PQA=0.0;SRF=57;SRR=60;SAF=155;SAR=152;SRP=3.17734;SAP=3.07396;AB=0.624204;ABP=45.0843;RUN=1;RPP=7.43105;RPPR=3.02886;RPL=141.0;RPR=166.0;EPP=4.20567;EPPR=6.14687;DPRA=0.0;ODDS=70.2551;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983713;PAIREDR=0.991453;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.115;Dels=0.0;FS=0.2115;Haplot [...]
+chr13 41174534 . C T 8607.755000000001 REJECT NS=2;DP=372;DPB=427.0;AC=3;AN=4;AF=0.75;RO=120;AO=307;PRO=0.0;PAO=0.0;QR=4491;QA=11770;PQR=0.0;PQA=0.0;SRF=51;SRR=69;SAF=137;SAR=170;SRP=8.87328;SAP=10.713;AB=0.621451;ABP=43.6244;RUN=1;RPP=5.05445;RPPR=3.0103;RPL=145.0;RPR=162.0;EPP=3.07396;EPPR=3.08268;DPRA=0.0;ODDS=69.5903;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991667;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.873;Dels=0.0;FS=0.691;Hapl [...]
+chr13 41177259 . G T 9137.935000000001 REJECT NS=2;DP=409;DPB=464.0;AC=3;AN=4;AF=0.75;RO=128;AO=333;PRO=0.0;PAO=0.0;QR=4862;QA=12294;PQR=0.0;PQA=0.0;SRF=47;SRR=81;SAF=135;SAR=198;SRP=22.6214;SAP=28.8919;AB=0.638655;ABP=62.6254;RUN=1;RPP=3.32983;RPPR=3.07816;RPL=163.0;RPR=170.0;EPP=4.47751;EPPR=3.28173;DPRA=0.0;ODDS=66.3712;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984985;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.884;Dels=0.0;FS=1.8375; [...]
+chr13 41177488 . TCCA ACC 112.298 REJECT NS=2;DP=98;DPB=183.594;AC=2;AN=2;AF=0.0;RO=20;AO=8;PRO=66.6167;PAO=18.6167;QR=711;QA=117;PQR=2232.93;PQA=598.183;SRF=7;SRR=13;SAF=0;SAR=8;SRP=6.91895;SAP=20.3821;AB=0.0816327;ABP=152.0;RUN=1;RPP=3.0103;RPPR=3.44459;RPL=4.0;RPR=4.0;EPP=3.0103;EPPR=30.8051;DPRA=0.0;ODDS=7.43985;GTI=0;TYPE=complex;CIGAR=1X2M1D28M;NUMALT=4;MEANALT=17.0;LEN=31;MQM=59.875;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr13 41177490 . CA C 112.298 REJECT NS=2;DP=98;DPB=183.594;AC=3;AN=4;AF=0.5;RO=20;AO=13;PRO=66.6167;PAO=47.1167;QR=711;QA=258;PQR=2232.93;PQA=1587.43;SRF=7;SRR=13;SAF=3;SAR=10;SRP=6.91895;SAP=11.1951;AB=0.132653;ABP=117.877;RUN=1;RPP=3.17734;RPPR=3.44459;RPL=6.0;RPR=7.0;EPP=7.18621;EPPR=30.8051;DPRA=0.0;ODDS=7.43985;GTI=0;TYPE=del;CIGAR=3M1D28M;NUMALT=4;MEANALT=17.0;LEN=1;MQM=55.6154;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.067;FS=0.0;ML [...]
+chr13 41177490 . CAA C 112.298 REJECT NS=2;DP=98;DPB=183.594;AC=2;AN=2;AF=0.0;RO=20;AO=13;PRO=66.6167;PAO=41.45;QR=711;QA=247;PQR=2232.93;PQA=1384.6;SRF=7;SRR=13;SAF=4;SAR=9;SRP=6.91895;SAP=7.18621;AB=0.132653;ABP=117.877;RUN=1;RPP=4.51363;RPPR=3.44459;RPL=8.0;RPR=5.0;EPP=4.51363;EPPR=30.8051;DPRA=0.0;ODDS=7.43985;GTI=0;TYPE=del;CIGAR=3M2D27M;NUMALT=4;MEANALT=17.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr13 41177490 . CAAA C 112.298 REJECT NS=2;DP=98;DPB=183.594;AC=2;AN=2;AF=0.0;RO=20;AO=8;PRO=66.6167;PAO=36.2;QR=711;QA=204;PQR=2232.93;PQA=1222.85;SRF=7;SRR=13;SAF=5;SAR=3;SRP=6.91895;SAP=4.09604;AB=0.0816327;ABP=152.0;RUN=1;RPP=7.35324;RPPR=3.44459;RPL=2.0;RPR=6.0;EPP=4.09604;EPPR=30.8051;DPRA=0.0;ODDS=7.43985;GTI=0;TYPE=del;CIGAR=3M3D26M;NUMALT=4;MEANALT=17.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr13 41178320 . G GA 751.951 REJECT NS=2;DP=289;DPB=396.0;AC=2;AN=2;AF=0.0;RO=181;AO=25;PRO=102.167;PAO=71.1667;QR=6489;QA=840;PQR=3519.33;PQA=2423.33;SRF=88;SRR=93;SAF=12;SAR=13;SRP=3.31023;SAP=3.09716;AB=0.0865052;ABP=432.203;RUN=1;RPP=7.26639;RPPR=8.30101;RPL=9.0;RPR=16.0;EPP=5.18177;EPPR=5.70964;DPRA=0.0;ODDS=0.518537;GTI=0;TYPE=ins;CIGAR=1M1I25M;NUMALT=2;MEANALT=15.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994475;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr13 41178320 . GA G 751.951 REJECT NS=2;DP=289;DPB=396.0;AC=2;AN=4;AF=0.5;RO=181;AO=48;PRO=102.167;PAO=65.6667;QR=6489;QA=1605;PQR=3519.33;PQA=2256.33;SRF=88;SRR=93;SAF=23;SAR=25;SRP=3.31023;SAP=3.19126;AB=0.16609;ABP=282.89;RUN=1;RPP=3.19126;RPPR=8.30101;RPL=23.0;RPR=25.0;EPP=3.0103;EPPR=5.70964;DPRA=0.0;ODDS=0.518537;GTI=0;TYPE=del;CIGAR=1M1D24M;NUMALT=2;MEANALT=15.0;LEN=1;MQM=60.2083;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994475;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1 [...]
+chr13 41178521 . C CT 1792.4 REJECT NS=2;DP=253;DPB=365.667;AC=2;AN=4;AF=0.5;RO=92;AO=89;PRO=61.4167;PAO=63.4167;QR=3388;QA=2657;PQR=2149.75;PQA=2177.75;SRF=36;SRR=56;SAF=43;SAR=46;SRP=12.4515;SAP=3.22989;AB=0.351779;ABP=51.2891;RUN=1;RPP=11.8182;RPPR=14.4341;RPL=54.0;RPR=35.0;EPP=10.0615;EPPR=5.3706;DPRA=0.0;ODDS=96.272;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=3;MEANALT=16.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.98913;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.217 [...]
+chr13 41178521 . C CTT 2326.07 REJECT NS=2;DP=253;DPB=365.667;AC=2;AN=2;AF=0.0;RO=92;AO=16;PRO=61.4167;PAO=54.4167;QR=3388;QA=338;PQR=2149.75;PQA=1883.75;SRF=36;SRR=56;SAF=3;SAR=13;SRP=12.4515;SAP=16.582;AB=0.0632411;ABP=422.207;RUN=1;RPP=5.18177;RPPR=14.4341;RPL=6.0;RPR=10.0;EPP=3.55317;EPPR=5.3706;DPRA=0.0;ODDS=96.272;GTI=0;TYPE=ins;CIGAR=1M2I23M;NUMALT=3;MEANALT=16.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=0.9375;PAIREDR=0.98913;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr13 41178521 . CT C 2326.07 REJECT NS=2;DP=253;DPB=365.667;AC=2;AN=2;AF=0.0;RO=92;AO=19;PRO=61.4167;PAO=40.75;QR=3388;QA=635;PQR=2149.75;PQA=1382.75;SRF=36;SRR=56;SAF=8;SAR=11;SRP=12.4515;SAP=4.03889;AB=0.0750988;ABP=399.755;RUN=1;RPP=4.03889;RPPR=14.4341;RPL=11.0;RPR=8.0;EPP=3.12459;EPPR=5.3706;DPRA=0.0;ODDS=96.272;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=3;MEANALT=16.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.98913;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr13 41179580 . C G 9202.475 REJECT NS=2;DP=399;DPB=450.0;AC=3;AN=4;AF=0.75;RO=126;AO=324;PRO=0.0;PAO=0.0;QR=4802;QA=12240;PQR=0.0;PQA=0.0;SRF=59;SRR=67;SAF=176;SAR=148;SRP=4.11327;SAP=8.26473;AB=0.641026;ABP=63.6445;RUN=1;RPP=8.26473;RPPR=6.38815;RPL=148.0;RPR=176.0;EPP=3.43923;EPPR=3.28604;DPRA=0.0;ODDS=62.7259;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993827;PAIREDR=0.984127;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.632;Dels=0.0;FS=2.543;Haplo [...]
+chr13 41179798 . A G 10523.935000000001 REJECT NS=2;DP=442;DPB=502.0;AC=3;AN=4;AF=0.75;RO=132;AO=370;PRO=0.0;PAO=0.0;QR=5060;QA=14019;PQR=0.0;PQA=0.0;SRF=60;SRR=72;SAF=201;SAR=169;SRP=5.37918;SAP=9.02;AB=0.658854;ABP=87.1775;RUN=1;RPP=5.35784;RPPR=4.65535;RPL=175.0;RPR=195.0;EPP=4.91181;EPPR=3.60252;DPRA=0.0;ODDS=68.8896;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994595;PAIREDR=0.992424;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.694;Dels=0.0;FS=5.899 [...]
+chr13 41181774 . T A 10573.885 REJECT NS=2;DP=447;DPB=514.0;AC=3;AN=4;AF=0.75;RO=134;AO=380;PRO=0.0;PAO=0.0;QR=5125;QA=14383;PQR=0.0;PQA=0.0;SRF=69;SRR=65;SAF=189;SAR=191;SRP=3.26958;SAP=3.03316;AB=0.648294;ABP=75.786;RUN=1;RPP=3.37602;RPPR=4.6308;RPL=186.0;RPR=194.0;EPP=6.87324;EPPR=4.04742;DPRA=0.0;ODDS=83.917;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997368;PAIREDR=0.992537;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.455;Dels=0.0;FS=0.1935;Haploty [...]
+chr13 41182170 . CA C 9934.965 REJECT NS=2;DP=417;DPB=428.0;AC=3;AN=4;AF=0.75;RO=113;AO=355;PRO=17.5;PAO=17.5;QR=4253;QA=13175;PQR=534.0;PQA=530.0;SRF=61;SRR=52;SAF=180;SAR=175;SRP=4.56684;SAP=3.16322;AB=0.662857;ABP=83.6402;RUN=1;RPP=3.50576;RPPR=4.56684;RPL=173.0;RPR=182.0;EPP=3.75044;EPPR=3.49071;DPRA=0.0;ODDS=78.2401;GTI=0;TYPE=del;CIGAR=1M1D4M;NUMALT=1;MEANALT=3.5;LEN=1;MQM=60.1972;MQMR=60.0;PAIRED=0.991549;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=41182171;HOMLEN=1;HOMSEQ=A;SVL [...]
+chr13 41183050 . A G 14522.349999999999 REJECT NS=2;DP=385;DPB=447.0;AC=4;AN=4;AF=1.0;RO=0;AO=447;PRO=0.0;PAO=0.0;QR=0;QA=16987;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=221;SAR=226;SRP=0.0;SAP=3.13175;AB=0.0;ABP=0.0;RUN=1;RPP=15.6456;RPPR=0.0;RPL=198.0;RPR=249.0;EPP=5.58012;EPPR=0.0;DPRA=0.0;ODDS=81.6604;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993289;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8547;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=2 [...]
+chr13 41183716 . G A 10623.835 REJECT NS=2;DP=444;DPB=508.0;AC=3;AN=4;AF=0.75;RO=135;AO=372;PRO=0.0;PAO=0.0;QR=5144;QA=14329;PQR=0.0;PQA=0.0;SRF=76;SRR=59;SAF=188;SAR=184;SRP=7.65886;SAP=3.1037;AB=0.642105;ABP=69.6631;RUN=1;RPP=3.03365;RPPR=3.15506;RPL=185.0;RPR=187.0;EPP=4.15441;EPPR=3.79846;DPRA=0.0;ODDS=80.8101;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997312;PAIREDR=0.992593;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.385;Dels=0.0;FS=2.73;Haploty [...]
+chr13 41184078 . C G 8495.945 REJECT NS=2;DP=418;DPB=484.0;AC=3;AN=4;AF=0.75;RO=130;AO=346;PRO=0.0;PAO=0.0;QR=4564;QA=12007;PQR=0.0;PQA=0.0;SRF=70;SRR=60;SAF=166;SAR=180;SRP=4.68066;SAP=4.24038;AB=0.619318;ABP=46.5385;RUN=1;RPP=3.0354;RPPR=5.41562;RPL=174.0;RPR=172.0;EPP=3.63789;EPPR=4.07933;DPRA=0.0;ODDS=80.3823;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=59.9884;MQMR=60.0;PAIRED=0.99711;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.128;Dels=0.0;FS=1.7795;Haplotype [...]
+chr13 41186644 . T G 8906.69 REJECT NS=2;DP=399;DPB=446.0;AC=3;AN=4;AF=0.75;RO=132;AO=314;PRO=0.0;PAO=0.0;QR=5020;QA=11863;PQR=0.0;PQA=0.0;SRF=74;SRR=58;SAF=168;SAR=146;SRP=7.22164;SAP=6.35741;AB=0.625;ABP=50.7827;RUN=1;RPP=3.03796;RPPR=5.37918;RPL=156.0;RPR=158.0;EPP=7.68519;EPPR=3.0103;DPRA=0.0;ODDS=59.6114;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993631;PAIREDR=0.992424;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.008;Dels=0.0;FS=0.203;HaplotypeS [...]
+chr13 41187379 . T G 3990.54 PASS SOMATIC;NS=2;DP=483;DPB=483.0;AC=1;AN=3;AF=0.25;RO=335;AO=147;PRO=0.0;PAO=0.0;QR=12963;QA=5587;PQR=0.0;PQA=0.0;SRF=163;SRR=172;SAF=80;SAR=67;SRP=3.53534;SAP=5.50675;AB=0.410615;ABP=27.8549;RUN=1;RPP=4.7977;RPPR=4.46875;RPL=79.0;RPR=68.0;EPP=12.2428;EPPR=16.1364;DPRA=2.864;ODDS=79.0113;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986395;PAIREDR=0.99403;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.579;Dels=0.0;FS=3 [...]
+chr13 41187557 . T TA 4468.44 REJECT NS=2;DP=373;DPB=477.111;AC=2;AN=4;AF=0.5;RO=122;AO=208;PRO=44.3333;PAO=35.8333;QR=4575;QA=7349;PQR=1561.67;PQA=1236.17;SRF=54;SRR=68;SAF=112;SAR=96;SRP=6.49889;SAP=5.68288;AB=0.527919;ABP=5.67779;RUN=1;RPP=5.68288;RPPR=6.49889;RPL=96.0;RPR=112.0;EPP=5.68288;EPPR=6.49889;DPRA=0.0;ODDS=49.0773;GTI=0;TYPE=ins;CIGAR=1M1I17M;NUMALT=3;MEANALT=11.5;LEN=1;MQM=60.0962;MQMR=60.0;PAIRED=0.995192;PAIREDR=0.991803;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;Ba [...]
+chr13 41187557 . T TAA 5985.15 REJECT NS=2;DP=394;DPB=477.111;AC=2;AN=2;AF=0.0;RO=122;AO=20;PRO=44.3333;PAO=33.8333;QR=4575;QA=716;PQR=1561.67;PQA=1183.17;SRF=54;SRR=68;SAF=11;SAR=9;SRP=6.49889;SAP=3.44459;AB=0.0507614;ABP=693.671;RUN=1;RPP=6.91895;RPPR=6.49889;RPL=13.0;RPR=7.0;EPP=9.95901;EPPR=6.49889;DPRA=0.0;ODDS=49.0773;GTI=0;TYPE=ins;CIGAR=1M2I17M;NUMALT=3;MEANALT=11.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991803;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr13 41187557 . TA T 5985.15 REJECT NS=2;DP=394;DPB=477.111;AC=2;AN=2;AF=0.0;RO=122;AO=21;PRO=44.3333;PAO=27.0;QR=4575;QA=789;PQR=1561.67;PQA=932.0;SRF=54;SRR=68;SAF=14;SAR=7;SRP=6.49889;SAP=8.07707;AB=0.0532995;ABP=685.889;RUN=1;RPP=3.94093;RPPR=6.49889;RPL=12.0;RPR=9.0;EPP=5.59539;EPPR=6.49889;DPRA=0.0;ODDS=49.0773;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=3;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.952381;PAIREDR=0.991803;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr13 41188252 . A G 8806.185000000001 REJECT NS=2;DP=374;DPB=433.0;AC=3;AN=4;AF=0.75;RO=117;AO=316;PRO=0.0;PAO=0.0;QR=4540;QA=12162;PQR=0.0;PQA=0.0;SRF=51;SRR=66;SAF=155;SAR=161;SRP=7.18621;SAP=3.25768;AB=0.629747;ABP=49.2159;RUN=1;RPP=5.23675;RPPR=3.47429;RPL=149.0;RPR=167.0;EPP=3.12025;EPPR=7.18621;DPRA=0.0;ODDS=73.9752;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993671;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.894;Dels=0.0;FS=2.639;H [...]
+chr13 41188292 . A G 8901.005000000001 REJECT NS=2;DP=376;DPB=431.0;AC=3;AN=4;AF=0.75;RO=117;AO=314;PRO=0.0;PAO=0.0;QR=4554;QA=12053;PQR=0.0;PQA=0.0;SRF=52;SRR=65;SAF=157;SAR=157;SRP=6.14687;SAP=3.0103;AB=0.639752;ABP=57.6343;RUN=1;RPP=3.12095;RPPR=5.25601;RPL=159.0;RPR=155.0;EPP=3.25926;EPPR=3.47429;DPRA=0.0;ODDS=61.3003;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996815;PAIREDR=0.991453;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.118;Dels=0.0;FS=1.90 [...]
+chr13 41189143 . C A 10353.135 REJECT NS=2;DP=434;DPB=495.0;AC=3;AN=4;AF=0.75;RO=132;AO=362;PRO=0.0;PAO=0.0;QR=5002;QA=13911;PQR=0.0;PQA=0.0;SRF=63;SRR=69;SAF=165;SAR=197;SRP=3.60252;SAP=9.15281;AB=0.644385;ABP=70.7324;RUN=1;RPP=3.39421;RPPR=4.65535;RPL=177.0;RPR=185.0;EPP=5.91359;EPPR=3.0103;DPRA=0.0;ODDS=76.4605;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997238;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.311;Dels=0.0;FS=0.0;HaplotypeScor [...]
+chr13 41189665 . A AATACATAC 1509.33 REJECT SOMATIC;NS=2;DP=98;DPB=195.3;AC=1;AN=3;AF=0.25;RO=9;AO=10;PRO=49.8833;PAO=49.8833;QR=345;QA=362;PQR=1803.83;PQA=1803.83;SRF=7;SRR=2;SAF=9;SAR=1;SRP=9.04217;SAP=16.9077;AB=0.15625;ABP=68.6973;RUN=1;RPP=6.48466;RPPR=22.5536;RPL=3.0;RPR=7.0;EPP=10.8276;EPPR=9.04217;DPRA=0.0;ODDS=4.5056;GTI=0;TYPE=ins;CIGAR=1M8I49M;NUMALT=4;MEANALT=7.0;LEN=8;MQM=58.8;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;END=41189665;HOMLE [...]
+chr13 41189665 . AATAC A 1509.33 REJECT NS=2;DP=98;DPB=195.3;AC=2;AN=3;AF=0.25;RO=9;AO=22;PRO=49.8833;PAO=50.3833;QR=345;QA=828;PQR=1803.83;PQA=1817.33;SRF=7;SRR=2;SAF=19;SAR=3;SRP=9.04217;SAP=28.2783;AB=0.22449;ABP=67.6227;RUN=1;RPP=6.56362;RPPR=22.5536;RPL=8.0;RPR=14.0;EPP=3.0103;EPPR=9.04217;DPRA=0.0;ODDS=4.5056;GTI=0;TYPE=del;CIGAR=1M4D45M;NUMALT=4;MEANALT=5.5;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;END=41189669;HOMLEN=45;HOMSEQ=ATACA [...]
+chr13 41189665 . AATACATAC A 1541.53 REJECT NS=2;DP=98;DPB=195.3;AC=2;AN=2;AF=0.5;RO=9;AO=47;PRO=49.8833;PAO=44.05;QR=345;QA=1635;PQR=1803.83;PQA=1586.0;SRF=7;SRR=2;SAF=40;SAR=7;SRP=9.04217;SAP=53.3238;AB=0.479592;ABP=3.36483;RUN=1;RPP=19.6891;RPPR=22.5536;RPL=14.0;RPR=33.0;EPP=4.16534;EPPR=9.04217;DPRA=0.0;ODDS=4.5056;GTI=0;TYPE=del;CIGAR=1M8D41M;NUMALT=4;MEANALT=5.5;LEN=8;MQM=61.7021;MQMR=60.0;PAIRED=0.978723;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;END=41189673;HOML [...]
+chr13 41189665 . AATACATACATAC A 1509.33 REJECT NS=2;DP=98;DPB=195.3;AC=0;AN=4;AF=0.0;RO=9;AO=4;PRO=49.8833;PAO=38.8;QR=345;QA=146;PQR=1803.83;PQA=1382.0;SRF=7;SRR=2;SAF=3;SAR=1;SRP=9.04217;SAP=5.18177;AB=0.0408163;ABP=182.489;RUN=1;RPP=5.18177;RPPR=22.5536;RPL=3.0;RPR=1.0;EPP=11.6962;EPPR=9.04217;DPRA=0.0;ODDS=4.5056;GTI=0;TYPE=del;CIGAR=1M12D37M;NUMALT=4;MEANALT=5.5;LEN=12;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr13 41189773 . A T 7433.8550000000005 REJECT NS=2;DP=321;DPB=376.0;AC=3;AN=4;AF=0.75;RO=100;AO=275;PRO=0.0;PAO=0.0;QR=3778;QA=10464;PQR=0.0;PQA=0.0;SRF=67;SRR=33;SAF=152;SAR=123;SRP=28.1125;SAP=9.65106;AB=0.625926;ABP=40.1988;RUN=1;RPP=3.6499;RPPR=3.35774;RPL=142.0;RPR=133.0;EPP=3.96575;EPPR=3.79203;DPRA=0.0;ODDS=67.1163;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989091;PAIREDR=0.97;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.122;Dels=0.0;FS=8.5525 [...]
+chr13 41191363 . A G 4134.96 REJECT NS=2;DP=185;DPB=216.0;AC=3;AN=4;AF=0.75;RO=57;AO=158;PRO=0.0;PAO=0.0;QR=2190;QA=5949;PQR=0.0;PQA=0.0;SRF=13;SRR=44;SAF=25;SAR=133;SRP=39.6206;SAP=163.314;AB=0.625806;ABP=24.3187;RUN=1;RPP=12.3009;RPPR=16.763;RPL=66.0;RPR=92.0;EPP=8.5077;EPPR=14.02;DPRA=0.0;ODDS=39.0404;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=57.481;MQMR=58.0702;PAIRED=0.993671;PAIREDR=0.982456;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.318;Dels=0.0;FS=0.8655;HaplotypeS [...]
+chr13 41191381 . G A 4065.63 REJECT NS=2;DP=172;DPB=200.0;AC=3;AN=4;AF=0.75;RO=50;AO=150;PRO=0.0;PAO=0.0;QR=1808;QA=5678;PQR=0.0;PQA=0.0;SRF=11;SRR=39;SAF=30;SAR=120;SRP=37.059;SAP=120.27;AB=0.662069;ABP=36.0916;RUN=1;RPP=3.53145;RPPR=32.3686;RPL=78.0;RPR=72.0;EPP=3.53145;EPPR=28.0257;DPRA=0.0;ODDS=33.4678;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=57.34;MQMR=57.8;PAIRED=0.993333;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.591;Dels=0.0;FS=0.0;HaplotypeScore=5.857 [...]
+chr13 41191473 . C T 3021.8 REJECT NS=2;DP=159;DPB=179.0;AC=3;AN=4;AF=0.75;RO=46;AO=132;PRO=0.0;PAO=0.0;QR=1569;QA=4303;PQR=0.0;PQA=0.0;SRF=33;SRR=13;SAF=90;SAR=42;SRP=21.8927;SAP=40.9124;AB=0.661871;ABP=34.6451;RUN=1;RPP=3.27351;RPPR=6.03148;RPL=68.0;RPR=64.0;EPP=12.4858;EPPR=4.70971;DPRA=0.0;ODDS=25.8954;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=55.0379;MQMR=60.0;PAIRED=0.992424;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.362;Dels=0.0;FS=0.0;HaplotypeScore=8. [...]
+chr13 41191572 . C A 186.832 REJECT NS=2;DP=187;DPB=284.034;AC=2;AN=2;AF=0.0;RO=75;AO=4;PRO=45.8333;PAO=33.7833;QR=2736;QA=56;PQR=1647.77;PQA=1208.72;SRF=42;SRR=33;SAF=0;SAR=4;SRP=5.35549;SAP=11.6962;AB=0.0213904;ABP=375.075;RUN=1;RPP=5.18177;RPPR=84.3392;RPL=1.0;RPR=3.0;EPP=5.18177;EPPR=6.51361;DPRA=0.0;ODDS=8.16824;GTI=0;TYPE=snp;CIGAR=1X28M;NUMALT=5;MEANALT=24.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986667;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr13 41191572 . C CA 186.832 REJECT NS=2;DP=187;DPB=284.034;AC=2;AN=3;AF=0.25;RO=75;AO=17;PRO=45.8333;PAO=44.3333;QR=2736;QA=517;PQR=1647.77;PQA=1556.27;SRF=42;SRR=33;SAF=10;SAR=7;SRP=5.35549;SAP=4.1599;AB=0.0909091;ABP=274.839;RUN=1;RPP=24.5973;RPPR=84.3392;RPL=2.0;RPR=15.0;EPP=9.26925;EPPR=6.51361;DPRA=0.0;ODDS=8.16824;GTI=0;TYPE=ins;CIGAR=1M1I28M;NUMALT=5;MEANALT=24.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986667;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr13 41191572 . CA C 186.832 REJECT NS=2;DP=187;DPB=284.034;AC=2;AN=3;AF=0.25;RO=75;AO=20;PRO=45.8333;PAO=38.5833;QR=2736;QA=644;PQR=1647.77;PQA=1384.52;SRF=42;SRR=33;SAF=14;SAR=6;SRP=5.35549;SAP=9.95901;AB=0.106952;ABP=253.937;RUN=1;RPP=4.74748;RPPR=84.3392;RPL=8.0;RPR=12.0;EPP=4.74748;EPPR=6.51361;DPRA=0.0;ODDS=8.16824;GTI=0;TYPE=del;CIGAR=1M1D27M;NUMALT=5;MEANALT=24.0;LEN=1;MQM=59.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986667;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr13 41191587 . G A 186.832 REJECT NS=2;DP=187;DPB=284.034;AC=2;AN=2;AF=0.0;RO=75;AO=3;PRO=45.8333;PAO=26.0833;QR=2736;QA=42;PQR=1647.77;PQA=850.517;SRF=42;SRR=33;SAF=3;SAR=0;SRP=5.35549;SAP=9.52472;AB=0.0545455;ABP=97.8049;RUN=1;RPP=3.73412;RPPR=84.3392;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=6.51361;DPRA=0.0;ODDS=8.16824;GTI=0;TYPE=snp;CIGAR=15M1X13M;NUMALT=5;MEANALT=17.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986667;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr13 41191593 . T G 186.832 REJECT NS=2;DP=187;DPB=284.034;AC=2;AN=2;AF=0.0;RO=75;AO=14;PRO=45.8333;PAO=22.3833;QR=2736;QA=229;PQR=1647.77;PQA=720.217;SRF=42;SRR=33;SAF=14;SAR=0;SRP=5.35549;SAP=33.4109;AB=0.0748663;ABP=296.577;RUN=1;RPP=12.937;RPPR=84.3392;RPL=11.0;RPR=3.0;EPP=12.937;EPPR=6.51361;DPRA=0.0;ODDS=8.16824;GTI=0;TYPE=snp;CIGAR=21M1X7M;NUMALT=5;MEANALT=24.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986667;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr13 41192645 . G A 9733.335 REJECT NS=2;DP=406;DPB=475.0;AC=3;AN=4;AF=0.75;RO=122;AO=353;PRO=0.0;PAO=0.0;QR=4709;QA=13528;PQR=0.0;PQA=0.0;SRF=58;SRR=64;SAF=180;SAR=173;SRP=3.65106;SAP=3.31172;AB=0.640118;ABP=60.8201;RUN=1;RPP=5.23098;RPPR=5.57335;RPL=186.0;RPR=167.0;EPP=4.0499;EPPR=3.29508;DPRA=0.0;ODDS=85.8214;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994334;PAIREDR=0.991803;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.05;Dels=0.0;FS=0.2055;Haploty [...]
+chr13 41193475 . C T 7439.74 REJECT NS=2;DP=316;DPB=356.0;AC=3;AN=4;AF=0.75;RO=97;AO=258;PRO=0.0;PAO=0.0;QR=3722;QA=9922;PQR=0.0;PQA=0.0;SRF=72;SRR=25;SAF=178;SAR=80;SRP=52.4617;SAP=83.8429;AB=0.647482;ABP=55.5318;RUN=1;RPP=31.3236;RPPR=3.56996;RPL=100.0;RPR=158.0;EPP=3.3133;EPPR=11.0918;DPRA=0.0;ODDS=49.629;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992248;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.602;Dels=0.0;FS=2.8195;HaplotypeScore=2 [...]
+chr13 41194936 . C G 181.179 REJECT SOMATIC;NS=2;DP=56;DPB=120.76;AC=1;AN=3;AF=0.0;RO=14;AO=3;PRO=47.75;PAO=6.25;QR=470;QA=44;PQR=1700.17;PQA=208.5;SRF=2;SRR=12;SAF=0;SAR=3;SRP=18.5208;SAP=9.52472;AB=0.0625;ABP=82.8119;RUN=1;RPP=3.73412;RPPR=3.0103;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=5.49198;DPRA=6.0;ODDS=1.60634;GTI=0;TYPE=snp;CIGAR=1X24M;NUMALT=3;MEANALT=17.0;LEN=1;MQM=60.0;MQMR=58.5714;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr13 41194936 . C CT 181.179 REJECT NS=2;DP=56;DPB=120.76;AC=3;AN=4;AF=0.75;RO=14;AO=8;PRO=47.75;PAO=46.75;QR=470;QA=237;PQR=1700.17;PQA=1647.17;SRF=2;SRR=12;SAF=4;SAR=4;SRP=18.5208;SAP=3.0103;AB=0.145833;ABP=55.3066;RUN=1;RPP=7.35324;RPPR=3.0103;RPL=6.0;RPR=2.0;EPP=7.35324;EPPR=5.49198;DPRA=0.0;ODDS=1.60634;GTI=0;TYPE=ins;CIGAR=1M1I24M;NUMALT=3;MEANALT=12.5;LEN=1;MQM=57.5;MQMR=58.5714;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr13 41194936 . CT C 181.179 REJECT SOMATIC;NS=2;DP=56;DPB=120.76;AC=1;AN=3;AF=0.0;RO=14;AO=5;PRO=47.75;PAO=28.25;QR=470;QA=150;PQR=1700.17;PQA=973.167;SRF=2;SRR=12;SAF=2;SAR=3;SRP=18.5208;SAP=3.44459;AB=0.104167;ABP=68.3354;RUN=1;RPP=3.44459;RPPR=3.0103;RPL=3.0;RPR=2.0;EPP=6.91895;EPPR=5.49198;DPRA=6.0;ODDS=1.60634;GTI=0;TYPE=del;CIGAR=1M1D23M;NUMALT=3;MEANALT=17.0;LEN=1;MQM=60.0;MQMR=58.5714;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr13 41195411 . G A 7790.485000000001 REJECT NS=2;DP=350;DPB=401.0;AC=3;AN=4;AF=0.75;RO=117;AO=284;PRO=0.0;PAO=0.0;QR=4483;QA=10729;PQR=0.0;PQA=0.0;SRF=69;SRR=48;SAF=165;SAR=119;SRP=11.1951;SAP=19.1893;AB=0.614618;ABP=37.3571;RUN=1;RPP=22.1254;RPPR=6.14687;RPL=117.0;RPR=167.0;EPP=10.8398;EPPR=3.17734;DPRA=0.0;ODDS=54.6722;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9145;PAIRED=0.989437;PAIREDR=0.991453;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.424;Dels=0.0;FS [...]
+chr13 41195992 . T C 8432.985 REJECT NS=2;DP=378;DPB=439.0;AC=3;AN=4;AF=0.75;RO=125;AO=314;PRO=0.0;PAO=0.0;QR=4796;QA=11862;PQR=0.0;PQA=0.0;SRF=66;SRR=59;SAF=147;SAR=167;SRP=3.86152;SAP=5.77651;AB=0.606918;ABP=34.5854;RUN=1;RPP=11.9728;RPPR=3.16665;RPL=175.0;RPR=139.0;EPP=7.68519;EPPR=12.2;DPRA=0.0;ODDS=76.326;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.6178;MQMR=60.0;PAIRED=0.996815;PAIREDR=0.992;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.659;Dels=0.0;FS=1.5555;Haplotyp [...]
+chr13 41196006 . T G 8606.875 REJECT NS=2;DP=389;DPB=443.0;AC=3;AN=4;AF=0.75;RO=128;AO=314;PRO=0.0;PAO=0.0;QR=4853;QA=11917;PQR=0.0;PQA=0.0;SRF=73;SRR=55;SAF=156;SAR=158;SRP=8.50684;SAP=3.03796;AB=0.616071;ABP=42.3295;RUN=1;RPP=6.35741;RPPR=3.28173;RPL=168.0;RPR=146.0;EPP=20.2991;EPPR=8.50684;DPRA=0.0;ODDS=67.6107;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=57.8535;MQMR=60.0;PAIRED=0.990446;PAIREDR=0.992188;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.052;Dels=0.0;FS=1.512;Ha [...]
+chr13 41196016 . C T 9143.07 REJECT NS=2;DP=403;DPB=455.0;AC=3;AN=4;AF=0.75;RO=133;AO=322;PRO=0.0;PAO=0.0;QR=5095;QA=12423;PQR=0.0;PQA=0.0;SRF=74;SRR=59;SAF=162;SAR=160;SRP=6.68384;SAP=3.03727;AB=0.622159;ABP=48.6359;RUN=1;RPP=3.68467;RPPR=4.98585;RPL=156.0;RPR=166.0;EPP=9.07963;EPPR=16.7412;DPRA=0.0;ODDS=65.1469;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=57.8882;MQMR=60.0;PAIRED=0.990683;PAIREDR=0.992481;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.886;Dels=0.0;FS=1.4665;Hap [...]
+chr13 41196407 . C T 10018.735 REJECT NS=2;DP=427;DPB=493.0;AC=3;AN=4;AF=0.75;RO=134;AO=358;PRO=0.0;PAO=0.0;QR=5145;QA=13803;PQR=0.0;PQA=0.0;SRF=63;SRR=71;SAF=181;SAR=177;SRP=4.04742;SAP=3.10735;AB=0.627072;ABP=53.782;RUN=1;RPP=4.56308;RPPR=3.59368;RPL=171.0;RPR=187.0;EPP=5.94603;EPPR=15.715;DPRA=0.0;ODDS=82.7535;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988827;PAIREDR=0.985075;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.559;Dels=0.0;FS=2.8325;Haplot [...]
+chr13 41197260 . T TA 488.814 REJECT NS=2;DP=405;DPB=477.05;AC=2;AN=2;AF=0.0;RO=279;AO=33;PRO=70.5;PAO=51.5;QR=10282;QA=1120;PQR=2424.67;PQA=1754.67;SRF=132;SRR=147;SAF=16;SAR=17;SRP=4.76149;SAP=3.0761;AB=0.0814815;ABP=619.178;RUN=1;RPP=3.60252;RPPR=3.64073;RPL=18.0;RPR=15.0;EPP=3.0761;EPPR=3.64073;DPRA=0.0;ODDS=31.4713;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=2;MEANALT=17.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.982079;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr13 41197260 . TA T 488.814 REJECT NS=2;DP=405;DPB=477.05;AC=2;AN=4;AF=0.5;RO=279;AO=46;PRO=70.5;PAO=48.0;QR=10282;QA=1665;PQR=2424.67;PQA=1624.67;SRF=132;SRR=147;SAF=26;SAR=20;SRP=4.76149;SAP=4.70971;AB=0.11358;ABP=528.287;RUN=1;RPP=3.0103;RPPR=3.64073;RPL=23.0;RPR=23.0;EPP=6.03148;EPPR=3.64073;DPRA=0.0;ODDS=31.4713;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=2;MEANALT=17.0;LEN=1;MQM=61.3043;MQMR=60.0;PAIRED=1.0;PAIREDR=0.982079;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=1.913;FS= [...]
+chr13 41198058 . TA T 1363.69 REJECT SOMATIC;NS=2;DP=35;DPB=114.0;AC=1;AN=3;AF=0.0;RO=6;AO=2;PRO=30.369;PAO=27.619;QR=229;QA=73;PQR=1050.96;PQA=952.714;SRF=0;SRR=6;SAF=1;SAR=1;SRP=16.0391;SAP=3.0103;AB=0.0645161;ABP=54.0749;RUN=1;RPP=7.35324;RPPR=4.45795;RPL=2.0;RPR=0.0;EPP=3.0103;EPPR=4.45795;DPRA=0.0;ODDS=0.694892;GTI=1;TYPE=del;CIGAR=1M1D36M;NUMALT=6;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr13 41198074 . AA T 1363.69 REJECT SOMATIC;NS=2;DP=35;DPB=114.0;AC=1;AN=3;AF=0.0;RO=6;AO=2;PRO=30.369;PAO=17.2857;QR=229;QA=78;PQR=1050.96;PQA=539.548;SRF=0;SRR=6;SAF=2;SAR=0;SRP=16.0391;SAP=7.35324;AB=0.0645161;ABP=54.0749;RUN=1;RPP=3.0103;RPPR=4.45795;RPL=1.0;RPR=1.0;EPP=3.0103;EPPR=4.45795;DPRA=0.0;ODDS=0.694892;GTI=1;TYPE=complex;CIGAR=1M1D15M1X20M;NUMALT=6;MEANALT=13.0;LEN=37;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr13 41198075 . A T 1363.69 REJECT NS=2;DP=35;DPB=114.0;AC=2;AN=2;AF=0.25;RO=6;AO=7;PRO=30.369;PAO=24.9524;QR=229;QA=239;PQR=1050.96;PQA=862.881;SRF=0;SRR=6;SAF=2;SAR=5;SRP=16.0391;SAP=5.80219;AB=0.2;ABP=30.3709;RUN=1;RPP=3.32051;RPPR=4.45795;RPL=3.0;RPR=4.0;EPP=5.80219;EPPR=4.45795;DPRA=0.0;ODDS=0.694892;GTI=1;TYPE=snp;CIGAR=17M1X20M;NUMALT=6;MEANALT=8.0;LEN=1;MQM=59.8571;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=1;BaseQRankSum=0.751;Dels=0.01;FS=6. [...]
+chr13 41198075 . A AT 1363.69 REJECT NS=2;DP=35;DPB=114.0;AC=2;AN=3;AF=0.5;RO=6;AO=6;PRO=30.369;PAO=32.7024;QR=229;QA=205;PQR=1050.96;PQA=1119.13;SRF=0;SRR=6;SAF=3;SAR=3;SRP=16.0391;SAP=3.0103;AB=0.171429;ABP=35.8306;RUN=1;RPP=3.0103;RPPR=4.45795;RPL=3.0;RPR=3.0;EPP=16.0391;EPPR=4.45795;DPRA=0.0;ODDS=0.694892;GTI=1;TYPE=ins;CIGAR=18M1I20M;NUMALT=6;MEANALT=8.0;LEN=1;MQM=59.3333;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr13 41198075 . AT A 1363.69 REJECT SOMATIC;NS=2;DP=35;DPB=114.0;AC=1;AN=3;AF=0.0;RO=6;AO=2;PRO=30.369;PAO=17.869;QR=229;QA=78;PQR=1050.96;PQA=606.964;SRF=0;SRR=6;SAF=2;SAR=0;SRP=16.0391;SAP=7.35324;AB=0.0645161;ABP=54.0749;RUN=1;RPP=3.0103;RPPR=4.45795;RPL=1.0;RPR=1.0;EPP=3.0103;EPPR=4.45795;DPRA=0.0;ODDS=0.694892;GTI=1;TYPE=del;CIGAR=18M1D19M;NUMALT=6;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr13 41198091 . A T 1363.69 REJECT SOMATIC;NS=2;DP=35;DPB=114.0;AC=1;AN=3;AF=0.0;RO=6;AO=2;PRO=30.369;PAO=15.2024;QR=229;QA=32;PQR=1050.96;PQA=521.798;SRF=0;SRR=6;SAF=2;SAR=0;SRP=16.0391;SAP=7.35324;AB=0.0645161;ABP=54.0749;RUN=1;RPP=7.35324;RPPR=4.45795;RPL=2.0;RPR=0.0;EPP=7.35324;EPPR=4.45795;DPRA=0.0;ODDS=0.694892;GTI=1;TYPE=snp;CIGAR=33M1X4M;NUMALT=6;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr13 41198454 . T TTAA 1106.95 REJECT SOMATIC;NS=2;DP=145;DPB=231.4;AC=1;AN=3;AF=0.0;RO=56;AO=3;PRO=15.0;PAO=9.66667;QR=1859;QA=48;PQR=445.75;PQA=292.083;SRF=42;SRR=14;SAF=1;SAR=2;SRP=33.4109;SAP=3.73412;AB=0.00925926;ABP=228.924;RUN=1;RPP=9.52472;RPPR=15.5738;RPL=0.0;RPR=3.0;EPP=3.73412;EPPR=3.16541;DPRA=0.0;ODDS=8.02068;GTI=0;TYPE=ins;CIGAR=3M3I2M;NUMALT=3;MEANALT=11.0;LEN=3;MQM=58.6667;MQMR=56.5536;PAIRED=0.666667;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:A [...]
+chr13 41198454 . T TTAAA 1106.95 REJECT NS=2;DP=145;DPB=231.4;AC=3;AN=3;AF=0.5;RO=56;AO=30;PRO=15.0;PAO=9.66667;QR=1859;QA=794;PQR=445.75;PQA=292.083;SRF=42;SRR=14;SAF=19;SAR=11;SRP=33.4109;SAP=7.64277;AB=0.0277778;ABP=212.195;RUN=1;RPP=38.0434;RPPR=15.5738;RPL=26.0;RPR=4.0;EPP=13.4334;EPPR=3.16541;DPRA=0.0;ODDS=8.02068;GTI=0;TYPE=ins;CIGAR=3M4I2M;NUMALT=3;MEANALT=11.0;LEN=4;MQM=64.1;MQMR=56.5536;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;FS=0.0;MLEAC=2;MLEAF=1.0;MQ [...]
+chr13 41198454 . T TTAAAA 1106.95 REJECT SOMATIC;NS=2;DP=145;DPB=231.4;AC=1;AN=4;AF=0.25;RO=56;AO=35;PRO=15.0;PAO=9.66667;QR=1859;QA=881;PQR=445.75;PQA=292.083;SRF=42;SRR=14;SAF=27;SAR=8;SRP=33.4109;SAP=25.4075;AB=0.324074;ABP=32.0437;RUN=1;RPP=48.239;RPPR=15.5738;RPL=31.0;RPR=4.0;EPP=16.9698;EPPR=3.16541;DPRA=2.91892;ODDS=8.02068;GTI=0;TYPE=ins;CIGAR=3M5I2M;NUMALT=3;MEANALT=14.0;LEN=5;MQM=59.8;MQMR=56.5536;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankS [...]
+chr13 41199421 . G A 10258.935000000001 REJECT NS=2;DP=434;DPB=500.0;AC=3;AN=4;AF=0.75;RO=129;AO=371;PRO=0.0;PAO=0.0;QR=4869;QA=14044;PQR=0.0;PQA=0.0;SRF=61;SRR=68;SAF=195;SAR=176;SRP=3.83512;SAP=5.12324;AB=0.650407;ABP=75.5163;RUN=1;RPP=6.66844;RPPR=4.37378;RPL=173.0;RPR=198.0;EPP=13.8325;EPPR=11.915;DPRA=0.0;ODDS=82.6969;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997305;PAIREDR=0.992248;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.577;Dels=0.0;FS=1. [...]
+chr13 41199487 . A C 10278.735 REJECT NS=2;DP=441;DPB=516.0;AC=3;AN=4;AF=0.75;RO=138;AO=378;PRO=0.0;PAO=0.0;QR=5262;QA=14440;PQR=0.0;PQA=0.0;SRF=79;SRR=59;SAF=196;SAR=182;SRP=9.30442;SAP=4.13625;AB=0.623978;ABP=52.0075;RUN=1;RPP=3.21711;RPPR=4.01736;RPL=192.0;RPR=186.0;EPP=11.3056;EPPR=6.09442;DPRA=0.0;ODDS=93.9314;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997354;PAIREDR=0.992754;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.651;Dels=0.0;FS=2.765;Haplo [...]
+chr13 41199531 . A G 9813.485 REJECT NS=2;DP=417;DPB=483.0;AC=3;AN=4;AF=0.75;RO=127;AO=356;PRO=0.0;PAO=0.0;QR=4860;QA=13530;PQR=0.0;PQA=0.0;SRF=69;SRR=58;SAF=198;SAR=158;SRP=5.07918;SAP=12.7697;AB=0.639205;ABP=62.257;RUN=1;RPP=4.98658;RPPR=3.43776;RPL=169.0;RPR=187.0;EPP=3.22989;EPPR=3.16418;DPRA=0.0;ODDS=82.662;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997191;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.641;Dels=0.0;FS=0.0;HaplotypeScore= [...]
+chr13 41199697 . G A 2759.61 PASS SOMATIC;NS=2;DP=439;DPB=439.0;AC=1;AN=3;AF=0.25;RO=330;AO=108;PRO=0.0;PAO=0.0;QR=12397;QA=4089;PQR=0.0;PQA=0.0;SRF=137;SRR=193;SAF=39;SAR=69;SRP=23.6459;SAP=21.1059;AB=0.345048;ABP=68.2863;RUN=1;RPP=4.2971;RPPR=16.934;RPL=50.0;RPR=58.0;EPP=5.02092;EPPR=4.69484;DPRA=2.48413;ODDS=79.5066;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990741;PAIREDR=0.984848;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.547;Dels=0.0;FS= [...]
+chr13 41199795 . T TA 3786.08 REJECT NS=2;DP=267;DPB=348.72;AC=2;AN=2;AF=0.0;RO=60;AO=11;PRO=54.5833;PAO=46.5833;QR=2212;QA=394;PQR=1923.33;PQA=1626.33;SRF=23;SRR=37;SAF=7;SAR=4;SRP=10.1038;SAP=4.78696;AB=0.0411985;ABP=491.185;RUN=1;RPP=4.78696;RPPR=8.22183;RPL=4.0;RPR=7.0;EPP=4.78696;EPPR=4.31318;DPRA=0.0;ODDS=26.2498;GTI=0;TYPE=ins;CIGAR=1M1I24M;NUMALT=3;MEANALT=18.5;LEN=1;MQM=60.0;MQMR=59.8667;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr13 41199795 . TA T 3037.9049999999997 REJECT NS=2;DP=267;DPB=348.72;AC=2;AN=4;AF=0.5;RO=60;AO=130;PRO=54.5833;PAO=57.5833;QR=2212;QA=4443;PQR=1923.33;PQA=1957.83;SRF=23;SRR=37;SAF=69;SAR=61;SRP=10.1038;SAP=4.07933;AB=0.486891;ABP=3.40881;RUN=1;RPP=6.28421;RPPR=8.22183;RPL=58.0;RPR=72.0;EPP=4.07933;EPPR=4.31318;DPRA=0.0;ODDS=26.2498;GTI=0;TYPE=del;CIGAR=1M1D23M;NUMALT=3;MEANALT=18.5;LEN=1;MQM=60.5231;MQMR=59.8667;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;Ba [...]
+chr13 41199795 . TAA T 3786.08 REJECT NS=2;DP=267;DPB=348.72;AC=2;AN=2;AF=0.0;RO=60;AO=30;PRO=54.5833;PAO=41.25;QR=2212;QA=1066;PQR=1923.33;PQA=1426.5;SRF=23;SRR=37;SAF=17;SAR=13;SRP=10.1038;SAP=4.16842;AB=0.11236;ABP=351.495;RUN=1;RPP=4.16842;RPPR=8.22183;RPL=13.0;RPR=17.0;EPP=10.2485;EPPR=4.31318;DPRA=0.0;ODDS=26.2498;GTI=0;TYPE=del;CIGAR=1M2D22M;NUMALT=3;MEANALT=18.5;LEN=2;MQM=60.0;MQMR=59.8667;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr13 41200091 . A G 6219.030000000001 REJECT NS=2;DP=288;DPB=339.0;AC=3;AN=4;AF=0.75;RO=102;AO=237;PRO=0.0;PAO=0.0;QR=3969;QA=9011;PQR=0.0;PQA=0.0;SRF=33;SRR=69;SAF=80;SAR=157;SRP=30.6008;SAP=57.3338;AB=0.575;ABP=14.7363;RUN=1;RPP=39.3756;RPPR=15.2727;RPL=150.0;RPR=87.0;EPP=23.2499;EPPR=3.09546;DPRA=0.0;ODDS=62.7097;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987342;PAIREDR=0.980392;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.259;Dels=0.0;FS=0.0;Haplo [...]
+chr13 41201633 . G A 8262.125 REJECT NS=2;DP=377;DPB=427.0;AC=3;AN=4;AF=0.75;RO=130;AO=297;PRO=0.0;PAO=0.0;QR=5041;QA=11181;PQR=0.0;PQA=0.0;SRF=43;SRR=87;SAF=110;SAR=187;SRP=35.3485;SAP=46.3593;AB=0.604863;ABP=34.4339;RUN=1;RPP=5.12328;RPPR=11.0949;RPL=157.0;RPR=140.0;EPP=3.19308;EPPR=3.27756;DPRA=0.0;ODDS=62.0782;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983165;PAIREDR=0.984615;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.312;Dels=0.0;FS=2.657;Haplo [...]
+chr13 41202322 . T A 5896.3150000000005 REJECT NS=2;DP=365;DPB=424.0;AC=2;AN=4;AF=0.5;RO=203;AO=221;PRO=0.0;PAO=0.0;QR=7603;QA=8283;PQR=0.0;PQA=0.0;SRF=98;SRR=105;SAF=94;SAR=127;SRP=3.53445;SAP=13.7105;AB=0.521226;ABP=4.66963;RUN=1;RPP=5.22108;RPPR=3.021;RPL=118.0;RPR=103.0;EPP=5.22108;EPPR=4.30463;DPRA=0.0;ODDS=330.176;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9095;MQMR=60.0;PAIRED=0.995475;PAIREDR=0.995074;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.564;Dels=0.0;FS=4.1 [...]
+chr13 41202493 . T TAC 3332.72 REJECT NS=2;DP=222;DPB=365.949;AC=2;AN=3;AF=0.5;RO=47;AO=97;PRO=70.0;PAO=71.6667;QR=1745;QA=3411;PQR=2429.75;PQA=2449.75;SRF=30;SRR=17;SAF=57;SAR=40;SRP=10.8184;SAP=9.47994;AB=0.436937;ABP=10.6789;RUN=1;RPP=8.04722;RPPR=6.75262;RPL=56.0;RPR=41.0;EPP=4.82359;EPPR=3.42611;DPRA=0.0;ODDS=47.042;GTI=0;TYPE=ins;CIGAR=1M2I38M;NUMALT=3;MEANALT=15.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=0.989691;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.4 [...]
+chr13 41202493 . T TACAC 3332.72 REJECT SOMATIC;NS=2;DP=222;DPB=365.949;AC=1;AN=3;AF=0.0;RO=47;AO=16;PRO=70.0;PAO=69.6667;QR=1745;QA=504;PQR=2429.75;PQA=2403.75;SRF=30;SRR=17;SAF=11;SAR=5;SRP=10.8184;SAP=7.89611;AB=0.0720721;ABP=356.119;RUN=1;RPP=5.18177;RPPR=6.75262;RPL=10.0;RPR=6.0;EPP=3.55317;EPPR=3.42611;DPRA=0.0;ODDS=47.042;GTI=0;TYPE=ins;CIGAR=1M4I38M;NUMALT=3;MEANALT=15.0;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr13 41202493 . T TACACAC 3332.72 REJECT NS=2;DP=222;DPB=365.949;AC=2;AN=2;AF=0.25;RO=47;AO=22;PRO=70.0;PAO=69.6667;QR=1745;QA=772;PQR=2429.75;PQA=2403.75;SRF=30;SRR=17;SAF=12;SAR=10;SRP=10.8184;SAP=3.40511;AB=0.0990991;ABP=312.924;RUN=1;RPP=9.32731;RPPR=6.75262;RPL=7.0;RPR=15.0;EPP=3.0103;EPPR=3.42611;DPRA=0.0;ODDS=47.042;GTI=0;TYPE=ins;CIGAR=1M6I38M;NUMALT=3;MEANALT=15.0;LEN=6;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.782;FS=0. [...]
+chr13 41202948 . T C 9365.285 REJECT NS=2;DP=389;DPB=443.0;AC=3;AN=4;AF=0.75;RO=116;AO=327;PRO=0.0;PAO=0.0;QR=4466;QA=12565;PQR=0.0;PQA=0.0;SRF=67;SRR=49;SAF=198;SAR=129;SRP=9.07545;SAP=34.6261;AB=0.655786;ABP=74.0503;RUN=1;RPP=3.07007;RPPR=6.67934;RPL=165.0;RPR=162.0;EPP=27.7199;EPPR=13.7928;DPRA=0.0;ODDS=67.1083;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990826;PAIREDR=0.991379;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.159;Dels=0.0;FS=0.6965;Haplo [...]
+chr13 41203281 . C T 1254.12 REJECT SOMATIC;NS=2;DP=151;DPB=211.2;AC=1;AN=3;AF=0.0;RO=28;AO=8;PRO=27.3667;PAO=3.45;QR=1020;QA=113;PQR=988.55;PQA=122.3;SRF=10;SRR=18;SAF=0;SAR=8;SRP=7.97367;SAP=20.3821;AB=0.0529801;ABP=265.097;RUN=1;RPP=7.35324;RPPR=22.8638;RPL=2.0;RPR=6.0;EPP=7.35324;EPPR=3.0103;DPRA=0.0;ODDS=24.4928;GTI=0;TYPE=snp;CIGAR=1X19M;NUMALT=5;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=59.2857;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr13 41203281 . C CT 976.925 REJECT NS=2;DP=151;DPB=211.2;AC=2;AN=3;AF=0.5;RO=28;AO=52;PRO=27.3667;PAO=28.6167;QR=1020;QA=1333;PQR=988.55;PQA=1024.05;SRF=10;SRR=18;SAF=18;SAR=34;SRP=7.97367;SAP=13.7006;AB=0.344371;ABP=34.7771;RUN=1;RPP=27.0635;RPPR=22.8638;RPL=38.0;RPR=14.0;EPP=3.0103;EPPR=3.0103;DPRA=0.0;ODDS=24.4928;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=5;MEANALT=12.5;LEN=1;MQM=59.6154;MQMR=59.2857;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.168 [...]
+chr13 41203281 . C TT 1254.12 REJECT SOMATIC;NS=2;DP=151;DPB=211.2;AC=1;AN=3;AF=0.0;RO=28;AO=5;PRO=27.3667;PAO=3.45;QR=1020;QA=71;PQR=988.55;PQA=122.3;SRF=10;SRR=18;SAF=0;SAR=5;SRP=7.97367;SAP=13.8677;AB=0.0331126;ABP=288.911;RUN=1;RPP=13.8677;RPPR=22.8638;RPL=0.0;RPR=5.0;EPP=13.8677;EPPR=3.0103;DPRA=0.0;ODDS=24.4928;GTI=0;TYPE=complex;CIGAR=1X1I19M;NUMALT=5;MEANALT=12.5;LEN=21;MQM=70.0;MQMR=59.2857;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr13 41203281 . C CTT 1254.12 REJECT NS=2;DP=151;DPB=211.2;AC=2;AN=2;AF=0.25;RO=28;AO=18;PRO=27.3667;PAO=26.6167;QR=1020;QA=480;PQR=988.55;PQA=949.05;SRF=10;SRR=18;SAF=4;SAR=14;SRP=7.97367;SAP=15.074;AB=0.119205;ABP=193.194;RUN=1;RPP=10.7311;RPPR=22.8638;RPL=13.0;RPR=5.0;EPP=4.9405;EPPR=3.0103;DPRA=0.0;ODDS=24.4928;GTI=0;TYPE=ins;CIGAR=1M2I19M;NUMALT=5;MEANALT=12.5;LEN=2;MQM=57.3333;MQMR=59.2857;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr13 41203281 . CT C 1254.12 REJECT SOMATIC;NS=2;DP=151;DPB=211.2;AC=1;AN=3;AF=0.0;RO=28;AO=19;PRO=27.3667;PAO=20.5;QR=1020;QA=551;PQR=988.55;PQA=728.75;SRF=10;SRR=18;SAF=4;SAR=15;SRP=7.97367;SAP=16.8392;AB=0.125828;ABP=186.636;RUN=1;RPP=5.8675;RPPR=22.8638;RPL=12.0;RPR=7.0;EPP=5.8675;EPPR=3.0103;DPRA=0.0;ODDS=24.4928;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=5;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=59.2857;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr13 41203905 . C T 9602.535 REJECT NS=2;DP=430;DPB=491.0;AC=3;AN=4;AF=0.75;RO=147;AO=344;PRO=0.0;PAO=0.0;QR=5577;QA=13184;PQR=0.0;PQA=0.0;SRF=82;SRR=65;SAF=197;SAR=147;SRP=7.27939;SAP=18.7913;AB=0.602703;ABP=36.9087;RUN=1;RPP=10.3075;RPPR=8.34296;RPL=155.0;RPR=189.0;EPP=11.1912;EPPR=7.27939;DPRA=0.0;ODDS=76.1623;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.843;MQMR=60.0;PAIRED=0.991279;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=4.174;Dels=0.0;FS=0.0;HaplotypeSc [...]
+chr13 41204242 . A G 10110.035 REJECT NS=2;DP=408;DPB=471.0;AC=3;AN=4;AF=0.75;RO=112;AO=359;PRO=0.0;PAO=0.0;QR=4221;QA=13710;PQR=0.0;PQA=0.0;SRF=58;SRR=54;SAF=173;SAR=186;SRP=3.32051;SAP=4.03253;AB=0.676301;ABP=96.4213;RUN=1;RPP=3.01635;RPPR=3.0103;RPL=180.0;RPR=179.0;EPP=8.09723;EPPR=3.32051;DPRA=0.0;ODDS=78.9389;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994429;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.324;Dels=0.0;FS=1.2545;HaplotypeS [...]
+chr13 41204788 . C CA 1092.37 PASS SOMATIC;NS=2;DP=240;DPB=306.64;AC=2;AN=2;AF=0.0;RO=130;AO=24;PRO=41.25;PAO=30.25;QR=4664;QA=774;PQR=1395.67;PQA=1043.67;SRF=82;SRR=48;SAF=14;SAR=10;SRP=22.3197;SAP=4.45795;AB=0.1;ABP=336.548;RUN=1;RPP=12.0581;RPPR=59.2013;RPL=7.0;RPR=17.0;EPP=3.37221;EPPR=6.28421;DPRA=0.0;ODDS=57.1542;GTI=0;TYPE=ins;CIGAR=1M1I24M;NUMALT=3;MEANALT=13.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr13 41204788 . CA C 807.05 REJECT NS=2;DP=222;DPB=306.64;AC=2;AN=4;AF=0.5;RO=130;AO=52;PRO=41.25;PAO=33.25;QR=4664;QA=1725;PQR=1395.67;PQA=1160.67;SRF=82;SRR=48;SAF=35;SAR=17;SRP=22.3197;SAP=16.5402;AB=0.216667;ABP=170.358;RUN=1;RPP=35.7494;RPPR=59.2013;RPL=12.0;RPR=40.0;EPP=3.17734;EPPR=6.28421;DPRA=0.0;ODDS=57.1542;GTI=0;TYPE=del;CIGAR=1M1D23M;NUMALT=3;MEANALT=13.5;LEN=1;MQM=60.3846;MQMR=60.0;PAIRED=0.980769;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.6 [...]
+chr13 41204788 . CAA C 1092.37 REJECT NS=2;DP=240;DPB=306.64;AC=2;AN=2;AF=0.0;RO=130;AO=7;PRO=41.25;PAO=26.25;QR=4664;QA=236;PQR=1395.67;PQA=900.0;SRF=82;SRR=48;SAF=6;SAR=1;SRP=22.3197;SAP=10.7656;AB=0.0291667;ABP=465.136;RUN=1;RPP=5.80219;RPPR=59.2013;RPL=2.0;RPR=5.0;EPP=3.32051;EPPR=6.28421;DPRA=0.0;ODDS=57.1542;GTI=0;TYPE=del;CIGAR=1M2D22M;NUMALT=3;MEANALT=13.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr13 41205289 . G A 4082.15 PASS SOMATIC;NS=2;DP=485;DPB=485.0;AC=1;AN=3;AF=0.25;RO=333;AO=151;PRO=0.0;PAO=0.0;QR=12706;QA=5721;PQR=0.0;PQA=0.0;SRF=184;SRR=149;SAF=79;SAR=72;SRP=10.9984;SAP=3.71495;AB=0.405914;ABP=31.613;RUN=1;RPP=7.1663;RPPR=7.08589;RPL=84.0;RPR=67.0;EPP=3.13973;EPPR=12.9286;DPRA=3.29204;ODDS=71.5045;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993377;PAIREDR=0.996997;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.354;Dels=0.0;FS [...]
+chr13 41206298 . C T 2531.295 REJECT NS=2;DP=130;DPB=148.0;AC=3;AN=4;AF=0.75;RO=51;AO=97;PRO=0.0;PAO=0.0;QR=1871;QA=3606;PQR=0.0;PQA=0.0;SRF=43;SRR=8;SAF=77;SAR=20;SRP=55.1682;SAP=75.7434;AB=0.552632;ABP=5.75321;RUN=1;RPP=14.8527;RPPR=3.05288;RPL=37.0;RPR=60.0;EPP=24.5235;EPPR=15.3153;DPRA=0.0;ODDS=22.2069;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.7423;MQMR=59.3529;PAIRED=0.979381;PAIREDR=0.980392;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.87;Dels=0.0;FS=0.9995;Haplotyp [...]
+chr13 41206612 . T C 635.792 REJECT NS=2;DP=144;DPB=172.0;AC=2;AN=4;AF=0.5;RO=136;AO=36;PRO=0.0;PAO=0.0;QR=5195;QA=1324;PQR=0.0;PQA=0.0;SRF=16;SRR=120;SAF=6;SAR=30;SRP=175.706;SAP=37.7539;AB=0.209302;ABP=129.259;RUN=1;RPP=5.18177;RPPR=7.09778;RPL=21.0;RPR=15.0;EPP=5.18177;EPPR=7.09778;DPRA=0.0;ODDS=12.3212;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.985294;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.393;Dels=0.0;FS=5.2865;HaplotypeScore=1.9 [...]
+chr13 41208607 . A C 5424.19 REJECT NS=2;DP=363;DPB=409.0;AC=2;AN=4;AF=0.5;RO=210;AO=199;PRO=0.0;PAO=0.0;QR=8160;QA=7375;PQR=0.0;PQA=0.0;SRF=74;SRR=136;SAF=75;SAR=124;SRP=42.7586;SAP=29.2098;AB=0.486553;ABP=3.65272;RUN=1;RPP=16.3774;RPPR=16.4114;RPL=117.0;RPR=82.0;EPP=5.46548;EPPR=5.65743;DPRA=0.0;ODDS=180.322;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.979899;PAIREDR=0.995238;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.954;Dels=0.0;FS=4.162;Haplotype [...]
+chr13 41208820 . C CTT 7.505 REJECT NS=2;DP=47;DPB=66.35;AC=2;AN=2;AF=0.0;RO=26;AO=3;PRO=13.9167;PAO=8.91667;QR=887;QA=42;PQR=472.333;PQA=303.333;SRF=6;SRR=20;SAF=0;SAR=3;SRP=19.3799;SAP=9.52472;AB=0.0638298;ABP=80.6751;RUN=1;RPP=3.73412;RPPR=3.34437;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=6.01695;DPRA=0.0;ODDS=1.06705;GTI=1;TYPE=ins;CIGAR=1M2I19M;NUMALT=3;MEANALT=7.5;LEN=2;MQM=60.0;MQMR=59.8462;PAIRED=1.0;PAIREDR=0.961538;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr13 41208820 . CT C 7.505 REJECT NS=2;DP=47;DPB=66.35;AC=2;AN=4;AF=0.5;RO=26;AO=6;PRO=13.9167;PAO=8.41667;QR=887;QA=173;PQR=472.333;PQA=284.333;SRF=6;SRR=20;SAF=1;SAR=5;SRP=19.3799;SAP=8.80089;AB=0.12766;ABP=59.6072;RUN=1;RPP=8.80089;RPPR=3.34437;RPL=5.0;RPR=1.0;EPP=4.45795;EPPR=6.01695;DPRA=0.0;ODDS=1.06705;GTI=1;TYPE=del;CIGAR=1M1D18M;NUMALT=3;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=59.8462;PAIRED=1.0;PAIREDR=0.961538;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr13 41208820 . CTT C 7.505 REJECT NS=2;DP=47;DPB=66.35;AC=2;AN=2;AF=0.0;RO=26;AO=3;PRO=13.9167;PAO=8.75;QR=887;QA=65;PQR=472.333;PQA=294.0;SRF=6;SRR=20;SAF=1;SAR=2;SRP=19.3799;SAP=3.73412;AB=0.0638298;ABP=80.6751;RUN=1;RPP=3.73412;RPPR=3.34437;RPL=2.0;RPR=1.0;EPP=9.52472;EPPR=6.01695;DPRA=0.0;ODDS=1.06705;GTI=1;TYPE=del;CIGAR=1M2D17M;NUMALT=3;MEANALT=7.5;LEN=2;MQM=53.3333;MQMR=59.8462;PAIRED=1.0;PAIREDR=0.961538;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr13 41209338 . C CA 7602.315 REJECT NS=2;DP=381;DPB=508.214;AC=3;AN=4;AF=0.75;RO=114;AO=297;PRO=56.0;PAO=70.0;QR=4346;QA=11083;PQR=1941.0;PQA=2450.0;SRF=54;SRR=60;SAF=148;SAR=149;SRP=3.69603;SAP=3.01761;AB=0.606667;ABP=32.6581;RUN=1;RPP=3.89497;RPPR=3.31507;RPL=143.0;RPR=154.0;EPP=3.0761;EPPR=10.6295;DPRA=0.0;ODDS=76.3251;GTI=0;TYPE=ins;CIGAR=1M1I13M;NUMALT=1;MEANALT=3.5;LEN=1;MQM=60.1684;MQMR=60.0;PAIRED=0.989899;PAIREDR=0.973684;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.148;FS=0.2 [...]
+chr13 41209883 . G A 12185.95 REJECT NS=2;DP=318;DPB=364.0;AC=4;AN=4;AF=1.0;RO=0;AO=364;PRO=0.0;PAO=0.0;QR=0;QA=14079;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=157;SAR=207;SRP=0.0;SAP=17.9243;AB=0.0;ABP=0.0;RUN=1;RPP=21.7184;RPPR=0.0;RPL=210.0;RPR=154.0;EPP=3.22506;EPPR=0.0;DPRA=0.0;ODDS=61.7428;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997253;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9661;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.32;SOR=0 [...]
+chr13 41210041 . G A 3951.3500000000004 REJECT NS=2;DP=175;DPB=196.0;AC=3;AN=4;AF=0.75;RO=57;AO=139;PRO=0.0;PAO=0.0;QR=2166;QA=5323;PQR=0.0;PQA=0.0;SRF=12;SRR=45;SAF=36;SAR=103;SRP=44.4969;SAP=73.1379;AB=0.62987;ABP=25.5711;RUN=1;RPP=18.0231;RPPR=23.1631;RPL=85.0;RPR=54.0;EPP=18.0231;EPPR=7.61992;DPRA=0.0;ODDS=27.2428;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992806;PAIREDR=0.947368;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.528;Dels=0.0;FS=2.913;Ha [...]
+chr13 41213098 . A G 3080.45 REJECT NS=2;DP=153;DPB=181.0;AC=3;AN=4;AF=0.75;RO=57;AO=124;PRO=0.0;PAO=0.0;QR=2151;QA=4715;PQR=0.0;PQA=0.0;SRF=9;SRR=48;SAF=12;SAR=112;SRP=60.9543;SAP=178.129;AB=0.544;ABP=5.11229;RUN=1;RPP=4.13106;RPPR=6.09608;RPL=66.0;RPR=58.0;EPP=3.29049;EPPR=3.0484;DPRA=0.0;ODDS=35.9373;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.574;Dels=0.0;FS=0.4855;HaplotypeScore=1.9577;MLEA [...]
+chr13 41213337 . T TA 200.871 REJECT NS=2;DP=208;DPB=266.682;AC=2;AN=4;AF=0.5;RO=146;AO=24;PRO=46.5;PAO=34.5;QR=5364;QA=866;PQR=1625.0;PQA=1181.0;SRF=106;SRR=40;SAF=20;SAR=4;SRP=67.7975;SAP=26.1727;AB=0.115385;ABP=270.268;RUN=1;RPP=16.0391;RPPR=60.1825;RPL=6.0;RPR=18.0;EPP=4.45795;EPPR=7.82918;DPRA=0.0;ODDS=9.95694;GTI=0;TYPE=ins;CIGAR=1M1I21M;NUMALT=2;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993151;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr13 41213337 . TA T 200.871 REJECT NS=2;DP=208;DPB=266.682;AC=2;AN=2;AF=0.0;RO=146;AO=11;PRO=46.5;PAO=34.0;QR=5364;QA=372;PQR=1625.0;PQA=1165.0;SRF=106;SRR=40;SAF=8;SAR=3;SRP=67.7975;SAP=7.94546;AB=0.0528846;ABP=364.185;RUN=1;RPP=3.20771;RPPR=60.1825;RPL=6.0;RPR=5.0;EPP=4.78696;EPPR=7.82918;DPRA=0.0;ODDS=9.95694;GTI=0;TYPE=del;CIGAR=1M1D20M;NUMALT=2;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993151;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr13 41214934 . GTT G 2579.73 REJECT SOMATIC;NS=2;DP=169;DPB=184.5;AC=1;AN=3;AF=0.0;RO=54;AO=24;PRO=7.33333;PAO=5.33333;QR=2069;QA=898;PQR=253.333;PQA=190.833;SRF=4;SRR=50;SAF=1;SAR=23;SRP=88.0998;SAP=46.8017;AB=0.166667;ABP=124.613;RUN=1;RPP=12.0581;RPPR=16.0391;RPL=7.0;RPR=17.0;EPP=16.0391;EPPR=7.03155;DPRA=0.0;ODDS=14.0471;GTI=0;TYPE=del;CIGAR=1M2D3M;NUMALT=2;MEANALT=2.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr13 41214936 . T TG 2579.73 REJECT NS=2;DP=149;DPB=184.5;AC=2;AN=4;AF=0.625;RO=54;AO=90;PRO=7.33333;PAO=8.33333;QR=2069;QA=3307;PQR=253.333;PQA=290.833;SRF=4;SRR=50;SAF=8;SAR=82;SRP=88.0998;SAP=135.132;AB=0.396825;ABP=14.6604;RUN=1;RPP=24.725;RPPR=16.0391;RPL=60.0;RPR=30.0;EPP=24.725;EPPR=7.03155;DPRA=0.0;ODDS=14.0471;GTI=0;TYPE=ins;CIGAR=3M1I3M;NUMALT=2;MEANALT=2.5;LEN=1;MQM=60.9444;MQMR=60.0;PAIRED=0.988889;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;END=41214936;HOML [...]
+chr13 41215256 . A T 7593.175 REJECT NS=2;DP=326;DPB=367.0;AC=3;AN=4;AF=0.75;RO=100;AO=267;PRO=0.0;PAO=0.0;QR=3875;QA=10071;PQR=0.0;PQA=0.0;SRF=50;SRR=50;SAF=161;SAR=106;SRP=3.0103;SAP=27.6122;AB=0.65035;ABP=59.1649;RUN=1;RPP=3.40881;RPPR=4.40004;RPL=130.0;RPR=137.0;EPP=3.0835;EPPR=11.6962;DPRA=0.0;ODDS=51.4989;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996255;PAIREDR=0.99;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.933;Dels=0.0;FS=3.847;HaplotypeSco [...]
+chr13 41215696 . C T 7214.245000000001 REJECT NS=2;DP=329;DPB=369.0;AC=3;AN=4;AF=0.75;RO=114;AO=255;PRO=0.0;PAO=0.0;QR=4424;QA=9700;PQR=0.0;PQA=0.0;SRF=43;SRR=71;SAF=100;SAR=155;SRP=17.9439;SAP=28.7699;AB=0.608247;ABP=32.6274;RUN=1;RPP=3.08694;RPPR=4.22937;RPL=126.0;RPR=129.0;EPP=3.70006;EPPR=3.69603;DPRA=0.0;ODDS=49.6239;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988235;PAIREDR=0.991228;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.105;Dels=0.0;FS=0.0 [...]
+chr13 41215802 . G T 4440.185 REJECT NS=2;DP=228;DPB=261.0;AC=3;AN=4;AF=0.75;RO=93;AO=168;PRO=0.0;PAO=0.0;QR=3428;QA=6373;PQR=0.0;PQA=0.0;SRF=32;SRR=61;SAF=67;SAR=101;SRP=22.6469;SAP=17.9521;AB=0.523077;ABP=3.9123;RUN=1;RPP=14.6432;RPPR=20.0318;RPL=99.0;RPR=69.0;EPP=3.83753;EPPR=4.15441;DPRA=0.0;ODDS=42.162;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.982143;PAIREDR=0.989247;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.513;Dels=0.0;FS=3.091;HaplotypeScor [...]
+chr13 41215972 . A G 2078.535 REJECT NS=2;DP=96;DPB=110.0;AC=3;AN=4;AF=0.75;RO=30;AO=80;PRO=0.0;PAO=0.0;QR=1135;QA=2937;PQR=0.0;PQA=0.0;SRF=14;SRR=16;SAF=42;SAR=38;SRP=3.29983;SAP=3.44459;AB=0.638554;ABP=16.8502;RUN=1;RPP=3.44459;RPPR=7.64277;RPL=42.0;RPR=38.0;EPP=76.4061;EPPR=21.5402;DPRA=0.0;ODDS=17.86;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.925;MQMR=60.0;PAIRED=0.9875;PAIREDR=0.966667;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.436;Dels=0.0;FS=0.0;HaplotypeScore=3. [...]
+chr13 41216052 . G A 3299.33 REJECT NS=2;DP=139;DPB=157.0;AC=3;AN=4;AF=0.75;RO=39;AO=117;PRO=0.0;PAO=0.0;QR=1459;QA=4440;PQR=0.0;PQA=0.0;SRF=30;SRR=9;SAF=100;SAR=17;SRP=27.5646;SAP=130.867;AB=0.669421;ABP=33.1776;RUN=1;RPP=3.47429;RPPR=7.52028;RPL=56.0;RPR=61.0;EPP=3.02886;EPPR=3.51141;DPRA=0.0;ODDS=23.4537;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=59.7949;PAIRED=0.982906;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.855;Dels=0.0;FS=1.084;HaplotypeScore= [...]
+chr13 41216437 . C A 8603.970000000001 REJECT NS=2;DP=387;DPB=446.0;AC=3;AN=4;AF=0.75;RO=127;AO=318;PRO=0.0;PAO=0.0;QR=4859;QA=11922;PQR=0.0;PQA=0.0;SRF=69;SRR=58;SAF=167;SAR=151;SRP=5.07918;SAP=4.7584;AB=0.612121;ABP=39.0436;RUN=1;RPP=3.69315;RPPR=3.16418;RPL=154.0;RPR=164.0;EPP=5.74171;EPPR=3.0274;DPRA=0.0;ODDS=73.2696;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987421;PAIREDR=0.992126;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.009;Dels=0.0;FS=2.18 [...]
+chr13 41216534 . C T 9319.835 REJECT NS=2;DP=401;DPB=461.0;AC=3;AN=4;AF=0.75;RO=128;AO=333;PRO=0.0;PAO=0.0;QR=4805;QA=12766;PQR=0.0;PQA=0.0;SRF=59;SRR=69;SAF=138;SAR=195;SRP=4.70676;SAP=24.1968;AB=0.627907;ABP=51.8937;RUN=1;RPP=6.45988;RPPR=4.09604;RPL=178.0;RPR=155.0;EPP=3.17332;EPPR=3.62103;DPRA=0.0;ODDS=73.9521;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993994;PAIREDR=0.984375;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.996;Dels=0.0;FS=1.8395;Haplo [...]
+chr13 41216646 . T C 8888.535 REJECT NS=2;DP=382;DPB=448.0;AC=3;AN=4;AF=0.75;RO=124;AO=324;PRO=0.0;PAO=0.0;QR=4763;QA=12506;PQR=0.0;PQA=0.0;SRF=58;SRR=66;SAF=169;SAR=155;SRP=4.13106;SAP=4.32391;AB=0.610063;ABP=36.4701;RUN=1;RPP=3.9754;RPPR=3.29049;RPL=156.0;RPR=168.0;EPP=48.0751;EPPR=10.015;DPRA=0.0;ODDS=82.0805;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996914;PAIREDR=0.983871;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.43;Dels=0.0;FS=2.24;HaplotypeS [...]
+chr13 41216831 . A G 4400.495 REJECT NS=2;DP=182;DPB=208.0;AC=3;AN=4;AF=0.75;RO=49;AO=159;PRO=0.0;PAO=0.0;QR=1916;QA=6004;PQR=0.0;PQA=0.0;SRF=5;SRR=44;SAF=26;SAR=133;SRP=70.4146;SAP=159.37;AB=0.687898;ABP=51.1561;RUN=1;RPP=3.35173;RPPR=4.11819;RPL=82.0;RPR=77.0;EPP=3.35173;EPPR=5.18177;DPRA=0.0;ODDS=32.8116;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993711;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.771;Dels=0.0;FS=1.063;HaplotypeScore=1. [...]
+chr13 41217351 . C T 1464.895 REJECT NS=2;DP=80;DPB=95.0;AC=3;AN=4;AF=0.75;RO=27;AO=67;PRO=0.0;PAO=0.0;QR=956;QA=2247;PQR=0.0;PQA=0.0;SRF=12;SRR=15;SAF=33;SAR=34;SRP=3.73412;SAP=3.04271;AB=0.575758;ABP=6.30041;RUN=1;RPP=3.82055;RPPR=3.09072;RPL=31.0;RPR=36.0;EPP=17.3031;EPPR=3.09072;DPRA=0.0;ODDS=19.0513;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=57.6119;MQMR=58.5926;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.659;Dels=0.0;FS=0.0;HaplotypeScore=0.9665 [...]
+chr13 41217410 . C G 1537.6799999999998 REJECT NS=2;DP=93;DPB=111.0;AC=3;AN=4;AF=0.75;RO=31;AO=79;PRO=0.0;PAO=0.0;QR=985;QA=2404;PQR=0.0;PQA=0.0;SRF=17;SRR=14;SAF=56;SAR=23;SRP=3.64073;SAP=32.9436;AB=0.586667;ABP=7.90335;RUN=1;RPP=4.35716;RPPR=3.64073;RPL=36.0;RPR=43.0;EPP=3.69747;EPPR=11.486;DPRA=0.0;ODDS=22.6015;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.6962;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.941;Dels=0.0;FS=2.292;HaplotypeSco [...]
+chr13 41217484 . G A 104.943 REJECT NS=2;DP=117;DPB=199.559;AC=2;AN=2;AF=0.0;RO=34;AO=14;PRO=47.7667;PAO=33.85;QR=1180;QA=360;PQR=1642.95;PQA=1165.45;SRF=27;SRR=7;SAF=0;SAR=14;SRP=28.557;SAP=33.4109;AB=0.119658;ABP=150.021;RUN=1;RPP=18.5208;RPPR=46.1843;RPL=2.0;RPR=12.0;EPP=18.5208;EPPR=19.3602;DPRA=0.0;ODDS=4.67864;GTI=0;TYPE=snp;CIGAR=1X33M;NUMALT=4;MEANALT=24.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.928571;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr13 41217484 . G GA 104.943 REJECT NS=2;DP=117;DPB=199.559;AC=2;AN=2;AF=0.25;RO=34;AO=9;PRO=47.7667;PAO=41.7667;QR=1180;QA=271;PQR=1642.95;PQA=1448.95;SRF=27;SRR=7;SAF=7;SAR=2;SRP=28.557;SAP=9.04217;AB=0.0769231;ABP=184.913;RUN=1;RPP=14.8328;RPPR=46.1843;RPL=1.0;RPR=8.0;EPP=14.8328;EPPR=19.3602;DPRA=0.0;ODDS=4.67864;GTI=0;TYPE=ins;CIGAR=1M1I33M;NUMALT=4;MEANALT=24.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.3575;FS=6 [...]
+chr13 41217484 . GA G 104.943 REJECT NS=2;DP=117;DPB=199.559;AC=2;AN=4;AF=0.5;RO=34;AO=10;PRO=47.7667;PAO=41.1;QR=1180;QA=304;PQR=1642.95;PQA=1428.95;SRF=27;SRR=7;SAF=7;SAR=3;SRP=28.557;SAP=6.48466;AB=0.0854701;ABP=177.638;RUN=1;RPP=10.8276;RPPR=46.1843;RPL=2.0;RPR=8.0;EPP=6.48466;EPPR=19.3602;DPRA=0.0;ODDS=4.67864;GTI=0;TYPE=del;CIGAR=1M1D32M;NUMALT=4;MEANALT=24.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr13 41217501 . GAAAAG AAAAAA 104.943 REJECT NS=2;DP=117;DPB=199.559;AC=2;AN=2;AF=0.0;RO=34;AO=5;PRO=47.7667;PAO=25.5167;QR=1180;QA=58;PQR=1642.95;PQA=719.7;SRF=27;SRR=7;SAF=5;SAR=0;SRP=28.557;SAP=13.8677;AB=0.042735;ABP=215.499;RUN=1;RPP=3.44459;RPPR=46.1843;RPL=3.0;RPR=2.0;EPP=3.44459;EPPR=19.3602;DPRA=0.0;ODDS=4.67864;GTI=0;TYPE=complex;CIGAR=17M1X4M1X11M;NUMALT=4;MEANALT=24.0;LEN=34;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO [...]
+chr13 41217849 . A G 8482.400000000001 REJECT NS=2;DP=379;DPB=438.0;AC=3;AN=4;AF=0.75;RO=116;AO=322;PRO=0.0;PAO=0.0;QR=4198;QA=11752;PQR=0.0;PQA=0.0;SRF=52;SRR=64;SAF=158;SAR=164;SRP=5.70592;SAP=3.25307;AB=0.639752;ABP=57.6343;RUN=1;RPP=16.0661;RPPR=4.88226;RPL=183.0;RPR=139.0;EPP=18.5478;EPPR=3.08518;DPRA=0.0;ODDS=73.2063;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987578;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.041;Dels=0.0;FS=1.2555;H [...]
+chr13 41217991 . C T 8385.26 REJECT NS=2;DP=347;DPB=395.0;AC=3;AN=4;AF=0.75;RO=103;AO=290;PRO=0.0;PAO=0.0;QR=3959;QA=11213;PQR=0.0;PQA=0.0;SRF=51;SRR=52;SAF=153;SAR=137;SRP=3.03138;SAP=4.92719;AB=0.653333;ABP=64.2748;RUN=1;RPP=3.75908;RPPR=4.04333;RPL=140.0;RPR=150.0;EPP=7.32329;EPPR=5.56125;DPRA=0.0;ODDS=59.6769;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993103;PAIREDR=0.990291;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.197;Dels=0.0;FS=2.043;Haploty [...]
+chr13 41218134 . T C 9535.635 REJECT NS=2;DP=392;DPB=447.0;AC=3;AN=4;AF=0.75;RO=114;AO=331;PRO=0.0;PAO=0.0;QR=4383;QA=12735;PQR=0.0;PQA=0.0;SRF=58;SRR=56;SAF=169;SAR=162;SRP=3.08649;SAP=3.33176;AB=0.656805;ABP=75.1957;RUN=1;RPP=3.01686;RPPR=6.74371;RPL=166.0;RPR=165.0;EPP=4.48638;EPPR=3.69603;DPRA=0.0;ODDS=68.9854;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993958;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.537;Dels=0.0;FS=0.208;HaplotypeS [...]
+chr13 41218451 . C T 9382.135 REJECT NS=2;DP=408;DPB=467.0;AC=3;AN=4;AF=0.75;RO=130;AO=337;PRO=0.0;PAO=0.0;QR=4992;QA=12818;PQR=0.0;PQA=0.0;SRF=70;SRR=60;SAF=186;SAR=151;SRP=4.68066;SAP=10.9036;AB=0.628571;ABP=53.2644;RUN=1;RPP=17.2441;RPPR=3.0103;RPL=145.0;RPR=192.0;EPP=13.8419;EPPR=3.27756;DPRA=0.0;ODDS=73.9297;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.598;Dels=0.0;FS=0.4195;HaplotypeScore=5 [...]
+chr13 41218670 . C T 9736.085 REJECT NS=2;DP=433;DPB=501.0;AC=3;AN=4;AF=0.75;RO=140;AO=360;PRO=0.0;PAO=0.0;QR=5340;QA=13522;PQR=0.0;PQA=0.0;SRF=70;SRR=70;SAF=181;SAR=179;SRP=3.0103;SAP=3.03443;AB=0.614754;ABP=44.8734;RUN=1;RPP=3.39634;RPPR=10.5174;RPL=176.0;RPR=184.0;EPP=3.03443;EPPR=3.07234;DPRA=0.0;ODDS=85.146;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997222;PAIREDR=0.992857;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.784;Dels=0.0;FS=0.6315;Haploty [...]
+chr13 41218685 . G A 10141.235 REJECT NS=2;DP=435;DPB=499.0;AC=3;AN=4;AF=0.75;RO=139;AO=360;PRO=0.0;PAO=0.0;QR=5320;QA=13822;PQR=0.0;PQA=0.0;SRF=68;SRR=71;SAF=188;SAR=172;SRP=3.1509;SAP=4.55446;AB=0.625337;ABP=53.6331;RUN=1;RPP=4.96463;RPPR=7.52509;RPL=171.0;RPR=189.0;EPP=3.61349;EPPR=3.02592;DPRA=0.0;ODDS=80.7834;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992806;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.909;Dels=0.0;FS=0.0;HaplotypeScor [...]
+chr13 41219125 . G A 9753.435000000001 REJECT NS=2;DP=387;DPB=446.0;AC=3;AN=4;AF=0.75;RO=104;AO=339;PRO=0.0;PAO=0.0;QR=3972;QA=13084;PQR=0.0;PQA=0.0;SRF=47;SRR=57;SAF=173;SAR=166;SRP=5.09825;SAP=3.32417;AB=0.677812;ABP=93.3607;RUN=1;RPP=3.32417;RPPR=7.10269;RPL=166.0;RPR=173.0;EPP=3.52915;EPPR=3.34437;DPRA=0.0;ODDS=73.3471;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.9941;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.082;Dels=0.0;FS=2.701;Hapl [...]
+chr13 41219434 . T A 10809.235 REJECT NS=2;DP=453;DPB=521.0;AC=3;AN=4;AF=0.75;RO=134;AO=387;PRO=0.0;PAO=0.0;QR=5102;QA=14678;PQR=0.0;PQA=0.0;SRF=72;SRR=62;SAF=199;SAR=188;SRP=4.6308;SAP=3.68924;AB=0.654545;ABP=82.881;RUN=1;RPP=3.46479;RPPR=4.6308;RPL=189.0;RPR=198.0;EPP=7.72918;EPPR=6.18648;DPRA=0.0;ODDS=80.2419;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.782;Dels=0.0;FS=0.6285;HaplotypeScore=3. [...]
+chr13 41220204 . C CA 271.988 REJECT NS=2;DP=161;DPB=240.304;AC=2;AN=4;AF=0.5;RO=60;AO=21;PRO=40.8833;PAO=36.3833;QR=2150;QA=634;PQR=1436.58;PQA=1277.58;SRF=34;SRR=26;SAF=14;SAR=7;SRP=5.32654;SAP=8.07707;AB=0.130435;ABP=194.005;RUN=1;RPP=11.386;RPPR=49.9141;RPL=6.0;RPR=15.0;EPP=8.07707;EPPR=3.58936;DPRA=0.0;ODDS=2.78976;GTI=0;TYPE=ins;CIGAR=1M1I22M;NUMALT=5;MEANALT=23.5;LEN=1;MQM=60.0;MQMR=59.4833;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.226;F [...]
+chr13 41220204 . CA C 271.988 REJECT NS=2;DP=161;DPB=240.304;AC=2;AN=2;AF=0.0;RO=60;AO=18;PRO=40.8833;PAO=25.55;QR=2150;QA=569;PQR=1436.58;PQA=902.25;SRF=34;SRR=26;SAF=9;SAR=9;SRP=5.32654;SAP=3.0103;AB=0.111801;ABP=213.751;RUN=1;RPP=10.7311;RPPR=49.9141;RPL=5.0;RPR=13.0;EPP=7.35324;EPPR=3.58936;DPRA=0.0;ODDS=2.78976;GTI=0;TYPE=del;CIGAR=1M1D21M;NUMALT=5;MEANALT=23.5;LEN=1;MQM=60.0;MQMR=59.4833;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr13 41220204 . CAA C 271.988 REJECT NS=2;DP=161;DPB=240.304;AC=2;AN=2;AF=0.0;RO=60;AO=6;PRO=40.8833;PAO=24.0833;QR=2150;QA=205;PQR=1436.58;PQA=848.25;SRF=34;SRR=26;SAF=5;SAR=1;SRP=5.32654;SAP=8.80089;AB=0.0372671;ABP=302.444;RUN=1;RPP=3.0103;RPPR=49.9141;RPL=3.0;RPR=3.0;EPP=4.45795;EPPR=3.58936;DPRA=0.0;ODDS=2.78976;GTI=0;TYPE=del;CIGAR=1M2D20M;NUMALT=5;MEANALT=23.5;LEN=2;MQM=60.0;MQMR=59.4833;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr13 41220220 . AGT GA 271.988 REJECT NS=2;DP=161;DPB=240.304;AC=2;AN=2;AF=0.0;RO=60;AO=3;PRO=40.8833;PAO=9.13333;QR=2150;QA=48;PQR=1436.58;PQA=291.5;SRF=34;SRR=26;SAF=3;SAR=0;SRP=5.32654;SAP=9.52472;AB=0.0186335;ABP=327.045;RUN=1;RPP=9.52472;RPPR=49.9141;RPL=3.0;RPR=0.0;EPP=9.52472;EPPR=3.58936;DPRA=0.0;ODDS=2.78976;GTI=0;TYPE=complex;CIGAR=1M1D16M1X4M;NUMALT=5;MEANALT=23.5;LEN=22;MQM=60.0;MQMR=59.4833;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:Q [...]
+chr13 41220222 . T A 271.988 REJECT NS=2;DP=161;DPB=240.304;AC=2;AN=2;AF=0.0;RO=60;AO=4;PRO=40.8833;PAO=21.9667;QR=2150;QA=64;PQR=1436.58;PQA=738.833;SRF=34;SRR=26;SAF=4;SAR=0;SRP=5.32654;SAP=11.6962;AB=0.0248447;ABP=318.737;RUN=1;RPP=5.18177;RPPR=49.9141;RPL=3.0;RPR=1.0;EPP=5.18177;EPPR=3.58936;DPRA=0.0;ODDS=2.78976;GTI=0;TYPE=snp;CIGAR=18M1X4M;NUMALT=5;MEANALT=23.5;LEN=1;MQM=60.0;MQMR=59.4833;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr13 41220428 . CCTTTTTTTTTTTTTTTTTGAGAT GCTTTTTTTTTTTTTTTTGAGAC 4313.38 REJECT SOMATIC;NS=2;DP=141;DPB=207.154;AC=1;AN=3;AF=0.0;RO=18;AO=3;PRO=40.5548;PAO=7.07143;QR=609;QA=57;PQR=1411.54;PQA=187.31;SRF=7;SRR=11;SAF=0;SAR=3;SRP=4.9405;SAP=9.52472;AB=0.0212766;ABP=283.685;RUN=1;RPP=3.73412;RPPR=3.49285;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=10.7311;DPRA=0.0;ODDS=40.1102;GTI=0;TYPE=complex;CIGAR=1X1M1D20M1X2M;NUMALT=6;MEANALT=21.5;LEN=25;MQM=53.3333;MQMR=57.7778;PAIRED=1.0;PAIREDR=1.0;technolo [...]
+chr13 41220429 . CT C 516.76 PASS DP=131;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.212;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.4;MQRankSum=0.9995;QD=4.405;RPA=17,16;RU=T;ReadPosRankSum=1.1765;SOR=1.2015;STR;ClippingRankSum=-0.397 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:6,18:24:40.0:292,0,40:18:75:24:1:.:.:.:.:.:-0.480745 0/1:63,70:204:99.0:797,0,786:70:53:133:.:1:.:.:.:.:-0.0152891
+chr13 41220443 . TTTTGAGAT GAGAC 4313.38 REJECT SOMATIC;NS=2;DP=141;DPB=207.154;AC=1;AN=3;AF=0.0;RO=18;AO=3;PRO=40.5548;PAO=16.9048;QR=609;QA=82;PQR=1411.54;PQA=562.976;SRF=7;SRR=11;SAF=1;SAR=2;SRP=4.9405;SAP=3.73412;AB=0.0212766;ABP=283.685;RUN=1;RPP=3.73412;RPPR=3.49285;RPL=2.0;RPR=1.0;EPP=9.52472;EPPR=10.7311;DPRA=0.0;ODDS=40.1102;GTI=0;TYPE=complex;CIGAR=2M4D17M1X2M;NUMALT=6;MEANALT=21.5;LEN=22;MQM=60.0;MQMR=57.7778;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT: [...]
+chr13 41220444 . TTTGAGAT GAGAC 4313.38 REJECT SOMATIC;NS=2;DP=141;DPB=207.154;AC=1;AN=3;AF=0.0;RO=18;AO=6;PRO=40.5548;PAO=18.3048;QR=609;QA=133;PQR=1411.54;PQA=616.376;SRF=7;SRR=11;SAF=1;SAR=5;SRP=4.9405;SAP=8.80089;AB=0.0540541;ABP=194.745;RUN=1;RPP=8.80089;RPPR=3.49285;RPL=5.0;RPR=1.0;EPP=4.45795;EPPR=10.7311;DPRA=0.0;ODDS=40.1102;GTI=0;TYPE=complex;CIGAR=2M3D18M1X2M;NUMALT=6;MEANALT=33.0;LEN=23;MQM=60.0;MQMR=57.7778;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT: [...]
+chr13 41220445 . TTGAGAT GAGAC 4313.38 REJECT SOMATIC;NS=2;DP=141;DPB=207.154;AC=1;AN=3;AF=0.0;RO=18;AO=10;PRO=40.5548;PAO=19.5548;QR=609;QA=225;PQR=1411.54;PQA=662.376;SRF=7;SRR=11;SAF=2;SAR=8;SRP=4.9405;SAP=10.8276;AB=0.070922;ABP=228.489;RUN=1;RPP=16.9077;RPPR=3.49285;RPL=9.0;RPR=1.0;EPP=6.48466;EPPR=10.7311;DPRA=0.0;ODDS=40.1102;GTI=0;TYPE=complex;CIGAR=2M2D19M1X2M;NUMALT=6;MEANALT=21.5;LEN=24;MQM=58.0;MQMR=57.7778;PAIRED=0.9;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:G [...]
+chr13 41220446 . TGAGAT GAGAC 4313.38 REJECT NS=2;DP=141;DPB=207.154;AC=2;AN=3;AF=0.5;RO=18;AO=41;PRO=40.5548;PAO=28.5548;QR=609;QA=892;PQR=1411.54;PQA=972.21;SRF=7;SRR=11;SAF=18;SAR=23;SRP=4.9405;SAP=4.33437;AB=0.29078;ABP=56.6195;RUN=1;RPP=4.33437;RPPR=3.49285;RPL=23.0;RPR=18.0;EPP=4.33437;EPPR=10.7311;DPRA=0.0;ODDS=40.1102;GTI=0;TYPE=complex;CIGAR=2M1D20M1X2M;NUMALT=6;MEANALT=21.5;LEN=25;MQM=59.2683;MQMR=57.7778;PAIRED=0.97561;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:G [...]
+chr13 41220451 . T C 3681.075 REJECT NS=2;DP=141;DPB=207.154;AC=2;AN=2;AF=0.375;RO=18;AO=15;PRO=40.5548;PAO=35.0548;QR=609;QA=326;PQR=1411.54;PQA=1161.21;SRF=7;SRR=11;SAF=7;SAR=8;SRP=4.9405;SAP=3.15506;AB=0.106383;ABP=192.76;RUN=1;RPP=6.62942;RPPR=3.49285;RPL=10.0;RPR=5.0;EPP=3.15506;EPPR=10.7311;DPRA=0.0;ODDS=40.1102;GTI=0;TYPE=snp;CIGAR=23M1X2M;NUMALT=6;MEANALT=21.5;LEN=1;MQM=54.8667;MQMR=57.7778;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=1;BaseQRankSum=-2.885 [...]
+chr13 41220777 . G C 2529.565 REJECT NS=2;DP=123;DPB=143.0;AC=3;AN=4;AF=0.75;RO=43;AO=100;PRO=0.0;PAO=0.0;QR=1609;QA=3696;PQR=0.0;PQA=0.0;SRF=8;SRR=35;SAF=21;SAR=79;SRP=39.8243;SAP=76.0586;AB=0.590476;ABP=10.476;RUN=1;RPP=6.13722;RPPR=4.27278;RPL=56.0;RPR=44.0;EPP=22.5536;EPPR=3.0608;DPRA=0.0;ODDS=24.7252;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8;MQMR=60.0;PAIRED=1.0;PAIREDR=0.930233;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.947;Dels=0.0;FS=1.039;HaplotypeScore=0.0; [...]
+chr13 41221589 . G T 3464.91 REJECT NS=2;DP=137;DPB=153.0;AC=3;AN=4;AF=0.75;RO=34;AO=119;PRO=0.0;PAO=0.0;QR=1320;QA=4530;PQR=0.0;PQA=0.0;SRF=6;SRR=28;SAF=18;SAR=101;SRP=33.9218;SAP=128.718;AB=0.721311;ABP=54.9121;RUN=1;RPP=3.17453;RPPR=7.09778;RPL=61.0;RPR=58.0;EPP=3.46649;EPPR=7.09778;DPRA=0.0;ODDS=20.3322;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8319;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.642;Dels=0.0;FS=1.181;HaplotypeScore=4.86 [...]
+chr13 41222067 . C A 2954.28 PASS SOMATIC;NS=2;DP=397;DPB=397.0;AC=1;AN=3;AF=0.25;RO=285;AO=112;PRO=0.0;PAO=0.0;QR=11085;QA=4280;PQR=0.0;PQA=0.0;SRF=146;SRR=139;SAF=67;SAR=45;SRP=3.38364;SAP=12.3942;AB=0.367213;ABP=49.7219;RUN=1;RPP=4.25114;RPPR=5.76083;RPL=52.0;RPR=60.0;EPP=9.29206;EPPR=4.29794;DPRA=3.31522;ODDS=58.431;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996491;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.412;Dels=0.0;FS=5.4 [...]
+chr13 41222112 . C T 8384.970000000001 REJECT NS=2;DP=379;DPB=430.0;AC=3;AN=4;AF=0.75;RO=128;AO=302;PRO=0.0;PAO=0.0;QR=4908;QA=11409;PQR=0.0;PQA=0.0;SRF=73;SRR=55;SAF=141;SAR=161;SRP=8.50684;SAP=5.88642;AB=0.610942;ABP=38.1829;RUN=1;RPP=8.6475;RPPR=3.28173;RPL=137.0;RPR=165.0;EPP=6.49041;EPPR=14.4784;DPRA=0.0;ODDS=63.9461;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996689;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.837;Dels=0.0;FS=4.7835;Ha [...]
+chr13 41222213 . A AT 23.8885 REJECT NS=2;DP=368;DPB=463.05;AC=2;AN=3;AF=0.25;RO=329;AO=18;PRO=91.8333;PAO=63.8333;QR=12459;QA=640;PQR=3273.83;PQA=2262.83;SRF=210;SRR=119;SAF=14;SAR=4;SRP=57.6667;SAP=15.074;AB=0.0833333;ABP=111.584;RUN=1;RPP=3.49285;RPPR=20.1775;RPL=8.0;RPR=10.0;EPP=3.49285;EPPR=14.1053;DPRA=0.0;ODDS=5.49643;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=2;MEANALT=6.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987842;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr13 41222213 . AT A 23.8885 REJECT NS=2;DP=368;DPB=463.05;AC=2;AN=2;AF=0.0;RO=329;AO=11;PRO=91.8333;PAO=56.3333;QR=12459;QA=414;PQR=3273.83;PQA=1985.33;SRF=210;SRR=119;SAF=7;SAR=4;SRP=57.6667;SAP=4.78696;AB=0.0555556;ABP=126.543;RUN=1;RPP=3.20771;RPPR=20.1775;RPL=6.0;RPR=5.0;EPP=7.94546;EPPR=14.1053;DPRA=0.0;ODDS=5.49643;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=2;MEANALT=6.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987842;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr13 41223886 . C T 3579.07 PASS SOMATIC;NS=2;DP=519;DPB=519.0;AC=1;AN=3;AF=0.25;RO=380;AO=139;PRO=0.0;PAO=0.0;QR=14360;QA=5213;PQR=0.0;PQA=0.0;SRF=202;SRR=178;SAF=73;SAR=66;SRP=6.30179;SAP=3.77578;AB=0.363874;ABP=64.4937;RUN=1;RPP=4.90057;RPPR=3.58174;RPL=75.0;RPR=64.0;EPP=22.1474;EPPR=9.61615;DPRA=2.78832;ODDS=86.4005;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992806;PAIREDR=0.989474;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.091;Dels=0.0;F [...]
+chr13 41224287 . CTATA C 1251.91 REJECT NS=2;DP=58;DPB=57.0833;AC=3;AN=4;AF=0.75;RO=20;AO=43;PRO=9.5;PAO=8.5;QR=755;QA=1583;PQR=338.0;PQA=298.0;SRF=12;SRR=8;SAF=20;SAR=23;SRP=4.74748;SAP=3.46479;AB=0.555556;ABP=4.21667;RUN=1;RPP=7.10075;RPPR=3.44459;RPL=17.0;RPR=26.0;EPP=3.46479;EPPR=3.44459;DPRA=0.0;ODDS=12.2561;GTI=0;TYPE=del;CIGAR=1M4D7M;NUMALT=1;MEANALT=1.5;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=41224291;HOMLEN=6;HOMSEQ=TATATA;SVLEN=-4;SVTYP [...]
+chr13 41224442 . C T 1754.0 REJECT NS=2;DP=83;DPB=96.0;AC=3;AN=4;AF=0.75;RO=29;AO=67;PRO=0.0;PAO=0.0;QR=1118;QA=2518;PQR=0.0;PQA=0.0;SRF=17;SRR=12;SAF=43;SAR=24;SRP=4.88226;SAP=14.7103;AB=0.585714;ABP=7.47733;RUN=1;RPP=3.04271;RPPR=3.68421;RPL=33.0;RPR=34.0;EPP=5.63551;EPPR=15.6647;DPRA=0.0;ODDS=17.2545;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.9552;MQMR=60.0;PAIRED=0.985075;PAIREDR=0.931034;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.644;Dels=0.0;FS=0.0;HaplotypeScore=0 [...]
+chr13 41224813 . C T 9709.585 REJECT NS=2;DP=419;DPB=474.0;AC=3;AN=4;AF=0.75;RO=135;AO=339;PRO=0.0;PAO=0.0;QR=5098;QA=13032;PQR=0.0;PQA=0.0;SRF=54;SRR=81;SAF=117;SAR=222;SRP=14.7363;SAP=73.6312;AB=0.63388;ABP=59.9907;RUN=1;RPP=3.01671;RPPR=3.79846;RPL=170.0;RPR=169.0;EPP=7.01375;EPPR=3.15506;DPRA=0.0;ODDS=64.738;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.9941;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.233;Dels=0.0;FS=5.7805;HaplotypeScore [...]
+chr13 41225094 . G T 117.27000000000001 PASS DP=24;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-0.039;Dels=0.0;FS=4.917;HaplotypeScore=7.9652;MLEAC=1;MLEAF=0.5;MQ=59.82;MQRankSum=-0.821;QD=5.27;ReadPosRankSum=0.2065;SOR=0.5975;ClippingRankSum=-0.715 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:8,3:11:94.0:94,0,317:3:27:11:1:.:.:.:.:.:-0.480745 0/1:30,7:37:99.0:197,0,1108:7:19:37:.:1:.:.:.:.:-0.0152891
+chr13 41225094 . GTTA TTTG 654.47 REJECT NS=2;DP=49;DPB=49.75;AC=2;AN=2;AF=0.25;RO=15;AO=12;PRO=0.5;PAO=0.0;QR=556;QA=385;PQR=17.0;PQA=0.0;SRF=5;SRR=10;SAF=5;SAR=7;SRP=6.62942;SAP=3.73412;AB=0.244898;ABP=30.7077;RUN=1;RPP=9.52472;RPPR=4.31318;RPL=3.0;RPR=9.0;EPP=5.9056;EPPR=10.1038;DPRA=0.0;ODDS=12.5262;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=2;MEANALT=2.0;LEN=4;MQM=58.75;MQMR=60.0;PAIRED=0.916667;PAIREDR=0.866667;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr13 41225097 . A G 654.47 REJECT NS=2;DP=42;DPB=49.75;AC=2;AN=3;AF=0.5;RO=15;AO=22;PRO=0.5;PAO=0.5;QR=556;QA=831;PQR=17.0;PQA=17.0;SRF=5;SRR=10;SAF=6;SAR=16;SRP=6.62942;SAP=12.8806;AB=0.44898;ABP=4.11819;RUN=1;RPP=9.32731;RPPR=4.31318;RPL=15.0;RPR=7.0;EPP=17.2236;EPPR=10.1038;DPRA=0.0;ODDS=12.5262;GTI=0;TYPE=snp;CIGAR=3M1X;NUMALT=2;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.866667;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.834;Dels=0.0;FS=0.0;Haplotyp [...]
+chr13 41225228 . G T 580.77 PASS DP=31;AC=3;AN=4;AF=0.75;MQ0=0;ALERT;BaseQRankSum=0.312;Dels=0.02;FS=1.797;HaplotypeScore=31.9948;MLEAC=1;MLEAF=0.75;MQ=59.745;MQRankSum=-0.918;QD=21.285;ReadPosRankSum=1.846;SOR=2.198 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:0,10:10:30.0:450,30,0:10:100:10:1:.:.:.:.:.:-0.480745 0/1:28,23:51:99.0:768,0,1017:23:45:51:.:1:.:.:.:.:-0.0152891
+chr13 41225228 . GTTTTTTGTTTTTTGTTTTTG TGTTTTTGTTTTTGTTTTTT 1066.91 REJECT NS=2;DP=40;DPB=74.5238;AC=3;AN=4;AF=0.75;RO=12;AO=24;PRO=54.5;PAO=52.5;QR=445;QA=810;PQR=1850.5;PQA=1768.5;SRF=12;SRR=0;SAF=22;SAR=2;SRP=29.068;SAP=39.2015;AB=0.558824;ABP=4.03217;RUN=1;RPP=3.37221;RPPR=5.9056;RPL=13.0;RPR=11.0;EPP=3.37221;EPPR=5.9056;DPRA=0.0;ODDS=7.86986;GTI=0;TYPE=complex;CIGAR=6M2X6M1D11M1X15M;NUMALT=1;MEANALT=3.0;LEN=41;MQM=59.5417;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:G [...]
+chr13 41225229 . T G 566.77 PASS DP=31;AC=3;AN=4;AF=0.75;MQ0=0;ALERT;BaseQRankSum=0.074;Dels=0.0;FS=2.833;HaplotypeScore=31.9948;MLEAC=1;MLEAF=0.75;MQ=59.745;MQRankSum=-2.008;QD=24.4;ReadPosRankSum=1.842;SOR=2.1595 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:0,10:10:30.0:450,30,0:10:100:10:1:.:.:.:.:.:-0.480745 0/1:29,23:52:99.0:740,0,1091:23:44:52:.:1:.:.:.:.:-0.0152891
+chr13 41225235 . GT G 705.73 PASS DP=34;AC=3;AN=4;AF=0.75;MQ0=0;BaseQRankSum=-0.081;FS=0.9755;MLEAC=1;MLEAF=0.75;MQ=59.765;MQRankSum=-1.796;QD=22.145;RPA=6,5;RU=T;ReadPosRankSum=-0.424;SOR=2.1395;STR GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:0,12:12:41.0:561,41,0:12:100:12:1:.:.:.:.:.:-0.480745 0/1:22,31:56:99.0:925,0,623:31:58:53:.:1:.:.:.:.:-0.0152891
+chr13 41225248 . G T 871.77 PASS DP=37;AC=3;AN=4;AF=0.75;MQ0=0;BaseQRankSum=2.344;Dels=0.03;FS=0.0;HaplotypeScore=6.8566;MLEAC=1;MLEAF=0.75;MQ=59.645;MQRankSum=0.481;QD=25.675;ReadPosRankSum=0.053;SOR=1.9015 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:0,13:13:38.0:516,38,0:13:100:13:1:.:.:.:.:.:-0.480745 0/1:26,33:59:99.0:1284,0,894:33:56:59:.:1:.:.:.:.:-0.0152891
+chr13 41225361 . G C 4905.475 REJECT NS=2;DP=200;DPB=226.0;AC=3;AN=4;AF=0.75;RO=55;AO=170;PRO=0.0;PAO=0.0;QR=2096;QA=6569;PQR=0.0;PQA=0.0;SRF=37;SRR=18;SAF=137;SAR=33;SRP=17.2631;SAP=141.167;AB=0.678161;ABP=50.9824;RUN=1;RPP=13.0246;RPPR=7.78754;RPL=71.0;RPR=99.0;EPP=5.51388;EPPR=3.04978;DPRA=0.0;ODDS=33.4599;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994118;PAIREDR=0.981818;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.416;Dels=0.0;FS=4.2885;HaplotypeS [...]
+chr13 41225666 . ACTT A 8082.99 REJECT NS=2;DP=352;DPB=233.6;AC=3;AN=4;AF=0.75;RO=99;AO=279;PRO=30.5;PAO=23.5;QR=3695;QA=9946;PQR=934.5;PQA=694.5;SRF=47;SRR=52;SAF=131;SAR=148;SRP=3.55865;SAP=5.2596;AB=0.652921;ABP=62.1176;RUN=1;RPP=3.20488;RPPR=7.94546;RPL=142.0;RPR=137.0;EPP=6.44263;EPPR=3.03223;DPRA=0.0;ODDS=56.2995;GTI=0;TYPE=del;CIGAR=1M3D1M;NUMALT=1;MEANALT=2.5;LEN=3;MQM=60.5735;MQMR=60.0;PAIRED=0.992832;PAIREDR=0.989899;technology.ILLUMINA=1.0;MQ0=0;END=41225669;HOMLEN=1;HOMSEQ=C; [...]
+chr13 41225874 . G C 8089.81 REJECT NS=2;DP=344;DPB=388.0;AC=3;AN=4;AF=0.75;RO=100;AO=287;PRO=0.0;PAO=0.0;QR=3790;QA=10728;PQR=0.0;PQA=0.0;SRF=60;SRR=40;SAF=181;SAR=106;SRP=11.6962;SAP=45.5696;AB=0.666667;ABP=75.3927;RUN=1;RPP=4.28897;RPPR=7.26639;RPL=137.0;RPR=150.0;EPP=18.3317;EPPR=13.5202;DPRA=0.0;ODDS=55.2145;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996516;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.829;Dels=0.0;FS=1.387;HaplotypeSco [...]
+chr13 41226426 . C T 11.015 REJECT NS=2;DP=83;DPB=149.679;AC=2;AN=2;AF=0.0;RO=28;AO=9;PRO=40.1;PAO=13.6333;QR=1009;QA=99;PQR=1413.88;PQA=405.5;SRF=6;SRR=22;SAF=0;SAR=9;SRP=22.8638;SAP=22.5536;AB=0.108434;ABP=113.546;RUN=1;RPP=5.18177;RPPR=14.1779;RPL=3.0;RPR=6.0;EPP=5.18177;EPPR=7.97367;DPRA=0.0;ODDS=1.23446;GTI=0;TYPE=snp;CIGAR=1X27M;NUMALT=5;MEANALT=13.5;LEN=1;MQM=58.7778;MQMR=60.0;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr13 41226426 . CT C 11.015 REJECT NS=2;DP=83;DPB=149.679;AC=2;AN=4;AF=0.5;RO=28;AO=12;PRO=40.1;PAO=32.1;QR=1009;QA=240;PQR=1413.88;PQA=1100.38;SRF=6;SRR=22;SAF=2;SAR=10;SRP=22.8638;SAP=14.5915;AB=0.144578;ABP=94.0813;RUN=1;RPP=9.52472;RPPR=14.1779;RPL=9.0;RPR=3.0;EPP=3.73412;EPPR=7.97367;DPRA=0.0;ODDS=1.23446;GTI=0;TYPE=del;CIGAR=1M1D26M;NUMALT=5;MEANALT=13.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr13 41226426 . CTT C 11.015 REJECT NS=2;DP=83;DPB=149.679;AC=2;AN=2;AF=0.0;RO=28;AO=8;PRO=40.1;PAO=26.4333;QR=1009;QA=191;PQR=1413.88;PQA=923.05;SRF=6;SRR=22;SAF=2;SAR=6;SRP=22.8638;SAP=7.35324;AB=0.0963855;ABP=120.453;RUN=1;RPP=7.35324;RPPR=14.1779;RPL=6.0;RPR=2.0;EPP=3.0103;EPPR=7.97367;DPRA=0.0;ODDS=1.23446;GTI=0;TYPE=del;CIGAR=1M2D25M;NUMALT=5;MEANALT=13.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr13 41226426 . CTTT C 11.015 REJECT NS=2;DP=83;DPB=149.679;AC=2;AN=2;AF=0.0;RO=28;AO=4;PRO=40.1;PAO=24.9333;QR=1009;QA=105;PQR=1413.88;PQA=869.8;SRF=6;SRR=22;SAF=1;SAR=3;SRP=22.8638;SAP=5.18177;AB=0.0481928;ABP=150.173;RUN=1;RPP=3.0103;RPPR=14.1779;RPL=2.0;RPR=2.0;EPP=5.18177;EPPR=7.97367;DPRA=0.0;ODDS=1.23446;GTI=0;TYPE=del;CIGAR=1M3D24M;NUMALT=5;MEANALT=13.5;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr13 41226452 . A G 11.015 REJECT NS=2;DP=83;DPB=149.679;AC=2;AN=2;AF=0.0;RO=28;AO=3;PRO=40.1;PAO=29.8;QR=1009;QA=42;PQR=1413.88;PQA=1055.38;SRF=6;SRR=22;SAF=3;SAR=0;SRP=22.8638;SAP=9.52472;AB=0.0545455;ABP=97.8049;RUN=1;RPP=3.73412;RPPR=14.1779;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=7.97367;DPRA=0.0;ODDS=1.23446;GTI=0;TYPE=snp;CIGAR=26M1X1M;NUMALT=5;MEANALT=17.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr13 41226485 . A C 2590.44 REJECT NS=2;DP=136;DPB=154.0;AC=3;AN=4;AF=0.75;RO=51;AO=102;PRO=0.0;PAO=0.0;QR=1899;QA=3680;PQR=0.0;PQA=0.0;SRF=16;SRR=35;SAF=29;SAR=73;SRP=18.3809;SAP=44.2257;AB=0.571429;ABP=8.28388;RUN=1;RPP=33.7515;RPPR=10.206;RPL=32.0;RPR=70.0;EPP=4.37279;EPPR=8.16222;DPRA=0.0;ODDS=22.1991;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.4314;MQMR=60.0;PAIRED=0.960784;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.507;Dels=0.0;FS=0.8305;HaplotypeScore [...]
+chr13 41226561 . C G 2681.895 REJECT NS=2;DP=122;DPB=141.0;AC=3;AN=4;AF=0.75;RO=37;AO=104;PRO=0.0;PAO=0.0;QR=1362;QA=3810;PQR=0.0;PQA=0.0;SRF=22;SRR=15;SAF=71;SAR=33;SRP=5.88603;SAP=33.1604;AB=0.644231;ABP=21.8019;RUN=1;RPP=17.1249;RPPR=5.88603;RPL=39.0;RPR=65.0;EPP=51.1168;EPPR=3.06899;DPRA=0.0;ODDS=24.1029;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990385;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.591;Dels=0.0;FS=2.787;HaplotypeScore=1 [...]
+chr13 41227108 . C CT 336.667 REJECT NS=2;DP=262;DPB=346.778;AC=2;AN=4;AF=0.5;RO=200;AO=34;PRO=70.1667;PAO=47.1667;QR=7426;QA=1171;PQR=2493.5;PQA=1650.5;SRF=50;SRR=150;SAF=7;SAR=27;SRP=111.584;SAP=28.557;AB=0.129771;ABP=314.94;RUN=1;RPP=28.557;RPPR=42.0968;RPL=27.0;RPR=7.0;EPP=15.5282;EPPR=3.70517;DPRA=0.0;ODDS=4.46273;GTI=0;TYPE=ins;CIGAR=1M1I17M;NUMALT=2;MEANALT=7.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr13 41227108 . CT C 336.667 REJECT NS=2;DP=262;DPB=346.778;AC=2;AN=2;AF=0.0;RO=200;AO=15;PRO=70.1667;PAO=37.6667;QR=7426;QA=539;PQR=2493.5;PQA=1341.0;SRF=50;SRR=150;SAF=3;SAR=12;SRP=111.584;SAP=14.7363;AB=0.0572519;ABP=449.107;RUN=1;RPP=4.31318;RPPR=42.0968;RPL=9.0;RPR=6.0;EPP=3.15506;EPPR=3.70517;DPRA=0.0;ODDS=4.46273;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=2;MEANALT=7.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr13 41227865 . G A 11186.75 REJECT NS=2;DP=463;DPB=522.0;AC=3;AN=4;AF=0.75;RO=139;AO=383;PRO=0.0;PAO=0.0;QR=5303;QA=14706;PQR=0.0;PQA=0.0;SRF=64;SRR=75;SAF=193;SAR=190;SRP=4.90057;SAP=3.06133;AB=0.657635;ABP=90.6394;RUN=1;RPP=5.51061;RPPR=4.90057;RPL=202.0;RPR=181.0;EPP=5.05704;EPPR=3.02592;DPRA=0.0;ODDS=73.2589;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989556;PAIREDR=0.992806;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.366;Dels=0.0;FS=1.2895;Haplo [...]
+chr13 41228210 . T A 9459.985 REJECT NS=2;DP=406;DPB=466.0;AC=3;AN=4;AF=0.75;RO=124;AO=342;PRO=0.0;PAO=0.0;QR=4737;QA=12879;PQR=0.0;PQA=0.0;SRF=61;SRR=63;SAF=160;SAR=182;SRP=3.08035;SAP=6.08338;AB=0.642651;ABP=64.3434;RUN=1;RPP=7.30245;RPPR=10.015;RPL=184.0;RPR=158.0;EPP=16.4455;EPPR=6.44263;DPRA=0.0;ODDS=74.2921;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994152;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.148;Dels=0.0;FS=0.6695;HaplotypeS [...]
+chr13 41228392 . G A 3587.4700000000003 REJECT NS=2;DP=156;DPB=173.0;AC=3;AN=4;AF=0.75;RO=49;AO=124;PRO=0.0;PAO=0.0;QR=1854;QA=4719;PQR=0.0;PQA=0.0;SRF=1;SRR=48;SAF=21;SAR=103;SRP=100.904;SAP=120.76;AB=0.65493;ABP=32.6157;RUN=1;RPP=25.7057;RPPR=3.40914;RPL=80.0;RPR=44.0;EPP=6.44263;EPPR=4.11819;DPRA=0.0;ODDS=20.3618;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.6129;MQMR=60.0;PAIRED=0.983871;PAIREDR=0.938776;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.346;Dels=0.0;FS=9.6745 [...]
+chr13 41228459 . TAAAAAAAAAAAA T 263.256 REJECT SOMATIC;NS=2;DP=33;DPB=51.9756;AC=1;AN=3;AF=0.0;RO=0;AO=1;PRO=24.6405;PAO=17.6405;QR=0;QA=16;PQR=846.236;PQA=602.236;SRF=0;SRR=0;SAF=0;SAR=1;SRP=0.0;SAP=5.18177;AB=0.0833333;ABP=21.1059;RUN=1;RPP=5.18177;RPPR=0.0;RPL=0.0;RPR=1.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=8.5517;GTI=0;TYPE=del;CIGAR=1M12D28M;NUMALT=6;MEANALT=6.0;LEN=12;MQM=42.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr13 41228459 . TAAAAAAAAAAAAA T 263.256 REJECT NS=2;DP=33;DPB=51.9756;AC=2;AN=2;AF=0.25;RO=0;AO=4;PRO=24.6405;PAO=16.6405;QR=0;QA=104;PQR=846.236;PQA=571.236;SRF=0;SRR=0;SAF=1;SAR=3;SRP=0.0;SAP=5.18177;AB=0.121212;ABP=44.1367;RUN=1;RPP=5.18177;RPPR=0.0;RPL=1.0;RPR=3.0;EPP=3.0103;EPPR=0.0;DPRA=0.0;ODDS=8.5517;GTI=0;TYPE=del;CIGAR=1M13D27M;NUMALT=6;MEANALT=6.5;LEN=13;MQM=47.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr13 41228459 . TAAAAAAAAAAAAAA T 263.256 REJECT NS=2;DP=33;DPB=51.9756;AC=2;AN=3;AF=0.5;RO=0;AO=17;PRO=24.6405;PAO=15.3071;QR=0;QA=412;PQR=846.236;PQA=524.236;SRF=0;SRR=0;SAF=8;SAR=9;SRP=0.0;SAP=3.13803;AB=0.515152;ABP=3.0761;RUN=1;RPP=3.13803;RPPR=0.0;RPL=9.0;RPR=8.0;EPP=3.13803;EPPR=0.0;DPRA=0.0;ODDS=8.5517;GTI=0;TYPE=del;CIGAR=1M14D26M;NUMALT=6;MEANALT=6.5;LEN=14;MQM=48.3529;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.207;FS=1.373;M [...]
+chr13 41228459 . TAAAAAAAAAAAAAAA T 263.256 REJECT SOMATIC;NS=2;DP=33;DPB=51.9756;AC=1;AN=3;AF=0.0;RO=0;AO=5;PRO=24.6405;PAO=14.5571;QR=0;QA=99;PQR=846.236;PQA=493.986;SRF=0;SRR=0;SAF=1;SAR=4;SRP=0.0;SAP=6.91895;AB=0.151515;ABP=37.8197;RUN=1;RPP=3.44459;RPPR=0.0;RPL=2.0;RPR=3.0;EPP=6.91895;EPPR=0.0;DPRA=0.0;ODDS=8.5517;GTI=0;TYPE=del;CIGAR=1M15D25M;NUMALT=6;MEANALT=6.5;LEN=15;MQM=45.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr13 41228473 . AAAAAAAAAAAAAAAAAT A 263.256 REJECT SOMATIC;NS=2;DP=33;DPB=51.9756;AC=1;AN=3;AF=0.0;RO=0;AO=1;PRO=24.6405;PAO=5.85714;QR=0;QA=14;PQR=846.236;PQA=189.286;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.0833333;ABP=21.1059;RUN=1;RPP=5.18177;RPPR=0.0;RPL=0.0;RPR=1.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=8.5517;GTI=0;TYPE=del;CIGAR=15M17D9M;NUMALT=6;MEANALT=6.0;LEN=17;MQM=40.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr13 41228475 . AAAAAAAAAAAAAAATTA TTT 263.256 REJECT SOMATIC;NS=2;DP=33;DPB=51.9756;AC=1;AN=3;AF=0.0;RO=0;AO=1;PRO=24.6405;PAO=5.35714;QR=0;QA=14;PQR=846.236;PQA=170.786;SRF=0;SRR=0;SAF=0;SAR=1;SRP=0.0;SAP=5.18177;AB=0.0833333;ABP=21.1059;RUN=1;RPP=5.18177;RPPR=0.0;RPL=1.0;RPR=0.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=8.5517;GTI=0;TYPE=complex;CIGAR=1M15D17M1X7M;NUMALT=6;MEANALT=6.0;LEN=26;MQM=47.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO [...]
+chr13 41228504 . TGGTGGC GGGGGGG 2997.03 REJECT SOMATIC;NS=2;DP=124;DPB=130.143;AC=1;AN=3;AF=0.0;RO=13;AO=3;PRO=2.0;PAO=1.5;QR=377;QA=53;PQR=70.5;PQA=49.0;SRF=9;SRR=4;SAF=3;SAR=0;SRP=7.18621;SAP=9.52472;AB=0.0119048;ABP=176.831;RUN=1;RPP=3.73412;RPPR=7.18621;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=16.5402;DPRA=0.0;ODDS=18.3351;GTI=0;TYPE=complex;CIGAR=1X2M1X2M1X;NUMALT=2;MEANALT=4.5;LEN=7;MQM=48.3333;MQMR=56.3846;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO [...]
+chr13 41228510 . C G 2739.9 REJECT NS=2;DP=108;DPB=130.143;AC=3;AN=4;AF=0.75;RO=13;AO=102;PRO=2.0;PAO=6.5;QR=377;QA=3495;PQR=70.5;PQA=232.5;SRF=9;SRR=4;SAF=60;SAR=42;SRP=7.18621;SAP=9.90792;AB=0.761905;ABP=53.0576;RUN=1;RPP=48.0577;RPPR=7.18621;RPL=28.0;RPR=74.0;EPP=65.0889;EPPR=16.5402;DPRA=0.0;ODDS=18.3351;GTI=0;TYPE=snp;CIGAR=6M1X;NUMALT=2;MEANALT=4.5;LEN=1;MQM=54.9706;MQMR=56.3846;PAIRED=0.990196;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=1;BaseQRankSum=1.46;Dels=0.0;F [...]
+chr13 41228637 . CA C 1099.23 PASS DP=91;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.961;FS=6.6455;MLEAC=1;MLEAF=0.5;MQ=59.84;MQRankSum=-0.141;QD=12.24;RPA=15,14;RU=A;ReadPosRankSum=0.78;SOR=1.574;STR;ClippingRankSum=1.558 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:10,40:50:97.0:784,0,97:40:80:50:1:.:.:.:.:.:-0.480745 0/1:24,72:118:99.0:1489,0,139:72:75:96:.:1:.:.:.:.:-0.0152891
+chr13 41228650 . A G 3982.6949999999997 REJECT NS=2;DP=195;DPB=230.0;AC=3;AN=4;AF=0.75;RO=54;AO=176;PRO=0.0;PAO=0.0;QR=1900;QA=5868;PQR=0.0;PQA=0.0;SRF=35;SRR=19;SAF=117;SAR=59;SRP=13.3047;SAP=44.515;AB=0.685185;ABP=51.2652;RUN=1;RPP=136.457;RPPR=26.1727;RPL=36.0;RPR=140.0;EPP=3.05965;EPPR=4.45795;DPRA=0.0;ODDS=29.7781;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9716;MQMR=58.6481;PAIRED=0.960227;PAIREDR=0.962963;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.039;Dels=0.0;FS= [...]
+chr13 41229485 . C A 78.1639 REJECT NS=2;DP=103;DPB=182.5;AC=2;AN=2;AF=0.0;RO=29;AO=8;PRO=44.6167;PAO=19.7167;QR=976;QA=121;PQR=1503.65;PQA=651.767;SRF=20;SRR=9;SAF=1;SAR=7;SRP=12.0706;SAP=12.7819;AB=0.0776699;ABP=162.582;RUN=1;RPP=4.09604;RPPR=6.67934;RPL=3.0;RPR=5.0;EPP=3.0103;EPPR=4.88226;DPRA=0.0;ODDS=2.69455;GTI=0;TYPE=snp;CIGAR=1X29M;NUMALT=5;MEANALT=20.5;LEN=1;MQM=59.875;MQMR=60.0;PAIRED=1.0;PAIREDR=0.965517;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr13 41229485 . C CA 78.1639 REJECT NS=2;DP=103;DPB=182.5;AC=2;AN=2;AF=0.0;RO=29;AO=4;PRO=44.6167;PAO=35.6167;QR=976;QA=98;PQR=1503.65;PQA=1215.65;SRF=20;SRR=9;SAF=2;SAR=2;SRP=12.0706;SAP=3.0103;AB=0.038835;ABP=193.278;RUN=1;RPP=5.18177;RPPR=6.67934;RPL=1.0;RPR=3.0;EPP=5.18177;EPPR=4.88226;DPRA=0.0;ODDS=2.69455;GTI=0;TYPE=ins;CIGAR=1M1I29M;NUMALT=5;MEANALT=20.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.965517;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.3 [...]
+chr13 41229485 . CA C 78.1639 REJECT NS=2;DP=103;DPB=182.5;AC=2;AN=4;AF=0.5;RO=29;AO=14;PRO=44.6167;PAO=27.7833;QR=976;QA=409;PQR=1503.65;PQA=936.817;SRF=20;SRR=9;SAF=11;SAR=3;SRP=12.0706;SAP=12.937;AB=0.135922;ABP=121.598;RUN=1;RPP=8.59409;RPPR=6.67934;RPL=4.0;RPR=10.0;EPP=12.937;EPPR=4.88226;DPRA=0.0;ODDS=2.69455;GTI=0;TYPE=del;CIGAR=1M1D28M;NUMALT=5;MEANALT=20.5;LEN=1;MQM=62.1429;MQMR=60.0;PAIRED=1.0;PAIREDR=0.965517;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr13 41229485 . CAA C 78.1639 REJECT NS=2;DP=103;DPB=182.5;AC=2;AN=2;AF=0.0;RO=29;AO=7;PRO=44.6167;PAO=26.0333;QR=976;QA=184;PQR=1503.65;PQA=861.983;SRF=20;SRR=9;SAF=4;SAR=3;SRP=12.0706;SAP=3.32051;AB=0.0679612;ABP=170.003;RUN=1;RPP=5.80219;RPPR=6.67934;RPL=2.0;RPR=5.0;EPP=5.80219;EPPR=4.88226;DPRA=0.0;ODDS=2.69455;GTI=0;TYPE=del;CIGAR=1M2D27M;NUMALT=5;MEANALT=20.5;LEN=2;MQM=59.5714;MQMR=60.0;PAIRED=1.0;PAIREDR=0.965517;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr13 41229485 . CAAAA C 78.1639 REJECT NS=2;DP=103;DPB=182.5;AC=2;AN=2;AF=0.0;RO=29;AO=3;PRO=44.6167;PAO=21.2333;QR=976;QA=103;PQR=1503.65;PQA=707.133;SRF=20;SRR=9;SAF=3;SAR=0;SRP=12.0706;SAP=9.52472;AB=0.0291262;ABP=201.373;RUN=1;RPP=3.73412;RPPR=6.67934;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=4.88226;DPRA=0.0;ODDS=2.69455;GTI=0;TYPE=del;CIGAR=1M4D25M;NUMALT=5;MEANALT=20.5;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.965517;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr13 41229905 . A G 998.18 REJECT NS=2;DP=65;DPB=76.0;AC=3;AN=4;AF=0.75;RO=22;AO=53;PRO=0.0;PAO=0.0;QR=761;QA=1638;PQR=0.0;PQA=0.0;SRF=11;SRR=11;SAF=29;SAR=24;SRP=3.0103;SAP=4.03458;AB=0.592593;ABP=7.03155;RUN=1;RPP=3.37904;RPPR=3.40511;RPL=25.0;RPR=28.0;EPP=7.96781;EPPR=4.58955;DPRA=0.0;ODDS=14.0535;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.4;Dels=0.0;FS=0.0;HaplotypeScore=7.7433;MLEAC=1;ML [...]
+chr13 41230062 . C T 1532.03 PASS SOMATIC;NS=2;DP=197;DPB=197.0;AC=1;AN=3;AF=0.25;RO=139;AO=58;PRO=0.0;PAO=0.0;QR=5211;QA=2253;PQR=0.0;PQA=0.0;SRF=114;SRR=25;SAF=48;SAR=10;SRP=126.753;SAP=57.0725;AB=0.411348;ABP=12.6356;RUN=1;RPP=5.40641;RPPR=4.90057;RPL=25.0;RPR=33.0;EPP=8.40154;EPPR=11.2744;DPRA=2.51786;ODDS=35.8861;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.982759;PAIREDR=0.985612;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.121;Dels=0.0;FS=0 [...]
+chr13 41230141 . T C 7738.445000000001 REJECT NS=2;DP=340;DPB=381.0;AC=3;AN=4;AF=0.75;RO=112;AO=269;PRO=0.0;PAO=0.0;QR=4407;QA=10286;PQR=0.0;PQA=0.0;SRF=68;SRR=44;SAF=162;SAR=107;SRP=14.1779;SAP=27.4293;AB=0.626667;ABP=44.8184;RUN=1;RPP=9.79918;RPPR=28.1373;RPL=120.0;RPR=149.0;EPP=3.01837;EPPR=3.32051;DPRA=0.0;ODDS=51.4803;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.814;Dels=0.0;FS=0.7375;Haplo [...]
+chr13 41230970 . A AT 143.548 REJECT NS=2;DP=130;DPB=194.143;AC=2;AN=2;AF=0.0;RO=87;AO=15;PRO=51.3333;PAO=42.3333;QR=3207;QA=500;PQR=1827.33;PQA=1477.33;SRF=29;SRR=58;SAF=5;SAR=10;SRP=24.0012;SAP=6.62942;AB=0.115385;ABP=170.047;RUN=1;RPP=3.15506;RPPR=12.0207;RPL=7.0;RPR=8.0;EPP=10.1038;EPPR=8.62618;DPRA=0.0;ODDS=0.237129;GTI=1;TYPE=ins;CIGAR=1M1I20M;NUMALT=2;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=59.7701;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr13 41230970 . AT A 143.548 REJECT NS=2;DP=130;DPB=194.143;AC=2;AN=4;AF=0.5;RO=87;AO=16;PRO=51.3333;PAO=39.3333;QR=3207;QA=560;PQR=1827.33;PQA=1399.33;SRF=29;SRR=58;SAF=5;SAR=11;SRP=24.0012;SAP=7.89611;AB=0.123077;ABP=163.432;RUN=1;RPP=5.18177;RPPR=12.0207;RPL=6.0;RPR=10.0;EPP=3.55317;EPPR=8.62618;DPRA=0.0;ODDS=0.237129;GTI=1;TYPE=del;CIGAR=1M1D19M;NUMALT=2;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=59.7701;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr13 41231456 . C T 431.281 REJECT NS=2;DP=89;DPB=143.292;AC=2;AN=2;AF=0.25;RO=19;AO=29;PRO=36.4167;PAO=12.0833;QR=665;QA=807;PQR=1286.25;PQA=302.25;SRF=5;SRR=14;SAF=0;SAR=29;SRP=12.2676;SAP=65.983;AB=0.325843;ABP=26.4573;RUN=1;RPP=19.8579;RPPR=44.2683;RPL=7.0;RPR=22.0;EPP=19.8579;EPPR=12.2676;DPRA=0.0;ODDS=3.41734;GTI=0;TYPE=snp;CIGAR=1X23M;NUMALT=3;MEANALT=8.5;LEN=1;MQM=53.4828;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-3.832;Dels=0. [...]
+chr13 41231456 . C CT 431.281 REJECT NS=2;DP=89;DPB=143.292;AC=2;AN=3;AF=0.5;RO=19;AO=22;PRO=36.4167;PAO=38.4167;QR=665;QA=554;PQR=1286.25;PQA=1336.25;SRF=5;SRR=14;SAF=6;SAR=16;SRP=12.2676;SAP=12.8806;AB=0.247191;ABP=52.4174;RUN=1;RPP=12.8806;RPPR=44.2683;RPL=16.0;RPR=6.0;EPP=3.40511;EPPR=12.2676;DPRA=0.0;ODDS=3.41734;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=3;MEANALT=8.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.067;FS=3.802;MLEA [...]
+chr13 41231456 . CT C 431.281 REJECT SOMATIC;NS=2;DP=89;DPB=143.292;AC=1;AN=3;AF=0.0;RO=19;AO=6;PRO=36.4167;PAO=28.0833;QR=665;QA=145;PQR=1286.25;PQA=971.25;SRF=5;SRR=14;SAF=1;SAR=5;SRP=12.2676;SAP=8.80089;AB=0.0674157;ABP=147.669;RUN=1;RPP=3.0103;RPPR=44.2683;RPL=3.0;RPR=3.0;EPP=4.45795;EPPR=12.2676;DPRA=0.0;ODDS=3.41734;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=3;MEANALT=8.5;LEN=1;MQM=56.6667;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr13 41231542 . A G 1790.155 REJECT NS=2;DP=77;DPB=90.0;AC=3;AN=4;AF=0.75;RO=18;AO=72;PRO=0.0;PAO=0.0;QR=651;QA=2465;PQR=0.0;PQA=0.0;SRF=8;SRR=10;SAF=33;SAR=39;SRP=3.49285;SAP=4.09604;AB=0.723077;ABP=31.1058;RUN=1;RPP=4.9405;RPPR=4.9405;RPL=40.0;RPR=32.0;EPP=4.09604;EPPR=3.0103;DPRA=0.0;ODDS=15.6383;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.459;Dels=0.0;FS=0.0;HaplotypeScore=5.7512;MLEAC=1;M [...]
+chr13 41232340 . G A 2008.48 REJECT NS=2;DP=351;DPB=400.0;AC=2;AN=4;AF=0.5;RO=307;AO=93;PRO=0.0;PAO=0.0;QR=11697;QA=3505;PQR=0.0;PQA=0.0;SRF=135;SRR=172;SAF=43;SAR=50;SRP=12.6935;SAP=4.15441;AB=0.2325;ABP=251.622;RUN=1;RPP=8.26386;RPPR=9.80765;RPL=39.0;RPR=54.0;EPP=3.59403;EPPR=13.7686;DPRA=0.0;ODDS=87.7174;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993485;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4995;Dels=0.0;FS=3.545;HaplotypeScore=8. [...]
+chr13 41233345 . G A 422.186 REJECT NS=2;DP=37;DPB=42.0;AC=3;AN=4;AF=0.75;RO=17;AO=25;PRO=0.0;PAO=0.0;QR=438;QA=722;PQR=0.0;PQA=0.0;SRF=15;SRR=2;SAF=25;SAR=0;SRP=24.5973;SAP=57.2971;AB=0.46875;ABP=3.28173;RUN=1;RPP=17.6895;RPPR=13.3567;RPL=6.0;RPR=19.0;EPP=17.6895;EPPR=13.3567;DPRA=0.0;ODDS=7.2239;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=55.12;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.359;Dels=0.0;FS=1.5675;HaplotypeScore=5.799;MLEAC=1;ML [...]
+chr13 41233451 . C CA 80.8395 REJECT NS=2;DP=44;DPB=133.429;AC=2;AN=2;AF=0.0;RO=4;AO=3;PRO=42.9;PAO=41.9;QR=135;QA=90;PQR=1525.02;PQA=1466.52;SRF=4;SRR=0;SAF=3;SAR=0;SRP=11.6962;SAP=9.52472;AB=0.0833333;ABP=57.2971;RUN=1;RPP=9.52472;RPPR=5.18177;RPL=0.0;RPR=3.0;EPP=9.52472;EPPR=5.18177;DPRA=0.0;ODDS=2.0859;GTI=0;TYPE=ins;CIGAR=1M1I41M;NUMALT=4;MEANALT=24.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICO [...]
+chr13 41233451 . C CAA 80.8395 REJECT NS=2;DP=44;DPB=133.429;AC=2;AN=4;AF=0.5;RO=4;AO=5;PRO=42.9;PAO=41.9;QR=135;QA=129;PQR=1525.02;PQA=1466.52;SRF=4;SRR=0;SAF=3;SAR=2;SRP=11.6962;SAP=3.44459;AB=0.113636;ABP=60.0608;RUN=1;RPP=13.8677;RPPR=5.18177;RPL=0.0;RPR=5.0;EPP=3.44459;EPPR=5.18177;DPRA=0.0;ODDS=2.0859;GTI=0;TYPE=ins;CIGAR=1M2I41M;NUMALT=4;MEANALT=15.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.294;FS=0.0;MLEAC=1;ML [...]
+chr13 41233451 . CA C 80.8395 REJECT NS=2;DP=44;DPB=133.429;AC=2;AN=2;AF=0.0;RO=4;AO=2;PRO=42.9;PAO=38.9;QR=135;QA=66;PQR=1525.02;PQA=1382.35;SRF=4;SRR=0;SAF=1;SAR=1;SRP=11.6962;SAP=3.0103;AB=0.0555556;ABP=64.7766;RUN=1;RPP=7.35324;RPPR=5.18177;RPL=0.0;RPR=2.0;EPP=3.0103;EPPR=5.18177;DPRA=0.0;ODDS=2.0859;GTI=0;TYPE=del;CIGAR=1M1D40M;NUMALT=4;MEANALT=24.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV: [...]
+chr13 41233451 . CAAAA C 80.8395 REJECT NS=2;DP=44;DPB=133.429;AC=2;AN=2;AF=0.0;RO=4;AO=2;PRO=42.9;PAO=37.4;QR=135;QA=48;PQR=1525.02;PQA=1329.6;SRF=4;SRR=0;SAF=1;SAR=1;SRP=11.6962;SAP=3.0103;AB=0.0555556;ABP=64.7766;RUN=1;RPP=3.0103;RPPR=5.18177;RPL=1.0;RPR=1.0;EPP=7.35324;EPPR=5.18177;DPRA=0.0;ODDS=2.0859;GTI=0;TYPE=del;CIGAR=1M4D37M;NUMALT=4;MEANALT=24.0;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICO [...]
+chr13 41233469 . G A 162.77 PASS SOMATIC;DP=128;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-0.044;Dels=0.02;FS=6.75;HaplotypeScore=28.275;MLEAC=1;MLEAF=0.5;MQ=56.61;MQRankSum=-3.209;QD=1.27;ReadPosRankSum=-0.478;SOR=2.142 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.480745 0/1:108,15:126:99.0:191,0,2710:15:12:123:.:1:.:.:.:.:-0.0152891
+chr13 41233505 . G C 5282.73 REJECT NS=2;DP=256;DPB=297.0;AC=3;AN=4;AF=0.75;RO=88;AO=207;PRO=0.0;PAO=0.0;QR=2985;QA=7721;PQR=0.0;PQA=0.0;SRF=62;SRR=26;SAF=163;SAR=44;SRP=34.9902;SAP=151.562;AB=0.6;ABP=22.5536;RUN=1;RPP=261.583;RPPR=28.2783;RPL=25.0;RPR=182.0;EPP=78.802;EPPR=6.56362;DPRA=0.0;ODDS=45.8119;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.7343;MQMR=59.2841;PAIRED=0.937198;PAIREDR=0.965909;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.27;Dels=0.0;FS=6.1475;HaplotypeSc [...]
+chr13 41233601 . A AT 200.988 REJECT NS=2;DP=305;DPB=363.0;AC=2;AN=2;AF=0.0;RO=232;AO=24;PRO=52.6667;PAO=40.6667;QR=8637;QA=806;PQR=1861.67;PQA=1424.67;SRF=117;SRR=115;SAF=11;SAR=13;SRP=3.04774;SAP=3.37221;AB=0.0786885;ABP=473.252;RUN=1;RPP=4.45795;RPPR=6.75422;RPL=14.0;RPR=10.0;EPP=3.37221;EPPR=3.04774;DPRA=0.0;ODDS=14.1757;GTI=0;TYPE=ins;CIGAR=1M1I18M;NUMALT=2;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.958333;PAIREDR=0.956897;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR: [...]
+chr13 41233601 . AT A 200.988 REJECT NS=2;DP=305;DPB=363.0;AC=2;AN=4;AF=0.5;RO=232;AO=31;PRO=52.6667;PAO=36.6667;QR=8637;QA=1143;PQR=1861.67;PQA=1274.67;SRF=117;SRR=115;SAF=17;SAR=14;SRP=3.04774;SAP=3.64073;AB=0.101639;ABP=423.414;RUN=1;RPP=8.68415;RPPR=6.75422;RPL=11.0;RPR=20.0;EPP=3.64073;EPPR=3.04774;DPRA=0.0;ODDS=14.1757;GTI=0;TYPE=del;CIGAR=1M1D17M;NUMALT=2;MEANALT=7.5;LEN=1;MQM=60.6452;MQMR=60.0;PAIRED=0.967742;PAIREDR=0.956897;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum [...]
+chr13 41233931 . A G 8845.585 REJECT NS=2;DP=389;DPB=456.0;AC=3;AN=4;AF=0.75;RO=128;AO=328;PRO=0.0;PAO=0.0;QR=4936;QA=12487;PQR=0.0;PQA=0.0;SRF=55;SRR=73;SAF=148;SAR=180;SRP=8.50684;SAP=9.78953;AB=0.604938;ABP=34.0007;RUN=1;RPP=3.96363;RPPR=6.33537;RPL=170.0;RPR=158.0;EPP=3.96363;EPPR=4.09604;DPRA=0.0;ODDS=83.2021;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.981707;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.861;Dels=0.0;FS=0.678;HaplotypeSc [...]
+chr13 41234397 . T C 10312.635 REJECT NS=2;DP=452;DPB=508.0;AC=3;AN=4;AF=0.75;RO=147;AO=358;PRO=0.0;PAO=0.0;QR=5683;QA=13766;PQR=0.0;PQA=0.0;SRF=71;SRR=76;SAF=171;SAR=187;SRP=3.3796;SAP=4.56308;AB=0.623116;ABP=55.4093;RUN=1;RPP=4.97554;RPPR=4.7977;RPL=188.0;RPR=170.0;EPP=4.56308;EPPR=7.27939;DPRA=0.0;ODDS=69.6039;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99162;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.567;Dels=0.0;FS=0.3905;HaplotypeSco [...]
+chr13 41235085 . AAACAAC A 2655.11 REJECT NS=2;DP=125;DPB=210.261;AC=3;AN=4;AF=0.75;RO=27;AO=89;PRO=113.0;PAO=113.0;QR=1024;QA=3082;PQR=3980.0;PQA=3940.0;SRF=17;SRR=10;SAF=65;SAR=24;SRP=6.95112;SAP=44.0243;AB=0.613636;ABP=12.8806;RUN=1;RPP=8.49998;RPPR=5.02092;RPL=37.0;RPR=52.0;EPP=3.0347;EPPR=3.09072;DPRA=0.0;ODDS=23.9828;GTI=0;TYPE=del;CIGAR=1M6D39M;NUMALT=1;MEANALT=5.0;LEN=6;MQM=60.4045;MQMR=60.0;PAIRED=0.988764;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.135;FS=1.5135;ML [...]
+chr13 41235213 . C T 9950.685000000001 REJECT NS=2;DP=430;DPB=498.0;AC=3;AN=4;AF=0.75;RO=137;AO=361;PRO=0.0;PAO=0.0;QR=5219;QA=13823;PQR=0.0;PQA=0.0;SRF=76;SRR=61;SAF=193;SAR=168;SRP=6.57659;SAP=6.76977;AB=0.62259;ABP=50.3939;RUN=1;RPP=6.19232;RPPR=4.29416;RPL=192.0;RPR=169.0;EPP=10.3789;EPPR=10.0002;DPRA=0.0;ODDS=85.2222;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9668;MQMR=60.0;PAIRED=0.99169;PAIREDR=0.992701;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.952;Dels=0.0;FS=0. [...]
+chr13 41235418 . C CT 318.026 REJECT NS=2;DP=246;DPB=305.125;AC=2;AN=4;AF=0.5;RO=177;AO=31;PRO=46.0;PAO=41.0;QR=6530;QA=943;PQR=1671.0;PQA=1462.0;SRF=54;SRR=123;SAF=8;SAR=23;SRP=61.4192;SAP=18.771;AB=0.126016;ABP=301.861;RUN=1;RPP=8.68415;RPPR=21.6702;RPL=20.0;RPR=11.0;EPP=3.64073;EPPR=23.6332;DPRA=0.0;ODDS=18.0607;GTI=0;TYPE=ins;CIGAR=1M1I15M;NUMALT=2;MEANALT=9.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.967742;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-2.156;FS=1.446;M [...]
+chr13 41235418 . CT C 318.026 REJECT NS=2;DP=246;DPB=305.125;AC=2;AN=2;AF=0.0;RO=177;AO=15;PRO=46.0;PAO=33.0;QR=6530;QA=499;PQR=1671.0;PQA=1161.0;SRF=54;SRR=123;SAF=3;SAR=12;SRP=61.4192;SAP=14.7363;AB=0.0609756;ABP=414.849;RUN=1;RPP=6.62942;RPPR=21.6702;RPL=10.0;RPR=5.0;EPP=3.15506;EPPR=23.6332;DPRA=0.0;ODDS=18.0607;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=2;MEANALT=9.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr13 41235587 . C T 892.502 REJECT NS=2;DP=119;DPB=142.0;AC=2;AN=4;AF=0.5;RO=102;AO=40;PRO=0.0;PAO=0.0;QR=3835;QA=1491;PQR=0.0;PQA=0.0;SRF=48;SRR=54;SAF=21;SAR=19;SRP=3.7767;SAP=3.22745;AB=0.28169;ABP=61.793;RUN=1;RPP=4.96463;RPPR=3.09546;RPL=23.0;RPR=17.0;EPP=16.9077;EPPR=7.18293;DPRA=0.0;ODDS=46.8925;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.902;PAIRED=0.975;PAIREDR=0.980392;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1;Dels=0.0;FS=0.577;HaplotypeScore=3.930 [...]
+chr13 41238944 . ACGCCAC A 2037.39 REJECT NS=2;DP=116;DPB=137.385;AC=3;AN=4;AF=0.5;RO=34;AO=79;PRO=36.8333;PAO=26.8333;QR=1282;QA=2718;PQR=1331.83;PQA=953.333;SRF=12;SRR=22;SAF=28;SAR=51;SRP=9.39698;SAP=17.5509;AB=0.681034;ABP=36.0317;RUN=1;RPP=3.25768;RPPR=3.26577;RPL=38.0;RPR=41.0;EPP=3.69747;EPPR=5.30951;DPRA=0.0;ODDS=7.74891;GTI=0;TYPE=del;CIGAR=1M6D19M;NUMALT=2;MEANALT=2.0;LEN=6;MQM=60.2532;MQMR=60.0;PAIRED=0.974684;PAIREDR=0.970588;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;EN [...]
+chr13 41238967 . AC CG 2037.39 REJECT NS=2;DP=116;DPB=137.385;AC=2;AN=2;AF=0.25;RO=34;AO=2;PRO=36.8333;PAO=18.3333;QR=1282;QA=78;PQR=1331.83;PQA=635.833;SRF=12;SRR=22;SAF=1;SAR=1;SRP=9.39698;SAP=3.0103;AB=0.0571429;ABP=62.6327;RUN=1;RPP=7.35324;RPPR=3.26577;RPL=2.0;RPR=0.0;EPP=3.0103;EPPR=5.30951;DPRA=0.0;ODDS=7.74891;GTI=0;TYPE=mnp;CIGAR=23M2X1M;NUMALT=2;MEANALT=3.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.970588;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr13 41239178 . A C 3883.4849999999997 REJECT NS=2;DP=185;DPB=212.0;AC=3;AN=4;AF=0.75;RO=67;AO=145;PRO=0.0;PAO=0.0;QR=2576;QA=5465;PQR=0.0;PQA=0.0;SRF=43;SRR=24;SAF=77;SAR=68;SRP=14.7103;SAP=4.22333;AB=0.578616;ABP=11.546;RUN=1;RPP=6.37983;RPPR=3.82055;RPL=65.0;RPR=80.0;EPP=6.37983;EPPR=5.63551;DPRA=0.0;ODDS=33.2072;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993103;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.123;Dels=0.0;FS=4.9545;Haplot [...]
+chr13 42701717 . A G 1248.175 REJECT NS=2;DP=304;DPB=344.0;AC=2;AN=4;AF=0.5;RO=276;AO=67;PRO=0.0;PAO=0.0;QR=10624;QA=2511;PQR=0.0;PQA=0.0;SRF=109;SRR=167;SAF=24;SAR=43;SRP=29.4771;SAP=14.7103;AB=0.194767;ABP=281.388;RUN=1;RPP=5.63551;RPPR=39.3903;RPL=38.0;RPR=29.0;EPP=10.3026;EPPR=14.3712;DPRA=0.0;ODDS=69.5768;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.56;Dels=0.0;FS=1.279;HaplotypeScore=1.9577 [...]
+chr13 42701739 . A T 8058.5650000000005 REJECT NS=2;DP=216;DPB=248.0;AC=4;AN=4;AF=1.0;RO=0;AO=248;PRO=0.0;PAO=0.0;QR=0;QA=9494;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=89;SAR=159;SRP=0.0;SAP=45.9144;AB=0.0;ABP=0.0;RUN=1;RPP=174.627;RPPR=0.0;RPL=194.0;RPR=54.0;EPP=4.72646;EPPR=0.0;DPRA=0.0;ODDS=44.2566;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9552;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.465;SO [...]
+chr13 42703682 . T C 7037.41 REJECT NS=2;DP=318;DPB=358.0;AC=3;AN=4;AF=0.75;RO=102;AO=256;PRO=0.0;PAO=0.0;QR=3930;QA=9493;PQR=0.0;PQA=0.0;SRF=75;SRR=27;SAF=178;SAR=78;SRP=52.06;SAP=87.8334;AB=0.634409;ABP=46.79;RUN=1;RPP=27.7447;RPPR=4.37279;RPL=101.0;RPR=155.0;EPP=7.11574;EPPR=22.1704;DPRA=0.0;ODDS=50.1624;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992188;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.708;Dels=0.0;FS=1.525;HaplotypeScore=6. [...]
+chr13 42729441 . C T 5288.555 REJECT NS=2;DP=302;DPB=349.0;AC=2;AN=4;AF=0.5;RO=160;AO=189;PRO=0.0;PAO=0.0;QR=6174;QA=7343;PQR=0.0;PQA=0.0;SRF=104;SRR=56;SAF=125;SAR=64;SRP=34.2795;SAP=45.7619;AB=0.541547;ABP=8.24299;RUN=1;RPP=10.1911;RPPR=29.2851;RPL=82.0;RPR=107.0;EPP=14.0515;EPPR=20.5992;DPRA=0.0;ODDS=247.396;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7735;Dels=0.0;FS=1.524;HaplotypeScore=5.8 [...]
+chr13 42764564 . C G 5591.07 REJECT NS=2;DP=349;DPB=398.0;AC=2;AN=4;AF=0.5;RO=199;AO=198;PRO=0.0;PAO=0.0;QR=7579;QA=7643;PQR=0.0;PQA=0.0;SRF=138;SRR=61;SAF=126;SAR=72;SRP=67.7071;SAP=34.9902;AB=0.497487;ABP=3.03212;RUN=1;RPP=3.05417;RPPR=3.89417;RPL=100.0;RPR=98.0;EPP=10.424;EPPR=7.82246;DPRA=0.0;ODDS=293.639;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994949;PAIREDR=0.98995;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.599;Dels=0.0;FS=7.273;HaplotypeSco [...]
+chr13 42772717 . G T 5181.91 REJECT NS=2;DP=326;DPB=373.0;AC=2;AN=4;AF=0.5;RO=187;AO=186;PRO=0.0;PAO=0.0;QR=6765;QA=7011;PQR=0.0;PQA=0.0;SRF=47;SRR=140;SAF=67;SAR=119;SRP=103.444;SAP=34.5784;AB=0.49866;ABP=3.01612;RUN=1;RPP=34.5784;RPPR=10.2679;RPL=119.0;RPR=67.0;EPP=3.43058;EPPR=7.20229;DPRA=0.0;ODDS=273.41;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.1075;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.8075;Dels=0.0;FS=9.355;HaplotypeScore=37. [...]
+chr13 42793479 . G A 5465.8 REJECT NS=2;DP=335;DPB=381.0;AC=2;AN=4;AF=0.5;RO=188;AO=193;PRO=0.0;PAO=0.0;QR=7111;QA=7430;PQR=0.0;PQA=0.0;SRF=73;SRR=115;SAF=76;SAR=117;SRP=23.3852;SAP=21.9235;AB=0.506562;ABP=3.15279;RUN=1;RPP=3.92164;RPPR=4.16534;RPL=101.0;RPR=92.0;EPP=16.793;EPPR=14.8379;DPRA=0.0;ODDS=294.111;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.404;Dels=0.0;FS=4.412;HaplotypeScore=3.9236; [...]
+chr13 42803341 . T C 9240.73 REJECT NS=2;DP=247;DPB=284.0;AC=4;AN=4;AF=1.0;RO=0;AO=284;PRO=0.0;PAO=0.0;QR=0;QA=10864;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=69;SAR=215;SRP=0.0;SAP=165.993;AB=0.0;ABP=0.0;RUN=1;RPP=40.4758;RPPR=0.0;RPL=177.0;RPR=107.0;EPP=3.49965;EPPR=0.0;DPRA=0.0;ODDS=49.9136;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.985915;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9973;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.41;SOR=2.3 [...]
+chr13 48797661 . T C 1456.425 REJECT NS=2;DP=341;DPB=391.0;AC=2;AN=4;AF=0.5;RO=309;AO=82;PRO=0.0;PAO=0.0;QR=11943;QA=3098;PQR=0.0;PQA=0.0;SRF=141;SRR=168;SAF=46;SAR=36;SRP=8.13329;SAP=5.65844;AB=0.209719;ABP=289.184;RUN=1;RPP=6.82362;RPPR=6.7278;RPL=35.0;RPR=47.0;EPP=3.0103;EPPR=7.40244;DPRA=0.0;ODDS=147.421;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990291;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.8955;Dels=0.0;FS=7.187;HaplotypeScore=0 [...]
+chr13 48919358 . T G 8654.16 REJECT NS=2;DP=231;DPB=266.0;AC=4;AN=4;AF=1.0;RO=0;AO=266;PRO=0.0;PAO=0.0;QR=0;QA=10153;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=82;SAR=184;SRP=0.0;SAP=87.9426;AB=0.0;ABP=0.0;RUN=1;RPP=112.857;RPPR=0.0;RPL=191.0;RPR=75.0;EPP=5.10014;EPPR=0.0;DPRA=0.0;ODDS=46.7255;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996241;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9993;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.945;SOR=1.7 [...]
+chr13 48934289 . T C 1359.25 REJECT NS=2;DP=216;DPB=252.0;AC=2;AN=4;AF=0.5;RO=190;AO=62;PRO=0.0;PAO=0.0;QR=7363;QA=2381;PQR=0.0;PQA=0.0;SRF=84;SRR=106;SAF=29;SAR=33;SRP=8.54184;SAP=3.57068;AB=0.246032;ABP=144.19;RUN=1;RPP=48.4011;RPPR=151.539;RPL=49.0;RPR=13.0;EPP=3.15039;EPPR=10.7362;DPRA=0.0;ODDS=61.3717;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994737;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.74;Dels=0.0;FS=8.039;HaplotypeScore=3.888 [...]
+chr13 49039122 . G T 1227.9 REJECT NS=2;DP=124;DPB=132.8;AC=2;AN=2;AF=0.0;RO=93;AO=5;PRO=12.5;PAO=9.5;QR=3139;QA=99;PQR=254.5;PQA=149.5;SRF=71;SRR=22;SAF=5;SAR=0;SRP=59.0716;SAP=13.8677;AB=0.0403226;ABP=230.595;RUN=1;RPP=3.44459;RPPR=187.959;RPL=2.0;RPR=3.0;EPP=3.44459;EPPR=50.2924;DPRA=0.0;ODDS=93.0607;GTI=0;TYPE=snp;CIGAR=1M1X3M;NUMALT=2;MEANALT=3.5;LEN=1;MQM=60.0;MQMR=60.1075;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV: [...]
+chr13 49039122 . GTTC TTTT 1227.9 REJECT NS=2;DP=124;DPB=132.8;AC=2;AN=4;AF=0.5;RO=93;AO=21;PRO=12.5;PAO=0.0;QR=3139;QA=346;PQR=254.5;PQA=0.0;SRF=71;SRR=22;SAF=21;SAR=0;SRP=59.0716;SAP=48.6112;AB=0.169355;ABP=120.76;RUN=1;RPP=5.59539;RPPR=187.959;RPL=13.0;RPR=8.0;EPP=5.59539;EPPR=50.2924;DPRA=0.0;ODDS=93.0607;GTI=0;TYPE=complex;CIGAR=1M1X2M1X;NUMALT=2;MEANALT=3.5;LEN=5;MQM=56.9524;MQMR=60.1075;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr13 49051481 . T A 1639.145 REJECT NS=2;DP=340;DPB=390.0;AC=2;AN=4;AF=0.5;RO=304;AO=86;PRO=0.0;PAO=0.0;QR=11841;QA=3245;PQR=0.0;PQA=0.0;SRF=188;SRR=116;SAF=53;SAR=33;SRP=40.0396;SAP=13.1102;AB=0.220513;ABP=267.618;RUN=1;RPP=13.1102;RPPR=18.1249;RPL=33.0;RPR=53.0;EPP=5.53527;EPPR=9.439;DPRA=0.0;ODDS=119.742;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9419;MQMR=60.0;PAIRED=0.965116;PAIREDR=0.986842;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.487;Dels=0.0;FS=3.9595;Haploty [...]
+chr13 49152343 . C CT 41.73 PASS DP=76;AC=1;AN=4;AF=0.5;BaseQRankSum=-1.657;FS=3.217;MLEAC=1;MLEAF=0.5;MQ=59.78;MQRankSum=1.73;QD=0.55;ReadPosRankSum=-1.587;SOR=1.227;ClippingRankSum=-0.736 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:30,11:41:79.0:79,0,481:11:27:41:1:.:.:.:.:.:-3.56049e-05 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0152891
+chr13 49153728 . G A 13340.0 REJECT NS=2;DP=352;DPB=393.0;AC=4;AN=4;AF=1.0;RO=0;AO=393;PRO=0.0;PAO=0.0;QR=0;QA=15019;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=220;SAR=173;SRP=0.0;SAP=15.2159;AB=0.0;ABP=0.0;RUN=1;RPP=3.01583;RPPR=0.0;RPL=196.0;RPR=197.0;EPP=14.1992;EPPR=0.0;DPRA=0.0;ODDS=55.5017;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994911;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8659;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.485;SOR=0 [...]
+chr13 49154010 . T C 3504.16 PASS SOMATIC;NS=2;DP=430;DPB=430.0;AC=1;AN=3;AF=0.25;RO=297;AO=133;PRO=0.0;PAO=0.0;QR=11254;QA=4963;PQR=0.0;PQA=0.0;SRF=144;SRR=153;SAF=77;SAR=56;SRP=3.60252;SAP=10.2104;AB=0.400602;ABP=31.5011;RUN=1;RPP=3.02663;RPPR=6.87801;RPL=67.0;RPR=66.0;EPP=3.02663;EPPR=3.19308;DPRA=3.38776;ODDS=62.0977;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986532;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.879;Dels=0.0;FS=5.0 [...]
+chr13 49154057 . G GA 1802.64 REJECT NS=2;DP=401;DPB=460.231;AC=2;AN=4;AF=0.5;RO=293;AO=88;PRO=61.5;PAO=54.5;QR=11072;QA=3237;PQR=2170.5;PQA=1908.5;SRF=159;SRR=134;SAF=52;SAR=36;SRP=7.64228;SAP=9.32731;AB=0.219451;ABP=277.152;RUN=1;RPP=4.58955;RPPR=3.6106;RPL=40.0;RPR=48.0;EPP=28.2783;EPPR=5.15213;DPRA=0.0;ODDS=134.838;GTI=0;TYPE=ins;CIGAR=1M1I12M;NUMALT=1;MEANALT=6.0;LEN=1;MQM=60.1136;MQMR=60.0;PAIRED=0.988636;PAIREDR=0.989761;technology.ILLUMINA=1.0;BaseQRankSum=0.323;FS=1.586;MLEAC=1; [...]
+chr13 49504810 . T C 2355.11 PASS SOMATIC;NS=2;DP=305;DPB=305.0;AC=1;AN=3;AF=0.25;RO=217;AO=88;PRO=0.0;PAO=0.0;QR=8380;QA=3389;PQR=0.0;PQA=0.0;SRF=71;SRR=146;SAF=27;SAR=61;SRP=59.2985;SAP=31.5356;AB=0.413146;ABP=16.9669;RUN=1;RPP=38.6422;RPPR=29.0379;RPL=63.0;RPR=25.0;EPP=3.40511;EPPR=10.3052;DPRA=2.31522;ODDS=58.3846;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995392;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.2;Dels=0.0;FS=0.0;Hapl [...]
+chr13 52506048 . A G 7890.805 REJECT NS=2;DP=217;DPB=248.0;AC=4;AN=4;AF=1.0;RO=0;AO=248;PRO=0.0;PAO=0.0;QR=0;QA=9363;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=157;SAR=91;SRP=0.0;SAP=41.1512;AB=0.0;ABP=0.0;RUN=1;RPP=160.232;RPPR=0.0;RPL=57.0;RPR=191.0;EPP=8.05372;EPPR=0.0;DPRA=0.0;ODDS=43.6774;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995968;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.01;FS=0.0;HaplotypeScore=6.8232;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.205;SOR=1. [...]
+chr13 52506159 . T C 2817.6 PASS SOMATIC;NS=2;DP=360;DPB=360.0;AC=1;AN=3;AF=0.25;RO=254;AO=106;PRO=0.0;PAO=0.0;QR=9859;QA=4019;PQR=0.0;PQA=0.0;SRF=93;SRR=161;SAF=30;SAR=76;SRP=42.5414;SAP=46.3578;AB=0.410853;ABP=20.8197;RUN=1;RPP=5.05886;RPPR=47.3289;RPL=58.0;RPR=48.0;EPP=3.09224;EPPR=7.14807;DPRA=2.52941;ODDS=64.6443;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.154;Dels=0.0;FS=9.622;Hapl [...]
+chr13 54018755 . A C 6269.785 REJECT NS=2;DP=288;DPB=327.0;AC=3;AN=4;AF=0.75;RO=98;AO=229;PRO=0.0;PAO=0.0;QR=3689;QA=8644;PQR=0.0;PQA=0.0;SRF=24;SRR=74;SAF=57;SAR=172;SRP=58.405;SAP=128.415;AB=0.612;ABP=30.2492;RUN=1;RPP=78.1205;RPPR=49.8964;RPL=159.0;RPR=70.0;EPP=5.75072;EPPR=3.09893;DPRA=0.0;ODDS=45.4354;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991266;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.628;Dels=0.0;FS=0.897;HaplotypeScore=3.89 [...]
+chr13 57019064 . C T 2524.08 REJECT NS=2;DP=375;DPB=432.0;AC=2;AN=4;AF=0.5;RO=313;AO=119;PRO=0.0;PAO=0.0;QR=12140;QA=4522;PQR=0.0;PQA=0.0;SRF=154;SRR=159;SAF=69;SAR=50;SRP=3.18374;SAP=9.59771;AB=0.275463;ABP=192.19;RUN=1;RPP=5.21827;RPPR=4.57126;RPL=54.0;RPR=65.0;EPP=6.09416;EPPR=27.1601;DPRA=0.0;ODDS=217.05;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991597;PAIREDR=0.996805;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1755;Dels=0.0;FS=7.366;HaplotypeS [...]
+chr13 57019098 . G A 9223.28 REJECT NS=2;DP=367;DPB=419.0;AC=2;AN=4;AF=0.5;RO=113;AO=306;PRO=0.0;PAO=0.0;QR=4283;QA=11634;PQR=0.0;PQA=0.0;SRF=58;SRR=55;SAF=121;SAR=185;SRP=3.18325;SAP=32.0768;AB=0.73031;ABP=196.054;RUN=1;RPP=3.0103;RPPR=3.18325;RPL=153.0;RPR=153.0;EPP=18.0261;EPPR=3.02952;DPRA=0.0;ODDS=230.756;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996732;PAIREDR=0.982301;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.634;Dels=0.0;FS=7.2675;Haplotype [...]
+chr13 67504048 . T G 5280.22 REJECT NS=2;DP=328;DPB=373.0;AC=2;AN=4;AF=0.5;RO=184;AO=189;PRO=0.0;PAO=0.0;QR=7076;QA=7176;PQR=0.0;PQA=0.0;SRF=115;SRR=69;SAF=122;SAR=67;SRP=27.9822;SAP=37.7653;AB=0.506702;ABP=3.15584;RUN=1;RPP=54.5856;RPPR=78.5398;RPL=61.0;RPR=128.0;EPP=20.4855;EPPR=20.0516;DPRA=0.0;ODDS=191.031;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994565;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.2375;Dels=0.0;FS=0.4235;HaplotypeSco [...]
+chr13 72010839 . C CA 325.335 REJECT NS=2;DP=266;DPB=285.2;AC=2;AN=2;AF=0.0;RO=206;AO=15;PRO=20.3333;PAO=11.3333;QR=7695;QA=492;PQR=729.833;PQA=399.833;SRF=47;SRR=159;SAF=3;SAR=12;SRP=135.238;SAP=14.7363;AB=0.056391;ABP=457.681;RUN=1;RPP=4.31318;RPPR=40.9584;RPL=9.0;RPR=6.0;EPP=6.62942;EPPR=3.05246;DPRA=0.0;ODDS=34.2352;GTI=0;TYPE=ins;CIGAR=1M1I14M;NUMALT=2;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995146;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr13 72010839 . CA C 325.335 REJECT NS=2;DP=266;DPB=285.2;AC=2;AN=4;AF=0.5;RO=206;AO=36;PRO=20.3333;PAO=9.33333;QR=7695;QA=1218;PQR=729.833;PQA=335.333;SRF=47;SRR=159;SAF=13;SAR=23;SRP=135.238;SAP=9.04217;AB=0.135338;ABP=310.249;RUN=1;RPP=11.6962;RPPR=40.9584;RPL=24.0;RPR=12.0;EPP=9.04217;EPPR=3.05246;DPRA=0.0;ODDS=34.2352;GTI=0;TYPE=del;CIGAR=1M1D13M;NUMALT=2;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995146;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.685;F [...]
+chr13 73343039 . C T 4426.790000000001 REJECT NS=2;DP=280;DPB=317.0;AC=2;AN=4;AF=0.5;RO=156;AO=161;PRO=0.0;PAO=0.0;QR=5797;QA=6213;PQR=0.0;PQA=0.0;SRF=43;SRR=113;SAF=32;SAR=129;SRP=71.2168;SAP=129.913;AB=0.507886;ABP=3.18155;RUN=1;RPP=23.5246;RPPR=3.51141;RPL=100.0;RPR=61.0;EPP=3.67118;EPPR=17.2641;DPRA=0.0;ODDS=197.852;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993789;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.764;Dels=0.0;FS=6.412;Haplo [...]
+chr13 73349359 . G C 4907.07 REJECT NS=2;DP=311;DPB=354.0;AC=2;AN=4;AF=0.5;RO=176;AO=177;PRO=0.0;PAO=0.0;QR=6662;QA=6713;PQR=0.0;PQA=0.0;SRF=108;SRR=68;SAF=134;SAR=43;SRP=22.751;SAP=104.603;AB=0.5;ABP=3.0103;RUN=1;RPP=13.3279;RPPR=5.42853;RPL=74.0;RPR=103.0;EPP=3.61144;EPPR=5.42853;DPRA=0.0;ODDS=243.326;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988701;PAIREDR=0.994318;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.231;Dels=0.0;FS=13.9195;HaplotypeScore= [...]
+chr13 78475313 . T C 9475.06 REJECT NS=2;DP=367;DPB=416.0;AC=2;AN=4;AF=0.5;RO=104;AO=311;PRO=0.0;PAO=0.0;QR=3999;QA=11868;PQR=0.0;PQA=0.0;SRF=50;SRR=54;SAF=136;SAR=175;SRP=3.34437;SAP=13.6303;AB=0.747596;ABP=224.521;RUN=1;RPP=3.01728;RPPR=3.76196;RPL=156.0;RPR=155.0;EPP=5.53088;EPPR=3.09382;DPRA=0.0;ODDS=183.008;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9839;MQMR=60.0;PAIRED=0.996785;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.4855;Dels=0.0;FS=5.991;Haplotype [...]
+chr13 78477674 . A G 14934.0 REJECT NS=2;DP=393;DPB=433.0;AC=4;AN=4;AF=1.0;RO=0;AO=433;PRO=0.0;PAO=0.0;QR=0;QA=16718;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=232;SAR=201;SRP=0.0;SAP=7.82966;AB=0.0;ABP=0.0;RUN=1;RPP=19.3039;RPPR=0.0;RPL=245.0;RPR=188.0;EPP=44.5391;EPPR=0.0;DPRA=0.0;ODDS=54.2821;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.988453;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.9045;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.925;SOR=0 [...]
+chr13 79504811 . T C 6861.055 REJECT NS=2;DP=272;DPB=318.0;AC=3;AN=4;AF=0.75;RO=71;AO=247;PRO=0.0;PAO=0.0;QR=2695;QA=9452;PQR=0.0;PQA=0.0;SRF=42;SRR=29;SAF=142;SAR=105;SRP=8.17902;SAP=15.0457;AB=0.685841;ABP=70.8064;RUN=1;RPP=63.5742;RPPR=19.1893;RPL=82.0;RPR=165.0;EPP=11.4588;EPPR=6.71098;DPRA=0.0;ODDS=58.3622;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991903;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.015;Dels=0.0;FS=0.0;HaplotypeScore=2 [...]
+chr13 80911511 . G A 2190.935 REJECT NS=2;DP=344;DPB=404.0;AC=2;AN=4;AF=0.5;RO=295;AO=109;PRO=0.0;PAO=0.0;QR=11218;QA=4052;PQR=0.0;PQA=0.0;SRF=160;SRR=135;SAF=64;SAR=45;SRP=7.61088;SAP=10.2021;AB=0.269802;ABP=188.961;RUN=1;RPP=3.50834;RPPR=3.07655;RPL=57.0;RPR=52.0;EPP=3.1896;EPPR=5.66759;DPRA=0.0;ODDS=215.292;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990826;PAIREDR=0.99661;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8015;Dels=0.0;FS=2.1715;Haplotype [...]
+chr13 80911525 . G A 5261.8 REJECT NS=2;DP=343;DPB=401.0;AC=2;AN=4;AF=0.5;RO=199;AO=201;PRO=0.0;PAO=0.0;QR=7371;QA=7405;PQR=0.0;PQA=0.0;SRF=112;SRR=87;SAF=110;SAR=91;SRP=9.83025;SAP=6.91031;AB=0.501247;ABP=3.01572;RUN=1;RPP=3.0211;RPPR=3.10851;RPL=101.0;RPR=100.0;EPP=4.3175;EPPR=4.85441;DPRA=0.0;ODDS=359.741;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995025;PAIREDR=0.994975;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3485;Dels=0.0;FS=3.1855;Haplotype [...]
+chr13 86369120 . C T 13474.7 REJECT NS=2;DP=351;DPB=402.0;AC=4;AN=4;AF=1.0;RO=0;AO=402;PRO=0.0;PAO=0.0;QR=0;QA=15545;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=197;SAR=205;SRP=0.0;SAP=3.35601;AB=0.0;ABP=0.0;RUN=1;RPP=16.5145;RPPR=0.0;RPL=226.0;RPR=176.0;EPP=3.35601;EPPR=0.0;DPRA=0.0;ODDS=67.3535;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997512;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.615;SOR=0 [...]
+chr13 87003817 . C T 75.313 REJECT NS=1;DP=47;DPB=68.1667;AC=1;AN=3;AF=0.0;RO=22;AO=3;PRO=13.3333;PAO=8.83333;QR=780;QA=54;PQR=461.917;PQA=290.25;SRF=18;SRR=4;SAF=0;SAR=3;SRP=22.3561;SAP=9.52472;AB=0.0638298;ABP=80.6751;RUN=1;RPP=9.52472;RPPR=3.0103;RPL=0.0;RPR=3.0;EPP=9.52472;EPPR=4.58955;DPRA=0.0;ODDS=15.8302;GTI=0;TYPE=snp;CIGAR=1X23M;NUMALT=3;MEANALT=12.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr13 87003817 . C CT 75.313 REJECT NS=1;DP=47;DPB=68.1667;AC=1;AN=3;AF=0.0;RO=22;AO=3;PRO=13.3333;PAO=12.3333;QR=780;QA=89;PQR=461.917;PQA=425.917;SRF=18;SRR=4;SAF=2;SAR=1;SRP=22.3561;SAP=3.73412;AB=0.0638298;ABP=80.6751;RUN=1;RPP=3.73412;RPPR=3.0103;RPL=1.0;RPR=2.0;EPP=3.73412;EPPR=4.58955;DPRA=0.0;ODDS=15.8302;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=3;MEANALT=12.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr13 87003817 . CT C 75.313 REJECT NS=1;DP=47;DPB=68.1667;AC=1;AN=4;AF=0.5;RO=22;AO=7;PRO=13.3333;PAO=10.5;QR=780;QA=233;PQR=461.917;PQA=355.917;SRF=18;SRR=4;SAF=4;SAR=3;SRP=22.3561;SAP=3.32051;AB=0.148936;ABP=53.3238;RUN=1;RPP=3.32051;RPPR=3.0103;RPL=3.0;RPR=4.0;EPP=3.32051;EPPR=4.58955;DPRA=0.0;ODDS=15.8302;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=3;MEANALT=12.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.085;FS=0.0;MLEAC=1;MLEA [...]
+chr13 90001033 . G A 12202.45 REJECT NS=2;DP=323;DPB=375.0;AC=4;AN=4;AF=1.0;RO=0;AO=375;PRO=0.0;PAO=0.0;QR=0;QA=14359;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=221;SAR=154;SRP=0.0;SAP=29.0043;AB=0.0;ABP=0.0;RUN=1;RPP=15.8017;RPPR=0.0;RPL=164.0;RPR=211.0;EPP=12.7443;EPPR=0.0;DPRA=0.0;ODDS=67.9995;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997333;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8547;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.095;SOR= [...]
+chr13 100507194 . G A 1766.83 REJECT NS=2;DP=366;DPB=421.0;AC=2;AN=4;AF=0.5;RO=332;AO=89;PRO=0.0;PAO=0.0;QR=12838;QA=3448;PQR=0.0;PQA=0.0;SRF=173;SRR=159;SAF=37;SAR=52;SRP=4.29225;SAP=8.49998;AB=0.211401;ABP=307.579;RUN=1;RPP=3.62026;RPPR=7.43173;RPL=47.0;RPR=42.0;EPP=23.5295;EPPR=3.11495;DPRA=0.0;ODDS=134.248;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996988;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.8305;Dels=0.0;FS=10.748;HaplotypeScor [...]
+chr13 106513956 . A C 8720.42 REJECT NS=2;DP=368;DPB=419.0;AC=3;AN=4;AF=0.75;RO=113;AO=306;PRO=0.0;PAO=0.0;QR=4337;QA=11733;PQR=0.0;PQA=0.0;SRF=62;SRR=51;SAF=187;SAR=119;SRP=5.3355;SAP=35.8237;AB=0.644654;ABP=60.807;RUN=1;RPP=16.7488;RPPR=19.1714;RPL=131.0;RPR=175.0;EPP=30.2885;EPPR=3.49071;DPRA=0.0;ODDS=63.9525;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993464;PAIREDR=0.99115;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.742;Dels=0.0;FS=1.5955;Haplotyp [...]
+chr13 109507359 . A G 2339.01 PASS SOMATIC;NS=2;DP=320;DPB=320.0;AC=1;AN=3;AF=0.25;RO=228;AO=92;PRO=0.0;PAO=0.0;QR=8773;QA=3443;PQR=0.0;PQA=0.0;SRF=145;SRR=83;SAF=64;SAR=28;SRP=39.6206;SAP=33.5997;AB=0.37551;ABP=35.9901;RUN=1;RPP=10.6577;RPPR=37.2967;RPL=37.0;RPR=55.0;EPP=7.63648;EPPR=7.61992;DPRA=3.26667;ODDS=47.7792;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991228;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.064;Dels=0.0;FS=2.411; [...]
+chr13 110408608 . C T 11661.55 REJECT NS=2;DP=306;DPB=350.0;AC=4;AN=4;AF=1.0;RO=0;AO=350;PRO=0.0;PAO=0.0;QR=0;QA=13524;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=243;SAR=107;SRP=0.0;SAP=117.763;AB=0.0;ABP=0.0;RUN=1;RPP=38.8458;RPPR=0.0;RPL=137.0;RPR=213.0;EPP=8.59409;EPPR=0.0;DPRA=0.0;ODDS=59.2488;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994286;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.866;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.175;SOR= [...]
+chr13 110435231 . C T 2444.4049999999997 REJECT NS=2;DP=463;DPB=529.0;AC=2;AN=4;AF=0.5;RO=399;AO=130;PRO=0.0;PAO=0.0;QR=15070;QA=4636;PQR=0.0;PQA=0.0;SRF=189;SRR=210;SAF=64;SAR=66;SRP=5.41035;SAP=3.07711;AB=0.245747;ABP=300.042;RUN=1;RPP=5.41562;RPPR=3.66882;RPL=59.0;RPR=71.0;EPP=3.0103;EPPR=24.6107;DPRA=0.0;ODDS=201.116;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997494;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.215;Dels=0.0;FS=0.702;Hap [...]
+chr13 110435914 . G A 4720.755 REJECT NS=2;DP=334;DPB=379.0;AC=2;AN=4;AF=0.5;RO=192;AO=186;PRO=0.0;PAO=0.0;QR=7291;QA=6660;PQR=0.0;PQA=0.0;SRF=116;SRR=76;SAF=111;SAR=75;SRP=21.1059;SAP=18.1406;AB=0.490765;ABP=3.29104;RUN=1;RPP=6.79286;RPPR=9.52472;RPL=84.0;RPR=102.0;EPP=7.68013;EPPR=4.6389;DPRA=0.0;ODDS=261.845;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994624;PAIREDR=0.994792;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.3835;Dels=0.0;FS=1.694;Haploty [...]
+chr13 110435953 . A G 2006.07 REJECT NS=2;DP=364;DPB=417.0;AC=2;AN=4;AF=0.5;RO=314;AO=103;PRO=0.0;PAO=0.0;QR=11800;QA=3905;PQR=0.0;PQA=0.0;SRF=174;SRR=140;SAF=59;SAR=44;SRP=11.0046;SAP=7.75381;AB=0.247002;ABP=234.848;RUN=1;RPP=5.56125;RPPR=4.00613;RPL=57.0;RPR=46.0;EPP=4.04333;EPPR=3.0103;DPRA=0.0;ODDS=222.513;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990446;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.5585;Dels=0.0;FS=0.801;HaplotypeScore [...]
+chr13 110436232 . G A 2348.17 REJECT NS=2;DP=307;DPB=359.0;AC=2;AN=4;AF=0.5;RO=255;AO=104;PRO=0.0;PAO=0.0;QR=9549;QA=3867;PQR=0.0;PQA=0.0;SRF=106;SRR=149;SAF=58;SAR=46;SRP=18.7556;SAP=6.01695;AB=0.289694;ABP=140.926;RUN=1;RPP=8.35546;RPPR=7.51504;RPL=44.0;RPR=60.0;EPP=6.01695;EPPR=6.08442;DPRA=0.0;ODDS=151.732;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990385;PAIREDR=0.996078;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.6375;Dels=0.0;FS=10.336;Haploty [...]
+chr14 20260241 . A G 3547.55 REJECT NS=2;DP=216;DPB=242.0;AC=2;AN=4;AF=0.5;RO=114;AO=128;PRO=0.0;PAO=0.0;QR=4245;QA=4888;PQR=0.0;PQA=0.0;SRF=87;SRR=27;SAF=94;SAR=34;SRP=71.5831;SAP=64.083;AB=0.528926;ABP=4.76901;RUN=1;RPP=68.2223;RPPR=30.5156;RPL=33.0;RPR=95.0;EPP=11.2212;EPPR=5.75321;DPRA=0.0;ODDS=136.463;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2445;Dels=0.0;FS=0.6675;HaplotypeScore=1.999;M [...]
+chr14 20386925 . C A 5799.370000000001 REJECT NS=2;DP=363;DPB=418.0;AC=2;AN=4;AF=0.5;RO=209;AO=209;PRO=0.0;PAO=0.0;QR=7900;QA=7925;PQR=0.0;PQA=0.0;SRF=107;SRR=102;SAF=110;SAR=99;SRP=3.27005;SAP=4.26747;AB=0.5;ABP=3.0103;RUN=1;RPP=22.2211;RPPR=9.50394;RPL=83.0;RPR=126.0;EPP=22.2211;EPPR=39.1773;DPRA=0.0;ODDS=327.526;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995215;PAIREDR=0.995215;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.2145;Dels=0.0;FS=2.1865;Ha [...]
+chr14 20387014 . C T 8862.76 REJECT NS=2;DP=236;DPB=275.0;AC=4;AN=4;AF=1.0;RO=0;AO=275;PRO=0.0;PAO=0.0;QR=0;QA=10573;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=62;SAR=213;SRP=0.0;SAP=183.053;AB=0.0;ABP=0.0;RUN=1;RPP=96.8258;RPPR=0.0;RPL=192.0;RPR=83.0;EPP=4.34477;EPPR=0.0;DPRA=0.0;ODDS=50.5161;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.989091;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=25.035;SOR=2.493 [...]
+chr14 23652346 . T A 459.159 REJECT NS=2;DP=68;DPB=232.2;AC=2;AN=2;AF=0.0;RO=15;AO=4;PRO=69.4333;PAO=15.7833;QR=560;QA=56;PQR=2438.89;PQA=558.886;SRF=2;SRR=13;SAF=0;SAR=4;SRP=20.5268;SAP=11.6962;AB=0.0588235;ABP=117.971;RUN=1;RPP=11.6962;RPPR=3.15506;RPL=0.0;RPR=4.0;EPP=11.6962;EPPR=3.15506;DPRA=0.0;ODDS=1.21601;GTI=1;TYPE=snp;CIGAR=1X29M;NUMALT=6;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr14 23652346 . T TA 459.159 REJECT NS=2;DP=68;DPB=232.2;AC=2;AN=3;AF=0.25;RO=15;AO=10;PRO=69.4333;PAO=63.6833;QR=560;QA=201;PQR=2438.89;PQA=2228.55;SRF=2;SRR=13;SAF=0;SAR=10;SRP=20.5268;SAP=24.725;AB=0.147059;ABP=76.5849;RUN=1;RPP=3.0103;RPPR=3.15506;RPL=5.0;RPR=5.0;EPP=3.0103;EPPR=3.15506;DPRA=0.0;ODDS=1.21601;GTI=1;TYPE=ins;CIGAR=1M1I29M;NUMALT=6;MEANALT=12.5;LEN=1;MQM=60.6;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr14 23652346 . T TAA 459.159 REJECT NS=2;DP=68;DPB=232.2;AC=2;AN=3;AF=0.25;RO=15;AO=13;PRO=69.4333;PAO=59.6833;QR=560;QA=217;PQR=2438.89;PQA=2125.55;SRF=2;SRR=13;SAF=1;SAR=12;SRP=20.5268;SAP=23.2217;AB=0.191176;ABP=59.3408;RUN=1;RPP=16.5402;RPPR=3.15506;RPL=11.0;RPR=2.0;EPP=11.1951;EPPR=3.15506;DPRA=0.0;ODDS=1.21601;GTI=1;TYPE=ins;CIGAR=1M2I29M;NUMALT=6;MEANALT=12.5;LEN=2;MQM=58.7692;MQMR=60.0;PAIRED=0.923077;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr14 23652346 . T TAAA 459.159 REJECT NS=2;DP=68;DPB=232.2;AC=2;AN=2;AF=0.0;RO=15;AO=3;PRO=69.4333;PAO=59.6833;QR=560;QA=59;PQR=2438.89;PQA=2125.55;SRF=2;SRR=13;SAF=0;SAR=3;SRP=20.5268;SAP=9.52472;AB=0.0441176;ABP=125.762;RUN=1;RPP=3.73412;RPPR=3.15506;RPL=1.0;RPR=2.0;EPP=3.73412;EPPR=3.15506;DPRA=0.0;ODDS=1.21601;GTI=1;TYPE=ins;CIGAR=1M3I29M;NUMALT=6;MEANALT=12.5;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr14 23652346 . TA T 459.159 REJECT NS=2;DP=68;DPB=232.2;AC=2;AN=2;AF=0.0;RO=15;AO=4;PRO=69.4333;PAO=38.7333;QR=560;QA=125;PQR=2438.89;PQA=1367.79;SRF=2;SRR=13;SAF=2;SAR=2;SRP=20.5268;SAP=3.0103;AB=0.0588235;ABP=117.971;RUN=1;RPP=11.6962;RPPR=3.15506;RPL=4.0;RPR=0.0;EPP=3.0103;EPPR=3.15506;DPRA=0.0;ODDS=1.21601;GTI=1;TYPE=del;CIGAR=1M1D28M;NUMALT=6;MEANALT=12.5;LEN=1;MQM=55.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr14 23652346 . TAA T 459.159 REJECT NS=2;DP=68;DPB=232.2;AC=2;AN=2;AF=0.0;RO=15;AO=4;PRO=69.4333;PAO=38.0;QR=560;QA=75;PQR=2438.89;PQA=1336.79;SRF=2;SRR=13;SAF=0;SAR=4;SRP=20.5268;SAP=11.6962;AB=0.0588235;ABP=117.971;RUN=1;RPP=3.0103;RPPR=3.15506;RPL=2.0;RPR=2.0;EPP=3.0103;EPPR=3.15506;DPRA=0.0;ODDS=1.21601;GTI=1;TYPE=del;CIGAR=1M2D27M;NUMALT=6;MEANALT=12.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr14 23777099 . G A 7534.21 REJECT NS=2;DP=298;DPB=340.0;AC=3;AN=4;AF=0.75;RO=80;AO=260;PRO=0.0;PAO=0.0;QR=3089;QA=9999;PQR=0.0;PQA=0.0;SRF=35;SRR=45;SAF=128;SAR=132;SRP=5.72464;SAP=3.14393;AB=0.688716;ABP=82.5098;RUN=1;RPP=3.31097;RPPR=3.98746;RPL=133.0;RPR=127.0;EPP=5.71629;EPPR=4.74748;DPRA=0.0;ODDS=52.8115;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992308;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.717;Dels=0.0;FS=0.2475;HaplotypeScor [...]
+chr14 23777374 . A G 12472.349999999999 REJECT NS=2;DP=332;DPB=389.0;AC=4;AN=4;AF=1.0;RO=0;AO=389;PRO=0.0;PAO=0.0;QR=0;QA=14913;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=132;SAR=257;SRP=0.0;SAP=90.232;AB=0.0;ABP=0.0;RUN=1;RPP=15.3414;RPPR=0.0;RPL=218.0;RPR=171.0;EPP=18.6907;EPPR=0.0;DPRA=0.0;ODDS=75.4676;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994859;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9134;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29 [...]
+chr14 25510841 . G GAC 11083.3 REJECT NS=2;DP=311;DPB=604.667;AC=4;AN=4;AF=1.0;RO=0;AO=342;PRO=19.0;PAO=24.0;QR=0;QA=12257;PQR=650.5;PQA=821.5;SRF=0;SRR=0;SAF=142;SAR=200;SRP=0.0;SAP=24.3695;AB=0.0;ABP=0.0;RUN=1;RPP=3.23888;RPPR=0.0;RPL=174.0;RPR=168.0;EPP=34.122;EPPR=0.0;DPRA=0.0;ODDS=62.4524;GTI=0;TYPE=ins;CIGAR=1M2I2M;NUMALT=1;MEANALT=2.5;LEN=2;MQM=60.0585;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=25510841;HOMLEN=1;HOMSEQ=A;SVLEN=2;SVTYPE=INS;FS=0.0;MLEAC=2;MLE [...]
+chr14 33003467 . T C 11262.599999999999 REJECT NS=2;DP=313;DPB=361.0;AC=4;AN=4;AF=1.0;RO=0;AO=361;PRO=0.0;PAO=0.0;QR=0;QA=13371;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=104;SAR=257;SRP=0.0;SAP=143.819;AB=0.0;ABP=0.0;RUN=1;RPP=79.8179;RPPR=0.0;RPL=237.0;RPR=124.0;EPP=23.9491;EPPR=0.0;DPRA=0.0;ODDS=63.4762;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99723;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9991;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31 [...]
+chr14 35871217 . G A 4790.35 REJECT NS=2;DP=360;DPB=406.0;AC=2;AN=4;AF=0.5;RO=225;AO=180;PRO=0.0;PAO=0.0;QR=8231;QA=6696;PQR=0.0;PQA=0.0;SRF=144;SRR=81;SAF=117;SAR=63;SRP=41.3151;SAP=38.1882;AB=0.44335;ABP=14.3276;RUN=1;RPP=8.84915;RPPR=30.1199;RPL=79.0;RPR=101.0;EPP=15.3636;EPPR=3.79203;DPRA=0.0;ODDS=260.354;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991111;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4155;Dels=0.0;FS=1.121;HaplotypeScore= [...]
+chr14 35871960 . G A 5604.035 REJECT NS=2;DP=354;DPB=403.0;AC=2;AN=4;AF=0.5;RO=200;AO=203;PRO=0.0;PAO=0.0;QR=7427;QA=7748;PQR=0.0;PQA=0.0;SRF=107;SRR=93;SAF=115;SAR=88;SRP=5.13834;SAP=10.8083;AB=0.503722;ABP=3.05879;RUN=1;RPP=3.10657;RPPR=3.0103;RPL=100.0;RPR=103.0;EPP=6.10171;EPPR=3.05373;DPRA=0.0;ODDS=268.249;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6665;Dels=0.0;FS=3.0695;HaplotypeScore= [...]
+chr14 35872926 . G A 8999.28 REJECT NS=2;DP=337;DPB=392.0;AC=2;AN=4;AF=0.5;RO=100;AO=292;PRO=0.0;PAO=0.0;QR=3862;QA=11274;PQR=0.0;PQA=0.0;SRF=41;SRR=59;SAF=142;SAR=150;SRP=10.0459;SAP=3.48624;AB=0.744898;ABP=207.217;RUN=1;RPP=11.607;RPPR=3.09716;RPL=129.0;RPR=163.0;EPP=11.607;EPPR=15.518;DPRA=0.0;ODDS=165.713;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993151;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.714;Dels=0.0;FS=4.3155;HaplotypeScore= [...]
+chr14 35873770 . G A 1909.66 REJECT NS=1;DP=116;DPB=116.0;AC=1;AN=4;AF=0.5;RO=50;AO=66;PRO=0.0;PAO=0.0;QR=1931;QA=2538;PQR=0.0;PQA=0.0;SRF=28;SRR=22;SAF=32;SAR=34;SRP=4.57376;SAP=3.1419;AB=0.568966;ABP=7.80251;RUN=1;RPP=9.45891;RPPR=3.70517;RPL=40.0;RPR=26.0;EPP=6.30041;EPPR=3.70517;DPRA=0.0;ODDS=315.943;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.454;FS=3.397;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.67 [...]
+chr14 38061742 . C T 5249.58 REJECT NS=2;DP=341;DPB=375.0;AC=2;AN=4;AF=0.5;RO=182;AO=193;PRO=0.0;PAO=0.0;QR=6930;QA=7156;PQR=0.0;PQA=0.0;SRF=130;SRR=52;SAF=141;SAR=52;SRP=75.5995;SAP=92.1307;AB=0.514667;ABP=3.71096;RUN=1;RPP=18.4131;RPPR=20.2389;RPL=78.0;RPR=115.0;EPP=8.96216;EPPR=11.0758;DPRA=0.0;ODDS=181.878;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989637;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.0165;Dels=0.0;FS=1.0375;HaplotypeSco [...]
+chr14 48011192 . G A 6609.76 REJECT NS=2;DP=414;DPB=477.0;AC=2;AN=4;AF=0.5;RO=239;AO=238;PRO=0.0;PAO=0.0;QR=9165;QA=9103;PQR=0.0;PQA=0.0;SRF=114;SRR=125;SAF=121;SAR=117;SRP=4.10966;SAP=3.15628;AB=0.498952;ABP=3.01485;RUN=1;RPP=20.674;RPPR=10.6513;RPL=141.0;RPR=97.0;EPP=33.7029;EPPR=16.8296;DPRA=0.0;ODDS=395.131;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995798;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.722;Dels=0.0;FS=7.7545;HaplotypeSco [...]
+chr14 50605507 . T TA 407.056 REJECT NS=2;DP=140;DPB=175.733;AC=2;AN=2;AF=0.0;RO=85;AO=10;PRO=44.0;PAO=17.0;QR=3177;QA=233;PQR=1586.17;PQA=535.167;SRF=6;SRR=79;SAF=0;SAR=10;SRP=139.149;SAP=24.725;AB=0.0714286;ABP=226.362;RUN=1;RPP=3.87889;RPPR=16.5245;RPL=6.0;RPR=4.0;EPP=3.87889;EPPR=6.10145;DPRA=0.0;ODDS=29.613;GTI=0;TYPE=ins;CIGAR=1M1I29M;NUMALT=2;MEANALT=9.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988235;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr14 50605507 . TA T 407.056 REJECT NS=2;DP=140;DPB=175.733;AC=2;AN=4;AF=0.5;RO=85;AO=28;PRO=44.0;PAO=13.0;QR=3177;QA=928;PQR=1586.17;PQA=450.667;SRF=6;SRR=79;SAF=2;SAR=26;SRP=139.149;SAP=47.6806;AB=0.2;ABP=112.453;RUN=1;RPP=10.7656;RPPR=16.5245;RPL=19.0;RPR=9.0;EPP=5.80219;EPPR=6.10145;DPRA=0.0;ODDS=29.613;GTI=0;TYPE=del;CIGAR=1M1D28M;NUMALT=2;MEANALT=9.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988235;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr14 50616878 . G A 6137.22 REJECT NS=2;DP=372;DPB=432.0;AC=2;AN=4;AF=0.5;RO=216;AO=216;PRO=0.0;PAO=0.0;QR=8362;QA=8315;PQR=0.0;PQA=0.0;SRF=104;SRR=112;SAF=101;SAR=115;SRP=3.6537;SAP=4.98071;AB=0.5;ABP=3.0103;RUN=1;RPP=4.98071;RPPR=3.6537;RPL=115.0;RPR=101.0;EPP=8.80089;EPPR=4.45795;DPRA=0.0;ODDS=353.568;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990741;PAIREDR=0.976852;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6775;Dels=0.0;FS=0.43;HaplotypeScore= [...]
+chr14 50623654 . A AAT . PASS SOMATIC;AC=1;AN=4;END=50623654;HOMLEN=2;HOMSEQ=AT;SVLEN=2;SVTYPE=INS GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:-0.000408587 0/1:93,30:30:24:123:.:.:.:1:.:.:-0.0130717
+chr14 50623657 . G A 3838.92 REJECT NS=2;DP=240;DPB=277.0;AC=2;AN=4;AF=0.5;RO=136;AO=141;PRO=0.0;PAO=0.0;QR=5212;QA=5365;PQR=0.0;PQA=0.0;SRF=121;SRR=15;SAF=120;SAR=21;SRP=182.412;SAP=153.951;AB=0.509025;ABP=3.20628;RUN=1;RPP=14.2373;RPPR=9.39698;RPL=57.0;RPR=84.0;EPP=6.47542;EPPR=4.60697;DPRA=0.0;ODDS=199.185;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.977941;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.2035;Dels=0.01;FS=3.125;HaplotypeScor [...]
+chr14 50623679 . G A 2481.27 PASS DP=171;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.7325;Dels=0.0;FS=4.364;HaplotypeScore=76.8779;MLEAC=1;MLEAF=0.5;MQ=59.835;MQRankSum=0.4575;QD=13.365;ReadPosRankSum=2.1235;SOR=0.6025;ClippingRankSum=-0.622 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:50,37:87:99.0:1087,0,3071:37:43:87:1:.:.:.:.:.:-0.000408587 0/1:134,111:245:99.0:3932,0,4824:111:45:245:.:1:.:.:.:.:-0.0130717
+chr14 50623679 . GTGTA ATGTG 4368.63 REJECT NS=2;DP=302;DPB=317.4;AC=2;AN=4;AF=0.5;RO=149;AO=144;PRO=14.0;PAO=15.0;QR=5657;QA=5413;PQR=469.0;PQA=531.0;SRF=115;SRR=34;SAF=108;SAR=36;SRP=98.628;SAP=81.1833;AB=0.476821;ABP=4.4196;RUN=1;RPP=27.1378;RPPR=9.43728;RPL=52.0;RPR=92.0;EPP=18.4519;EPPR=25.1768;DPRA=0.0;ODDS=284.225;GTI=0;TYPE=complex;CIGAR=1X3M1X;NUMALT=1;MEANALT=3.5;LEN=5;MQM=59.8611;MQMR=59.698;PAIRED=1.0;PAIREDR=0.973154;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr14 50623683 . A G 1052.77 PASS DP=100;AC=1;AN=4;AF=0.5;BaseQRankSum=0.941;FS=3.561;MLEAC=1;MLEAF=0.5;MQ=59.83;MQRankSum=-0.351;QD=10.53;ReadPosRankSum=2.016;SOR=0.327;ClippingRankSum=0.974 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:54,37:91:99.0:1081,0,3138:37:41:91:1:.:.:.:.:.:-0.000408587 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0130717
+chr14 50647273 . CTTC TTTA 151.245 REJECT NS=2;DP=208;DPB=213.0;AC=2;AN=2;AF=0.0;RO=181;AO=6;PRO=13.0;PAO=0.0;QR=5868;QA=99;PQR=171.0;PQA=0.0;SRF=115;SRR=66;SAF=6;SAR=0;SRP=31.8153;SAP=16.0391;AB=0.0288462;ABP=404.065;RUN=1;RPP=16.0391;RPPR=172.901;RPL=6.0;RPR=0.0;EPP=16.0391;EPPR=3.59816;DPRA=0.0;ODDS=3.86145;GTI=1;TYPE=complex;CIGAR=1X2M1X;NUMALT=2;MEANALT=4.0;LEN=4;MQM=56.6667;MQMR=60.2762;PAIRED=1.0;PAIREDR=0.994475;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr14 50647276 . C A 151.245 REJECT NS=2;DP=208;DPB=213.0;AC=2;AN=4;AF=0.5;RO=181;AO=13;PRO=13.0;PAO=0.0;QR=5868;QA=230;PQR=171.0;PQA=0.0;SRF=115;SRR=66;SAF=13;SAR=0;SRP=31.8153;SAP=31.2394;AB=0.0625;ABP=348.817;RUN=1;RPP=3.17734;RPPR=172.901;RPL=7.0;RPR=6.0;EPP=3.17734;EPPR=3.59816;DPRA=0.0;ODDS=3.86145;GTI=1;TYPE=snp;CIGAR=3M1X;NUMALT=2;MEANALT=4.0;LEN=1;MQM=53.8462;MQMR=60.2762;PAIRED=1.0;PAIREDR=0.994475;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr14 51020827 . G GT 535.456 REJECT NS=2;DP=233;DPB=284.667;AC=2;AN=4;AF=0.5;RO=155;AO=36;PRO=40.5;PAO=36.5;QR=5746;QA=1248;PQR=1342.67;PQA=1201.67;SRF=131;SRR=24;SAF=30;SAR=6;SRP=163.405;SAP=37.7539;AB=0.154506;ABP=244.584;RUN=1;RPP=6.8707;RPPR=24.3187;RPL=14.0;RPR=22.0;EPP=3.0103;EPPR=4.14507;DPRA=0.0;ODDS=18.1945;GTI=0;TYPE=ins;CIGAR=1M1I17M;NUMALT=2;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.972222;PAIREDR=0.993548;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-2.1 [...]
+chr14 51020827 . GT G 535.456 REJECT NS=2;DP=233;DPB=284.667;AC=2;AN=2;AF=0.0;RO=155;AO=24;PRO=40.5;PAO=34.0;QR=5746;QA=924;PQR=1342.67;PQA=1111.67;SRF=131;SRR=24;SAF=21;SAR=3;SRP=163.405;SAP=32.3252;AB=0.103004;ABP=321.974;RUN=1;RPP=16.0391;RPPR=24.3187;RPL=6.0;RPR=18.0;EPP=6.26751;EPPR=4.14507;DPRA=0.0;ODDS=18.1945;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=2;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993548;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr14 52501235 . A C 9333.27 REJECT NS=2;DP=254;DPB=292.0;AC=4;AN=4;AF=1.0;RO=1;AO=291;PRO=0.0;PAO=0.0;QR=16;QA=11015;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=187;SAR=104;SRP=5.18177;SAP=54.4167;AB=0.0;ABP=0.0;RUN=1;RPP=59.491;RPPR=5.18177;RPL=102.0;RPR=189.0;EPP=47.2531;EPPR=5.18177;DPRA=0.0;ODDS=51.161;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986254;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.716;Dels=0.0;FS=0.0;HaplotypeScore=4.8325;MLEAC=2;ML [...]
+chr14 58517788 . A G 10391.9 REJECT NS=2;DP=382;DPB=431.0;AC=2;AN=4;AF=0.5;RO=92;AO=339;PRO=0.0;PAO=0.0;QR=3532;QA=12928;PQR=0.0;PQA=0.0;SRF=48;SRR=44;SAF=178;SAR=161;SRP=3.38795;SAP=4.8615;AB=0.786543;ABP=310.387;RUN=1;RPP=5.32269;RPPR=3.86001;RPL=160.0;RPR=179.0;EPP=4.45154;EPPR=7.63648;DPRA=0.0;ODDS=117.914;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9735;MQMR=60.0;PAIRED=0.9941;PAIREDR=0.978261;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6985;Dels=0.0;FS=3.402;Haplotyp [...]
+chr14 58517852 . C G 10161.849999999999 REJECT NS=2;DP=267;DPB=301.0;AC=4;AN=4;AF=1.0;RO=0;AO=301;PRO=0.0;PAO=0.0;QR=0;QA=11642;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=88;SAR=213;SRP=0.0;SAP=115.732;AB=0.0;ABP=0.0;RUN=1;RPP=57.6145;RPPR=0.0;RPL=194.0;RPR=107.0;EPP=29.8543;EPPR=0.0;DPRA=0.0;ODDS=46.1492;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993355;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.44 [...]
+chr14 60027907 . C T 3184.25 PASS SOMATIC;NS=2;DP=450;DPB=450.0;AC=1;AN=3;AF=0.25;RO=328;AO=122;PRO=0.0;PAO=0.0;QR=12421;QA=4633;PQR=0.0;PQA=0.0;SRF=139;SRR=189;SAF=51;SAR=71;SRP=19.5612;SAP=10.1299;AB=0.356725;ABP=63.9893;RUN=1;RPP=3.65106;RPPR=8.20065;RPL=64.0;RPR=58.0;EPP=3.29508;EPPR=31.8485;DPRA=3.16667;ODDS=68.2692;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991803;PAIREDR=0.996951;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.629;Dels=0.0;F [...]
+chr14 61691100 . C T 8323.595000000001 REJECT NS=2;DP=361;DPB=410.0;AC=3;AN=4;AF=0.75;RO=115;AO=294;PRO=0.0;PAO=0.0;QR=4193;QA=11190;PQR=0.0;PQA=0.0;SRF=61;SRR=54;SAF=133;SAR=161;SRP=3.93554;SAP=8.80089;AB=0.636076;ABP=53.8337;RUN=1;RPP=3.7489;RPPR=3.93554;RPL=152.0;RPR=142.0;EPP=3.483;EPPR=3.48236;DPRA=0.0;ODDS=59.0063;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=59.8261;PAIRED=0.986395;PAIREDR=0.991304;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.015;Dels=0.0;FS=1.6 [...]
+chr14 61788816 . C T 1235.4099999999999 REJECT NS=2;DP=261;DPB=296.0;AC=2;AN=4;AF=0.5;RO=233;AO=62;PRO=0.0;PAO=0.0;QR=8924;QA=2351;PQR=0.0;PQA=0.0;SRF=145;SRR=88;SAF=38;SAR=24;SRP=33.2898;SAP=9.87495;AB=0.209459;ABP=220.04;RUN=1;RPP=14.358;RPPR=37.6886;RPL=22.0;RPR=40.0;EPP=4.27115;EPPR=14.4268;DPRA=0.0;ODDS=48.0907;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.131;Dels=0.0;FS=0.0;HaplotypeScore=3 [...]
+chr14 61789192 . G A 2171.89 PASS SOMATIC;NS=2;DP=340;DPB=340.0;AC=1;AN=3;AF=0.25;RO=253;AO=86;PRO=0.0;PAO=0.0;QR=9675;QA=3306;PQR=0.0;PQA=0.0;SRF=62;SRR=191;SAF=17;SAR=69;SRP=145.838;SAP=71.2854;AB=0.346774;ABP=53.5846;RUN=1;RPP=13.1102;RPPR=65.0217;RPL=53.0;RPR=33.0;EPP=3.1113;EPPR=3.43086;DPRA=2.69565;ODDS=58.3929;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.976744;PAIREDR=0.992095;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.447;Dels=0.0;FS=3. [...]
+chr14 61997226 . C T 12742.55 REJECT NS=2;DP=339;DPB=390.0;AC=4;AN=4;AF=1.0;RO=0;AO=390;PRO=0.0;PAO=0.0;QR=0;QA=14778;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=180;SAR=210;SRP=0.0;SAP=8.02139;AB=0.0;ABP=0.0;RUN=1;RPP=19.2462;RPPR=0.0;RPL=168.0;RPR=222.0;EPP=3.56709;EPPR=0.0;DPRA=0.0;ODDS=65.8084;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992308;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=13.7438;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.145;SOR [...]
+chr14 62114519 . G T 5762.885 REJECT NS=2;DP=368;DPB=423.0;AC=2;AN=4;AF=0.5;RO=212;AO=211;PRO=0.0;PAO=0.0;QR=8082;QA=8016;PQR=0.0;PQA=0.0;SRF=107;SRR=105;SAF=129;SAR=82;SRP=3.05127;SAP=25.7439;AB=0.498818;ABP=3.01543;RUN=1;RPP=3.8439;RPPR=3.05127;RPL=101.0;RPR=110.0;EPP=15.6172;EPPR=16.285;DPRA=0.0;ODDS=335.282;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995283;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1175;Dels=0.0;FS=9.34;HaplotypeScor [...]
+chr14 62116307 . G T 4872.085 REJECT NS=2;DP=325;DPB=366.0;AC=2;AN=4;AF=0.5;RO=189;AO=176;PRO=0.0;PAO=0.0;QR=7084;QA=6739;PQR=0.0;PQA=0.0;SRF=78;SRR=111;SAF=60;SAR=116;SRP=15.5221;SAP=41.702;AB=0.480874;ABP=4.17316;RUN=1;RPP=6.16881;RPPR=14.0515;RPL=96.0;RPR=80.0;EPP=6.16881;EPPR=4.4005;DPRA=0.0;ODDS=236.294;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989418;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.927;Dels=0.0;FS=6.3525;HaplotypeScore=1 [...]
+chr14 62117489 . C T 5665.39 REJECT NS=2;DP=350;DPB=400.0;AC=2;AN=4;AF=0.5;RO=203;AO=197;PRO=0.0;PAO=0.0;QR=7621;QA=7632;PQR=0.0;PQA=0.0;SRF=109;SRR=94;SAF=119;SAR=78;SRP=5.4171;SAP=21.5395;AB=0.4925;ABP=3.20573;RUN=1;RPP=38.8231;RPPR=24.6715;RPL=70.0;RPR=127.0;EPP=4.87314;EPPR=3.021;DPRA=0.0;ODDS=238.605;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994924;PAIREDR=0.995074;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.5895;Dels=0.0;FS=3.642;HaplotypeScore [...]
+chr14 64520800 . G A 12399.7 REJECT NS=2;DP=329;DPB=379.0;AC=4;AN=4;AF=1.0;RO=0;AO=379;PRO=0.0;PAO=0.0;QR=0;QA=14521;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=248;SAR=131;SRP=0.0;SAP=81.4411;AB=0.0;ABP=0.0;RUN=1;RPP=78.7827;RPPR=0.0;RPL=132.0;RPR=247.0;EPP=6.04119;EPPR=0.0;DPRA=0.0;ODDS=66.0857;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9472;MQMR=0.0;PAIRED=0.992084;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.7989;MLEAC=2;MLEAF=1.0;MQ=59.97;QD=28.49;SO [...]
+chr14 65008251 . C T 11674.7 REJECT NS=2;DP=310;DPB=357.0;AC=4;AN=4;AF=1.0;RO=0;AO=357;PRO=0.0;PAO=0.0;QR=0;QA=13570;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=152;SAR=205;SRP=0.0;SAP=20.0962;AB=0.0;ABP=0.0;RUN=1;RPP=4.76816;RPPR=0.0;RPL=187.0;RPR=170.0;EPP=7.44448;EPPR=0.0;DPRA=0.0;ODDS=62.3304;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991597;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.946;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.47;SOR=1.1 [...]
+chr14 71199452 . G A 6779.3150000000005 REJECT NS=2;DP=407;DPB=466.0;AC=2;AN=4;AF=0.5;RO=211;AO=255;PRO=0.0;PAO=0.0;QR=7956;QA=9289;PQR=0.0;PQA=0.0;SRF=104;SRR=107;SAF=124;SAR=131;SRP=3.10292;SAP=3.42756;AB=0.54721;ABP=12.0317;RUN=1;RPP=4.04068;RPPR=9.44239;RPL=133.0;RPR=122.0;EPP=3.22319;EPPR=3.26758;DPRA=0.0;ODDS=323.614;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992157;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.3245;Dels=0.0;FS=0.356; [...]
+chr14 71201179 . C G 1982.68 REJECT NS=2;DP=385;DPB=445.0;AC=2;AN=4;AF=0.5;RO=348;AO=97;PRO=0.0;PAO=0.0;QR=13286;QA=3698;PQR=0.0;PQA=0.0;SRF=178;SRR=170;SAF=54;SAR=43;SRP=3.40965;SAP=5.71904;AB=0.217978;ABP=310.437;RUN=1;RPP=3.03269;RPPR=12.0207;RPL=48.0;RPR=49.0;EPP=12.8827;EPPR=16.2139;DPRA=0.0;ODDS=127.671;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.979381;PAIREDR=0.988506;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.5845;Dels=0.0;FS=2.368;HaplotypeS [...]
+chr14 71201192 . T C 2002.82 REJECT NS=2;DP=396;DPB=458.0;AC=2;AN=4;AF=0.5;RO=357;AO=101;PRO=0.0;PAO=0.0;QR=13782;QA=3846;PQR=0.0;PQA=0.0;SRF=179;SRR=178;SAF=51;SAR=50;SRP=3.01638;SAP=3.0318;AB=0.220524;ABP=313.73;RUN=1;RPP=6.64375;RPPR=3.01638;RPL=57.0;RPR=44.0;EPP=21.0916;EPPR=7.44448;DPRA=0.0;ODDS=140.333;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.980198;PAIREDR=0.991597;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.802;Dels=0.0;FS=1.7925;HaplotypeS [...]
+chr14 71202650 . C T 10551.9 REJECT NS=2;DP=291;DPB=324.0;AC=4;AN=4;AF=1.0;RO=1;AO=321;PRO=0.0;PAO=0.0;QR=16;QA=11920;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=189;SAR=132;SRP=5.18177;SAP=24.9888;AB=0.0;ABP=0.0;RUN=1;RPP=66.6595;RPPR=5.18177;RPL=112.0;RPR=209.0;EPP=13.2994;EPPR=5.18177;DPRA=0.0;ODDS=44.8751;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993769;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.651;Dels=0.0;FS=0.0;HaplotypeScore=8.7121;MLEAC=2; [...]
+chr14 71215729 . G A 2356.15 PASS SOMATIC;NS=2;DP=328;DPB=328.0;AC=1;AN=3;AF=0.25;RO=240;AO=88;PRO=0.0;PAO=0.0;QR=9264;QA=3402;PQR=0.0;PQA=0.0;SRF=76;SRR=164;SAF=30;SAR=58;SRP=73.0765;SAP=22.3561;AB=0.384279;ABP=29.6464;RUN=1;RPP=12.8806;RPPR=17.4868;RPL=54.0;RPR=34.0;EPP=6.56362;EPPR=10.1038;DPRA=2.31313;ODDS=62.7041;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.9875;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.418;Dels=0.0;FS=0.529;H [...]
+chr14 71227913 . A C 6921.88 REJECT NS=2;DP=256;DPB=297.0;AC=2;AN=4;AF=0.5;RO=68;AO=229;PRO=0.0;PAO=0.0;QR=2545;QA=8812;PQR=0.0;PQA=0.0;SRF=23;SRR=45;SAF=63;SAR=166;SRP=18.4661;SAP=103.609;AB=0.771044;ABP=192.528;RUN=1;RPP=38.2944;RPPR=35.7101;RPL=145.0;RPR=84.0;EPP=4.15767;EPPR=6.20364;DPRA=0.0;ODDS=85.9359;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991266;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.185;Dels=0.0;FS=6.5005;HaplotypeScore=3 [...]
+chr14 75483812 . T C 7328.445 REJECT NS=2;DP=312;DPB=357.0;AC=3;AN=4;AF=0.75;RO=96;AO=261;PRO=0.0;PAO=0.0;QR=3704;QA=9987;PQR=0.0;PQA=0.0;SRF=64;SRR=32;SAF=162;SAR=99;SRP=26.1727;SAP=36.0317;AB=0.641791;ABP=49.8104;RUN=1;RPP=16.9959;RPPR=3.10078;RPL=110.0;RPR=151.0;EPP=42.621;EPPR=10.339;DPRA=0.0;ODDS=56.5561;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.282;Dels=0.0;FS=1.1255;HaplotypeScore=4.932 [...]
+chr14 75489632 . C T 2751.98 PASS SOMATIC;NS=2;DP=434;DPB=434.0;AC=1;AN=3;AF=0.25;RO=325;AO=108;PRO=0.0;PAO=0.0;QR=12510;QA=4132;PQR=0.0;PQA=0.0;SRF=176;SRR=149;SAF=52;SAR=56;SRP=7.88108;SAP=3.332;AB=0.333333;ABP=80.4595;RUN=1;RPP=11.0528;RPPR=16.5402;RPL=44.0;RPR=64.0;EPP=3.332;EPPR=3.07043;DPRA=0.0;ODDS=62.9663;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990741;PAIREDR=0.996923;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.695;Dels=0.0;FS=3.262; [...]
+chr14 75505008 . G C 6721.135 REJECT NS=2;DP=275;DPB=312.0;AC=3;AN=4;AF=0.75;RO=77;AO=235;PRO=0.0;PAO=0.0;QR=2905;QA=8997;PQR=0.0;PQA=0.0;SRF=54;SRR=23;SAF=167;SAR=68;SRP=30.1114;SAP=93.5746;AB=0.676471;ABP=67.3881;RUN=1;RPP=121.0;RPPR=60.1172;RPL=61.0;RPR=174.0;EPP=3.75876;EPPR=9.35551;DPRA=0.0;ODDS=47.1187;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991489;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.182;Dels=0.0;FS=0.0;HaplotypeScore=6.75 [...]
+chr14 75505016 . A G 11324.05 REJECT NS=2;DP=301;DPB=341.0;AC=4;AN=4;AF=1.0;RO=0;AO=340;PRO=0.0;PAO=0.0;QR=0;QA=13044;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=242;SAR=98;SRP=0.0;SAP=135.445;AB=0.0;ABP=0.0;RUN=1;RPP=117.69;RPPR=0.0;RPL=103.0;RPR=237.0;EPP=4.26209;EPPR=0.0;DPRA=0.0;ODDS=52.988;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994118;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8989;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.36;SOR=1.88 [...]
+chr14 75513828 . G A 2808.08 PASS SOMATIC;NS=2;DP=405;DPB=405.0;AC=1;AN=3;AF=0.25;RO=297;AO=108;PRO=0.0;PAO=0.0;QR=11370;QA=4144;PQR=0.0;PQA=0.0;SRF=152;SRR=145;SAF=47;SAR=61;SRP=3.36856;SAP=6.95112;AB=0.342857;ABP=70.5741;RUN=1;RPP=12.7417;RPPR=5.6497;RPL=65.0;RPR=43.0;EPP=3.332;EPPR=5.12328;DPRA=3.5;ODDS=57.179;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.174;Dels=0.0;FS=4.685;HaplotypeS [...]
+chr14 75513883 . T C 14554.8 REJECT NS=2;DP=382;DPB=434.0;AC=4;AN=4;AF=1.0;RO=0;AO=433;PRO=0.0;PAO=0.0;QR=0;QA=16609;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=219;SAR=214;SRP=0.0;SAP=3.13567;AB=0.0;ABP=0.0;RUN=1;RPP=10.638;RPPR=0.0;RPL=197.0;RPR=236.0;EPP=3.13567;EPPR=0.0;DPRA=0.0;ODDS=67.9111;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997691;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.465;SOR=0.7 [...]
+chr14 81574959 . A G 8679.985 REJECT NS=2;DP=385;DPB=440.0;AC=3;AN=4;AF=0.75;RO=119;AO=321;PRO=0.0;PAO=0.0;QR=4555;QA=11753;PQR=0.0;PQA=0.0;SRF=60;SRR=59;SAF=163;SAR=158;SRP=3.02855;SAP=3.17942;AB=0.645646;ABP=64.3658;RUN=1;RPP=4.53236;RPPR=4.48836;RPL=168.0;RPR=153.0;EPP=23.4736;EPPR=3.02855;DPRA=0.0;ODDS=64.1461;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993769;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.193;Dels=0.0;FS=0.0;HaplotypeScor [...]
+chr14 81575005 . C A 7500.42 REJECT NS=2;DP=323;DPB=367.0;AC=3;AN=4;AF=0.75;RO=95;AO=272;PRO=0.0;PAO=0.0;QR=3591;QA=10035;PQR=0.0;PQA=0.0;SRF=36;SRR=59;SAF=89;SAR=183;SRP=15.102;SAP=73.5512;AB=0.664311;ABP=69.3745;RUN=1;RPP=10.1953;RPPR=5.77607;RPL=151.0;RPR=121.0;EPP=13.3567;EPPR=22.2335;DPRA=0.0;ODDS=53.2674;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.981618;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.351;Dels=0.0;FS=0.793;HaplotypeScore= [...]
+chr14 81610583 . G C 13274.3 REJECT NS=2;DP=350;DPB=403.0;AC=4;AN=4;AF=1.0;RO=1;AO=401;PRO=0.0;PAO=0.0;QR=16;QA=15390;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=195;SAR=206;SRP=5.18177;SAP=3.66553;AB=0.0;ABP=0.0;RUN=1;RPP=4.22871;RPPR=5.18177;RPL=193.0;RPR=208.0;EPP=4.22871;EPPR=5.18177;DPRA=0.0;ODDS=69.1835;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997506;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.72;Dels=0.0;FS=0.0;HaplotypeScore=4.8967;MLEAC=2;M [...]
+chr14 95566105 . AC A 90.25 PASS DP=54;AC=1;AN=4;AF=0.5;ALERT;BaseQRankSum=1.464;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.2;MQRankSum=-1.235;QD=1.67;ReadPosRankSum=-1.784;SOR=0.613;ClippingRankSum=0.32 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:5,31:36:9.0:127,0,9:31:86:36:1:.:.:.:.:.:-0.000408587 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0130717
+chr14 95566107 . AC A 90.25 PASS DP=54;AC=1;AN=4;AF=0.5;ALERT;BaseQRankSum=2.79;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.2;MQRankSum=0.046;QD=1.67;ReadPosRankSum=-1.189;SOR=0.613;ClippingRankSum=0.366 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:5,31:36:9.0:127,0,9:31:86:36:1:.:.:.:.:.:-0.000408587 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0130717
+chr14 95566108 . C A 7567.12 REJECT NS=2;DP=242;DPB=242.0;AC=4;AN=4;AF=1.0;RO=0;AO=242;PRO=0.0;PAO=0.0;QR=0;QA=8614;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=174;SAR=68;SRP=0.0;SAP=103.831;AB=0.0;ABP=0.0;RUN=1;RPP=11.086;RPPR=0.0;RPL=106.0;RPR=136.0;EPP=33.1956;EPPR=0.0;DPRA=0.0;ODDS=42.8932;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8802;MQMR=0.0;PAIRED=0.983471;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=9.7626;MLEAC=2;MLEAF=1.0;MQ=59.85;QD=27.26;SOR=2 [...]
+chr14 96103099 . A G 5699.77 REJECT NS=2;DP=373;DPB=425.0;AC=2;AN=4;AF=0.5;RO=220;AO=205;PRO=0.0;PAO=0.0;QR=8258;QA=7837;PQR=0.0;PQA=0.0;SRF=108;SRR=112;SAF=91;SAR=114;SRP=3.16823;SAP=8.61376;AB=0.482353;ABP=4.1599;RUN=1;RPP=6.07155;RPPR=7.78754;RPL=111.0;RPR=94.0;EPP=14.5456;EPPR=11.8936;DPRA=0.0;ODDS=320.023;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6155;Dels=0.0;FS=2.196;HaplotypeScore=4.89 [...]
+chr14 96103115 . C T 5300.91 REJECT NS=2;DP=333;DPB=378.0;AC=2;AN=4;AF=0.5;RO=189;AO=189;PRO=0.0;PAO=0.0;QR=7249;QA=7117;PQR=0.0;PQA=0.0;SRF=81;SRR=108;SAF=83;SAR=106;SRP=11.386;SAP=9.08812;AB=0.5;ABP=3.0103;RUN=1;RPP=8.07707;RPPR=15.5221;RPL=105.0;RPR=84.0;EPP=10.1911;EPPR=22.3238;DPRA=0.0;ODDS=264.802;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994709;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.57;Dels=0.0;FS=0.2155;HaplotypeScore=2.9325 [...]
+chr14 103338324 . T A 5461.950000000001 REJECT NS=2;DP=328;DPB=371.0;AC=2;AN=4;AF=0.5;RO=181;AO=190;PRO=0.0;PAO=0.0;QR=6894;QA=7310;PQR=0.0;PQA=0.0;SRF=80;SRR=101;SAF=70;SAR=120;SRP=8.30101;SAP=31.5823;AB=0.512129;ABP=3.4844;RUN=1;RPP=14.7134;RPPR=10.5085;RPL=111.0;RPR=79.0;EPP=5.93607;EPPR=11.7562;DPRA=0.0;ODDS=285.301;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989474;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.052;Dels=0.0;FS=5.095;Haplo [...]
+chr14 103342049 . T C 4162.81 REJECT NS=2;DP=274;DPB=311.0;AC=2;AN=4;AF=0.5;RO=160;AO=151;PRO=0.0;PAO=0.0;QR=6034;QA=5669;PQR=0.0;PQA=0.0;SRF=64;SRR=96;SAF=60;SAR=91;SRP=16.9077;SAP=16.8301;AB=0.485531;ABP=3.57586;RUN=1;RPP=18.6708;RPPR=20.5992;RPL=92.0;RPR=59.0;EPP=10.6176;EPPR=8.43898;DPRA=0.0;ODDS=208.765;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993377;PAIREDR=0.99375;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6835;Dels=0.0;FS=0.0;HaplotypeScore [...]
+chr14 103370119 . C T 3830.34 REJECT NS=2;DP=242;DPB=271.0;AC=2;AN=4;AF=0.5;RO=133;AO=138;PRO=0.0;PAO=0.0;QR=4956;QA=5138;PQR=0.0;PQA=0.0;SRF=60;SRR=73;SAF=68;SAR=70;SRP=5.76954;SAP=3.07324;AB=0.509225;ABP=3.21062;RUN=1;RPP=8.10854;RPPR=5.76954;RPL=60.0;RPR=78.0;EPP=3.07324;EPPR=3.41847;DPRA=0.0;ODDS=155.204;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5865;Dels=0.0;FS=1.636;HaplotypeScore=3.8503 [...]
+chr14 103370163 . C T 4484.52 REJECT NS=2;DP=268;DPB=300.0;AC=2;AN=4;AF=0.5;RO=143;AO=157;PRO=0.0;PAO=0.0;QR=5478;QA=5971;PQR=0.0;PQA=0.0;SRF=54;SRR=89;SAF=66;SAR=91;SRP=21.6121;SAP=11.6547;AB=0.523333;ABP=4.429;RUN=1;RPP=7.00747;RPPR=3.14697;RPL=70.0;RPR=87.0;EPP=7.00747;EPPR=8.49213;DPRA=0.0;ODDS=187.663;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.2685;Dels=0.0;FS=1.4675;HaplotypeScore=4.8796 [...]
+chr14 105258892 . CA TG 9943.885 REJECT NS=2;DP=262;DPB=300.0;AC=4;AN=4;AF=1.0;RO=0;AO=296;PRO=0.0;PAO=4.0;QR=0;QA=11320;PQR=0.0;PQA=145.0;SRF=0;SRR=0;SAF=187;SAR=109;SRP=0.0;SAP=47.6429;AB=0.0;ABP=0.0;RUN=1;RPP=82.3571;RPPR=0.0;RPL=96.0;RPR=200.0;EPP=11.4908;EPPR=0.0;DPRA=0.0;ODDS=49.2435;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=1;MEANALT=2.0;LEN=2;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;JOINED;Dels=0.0;FS=0.0;HaplotypeScore=3.9327;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.91 [...]
+chr15 22772394 . C G 8223.244999999999 REJECT NS=2;DP=364;DPB=420.0;AC=3;AN=4;AF=0.75;RO=123;AO=297;PRO=0.0;PAO=0.0;QR=4691;QA=11409;PQR=0.0;PQA=0.0;SRF=44;SRR=79;SAF=129;SAR=168;SRP=24.6368;SAP=14.1309;AB=0.604502;ABP=32.5102;RUN=1;RPP=13.0195;RPPR=29.8624;RPL=167.0;RPR=130.0;EPP=4.24592;EPPR=6.98251;DPRA=0.0;ODDS=68.9813;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996633;PAIREDR=0.97561;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.439;Dels=0.0;FS=1.63 [...]
+chr15 24032467 . C T 13075.25 REJECT NS=2;DP=345;DPB=397.0;AC=4;AN=4;AF=1.0;RO=1;AO=396;PRO=0.0;PAO=0.0;QR=39;QA=15164;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=159;SAR=237;SRP=5.18177;SAP=36.372;AB=0.0;ABP=0.0;RUN=1;RPP=8.62542;RPPR=5.18177;RPL=214.0;RPR=182.0;EPP=12.6832;EPPR=5.18177;DPRA=0.0;ODDS=68.5101;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997475;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.177;Dels=0.0;FS=1.895;HaplotypeScore=7.7654;MLEAC= [...]
+chr15 34502467 . G A 12075.2 REJECT NS=2;DP=320;DPB=367.0;AC=4;AN=4;AF=1.0;RO=0;AO=366;PRO=0.0;PAO=0.0;QR=0;QA=13989;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=151;SAR=215;SRP=0.0;SAP=27.3118;AB=0.0;ABP=0.0;RUN=1;RPP=9.08568;RPPR=0.0;RPL=199.0;RPR=167.0;EPP=7.021;EPPR=0.0;DPRA=0.0;ODDS=62.339;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9329;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.79;SOR=1.084 GT:G [...]
+chr15 34638834 . G A 298.77 PASS SOMATIC;DP=138;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-3.683;Dels=0.0;FS=182.221;HaplotypeScore=10.7974;MLEAC=1;MLEAF=0.5;MQ=54.4;MQRankSum=2.089;QD=2.16;ReadPosRankSum=-2.115;SOR=5.889 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00690701 0/1:120,18:138:99.0:327,0,4664:18:13:138:.:1:.:.:.:.:-0.0142204
+chr15 34638841 . A G 2553.77 PASS SOMATIC;DP=87;AC=1;AN=4;AF=0.5;MQ0=0;ALERT;BaseQRankSum=5.022;Dels=0.03;FS=178.734;HaplotypeScore=8.8311;MLEAC=1;MLEAF=0.5;MQ=51.18;MQRankSum=-1.354;QD=29.35;ReadPosRankSum=2.713;SOR=8.379 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00690701 0/1:18,65:84:99.0:2582,0,448:65:78:83:.:1:.:.:.:.:-0.0142204
+chr15 34638841 . AGGAGGTC GGAAGGCT 2859.09 REJECT NS=2;DP=117;DPB=124.75;AC=3;AN=4;AF=0.75;RO=20;AO=96;PRO=0.0;PAO=22.0;QR=589;QA=3630;PQR=0.0;PQA=790.0;SRF=20;SRR=0;SAF=16;SAR=80;SRP=46.4397;SAP=95.6598;AB=0.786517;ABP=66.471;RUN=1;RPP=211.472;RPPR=24.2907;RPL=96.0;RPR=0.0;EPP=95.6598;EPPR=24.2907;DPRA=0.0;ODDS=14.3297;GTI=0;TYPE=complex;CIGAR=1X1M1X3M2X;NUMALT=1;MEANALT=1.5;LEN=8;MQM=44.1146;MQMR=56.8;PAIRED=0.822917;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr15 34638843 . G A 2377.77 PASS SOMATIC;DP=82;AC=1;AN=4;AF=0.5;MQ0=0;ALERT;BaseQRankSum=5.949;Dels=0.0;FS=114.357;HaplotypeScore=7.8646;MLEAC=1;MLEAF=0.5;MQ=50.6;MQRankSum=-2.305;QD=29.0;ReadPosRankSum=3.038;SOR=8.254 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00690701 0/1:21,61:82:99.0:2406,0,391:61:74:82:.:1:.:.:.:.:-0.0142204
+chr15 34638847 . T C 2412.77 PASS SOMATIC;DP=79;AC=1;AN=4;AF=0.5;MQ0=0;ALERT;BaseQRankSum=5.593;Dels=0.0;FS=154.534;HaplotypeScore=3.8602;MLEAC=1;MLEAF=0.5;MQ=50.21;MQRankSum=-2.881;QD=30.54;ReadPosRankSum=-0.707;SOR=8.254 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00690701 0/1:18,61:79:99.0:2441,0,341:61:77:79:.:1:.:.:.:.:-0.0142204
+chr15 34638848 . C T 2418.77 PASS SOMATIC;DP=79;AC=1;AN=4;AF=0.5;MQ0=0;ALERT;BaseQRankSum=5.756;Dels=0.0;FS=147.487;HaplotypeScore=5.765;MLEAC=1;MLEAF=0.5;MQ=50.21;MQRankSum=-2.11;QD=30.62;ReadPosRankSum=-1.642;SOR=8.254 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00690701 0/1:18,61:79:99.0:2447,0,311:61:77:79:.:1:.:.:.:.:-0.0142204
+chr15 34638862 . T C 73.7256 REJECT NS=2;DP=26;DPB=26.0;AC=2;AN=4;AF=0.5;RO=19;AO=7;PRO=0.0;PAO=0.0;QR=573;QA=246;PQR=0.0;PQA=0.0;SRF=19;SRR=0;SAF=3;SAR=4;SRP=44.2683;SAP=3.32051;AB=0.269231;ABP=15.0369;RUN=1;RPP=18.2106;RPPR=3.12459;RPL=7.0;RPR=0.0;EPP=3.32051;EPPR=3.12459;DPRA=0.0;ODDS=3.82582;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=44.5714;MQMR=58.7368;PAIRED=0.428571;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:C [...]
+chr15 34638910 . C A 741.238 REJECT NS=2;DP=26;DPB=29.0;AC=4;AN=4;AF=1.0;RO=0;AO=29;PRO=0.0;PAO=0.0;QR=0;QA=937;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=29;SAR=0;SRP=0.0;SAP=65.983;AB=0.0;ABP=0.0;RUN=1;RPP=4.88226;RPPR=0.0;RPL=12.0;RPR=17.0;EPP=4.88226;EPPR=0.0;DPRA=0.0;ODDS=7.50325;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.709;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.825;SOR=4.371 GT:GQ:DP:RO: [...]
+chr15 34639015 . C T 1768.02 REJECT NS=2;DP=67;DPB=75.0;AC=4;AN=4;AF=1.0;RO=1;AO=71;PRO=0.0;PAO=0.0;QR=15;QA=2232;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=71;SAR=0;SRP=5.18177;SAP=157.185;AB=0.0;ABP=0.0;RUN=1;RPP=4.50892;RPPR=5.18177;RPL=39.0;RPR=32.0;EPP=4.50892;EPPR=5.18177;DPRA=0.0;ODDS=13.7086;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=2;MEANALT=1.5;LEN=1;MQM=58.2958;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.55;Dels=0.0;FS=0.0;HaplotypeScore=21.2333;M [...]
+chr15 34639015 . C A 1768.02 REJECT NS=2;DP=75;DPB=75.0;AC=0;AN=4;AF=0.0;RO=1;AO=3;PRO=0.0;PAO=0.0;QR=15;QA=47;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=3;SAR=0;SRP=5.18177;SAP=9.52472;AB=0.0;ABP=0.0;RUN=1;RPP=9.52472;RPPR=5.18177;RPL=0.0;RPR=3.0;EPP=9.52472;EPPR=5.18177;DPRA=4.0;ODDS=13.7086;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=2;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI: [...]
+chr15 34639463 . C CT 976.19 REJECT NS=2;DP=69;DPB=103.556;AC=2;AN=4;AF=0.5;RO=9;AO=51;PRO=26.5;PAO=30.5;QR=332;QA=1503;PQR=929.5;PQA=1040.5;SRF=0;SRR=9;SAF=0;SAR=51;SRP=22.5536;SAP=113.755;AB=0.73913;ABP=37.2818;RUN=1;RPP=29.6215;RPPR=5.18177;RPL=38.0;RPR=13.0;EPP=29.6215;EPPR=5.18177;DPRA=0.0;ODDS=5.59969;GTI=0;TYPE=ins;CIGAR=1M1I17M;NUMALT=1;MEANALT=4.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.478;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.12;MQ [...]
+chr15 34640054 . AAAAAAT A 4594.17 REJECT NS=2;DP=158;DPB=333.75;AC=4;AN=4;AF=1.0;RO=0;AO=153;PRO=203.5;PAO=209.5;QR=0;QA=5056;PQR=7422.5;PQA=7627.5;SRF=0;SRR=0;SAF=106;SAR=47;SRP=0.0;SAP=52.4148;AB=0.0;ABP=0.0;RUN=1;RPP=52.4148;RPPR=0.0;RPL=47.0;RPR=106.0;EPP=3.36512;EPPR=0.0;DPRA=0.0;ODDS=25.4328;GTI=0;TYPE=del;CIGAR=1M6D45M;NUMALT=1;MEANALT=3.5;LEN=6;MQM=60.5882;MQMR=0.0;PAIRED=0.993464;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=34640060;HOMLEN=35;HOMSEQ=AAAAATAAAAATAAAAATAAAAATAAA [...]
+chr15 34640218 . C T 17874.5 REJECT NS=2;DP=473;DPB=534.0;AC=4;AN=4;AF=1.0;RO=0;AO=534;PRO=0.0;PAO=0.0;QR=0;QA=20268;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=277;SAR=257;SRP=0.0;SAP=4.63687;AB=0.0;ABP=0.0;RUN=1;RPP=3.27055;RPPR=0.0;RPL=271.0;RPR=263.0;EPP=3.41694;EPPR=0.0;DPRA=0.0;ODDS=79.6827;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992509;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8263;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.37;SOR=0. [...]
+chr15 34640378 . T C 18584.85 REJECT NS=2;DP=499;DPB=567.0;AC=4;AN=4;AF=1.0;RO=0;AO=567;PRO=0.0;PAO=0.0;QR=0;QA=21280;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=285;SAR=282;SRP=0.0;SAP=3.04477;AB=0.0;ABP=0.0;RUN=1;RPP=4.39284;RPPR=0.0;RPL=274.0;RPR=293.0;EPP=3.32051;EPPR=0.0;DPRA=0.0;ODDS=88.5051;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996473;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=17.4088;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.545;SOR [...]
+chr15 38614525 . G A 10460.0 REJECT NS=2;DP=391;DPB=447.0;AC=2;AN=4;AF=0.5;RO=109;AO=338;PRO=0.0;PAO=0.0;QR=4185;QA=13057;PQR=0.0;PQA=0.0;SRF=62;SRR=47;SAF=158;SAR=180;SRP=7.4927;SAP=6.11975;AB=0.756152;ABP=257.762;RUN=1;RPP=3.42147;RPPR=4.62396;RPL=173.0;RPR=165.0;EPP=9.58896;EPPR=4.62396;DPRA=0.0;ODDS=150.825;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994083;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.086;Dels=0.0;FS=4.4605;HaplotypeScor [...]
+chr15 38631930 . C A 6546.76 REJECT NS=2;DP=261;DPB=303.0;AC=2;AN=4;AF=0.5;RO=88;AO=215;PRO=0.0;PAO=0.0;QR=3296;QA=8316;PQR=0.0;PQA=0.0;SRF=52;SRR=36;SAF=132;SAR=83;SRP=9.32731;SAP=27.2601;AB=0.709571;ABP=118.6;RUN=1;RPP=23.4625;RPPR=7.84676;RPL=85.0;RPR=130.0;EPP=11.5043;EPPR=5.47788;DPRA=0.0;ODDS=179.138;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990698;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.929;Dels=0.0;FS=0.7475;HaplotypeScore=4.8 [...]
+chr15 38643574 . T C 10660.1 REJECT NS=2;DP=409;DPB=469.0;AC=2;AN=4;AF=0.5;RO=120;AO=349;PRO=0.0;PAO=0.0;QR=4628;QA=13342;PQR=0.0;PQA=0.0;SRF=71;SRR=49;SAF=181;SAR=168;SRP=11.7686;SAP=4.06182;AB=0.744136;ABP=245.812;RUN=1;RPP=5.75419;RPPR=3.08268;RPL=164.0;RPR=185.0;EPP=5.75419;EPPR=3.29983;DPRA=0.0;ODDS=212.672;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991404;PAIREDR=0.991667;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2175;Dels=0.0;FS=4.4605;Haplot [...]
+chr15 39000056 . T C 3752.7799999999997 REJECT NS=2;DP=240;DPB=279.0;AC=2;AN=4;AF=0.5;RO=142;AO=137;PRO=0.0;PAO=0.0;QR=5494;QA=5268;PQR=0.0;PQA=0.0;SRF=84;SRR=58;SAF=82;SAR=55;SRP=13.3477;SAP=14.5651;AB=0.491039;ABP=3.20488;RUN=1;RPP=101.931;RPPR=58.0617;RPL=29.0;RPR=108.0;EPP=3.40655;EPPR=3.25497;DPRA=0.0;ODDS=231.513;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.146;MQMR=60.0704;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.822;Dels=0.0;FS=5.06;Haploty [...]
+chr15 39000074 . C T 2523.18 PASS SOMATIC;NS=2;DP=347;DPB=347.0;AC=1;AN=3;AF=0.25;RO=252;AO=95;PRO=0.0;PAO=0.0;QR=9629;QA=3625;PQR=0.0;PQA=0.0;SRF=142;SRR=110;SAF=59;SAR=36;SRP=11.8341;SAP=15.102;AB=0.381526;ABP=33.3673;RUN=1;RPP=5.77607;RPPR=24.5527;RPL=42.0;RPR=53.0;EPP=4.13032;EPPR=7.18091;DPRA=2.54082;ODDS=62.103;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.1053;MQMR=60.0794;PAIRED=1.0;PAIREDR=0.996032;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.447;Dels=0.0;FS= [...]
+chr15 39000104 . C CTTTTATA 6854.34 REJECT NS=2;DP=299;DPB=620.143;AC=2;AN=4;AF=0.5;RO=82;AO=239;PRO=41.0;PAO=43.0;QR=3089;QA=8595;PQR=1462.0;PQA=1532.0;SRF=38;SRR=44;SAF=127;SAR=112;SRP=3.96363;SAP=5.05457;AB=0.737654;ABP=161.957;RUN=1;RPP=3.09207;RPPR=3.96363;RPL=121.0;RPR=118.0;EPP=6.29022;EPPR=3.11623;DPRA=0.0;ODDS=67.5888;GTI=0;TYPE=ins;CIGAR=1M7I6M;NUMALT=1;MEANALT=2.5;LEN=7;MQM=60.0;MQMR=60.0;PAIRED=0.995816;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=39000104;HOMLEN=5;HOMSEQ=TT [...]
+chr15 40681676 . T A 1578.22 PASS SOMATIC;NS=2;DP=248;DPB=248.0;AC=1;AN=3;AF=0.25;RO=183;AO=65;PRO=0.0;PAO=0.0;QR=7041;QA=2459;PQR=0.0;PQA=0.0;SRF=133;SRR=50;SAF=42;SAR=23;SRP=84.755;SAP=15.0703;AB=0.353261;ABP=37.4234;RUN=1;RPP=70.66;RPPR=62.8267;RPL=10.0;RPR=55.0;EPP=4.64726;EPPR=17.5461;DPRA=2.875;ODDS=40.9447;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989071;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.802;Dels=0.0;FS=6.278;Haplo [...]
+chr15 40683780 . G A 2550.08 PASS SOMATIC;NS=2;DP=384;DPB=384.0;AC=1;AN=3;AF=0.25;RO=286;AO=98;PRO=0.0;PAO=0.0;QR=10920;QA=3738;PQR=0.0;PQA=0.0;SRF=123;SRR=163;SAF=39;SAR=59;SRP=15.1584;SAP=11.8735;AB=0.356618;ABP=51.581;RUN=1;RPP=3.09893;RPPR=19.0762;RPL=50.0;RPR=48.0;EPP=4.4284;EPPR=17.7095;DPRA=0.0;ODDS=67.6447;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.982517;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.283;Dels=0.0;FS=1.54;Haplo [...]
+chr15 40684232 . G A 2443.29 PASS SOMATIC;NS=2;DP=381;DPB=381.0;AC=1;AN=3;AF=0.25;RO=284;AO=95;PRO=0.0;PAO=0.0;QR=10856;QA=3668;PQR=0.0;PQA=0.0;SRF=110;SRR=174;SAF=32;SAR=63;SRP=34.3284;SAP=24.9765;AB=0.338078;ABP=67.0031;RUN=1;RPP=13.0905;RPPR=3.49965;RPL=58.0;RPR=37.0;EPP=19.6735;EPPR=56.9607;DPRA=2.81;ODDS=63.3461;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.335;Dels=0.0;FS=0.484;Haplot [...]
+chr15 40685406 . A T 2952.95 PASS SOMATIC;NS=2;DP=395;DPB=395.0;AC=1;AN=3;AF=0.25;RO=286;AO=109;PRO=0.0;PAO=0.0;QR=11031;QA=4278;PQR=0.0;PQA=0.0;SRF=154;SRR=132;SAF=54;SAR=55;SRP=6.6851;SAP=3.03022;AB=0.353896;ABP=60.1172;RUN=1;RPP=8.76769;RPPR=12.8503;RPL=63.0;RPR=46.0;EPP=5.42083;EPPR=10.7851;DPRA=3.54023;ODDS=55.3092;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996503;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=4.349;Dels=0.0;FS=6.37 [...]
+chr15 41991315 . A T 7888.27 REJECT NS=2;DP=378;DPB=424.0;AC=3;AN=4;AF=0.75;RO=130;AO=293;PRO=0.0;PAO=0.0;QR=4989;QA=10741;PQR=0.0;PQA=0.0;SRF=65;SRR=65;SAF=133;SAR=160;SRP=3.0103;SAP=8.41304;AB=0.606607;ABP=35.8823;RUN=1;RPP=3.01771;RPPR=3.61163;RPL=147.0;RPR=146.0;EPP=51.635;EPPR=12.6316;DPRA=0.0;ODDS=57.6776;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993174;PAIREDR=0.992308;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-3.176;Dels=0.0;FS=0.0;HaplotypeS [...]
+chr15 41991391 . CT C 467.874 REJECT NS=2;DP=131;DPB=201.4;AC=2;AN=4;AF=0.5;RO=96;AO=26;PRO=89.0;PAO=47.0;QR=3647;QA=975;PQR=3233.5;PQA=1667.5;SRF=17;SRR=79;SAF=5;SAR=21;SRP=89.9597;SAP=24.391;AB=0.198473;ABP=106.462;RUN=1;RPP=24.391;RPPR=50.8732;RPL=21.0;RPR=5.0;EPP=6.01695;EPPR=12.0581;DPRA=0.0;ODDS=13.9044;GTI=0;TYPE=del;CIGAR=16M1D18M;NUMALT=1;MEANALT=4.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989583;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:C [...]
+chr15 42026764 . C T 7843.155000000001 REJECT NS=2;DP=380;DPB=432.0;AC=3;AN=4;AF=0.75;RO=135;AO=296;PRO=0.0;PAO=0.0;QR=5122;QA=10936;PQR=0.0;PQA=0.0;SRF=69;SRR=66;SAF=130;SAR=166;SRP=3.15506;SAP=12.5178;AB=0.585366;ABP=23.7717;RUN=1;RPP=29.4201;RPPR=8.81698;RPL=178.0;RPR=118.0;EPP=45.3834;EPPR=3.15506;DPRA=0.0;ODDS=65.7944;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996622;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.21;Dels=0.0;FS=6.295;Ha [...]
+chr15 42041712 . G A 7403.05 REJECT NS=2;DP=330;DPB=370.0;AC=3;AN=4;AF=0.75;RO=113;AO=257;PRO=0.0;PAO=0.0;QR=4294;QA=9894;PQR=0.0;PQA=0.0;SRF=48;SRR=65;SAF=121;SAR=136;SRP=8.56389;SAP=4.91139;AB=0.611684;ABP=34.5377;RUN=1;RPP=3.08634;RPPR=3.02952;RPL=130.0;RPR=127.0;EPP=3.69469;EPPR=17.0192;DPRA=0.0;ODDS=50.2975;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996109;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.479;Dels=0.0;FS=1.003;HaplotypeScor [...]
+chr15 54009339 . C T 5129.9 REJECT NS=2;DP=359;DPB=408.0;AC=2;AN=4;AF=0.5;RO=219;AO=188;PRO=0.0;PAO=0.0;QR=8418;QA=7207;PQR=0.0;PQA=0.0;SRF=107;SRR=112;SAF=67;SAR=121;SRP=3.25818;SAP=36.6912;AB=0.460784;ABP=8.46027;RUN=1;RPP=12.0658;RPPR=12.539;RPL=80.0;RPR=108.0;EPP=53.3238;EPPR=19.6781;DPRA=0.0;ODDS=313.395;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994681;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.219;Dels=0.0;FS=11.1565;HaplotypeScore [...]
+chr15 63004762 . T TA 10922.8 REJECT NS=2;DP=285;DPB=411.8;AC=4;AN=4;AF=1.0;RO=0;AO=325;PRO=11.0;PAO=19.0;QR=0;QA=12073;PQR=337.0;PQA=626.0;SRF=0;SRR=0;SAF=217;SAR=108;SRP=0.0;SAP=82.3926;AB=0.0;ABP=0.0;RUN=1;RPP=44.7093;RPPR=0.0;RPL=123.0;RPR=202.0;EPP=38.6158;EPPR=0.0;DPRA=0.0;ODDS=56.6564;GTI=0;TYPE=ins;CIGAR=1M1I4M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.1231;MQMR=0.0;PAIRED=0.996923;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=63004762;HOMLEN=0;SVLEN=1;SVTYPE=INS;BaseQRankSum=0.945;FS=0. [...]
+chr15 66745890 . G A 12881.15 REJECT NS=2;DP=341;DPB=391.0;AC=4;AN=4;AF=1.0;RO=0;AO=391;PRO=0.0;PAO=0.0;QR=0;QA=14961;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=158;SAR=233;SRP=0.0;SAP=34.2495;AB=0.0;ABP=0.0;RUN=1;RPP=16.3446;RPPR=0.0;RPL=220.0;RPR=171.0;EPP=34.2495;EPPR=0.0;DPRA=0.0;ODDS=66.7202;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994885;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.65;SOR=1.22 [...]
+chr15 67391394 . GT G 6762.62 REJECT NS=2;DP=186;DPB=167.4;AC=4;AN=4;AF=1.0;RO=0;AO=201;PRO=5.0;PAO=9.0;QR=0;QA=7558;PQR=184.0;PQA=332.0;SRF=0;SRR=0;SAF=69;SAR=132;SRP=0.0;SAP=45.8888;AB=0.0;ABP=0.0;RUN=1;RPP=92.4728;RPPR=0.0;RPL=146.0;RPR=55.0;EPP=3.10753;EPPR=0.0;DPRA=0.0;ODDS=30.5756;GTI=0;TYPE=del;CIGAR=1M1D3M;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=67391395;HOMLEN=1;HOMSEQ=T;SVLEN=-1;SVTYPE=DEL;FS=0.0;MLEAC=2;MLEAF=1.0;MQ [...]
+chr15 67457335 . A G 13997.4 REJECT NS=2;DP=372;DPB=421.0;AC=4;AN=4;AF=1.0;RO=0;AO=421;PRO=0.0;PAO=0.0;QR=0;QA=15977;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=209;SAR=212;SRP=0.0;SAP=3.05672;AB=0.0;ABP=0.0;RUN=1;RPP=3.6344;RPPR=0.0;RPL=205.0;RPR=216.0;EPP=10.0715;EPPR=0.0;DPRA=0.0;ODDS=64.8472;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992874;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.924;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.765;SOR=0.7 [...]
+chr15 73533057 . C A 1494.94 REJECT NS=2;DP=364;DPB=418.0;AC=2;AN=4;AF=0.5;RO=338;AO=80;PRO=0.0;PAO=0.0;QR=12735;QA=3102;PQR=0.0;PQA=0.0;SRF=158;SRR=180;SAF=32;SAR=48;SRP=6.11975;SAP=9.95901;AB=0.191388;ABP=348.804;RUN=1;RPP=6.91895;RPPR=3.036;RPL=46.0;RPR=34.0;EPP=3.44459;EPPR=21.7441;DPRA=0.0;ODDS=70.9787;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988166;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.55;Dels=0.0;FS=1.681;HaplotypeScore=1.96 [...]
+chr15 78003964 . C T 3109.31 PASS SOMATIC;NS=2;DP=420;DPB=420.0;AC=1;AN=3;AF=0.25;RO=304;AO=116;PRO=0.0;PAO=0.0;QR=11726;QA=4498;PQR=0.0;PQA=0.0;SRF=171;SRR=133;SAF=67;SAR=49;SRP=13.3248;SAP=9.07545;AB=0.371795;ABP=47.5533;RUN=1;RPP=17.6865;RPPR=16.8392;RPL=44.0;RPR=72.0;EPP=24.6501;EPPR=13.3248;DPRA=2.88889;ODDS=68.34;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.045;Dels=0.0;FS=0.898;Hapl [...]
+chr15 80259955 . TGTAA T 4284.86 REJECT NS=2;DP=331;DPB=268.167;AC=2;AN=4;AF=0.5;RO=197;AO=169;PRO=25.0;PAO=4.0;QR=7478;QA=6087;PQR=806.5;PQA=19.5;SRF=130;SRR=67;SAF=115;SAR=54;SRP=46.7594;SAP=50.8212;AB=0.459239;ABP=8.32097;RUN=1;RPP=33.8606;RPPR=7.87131;RPL=60.0;RPR=109.0;EPP=7.64877;EPPR=3.90314;DPRA=0.0;ODDS=221.156;GTI=0;TYPE=del;CIGAR=1M4D1M;NUMALT=1;MEANALT=2.0;LEN=4;MQM=60.2367;MQMR=59.8274;PAIRED=0.988166;PAIREDR=0.974619;technology.ILLUMINA=1.0;MQ0=0;END=80259959;HOMLEN=2;HOMSE [...]
+chr15 80259964 . C T 5078.72 REJECT NS=2;DP=343;DPB=390.0;AC=2;AN=4;AF=0.5;RO=207;AO=180;PRO=0.0;PAO=0.0;QR=7797;QA=6955;PQR=0.0;PQA=0.0;SRF=133;SRR=74;SAF=118;SAR=62;SRP=39.5267;SAP=40.8422;AB=0.461538;ABP=8.02139;RUN=1;RPP=24.2907;RPPR=8.55962;RPL=69.0;RPR=111.0;EPP=13.8677;EPPR=9.56668;DPRA=0.0;ODDS=263.391;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.1111;MQMR=59.8357;PAIRED=0.988889;PAIREDR=0.975845;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.3945;Dels=0.0;FS=0.4575;Ha [...]
+chr15 80260014 . T C 5482.57 REJECT NS=2;DP=363;DPB=416.0;AC=2;AN=4;AF=0.5;RO=218;AO=198;PRO=0.0;PAO=0.0;QR=8270;QA=7473;PQR=0.0;PQA=0.0;SRF=100;SRR=118;SAF=89;SAR=109;SRP=6.23763;SAP=7.39711;AB=0.475962;ABP=5.09825;RUN=1;RPP=24.2425;RPPR=4.44467;RPL=121.0;RPR=77.0;EPP=30.4279;EPPR=25.9602;DPRA=0.0;ODDS=277.938;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0404;MQMR=59.9587;PAIRED=0.989899;PAIREDR=0.986239;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1285;Dels=0.0;FS=2.5695;H [...]
+chr15 80263217 . C T 6830.475 REJECT NS=2;DP=369;DPB=424.0;AC=2;AN=4;AF=0.5;RO=180;AO=243;PRO=0.0;PAO=0.0;QR=6996;QA=9115;PQR=0.0;PQA=0.0;SRF=96;SRR=84;SAF=125;SAR=118;SRP=4.74748;SAP=3.44817;AB=0.573113;ABP=22.697;RUN=1;RPP=8.59536;RPPR=6.09862;RPL=109.0;RPR=134.0;EPP=3.44817;EPPR=4.74748;DPRA=0.0;ODDS=318.126;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.8;Dels=0.0;FS=2.8465;HaplotypeScore=7.77 [...]
+chr15 80263345 . A C 5941.935 REJECT NS=2;DP=357;DPB=409.0;AC=2;AN=4;AF=0.5;RO=197;AO=211;PRO=0.0;PAO=0.0;QR=7570;QA=7994;PQR=0.0;PQA=0.0;SRF=98;SRR=99;SAF=93;SAR=118;SRP=3.02132;SAP=9.44239;AB=0.515892;ABP=3.90756;RUN=1;RPP=4.74954;RPPR=3.55041;RPL=112.0;RPR=99.0;EPP=3.02059;EPPR=3.28587;DPRA=0.0;ODDS=320.09;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994924;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.2415;Dels=0.0;FS=3.3455;HaplotypeScore [...]
+chr15 80263406 . C T 4927.99 REJECT NS=2;DP=291;DPB=332.0;AC=2;AN=4;AF=0.5;RO=160;AO=172;PRO=0.0;PAO=0.0;QR=6139;QA=6628;PQR=0.0;PQA=0.0;SRF=58;SRR=102;SAF=68;SAR=104;SRP=29.2851;SAP=19.3721;AB=0.518072;ABP=3.95214;RUN=1;RPP=12.9082;RPPR=18.6992;RPL=100.0;RPR=72.0;EPP=4.82828;EPPR=15.2248;DPRA=0.0;ODDS=266.969;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.875;PAIRED=0.994186;PAIREDR=0.99375;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6825;Dels=0.0;FS=2.0575;Haploty [...]
+chr15 88576407 . T TTA 280.332 REJECT NS=2;DP=59;DPB=100.978;AC=2;AN=4;AF=0.5;RO=17;AO=18;PRO=17.3167;PAO=17.65;QR=640;QA=484;PQR=633.633;PQA=638.967;SRF=1;SRR=16;SAF=0;SAR=18;SRP=31.7504;SAP=42.0968;AB=0.305085;ABP=22.4799;RUN=1;RPP=4.9405;RPPR=4.1599;RPL=7.0;RPR=11.0;EPP=4.9405;EPPR=3.13803;DPRA=0.0;ODDS=2.0219;GTI=0;TYPE=ins;CIGAR=1M2I44M;NUMALT=5;MEANALT=7.0;LEN=2;MQM=58.8889;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.131;FS=3.452; [...]
+chr15 88576407 . T TTATA 280.332 REJECT NS=2;DP=59;DPB=100.978;AC=2;AN=2;AF=0.0;RO=17;AO=11;PRO=17.3167;PAO=17.65;QR=640;QA=289;PQR=633.633;PQA=638.967;SRF=1;SRR=16;SAF=0;SAR=11;SRP=31.7504;SAP=26.8965;AB=0.186441;ABP=53.3958;RUN=1;RPP=7.94546;RPPR=4.1599;RPL=3.0;RPR=8.0;EPP=7.94546;EPPR=3.13803;DPRA=0.0;ODDS=2.0219;GTI=0;TYPE=ins;CIGAR=1M4I44M;NUMALT=5;MEANALT=7.0;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr15 88576407 . T TTATATA 280.332 REJECT NS=2;DP=59;DPB=100.978;AC=2;AN=2;AF=0.0;RO=17;AO=3;PRO=17.3167;PAO=17.65;QR=640;QA=88;PQR=633.633;PQA=638.967;SRF=1;SRR=16;SAF=0;SAR=3;SRP=31.7504;SAP=9.52472;AB=0.0508475;ABP=106.394;RUN=1;RPP=3.73412;RPPR=4.1599;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=3.13803;DPRA=0.0;ODDS=2.0219;GTI=0;TYPE=ins;CIGAR=1M6I44M;NUMALT=5;MEANALT=7.0;LEN=6;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr15 88576407 . TTA T 280.332 REJECT NS=2;DP=59;DPB=100.978;AC=2;AN=2;AF=0.0;RO=17;AO=2;PRO=17.3167;PAO=16.5667;QR=640;QA=46;PQR=633.633;PQA=605.133;SRF=1;SRR=16;SAF=0;SAR=2;SRP=31.7504;SAP=7.35324;AB=0.133333;ABP=20.5268;RUN=1;RPP=7.35324;RPPR=4.1599;RPL=2.0;RPR=0.0;EPP=7.35324;EPPR=3.13803;DPRA=0.0;ODDS=2.0219;GTI=0;TYPE=del;CIGAR=1M2D42M;NUMALT=5;MEANALT=5.0;LEN=2;MQM=65.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr15 88576407 . TTATA T 280.332 REJECT NS=2;DP=59;DPB=100.978;AC=2;AN=2;AF=0.0;RO=17;AO=2;PRO=17.3167;PAO=17.1667;QR=640;QA=47;PQR=633.633;PQA=618.333;SRF=1;SRR=16;SAF=0;SAR=2;SRP=31.7504;SAP=7.35324;AB=0.0454545;ABP=81.9729;RUN=1;RPP=3.0103;RPPR=4.1599;RPL=1.0;RPR=1.0;EPP=3.0103;EPPR=3.13803;DPRA=0.0;ODDS=2.0219;GTI=0;TYPE=del;CIGAR=1M4D40M;NUMALT=5;MEANALT=9.0;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr15 88579653 . T TA 1752.48 REJECT NS=2;DP=328;DPB=401.636;AC=2;AN=2;AF=0.0;RO=181;AO=18;PRO=52.0;PAO=38.0;QR=6653;QA=565;PQR=1828.0;PQA=1305.0;SRF=65;SRR=116;SAF=7;SAR=11;SRP=34.2147;SAP=4.9405;AB=0.054878;ABP=567.487;RUN=1;RPP=3.49285;RPPR=21.2579;RPL=10.0;RPR=8.0;EPP=4.9405;EPPR=16.0751;DPRA=0.0;ODDS=149.438;GTI=0;TYPE=ins;CIGAR=1M1I21M;NUMALT=3;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994475;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr15 88579653 . TA T 1343.105 REJECT NS=2;DP=324;DPB=401.636;AC=2;AN=4;AF=0.5;RO=181;AO=80;PRO=52.0;PAO=41.0;QR=6653;QA=2611;PQR=1828.0;PQA=1465.0;SRF=65;SRR=116;SAF=31;SAR=49;SRP=34.2147;SAP=11.8048;AB=0.243902;ABP=189.863;RUN=1;RPP=3.0103;RPPR=21.2579;RPL=40.0;RPR=40.0;EPP=3.11887;EPPR=16.0751;DPRA=0.0;ODDS=149.438;GTI=0;TYPE=del;CIGAR=1M1D20M;NUMALT=3;MEANALT=13.0;LEN=1;MQM=60.225;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994475;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.068 [...]
+chr15 88579653 . TAA T 1752.48 REJECT NS=2;DP=328;DPB=401.636;AC=2;AN=2;AF=0.0;RO=181;AO=20;PRO=52.0;PAO=33.0;QR=6653;QA=668;PQR=1828.0;PQA=1163.0;SRF=65;SRR=116;SAF=8;SAR=12;SRP=34.2147;SAP=4.74748;AB=0.0609756;ABP=552.128;RUN=1;RPP=3.44459;RPPR=21.2579;RPL=11.0;RPR=9.0;EPP=3.44459;EPPR=16.0751;DPRA=0.0;ODDS=149.438;GTI=0;TYPE=del;CIGAR=1M2D19M;NUMALT=3;MEANALT=13.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=0.95;PAIREDR=0.994475;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr15 88582349 . AAC A 1773.88 REJECT SOMATIC;NS=2;DP=134;DPB=226.125;AC=1;AN=3;AF=0.25;RO=1;AO=31;PRO=53.6667;PAO=54.6667;QR=39;QA=843;PQR=1919.85;PQA=1908.85;SRF=1;SRR=0;SAF=14;SAR=17;SRP=5.18177;SAP=3.64073;AB=0.231343;ABP=87.0171;RUN=1;RPP=3.08035;RPPR=5.18177;RPL=16.0;RPR=15.0;EPP=4.76149;EPPR=5.18177;DPRA=0.0;ODDS=10.6384;GTI=0;TYPE=del;CIGAR=1M2D45M;NUMALT=4;MEANALT=10.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr15 88582349 . AACAC A 1773.88 REJECT NS=2;DP=134;DPB=226.125;AC=2;AN=2;AF=0.25;RO=1;AO=27;PRO=53.6667;PAO=51.6667;QR=39;QA=780;PQR=1919.85;PQA=1775.85;SRF=1;SRR=0;SAF=8;SAR=19;SRP=5.18177;SAP=12.7417;AB=0.201493;ABP=106.722;RUN=1;RPP=3.09072;RPPR=5.18177;RPL=14.0;RPR=13.0;EPP=3.09072;EPPR=5.18177;DPRA=0.0;ODDS=10.6384;GTI=0;TYPE=del;CIGAR=1M4D43M;NUMALT=4;MEANALT=10.5;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.275;FS= [...]
+chr15 88582349 . AACACAC A 1773.88 REJECT NS=2;DP=134;DPB=226.125;AC=2;AN=2;AF=0.5;RO=1;AO=50;PRO=53.6667;PAO=48.0;QR=39;QA=1530;PQR=1919.85;PQA=1709.85;SRF=1;SRR=0;SAF=26;SAR=24;SRP=5.18177;SAP=3.18402;AB=0.373134;ABP=21.7433;RUN=1;RPP=7.35324;RPPR=5.18177;RPL=30.0;RPR=20.0;EPP=4.57376;EPPR=5.18177;DPRA=0.0;ODDS=10.6384;GTI=0;TYPE=del;CIGAR=1M6D41M;NUMALT=4;MEANALT=10.5;LEN=6;MQM=61.6;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.73;FS= [...]
+chr15 88582349 . AACACACAC A 1773.88 REJECT NS=2;DP=134;DPB=226.125;AC=0;AN=4;AF=0.0;RO=1;AO=10;PRO=53.6667;PAO=48.0;QR=39;QA=333;PQR=1919.85;PQA=1711.6;SRF=1;SRR=0;SAF=7;SAR=3;SRP=5.18177;SAP=6.48466;AB=0.0746269;ABP=213.611;RUN=1;RPP=3.87889;RPPR=5.18177;RPL=6.0;RPR=4.0;EPP=3.0103;EPPR=5.18177;DPRA=0.0;ODDS=10.6384;GTI=0;TYPE=del;CIGAR=1M8D39M;NUMALT=4;MEANALT=10.5;LEN=8;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr15 88583867 . C T 13273.5 REJECT NS=2;DP=356;DPB=413.0;AC=4;AN=4;AF=1.0;RO=0;AO=413;PRO=0.0;PAO=0.0;QR=0;QA=15582;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=224;SAR=189;SRP=0.0;SAP=9.45111;AB=0.0;ABP=0.0;RUN=1;RPP=3.43618;RPPR=0.0;RPL=211.0;RPR=202.0;EPP=3.14175;EPPR=0.0;DPRA=0.0;ODDS=75.3636;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997579;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.9129;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.375;SOR=0 [...]
+chr15 88583988 . T G 3630.04 PASS SOMATIC;NS=2;DP=462;DPB=462.0;AC=1;AN=3;AF=0.25;RO=327;AO=133;PRO=0.0;PAO=0.0;QR=12261;QA=5102;PQR=0.0;PQA=0.0;SRF=159;SRR=168;SAF=64;SAR=69;SRP=3.54819;SAP=3.41847;AB=0.397015;ABP=33.8711;RUN=1;RPP=3.41847;RPPR=3.07007;RPL=64.0;RPR=69.0;EPP=5.76954;EPPR=15.2887;DPRA=2.6378;ODDS=80.0952;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987768;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.588;Dels=0.0;FS=0.41 [...]
+chr15 88585055 . T TAAA 203.73 PASS DP=40;AC=1;AN=4;AF=0.5;BaseQRankSum=0.751;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.31;MQRankSum=0.751;QD=5.09;SOR=3.056;ClippingRankSum=-0.751 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:4,8:12:50.0:174,0,50:8:67:12:1:.:.:.:.:.:-0.00690701 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0142204
+chr15 88587797 . C CA 614.73 PASS SOMATIC;DP=135;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-3.235;FS=97.662;MLEAC=1;MLEAF=0.5;MQ=53.52;MQRankSum=0.499;QD=4.55;RPA=1,2;RU=A;ReadPosRankSum=1.763;SOR=7.476;STR GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00690701 0/1:83,41:131:99.0:652,0,2395:41:33:124:.:1:.:.:.:.:-0.0142204
+chr15 88587802 . G C 968.652 REJECT NS=2;DP=178;DPB=184.0;AC=2;AN=4;AF=0.5;RO=66;AO=110;PRO=9.5;PAO=1.5;QR=2412;QA=2730;PQR=189.5;PQA=50.5;SRF=7;SRR=59;SAF=110;SAR=0;SRP=91.9749;SAP=241.872;AB=0.617978;ABP=24.5298;RUN=1;RPP=241.872;RPPR=91.9749;RPL=110.0;RPR=0.0;EPP=241.872;EPPR=113.69;DPRA=0.0;ODDS=49.9552;GTI=0;TYPE=snp;CIGAR=2M1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=45.7091;MQMR=58.9848;PAIRED=0.990909;PAIREDR=0.939394;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-7.212;Dels=0.0;FS=184.996;Ha [...]
+chr15 88587810 . A C 12.99 LowQual SOMATIC;DP=92;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-0.095;Dels=0.0;FS=30.02;HaplotypeScore=9.603;MLEAC=1;MLEAF=0.5;MQ=60.19;MQRankSum=0.801;QD=0.14;ReadPosRankSum=-2.71;SOR=4.398 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00690701 0/1:82,9:92:41.0:41,0,2583:9:10:91:.:1:.:.:.:.:-0.0142204
+chr15 88593717 . CGT C 433.332 REJECT NS=2;DP=185;DPB=251.562;AC=2;AN=4;AF=0.5;RO=128;AO=32;PRO=84.0;PAO=79.0;QR=4788;QA=1024;PQR=2984.5;PQA=2803.5;SRF=63;SRR=65;SAF=13;SAR=19;SRP=3.07816;SAP=5.45321;AB=0.172973;ABP=174.862;RUN=1;RPP=12.7819;RPPR=7.35324;RPL=22.0;RPR=10.0;EPP=9.79615;EPPR=3.62103;DPRA=0.0;ODDS=51.4842;GTI=0;TYPE=del;CIGAR=1M2D29M;NUMALT=1;MEANALT=10.5;LEN=2;MQM=60.625;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=0.232;FS=4.355;MLEAC=1;MLEAF=0.5;M [...]
+chr15 88597055 . T C 2050.85 REJECT NS=2;DP=384;DPB=439.0;AC=2;AN=4;AF=0.5;RO=338;AO=101;PRO=0.0;PAO=0.0;QR=12937;QA=3926;PQR=0.0;PQA=0.0;SRF=185;SRR=153;SAF=49;SAR=52;SRP=9.58896;SAP=3.2038;AB=0.230068;ABP=280.845;RUN=1;RPP=3.54779;RPPR=8.04709;RPL=53.0;RPR=48.0;EPP=7.84774;EPPR=3.24158;DPRA=0.0;ODDS=182.423;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994083;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.2585;Dels=0.0;FS=2.176;HaplotypeScore= [...]
+chr15 88597299 . C T 3580.0 PASS SOMATIC;NS=2;DP=487;DPB=487.0;AC=1;AN=3;AF=0.25;RO=353;AO=134;PRO=0.0;PAO=0.0;QR=13573;QA=5187;PQR=0.0;PQA=0.0;SRF=190;SRR=163;SAF=78;SAR=56;SRP=7.49473;SAP=10.8535;AB=0.354497;ABP=72.5204;RUN=1;RPP=3.07512;RPPR=15.467;RPL=66.0;RPR=68.0;EPP=3.07512;EPPR=3.01645;DPRA=3.46789;ODDS=69.0096;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.985836;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.842;Dels=0.0;FS=1.287 [...]
+chr15 88599431 . ATATTTT A 4098.02 REJECT SOMATIC;NS=2;DP=222;DPB=169.875;AC=1;AN=4;AF=0.0;RO=14;AO=17;PRO=12.9;PAO=2.5;QR=525;QA=625;PQR=415.5;PQA=46.5;SRF=4;SRR=10;SAF=7;SAR=10;SRP=8.59409;SAP=4.1599;AB=0.0765766;ABP=348.724;RUN=1;RPP=4.1599;RPPR=33.4109;RPL=10.0;RPR=7.0;EPP=6.20364;EPPR=8.59409;DPRA=0.0;ODDS=36.5588;GTI=0;TYPE=del;CIGAR=1M6D1M;NUMALT=5;MEANALT=8.0;LEN=6;MQM=60.0;MQMR=57.1429;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;END=88599437;HOMLEN=1;HOMSEQ= [...]
+chr15 88599433 . ATTTT A 4098.02 REJECT NS=2;DP=208;DPB=169.875;AC=2;AN=2;AF=0.5;RO=14;AO=109;PRO=12.9;PAO=5.23333;QR=525;QA=4012;PQR=415.5;PQA=151.167;SRF=4;SRR=10;SAF=32;SAR=77;SRP=8.59409;SAP=43.3519;AB=0.490991;ABP=3.1668;RUN=1;RPP=4.62396;RPPR=33.4109;RPL=50.0;RPR=59.0;EPP=8.76769;EPPR=8.59409;DPRA=0.0;ODDS=36.5588;GTI=0;TYPE=del;CIGAR=3M4D1M;NUMALT=5;MEANALT=8.0;LEN=4;MQM=59.9908;MQMR=57.1429;PAIRED=0.990826;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;ALERT;BaseQRan [...]
+chr15 88599434 . T TA 630.73 PASS DP=59;AC=1;AN=4;AF=0.5;ALERT;BaseQRankSum=-0.531;FS=5.368;MLEAC=1;MLEAF=0.5;MQ=59.53;MQRankSum=-0.809;QD=10.69;ReadPosRankSum=0.91;SOR=1.904;ClippingRankSum=-2.375 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:23,19:42:99.0:668,0,871:19:45:42:1:.:.:.:.:.:-0.00690701 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0142204
+chr15 88599435 . T A 4098.02 REJECT NS=2;DP=222;DPB=169.875;AC=0;AN=4;AF=0.0;RO=14;AO=15;PRO=12.9;PAO=5.56667;QR=525;QA=582;PQR=415.5;PQA=165.167;SRF=4;SRR=10;SAF=4;SAR=11;SRP=8.59409;SAP=10.1038;AB=0.0675676;ABP=363.592;RUN=1;RPP=14.7363;RPPR=33.4109;RPL=12.0;RPR=3.0;EPP=6.62942;EPPR=8.59409;DPRA=0.0;ODDS=36.5588;GTI=0;TYPE=snp;CIGAR=4M1X3M;NUMALT=5;MEANALT=8.0;LEN=1;MQM=57.6;MQMR=57.1429;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr15 88599435 . TTT A 4098.02 REJECT NS=2;DP=222;DPB=169.875;AC=0;AN=4;AF=0.0;RO=14;AO=17;PRO=12.9;PAO=5.9;QR=525;QA=642;PQR=415.5;PQA=177.833;SRF=4;SRR=10;SAF=8;SAR=9;SRP=8.59409;SAP=3.13803;AB=0.0765766;ABP=348.724;RUN=1;RPP=4.1599;RPPR=33.4109;RPL=10.0;RPR=7.0;EPP=4.1599;EPPR=8.59409;DPRA=0.0;ODDS=36.5588;GTI=0;TYPE=complex;CIGAR=3M2D1M1X1M;NUMALT=5;MEANALT=8.0;LEN=6;MQM=60.0;MQMR=57.1429;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr15 88599435 . TTT ATA 4098.02 REJECT NS=2;DP=222;DPB=169.875;AC=2;AN=2;AF=0.5;RO=14;AO=43;PRO=12.9;PAO=8.9;QR=525;QA=1498;PQR=415.5;PQA=278.833;SRF=4;SRR=10;SAF=13;SAR=30;SRP=8.59409;SAP=17.6046;AB=0.193694;ABP=183.927;RUN=1;RPP=11.5447;RPPR=33.4109;RPL=28.0;RPR=15.0;EPP=3.46479;EPPR=8.59409;DPRA=0.0;ODDS=36.5588;GTI=0;TYPE=complex;CIGAR=4M1X1M1X1M;NUMALT=5;MEANALT=8.0;LEN=8;MQM=52.2093;MQMR=57.1429;PAIRED=0.976744;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:A [...]
+chr15 88599437 . T A 532.77 PASS DP=59;AC=1;AN=4;AF=0.5;BaseQRankSum=0.693;FS=1.385;MLEAC=1;MLEAF=0.5;MQ=59.53;MQRankSum=0.51;QD=9.03;ReadPosRankSum=0.484;SOR=1.007;ClippingRankSum=0.745 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:22,19:41:99.0:561,0,660:19:46:41:1:.:.:.:.:.:-0.00690701 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0142204
+chr15 88600063 . G C 6509.64 REJECT NS=2;DP=255;DPB=300.0;AC=2;AN=4;AF=0.5;RO=79;AO=220;PRO=0.0;PAO=0.0;QR=2977;QA=8318;PQR=0.0;PQA=0.0;SRF=21;SRR=58;SAF=61;SAR=159;SRP=40.64;SAP=97.8049;AB=0.733333;ABP=144.88;RUN=1;RPP=8.69561;RPPR=5.23675;RPL=122.0;RPR=98.0;EPP=3.04978;EPPR=7.6556;DPRA=0.0;ODDS=91.6923;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.974684;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.119;Dels=0.0;FS=0.487;HaplotypeScore=4.8572 [...]
+chr15 88600091 . A G 5276.5 REJECT NS=2;DP=204;DPB=245.0;AC=2;AN=4;AF=0.5;RO=66;AO=179;PRO=0.0;PAO=0.0;QR=2581;QA=6891;PQR=0.0;PQA=0.0;SRF=14;SRR=52;SAF=39;SAR=140;SRP=50.5195;SAP=126.76;AB=0.730612;ABP=116.184;RUN=1;RPP=64.1633;RPPR=13.6703;RPL=125.0;RPR=54.0;EPP=10.5923;EPPR=6.30041;DPRA=0.0;ODDS=66.6473;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.954545;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.003;Dels=0.0;FS=0.522;HaplotypeScore=1.96 [...]
+chr15 88600730 . A C 4648.2 REJECT NS=2;DP=161;DPB=258.714;AC=2;AN=2;AF=0.25;RO=27;AO=9;PRO=35.55;PAO=39.2167;QR=968;QA=291;PQR=1240.9;PQA=1390.23;SRF=17;SRR=10;SAF=7;SAR=2;SRP=6.95112;SAP=9.04217;AB=0.0535714;ABP=293.832;RUN=1;RPP=3.25157;RPPR=12.7417;RPL=4.0;RPR=5.0;EPP=5.18177;EPPR=3.09072;DPRA=0.0;ODDS=41.1549;GTI=0;TYPE=snp;CIGAR=1X27M;NUMALT=4;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.296;Dels=0.0;FS= [...]
+chr15 88600730 . AAAGA CAAG 4648.2 REJECT NS=2;DP=168;DPB=258.714;AC=2;AN=4;AF=0.5;RO=27;AO=94;PRO=35.55;PAO=48.2167;QR=968;QA=3274;PQR=1240.9;PQA=1713.23;SRF=17;SRR=10;SAF=70;SAR=24;SRP=6.95112;SAP=51.8915;AB=0.559524;ABP=8.18047;RUN=1;RPP=29.7148;RPPR=12.7417;RPL=30.0;RPR=64.0;EPP=5.32038;EPPR=3.09072;DPRA=0.0;ODDS=41.1549;GTI=0;TYPE=complex;CIGAR=1X3M1D23M;NUMALT=4;MEANALT=13.0;LEN=27;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO [...]
+chr15 88600730 . AAAGAA CAAG 4648.2 REJECT NS=2;DP=168;DPB=258.714;AC=2;AN=2;AF=0.0;RO=27;AO=12;PRO=35.55;PAO=31.4667;QR=968;QA=408;PQR=1240.9;PQA=1104.73;SRF=17;SRR=10;SAF=7;SAR=5;SRP=6.95112;SAP=3.73412;AB=0.0714286;ABP=271.032;RUN=1;RPP=3.73412;RPPR=12.7417;RPL=5.0;RPR=7.0;EPP=5.9056;EPPR=3.09072;DPRA=0.0;ODDS=41.1549;GTI=0;TYPE=complex;CIGAR=1X3M2D22M;NUMALT=4;MEANALT=13.0;LEN=26;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr15 88600733 . GA G 3663.465 REJECT NS=2;DP=168;DPB=258.714;AC=2;AN=2;AF=0.25;RO=27;AO=7;PRO=35.55;PAO=34.55;QR=968;QA=224;PQR=1240.9;PQA=1197.9;SRF=17;SRR=10;SAF=5;SAR=2;SRP=6.95112;SAP=5.80219;AB=0.0416667;ABP=309.55;RUN=1;RPP=3.32051;RPPR=12.7417;RPL=3.0;RPR=4.0;EPP=5.80219;EPPR=3.09072;DPRA=0.0;ODDS=41.1549;GTI=0;TYPE=del;CIGAR=4M1D23M;NUMALT=4;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.08;FS=3.358;MLE [...]
+chr15 88601852 . G A 3304.57 PASS SOMATIC;NS=2;DP=510;DPB=510.0;AC=1;AN=3;AF=0.25;RO=380;AO=129;PRO=0.0;PAO=0.0;QR=14536;QA=4902;PQR=0.0;PQA=0.0;SRF=189;SRR=191;SAF=61;SAR=68;SRP=3.03316;SAP=3.83512;AB=0.335065;ABP=93.9809;RUN=1;RPP=5.8551;RPPR=3.0103;RPL=71.0;RPR=58.0;EPP=7.87507;EPPR=6.87324;DPRA=3.08;ODDS=77.4638;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992248;PAIREDR=0.997368;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.37;Dels=0.0;FS=0.0 [...]
+chr15 88602280 . AAC A 2595.07 REJECT NS=2;DP=193;DPB=256.121;AC=2;AN=3;AF=0.5;RO=42;AO=103;PRO=44.9167;PAO=41.9167;QR=1504;QA=3385;PQR=1613.5;PQA=1500.5;SRF=21;SRR=21;SAF=51;SAR=52;SRP=3.0103;SAP=3.03138;AB=0.530928;ABP=4.62211;RUN=1;RPP=9.10307;RPPR=10.4553;RPL=60.0;RPR=43.0;EPP=10.621;EPPR=3.21711;DPRA=0.0;ODDS=4.47553;GTI=0;TYPE=del;CIGAR=1M2D30M;NUMALT=3;MEANALT=10.5;LEN=2;MQM=60.3883;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.262 [...]
+chr15 88602280 . AACAC A 2595.07 REJECT NS=2;DP=194;DPB=256.121;AC=2;AN=2;AF=0.25;RO=42;AO=23;PRO=44.9167;PAO=38.4167;QR=1504;QA=812;PQR=1613.5;PQA=1356.5;SRF=21;SRR=21;SAF=17;SAR=6;SRP=3.0103;SAP=14.4341;AB=0.118557;ABP=248.185;RUN=1;RPP=3.10471;RPPR=10.4553;RPL=12.0;RPR=11.0;EPP=5.3706;EPPR=3.21711;DPRA=0.0;ODDS=4.47553;GTI=0;TYPE=del;CIGAR=1M4D28M;NUMALT=3;MEANALT=10.5;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.534;FS [...]
+chr15 88602280 . AACACAC A 2595.07 REJECT NS=2;DP=194;DPB=256.121;AC=1;AN=3;AF=0.0;RO=42;AO=10;PRO=44.9167;PAO=33.75;QR=1504;QA=295;PQR=1613.5;PQA=1199.5;SRF=21;SRR=21;SAF=5;SAR=5;SRP=3.0103;SAP=3.0103;AB=0.0515464;ABP=341.894;RUN=1;RPP=6.48466;RPPR=10.4553;RPL=3.0;RPR=7.0;EPP=3.87889;EPPR=3.21711;DPRA=0.0;ODDS=4.47553;GTI=0;TYPE=del;CIGAR=1M6D26M;NUMALT=3;MEANALT=10.5;LEN=6;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr15 88602841 . T C 10185.3 REJECT NS=2;DP=374;DPB=427.0;AC=2;AN=4;AF=0.5;RO=93;AO=333;PRO=0.0;PAO=0.0;QR=3450;QA=12680;PQR=0.0;PQA=0.0;SRF=50;SRR=43;SAF=171;SAR=162;SRP=4.15441;SAP=3.5385;AB=0.779859;ABP=293.494;RUN=1;RPP=3.5385;RPPR=3.03365;RPL=171.0;RPR=162.0;EPP=5.88603;EPPR=4.15441;DPRA=0.0;ODDS=162.781;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989247;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.0095;Dels=0.0;FS=0.0;HaplotypeScore=2. [...]
+chr15 88602867 . T G 10735.1 REJECT NS=2;DP=395;DPB=447.0;AC=2;AN=4;AF=0.5;RO=93;AO=354;PRO=0.0;PAO=0.0;QR=3575;QA=13373;PQR=0.0;PQA=0.0;SRF=43;SRR=50;SAF=163;SAR=191;SRP=4.15441;SAP=7.81944;AB=0.791946;ABP=333.934;RUN=1;RPP=14.8859;RPPR=3.59403;RPL=155.0;RPR=199.0;EPP=5.97921;EPPR=3.22044;DPRA=0.0;ODDS=164.805;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.078;Dels=0.0;FS=0.0;HaplotypeScore=9.7347 [...]
+chr15 88603103 . C T 10170.8 REJECT NS=2;DP=370;DPB=420.0;AC=2;AN=4;AF=0.5;RO=87;AO=333;PRO=0.0;PAO=0.0;QR=3362;QA=12654;PQR=0.0;PQA=0.0;SRF=49;SRR=38;SAF=171;SAR=162;SRP=6.03039;SAP=3.5385;AB=0.792857;ABP=315.888;RUN=1;RPP=7.76406;RPPR=3.23494;RPL=180.0;RPR=153.0;EPP=8.49441;EPPR=6.03039;DPRA=0.0;ODDS=130.694;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996997;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.488;Dels=0.0;FS=8.896;HaplotypeScore [...]
+chr15 88603614 . CA C 177.027 REJECT NS=2;DP=42;DPB=104.6;AC=2;AN=3;AF=0.25;RO=5;AO=14;PRO=44.5833;PAO=39.0833;QR=169;QA=352;PQR=1485.58;PQA=1269.58;SRF=3;SRR=2;SAF=9;SAR=5;SRP=3.44459;SAP=5.49198;AB=0.451613;ABP=3.64073;RUN=1;RPP=18.5208;RPPR=13.8677;RPL=2.0;RPR=12.0;EPP=5.49198;EPPR=3.44459;DPRA=2.81818;ODDS=5.35909;GTI=0;TYPE=del;CIGAR=1M1D28M;NUMALT=3;MEANALT=12.0;LEN=1;MQM=58.5714;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-2.103;FS [...]
+chr15 88603614 . CAA C 177.027 REJECT NS=2;DP=42;DPB=104.6;AC=2;AN=2;AF=0.0;RO=5;AO=3;PRO=44.5833;PAO=32.75;QR=169;QA=104;PQR=1485.58;PQA=1084.42;SRF=3;SRR=2;SAF=3;SAR=0;SRP=3.44459;SAP=9.52472;AB=0.0967742;ABP=46.79;RUN=1;RPP=9.52472;RPPR=13.8677;RPL=0.0;RPR=3.0;EPP=9.52472;EPPR=3.44459;DPRA=2.81818;ODDS=5.35909;GTI=0;TYPE=del;CIGAR=1M2D27M;NUMALT=3;MEANALT=12.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr15 88603636 . T G 177.027 REJECT NS=2;DP=42;DPB=104.6;AC=2;AN=2;AF=0.0;RO=5;AO=3;PRO=44.5833;PAO=24.5833;QR=169;QA=32;PQR=1485.58;PQA=796.417;SRF=3;SRR=2;SAF=3;SAR=0;SRP=3.44459;SAP=9.52472;AB=0.0645161;ABP=54.0749;RUN=1;RPP=3.73412;RPPR=13.8677;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=3.44459;DPRA=0.0;ODDS=5.35909;GTI=0;TYPE=snp;CIGAR=22M1X7M;NUMALT=3;MEANALT=10.5;LEN=1;MQM=53.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr15 88603957 . G A 9047.5 REJECT NS=2;DP=350;DPB=407.0;AC=2;AN=4;AF=0.5;RO=98;AO=309;PRO=0.0;PAO=0.0;QR=3635;QA=11363;PQR=0.0;PQA=0.0;SRF=45;SRR=53;SAF=165;SAR=144;SRP=4.4284;SAP=6.10939;AB=0.759214;ABP=240.544;RUN=1;RPP=3.86062;RPPR=10.1895;RPL=149.0;RPR=160.0;EPP=12.6308;EPPR=3.36483;DPRA=0.0;ODDS=161.113;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990291;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.533;Dels=0.0;FS=10.6;HaplotypeScore=3 [...]
+chr15 88605045 . C G 7790.68 REJECT NS=2;DP=286;DPB=332.0;AC=2;AN=4;AF=0.5;RO=76;AO=255;PRO=0.0;PAO=0.0;QR=2879;QA=9735;PQR=0.0;PQA=0.0;SRF=38;SRR=38;SAF=141;SAR=114;SRP=3.0103;SAP=9.21816;AB=0.768072;ABP=210.242;RUN=1;RPP=3.01882;RPPR=5.8675;RPL=127.0;RPR=128.0;EPP=6.08442;EPPR=3.12459;DPRA=0.0;ODDS=99.9081;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988235;PAIREDR=0.986842;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4275;Dels=0.0;FS=2.6605;Haplotype [...]
+chr15 88608074 . G A 10949.9 REJECT NS=2;DP=402;DPB=463.0;AC=2;AN=4;AF=0.5;RO=99;AO=364;PRO=0.0;PAO=0.0;QR=3772;QA=13639;PQR=0.0;PQA=0.0;SRF=45;SRR=54;SAF=179;SAR=185;SRP=4.78696;SAP=3.22506;AB=0.786177;ABP=332.366;RUN=1;RPP=3.3921;RPPR=3.20771;RPL=178.0;RPR=186.0;EPP=3.22506;EPPR=3.55865;DPRA=0.0;ODDS=102.078;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997253;PAIREDR=0.989899;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1275;Dels=0.0;FS=1.999;Haplotype [...]
+chr15 88608148 . T G 11222.0 REJECT NS=2;DP=413;DPB=475.0;AC=2;AN=4;AF=0.5;RO=108;AO=367;PRO=0.0;PAO=0.0;QR=4115;QA=13979;PQR=0.0;PQA=0.0;SRF=57;SRR=51;SAF=188;SAR=179;SRP=3.73412;SAP=3.48956;AB=0.772632;ABP=309.672;RUN=1;RPP=3.01622;RPPR=3.332;RPL=183.0;RPR=184.0;EPP=4.01024;EPPR=5.02092;DPRA=0.0;ODDS=150.611;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99455;PAIREDR=0.981481;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.5455;Dels=0.0;FS=2.9975;Haplotyp [...]
+chr15 88610457 . C T 9283.93 REJECT NS=2;DP=352;DPB=411.0;AC=2;AN=4;AF=0.5;RO=103;AO=307;PRO=0.0;PAO=0.0;QR=3954;QA=11632;PQR=0.0;PQA=0.0;SRF=50;SRR=53;SAF=146;SAR=161;SRP=3.20004;SAP=4.60177;AB=0.746959;ABP=220.733;RUN=1;RPP=3.86616;RPPR=3.03138;RPL=159.0;RPR=148.0;EPP=6.75202;EPPR=3.03138;DPRA=0.0;ODDS=92.8888;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.8935;Dels=0.0;FS=3.0795;HaplotypeScore= [...]
+chr15 88610905 . T G 9673.67 REJECT NS=2;DP=357;DPB=413.0;AC=2;AN=4;AF=0.5;RO=96;AO=317;PRO=0.0;PAO=0.0;QR=3680;QA=12072;PQR=0.0;PQA=0.0;SRF=41;SRR=55;SAF=161;SAR=156;SRP=7.44372;SAP=3.18155;AB=0.767554;ABP=259.807;RUN=1;RPP=5.48318;RPPR=5.27225;RPL=168.0;RPR=149.0;EPP=3.83916;EPPR=6.26751;DPRA=0.0;ODDS=147.236;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.019;Dels=0.0;FS=6.897;HaplotypeScore=7.7 [...]
+chr15 88611101 . T C 9564.43 REJECT NS=2;DP=370;DPB=420.0;AC=2;AN=4;AF=0.5;RO=107;AO=313;PRO=0.0;PAO=0.0;QR=3993;QA=11972;PQR=0.0;PQA=0.0;SRF=55;SRR=52;SAF=168;SAR=145;SRP=3.19295;SAP=6.6803;AB=0.745238;ABP=222.412;RUN=1;RPP=3.18374;RPPR=4.00471;RPL=154.0;RPR=159.0;EPP=3.18374;EPPR=3.03059;DPRA=0.0;ODDS=191.927;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99361;PAIREDR=0.990654;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.467;Dels=0.0;FS=2.534;HaplotypeS [...]
+chr15 88611122 . T C 10238.9 REJECT NS=2;DP=376;DPB=426.0;AC=2;AN=4;AF=0.5;RO=95;AO=331;PRO=0.0;PAO=0.0;QR=3577;QA=12738;PQR=0.0;PQA=0.0;SRF=48;SRR=47;SAF=168;SAR=163;SRP=3.03316;SAP=3.17431;AB=0.776995;ABP=286.912;RUN=1;RPP=4.119;RPPR=4.13032;RPL=172.0;RPR=159.0;EPP=3.54169;EPPR=3.03316;DPRA=0.0;ODDS=154.104;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993958;PAIREDR=0.989474;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.345;Dels=0.0;FS=0.0;HaplotypeScor [...]
+chr15 88611208 . T C 11367.2 REJECT NS=2;DP=404;DPB=454.0;AC=2;AN=4;AF=0.5;RO=85;AO=369;PRO=0.0;PAO=0.0;QR=3171;QA=14077;PQR=0.0;PQA=0.0;SRF=40;SRR=45;SAF=190;SAR=179;SRP=3.64897;SAP=3.72235;AB=0.812775;ABP=388.786;RUN=1;RPP=3.29865;RPPR=10.3933;RPL=188.0;RPR=181.0;EPP=3.01618;EPPR=6.10145;DPRA=0.0;ODDS=84.3777;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99729;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.2055;Dels=0.0;FS=1.052;HaplotypeScore [...]
+chr15 88611937 . G A 8863.92 REJECT NS=2;DP=335;DPB=387.0;AC=2;AN=4;AF=0.5;RO=85;AO=301;PRO=0.0;PAO=0.0;QR=3230;QA=11110;PQR=0.0;PQA=0.0;SRF=42;SRR=43;SAF=167;SAR=134;SRP=3.03585;SAP=10.8666;AB=0.777778;ABP=262.381;RUN=1;RPP=4.2295;RPPR=6.10145;RPL=144.0;RPR=157.0;EPP=16.3493;EPPR=6.10145;DPRA=0.0;ODDS=116.552;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9934;MQMR=60.0;PAIRED=0.996678;PAIREDR=0.988235;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0895;Dels=0.0;FS=3.657;Haplo [...]
+chr15 88612019 . A G 9770.84 REJECT NS=2;DP=333;DPB=386.0;AC=2;AN=4;AF=0.5;RO=68;AO=316;PRO=0.0;PAO=0.0;QR=2500;QA=12089;PQR=0.0;PQA=0.0;SRF=36;SRR=32;SAF=160;SAR=156;SRP=3.52123;SAP=3.12025;AB=0.818653;ABP=343.448;RUN=1;RPP=3.0103;RPPR=3.13803;RPL=158.0;RPR=158.0;EPP=3.99983;EPPR=3.13803;DPRA=0.0;ODDS=34.4917;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990506;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.8725;Dels=0.0;FS=1.185;HaplotypeScore [...]
+chr15 88612340 . C T 10303.5 REJECT NS=2;DP=376;DPB=425.0;AC=2;AN=4;AF=0.5;RO=93;AO=330;PRO=0.0;PAO=0.0;QR=3486;QA=12804;PQR=0.0;PQA=0.0;SRF=34;SRR=59;SAF=171;SAR=159;SRP=17.6035;SAP=3.95785;AB=0.776471;ABP=285.174;RUN=1;RPP=3.66832;RPPR=6.95631;RPL=160.0;RPR=170.0;EPP=5.64239;EPPR=3.03365;DPRA=0.0;ODDS=128.083;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993939;PAIREDR=0.967742;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.026;Dels=0.0;FS=10.3705;Haploty [...]
+chr15 88612515 . G A 1549.865 REJECT NS=2;DP=401;DPB=454.0;AC=2;AN=4;AF=0.5;RO=370;AO=83;PRO=0.0;PAO=0.0;QR=14089;QA=3199;PQR=0.0;PQA=0.0;SRF=191;SRR=179;SAF=47;SAR=36;SRP=3.85541;SAP=6.17594;AB=0.182819;ABP=399.73;RUN=1;RPP=3.03646;RPPR=4.51272;RPL=42.0;RPR=41.0;EPP=3.03646;EPPR=6.97764;DPRA=0.0;ODDS=85.1693;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997297;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.61;Dels=0.0;FS=3.1785;HaplotypeScore=4 [...]
+chr15 88614533 . T C 7560.42 REJECT NS=2;DP=276;DPB=319.0;AC=2;AN=4;AF=0.5;RO=70;AO=249;PRO=0.0;PAO=0.0;QR=2680;QA=9435;PQR=0.0;PQA=0.0;SRF=34;SRR=36;SAF=132;SAR=117;SRP=3.13438;SAP=4.97247;AB=0.780564;ABP=221.117;RUN=1;RPP=3.01902;RPPR=4.99565;RPL=125.0;RPR=124.0;EPP=3.43762;EPPR=3.0103;DPRA=0.0;ODDS=121.605;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.985714;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.617;Dels=0.0;FS=1.4905;HaplotypeScore= [...]
+chr15 88615235 . C T 204.809 REJECT NS=2;DP=63;DPB=104.414;AC=2;AN=2;AF=0.0;RO=16;AO=6;PRO=25.6;PAO=3.6;QR=564;QA=74;PQR=909.167;PQA=132.0;SRF=5;SRR=11;SAF=0;SAR=6;SRP=7.89611;SAP=16.0391;AB=0.0952381;ABP=92.6611;RUN=1;RPP=8.80089;RPPR=3.55317;RPL=1.0;RPR=5.0;EPP=8.80089;EPPR=3.0103;DPRA=0.0;ODDS=9.12803;GTI=0;TYPE=snp;CIGAR=1M1X27M;NUMALT=4;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:C [...]
+chr15 88615235 . C CT 204.809 REJECT NS=2;DP=63;DPB=104.414;AC=2;AN=3;AF=0.25;RO=16;AO=13;PRO=25.6;PAO=21.6;QR=564;QA=285;PQR=909.167;PQA=749.167;SRF=5;SRR=11;SAF=2;SAR=11;SRP=7.89611;SAP=16.5402;AB=0.270833;ABP=24.906;RUN=1;RPP=3.17734;RPPR=3.55317;RPL=7.0;RPR=6.0;EPP=7.18621;EPPR=3.0103;DPRA=0.0;ODDS=9.12803;GTI=0;TYPE=ins;CIGAR=2M1I27M;NUMALT=4;MEANALT=12.0;LEN=1;MQM=57.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.421;FS=1.494;MLEA [...]
+chr15 88615235 . CT C 204.809 REJECT NS=2;DP=63;DPB=104.414;AC=2;AN=3;AF=0.25;RO=16;AO=11;PRO=25.6;PAO=18.1;QR=564;QA=280;PQR=909.167;PQA=645.167;SRF=5;SRR=11;SAF=2;SAR=9;SRP=7.89611;SAP=12.6832;AB=0.174603;ABP=60.9507;RUN=1;RPP=4.78696;RPPR=3.55317;RPL=7.0;RPR=4.0;EPP=4.78696;EPPR=3.0103;DPRA=0.0;ODDS=9.12803;GTI=0;TYPE=del;CIGAR=2M1D26M;NUMALT=4;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr15 88615235 . CTT C 204.809 REJECT NS=2;DP=63;DPB=104.414;AC=2;AN=2;AF=0.0;RO=16;AO=3;PRO=25.6;PAO=16.1;QR=564;QA=45;PQR=909.167;PQA=575.5;SRF=5;SRR=11;SAF=0;SAR=3;SRP=7.89611;SAP=9.52472;AB=0.0625;ABP=82.8119;RUN=1;RPP=3.73412;RPPR=3.55317;RPL=1.0;RPR=2.0;EPP=3.73412;EPPR=3.0103;DPRA=0.0;ODDS=9.12803;GTI=0;TYPE=del;CIGAR=2M2D25M;NUMALT=4;MEANALT=12.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV: [...]
+chr15 88616092 . G A 9237.0 REJECT NS=2;DP=359;DPB=419.0;AC=2;AN=4;AF=0.5;RO=116;AO=303;PRO=0.0;PAO=0.0;QR=4502;QA=11615;PQR=0.0;PQA=0.0;SRF=53;SRR=63;SAF=135;SAR=168;SRP=4.88226;SAP=10.8147;AB=0.72315;ABP=184.238;RUN=1;RPP=3.0748;RPPR=3.68421;RPL=153.0;RPR=150.0;EPP=8.23473;EPPR=7.80251;DPRA=0.0;ODDS=203.436;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.9967;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3585;Dels=0.0;FS=2.1835;HaplotypeScore= [...]
+chr15 88617721 . C T 8825.85 REJECT NS=2;DP=322;DPB=373.0;AC=2;AN=4;AF=0.5;RO=83;AO=289;PRO=0.0;PAO=0.0;QR=3131;QA=11028;PQR=0.0;PQA=0.0;SRF=46;SRR=37;SAF=158;SAR=131;SRP=5.12945;SAP=8.48782;AB=0.774799;ABP=247.665;RUN=1;RPP=18.2256;RPPR=3.03646;RPL=167.0;RPR=122.0;EPP=6.98507;EPPR=14.5479;DPRA=0.0;ODDS=119.641;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=59.9639;PAIRED=0.99654;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.842;Dels=0.0;FS=2.975;HaplotypeSc [...]
+chr15 88619903 . TA T 523.375 REJECT NS=2;DP=118;DPB=224.692;AC=2;AN=4;AF=0.5;RO=27;AO=36;PRO=106.5;PAO=48.5;QR=994;QA=970;PQR=3755.33;PQA=1659.33;SRF=4;SRR=23;SAF=12;SAR=24;SRP=32.0437;SAP=11.6962;AB=0.305085;ABP=41.9496;RUN=1;RPP=9.04217;RPPR=9.52472;RPL=13.0;RPR=23.0;EPP=5.18177;EPPR=3.09072;DPRA=0.0;ODDS=20.9235;GTI=0;TYPE=del;CIGAR=1M1D24M;NUMALT=3;MEANALT=15.5;LEN=1;MQM=60.1667;MQMR=59.5185;PAIRED=1.0;PAIREDR=0.962963;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-1.684;FS [...]
+chr15 88619903 . TAA T 523.375 REJECT NS=2;DP=118;DPB=224.692;AC=2;AN=2;AF=0.0;RO=27;AO=16;PRO=106.5;PAO=43.5;QR=994;QA=394;PQR=3755.33;PQA=1476.83;SRF=4;SRR=23;SAF=4;SAR=12;SRP=32.0437;SAP=11.6962;AB=0.135593;ABP=139.114;RUN=1;RPP=3.55317;RPPR=9.52472;RPL=7.0;RPR=9.0;EPP=7.89611;EPPR=3.09072;DPRA=0.0;ODDS=20.9235;GTI=0;TYPE=del;CIGAR=1M2D23M;NUMALT=3;MEANALT=15.5;LEN=2;MQM=60.0;MQMR=59.5185;PAIRED=1.0;PAIREDR=0.962963;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.618;F [...]
+chr15 88619903 . TAAA T 523.375 REJECT NS=2;DP=118;DPB=224.692;AC=2;AN=2;AF=0.0;RO=27;AO=7;PRO=106.5;PAO=38.5;QR=994;QA=133;PQR=3755.33;PQA=1301.5;SRF=4;SRR=23;SAF=1;SAR=6;SRP=32.0437;SAP=10.7656;AB=0.0786517;ABP=140.252;RUN=1;RPP=3.32051;RPPR=9.52472;RPL=4.0;RPR=3.0;EPP=5.80219;EPPR=3.09072;DPRA=0.0;ODDS=20.9235;GTI=0;TYPE=del;CIGAR=1M3D22M;NUMALT=3;MEANALT=22.0;LEN=3;MQM=60.0;MQMR=59.5185;PAIRED=1.0;PAIREDR=0.962963;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr15 88623124 . A T 12951.2 REJECT NS=2;DP=466;DPB=534.0;AC=2;AN=4;AF=0.5;RO=107;AO=427;PRO=0.0;PAO=0.0;QR=4068;QA=16099;PQR=0.0;PQA=0.0;SRF=55;SRR=52;SAF=217;SAR=210;SRP=3.19295;SAP=3.25949;AB=0.799625;ABP=419.412;RUN=1;RPP=3.05607;RPPR=7.57648;RPL=215.0;RPR=212.0;EPP=20.7126;EPPR=3.51765;DPRA=0.0;ODDS=53.0665;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997658;PAIREDR=0.981308;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.5375;Dels=0.0;FS=0.3105;Haplo [...]
+chr15 88624621 . C G 9847.4 REJECT NS=2;DP=348;DPB=405.0;AC=2;AN=4;AF=0.5;RO=83;AO=321;PRO=0.0;PAO=0.0;QR=3213;QA=12239;PQR=0.0;PQA=0.0;SRF=33;SRR=50;SAF=161;SAR=160;SRP=10.5712;SAP=3.01706;AB=0.792593;ABP=304.169;RUN=1;RPP=7.23824;RPPR=3.03646;RPL=148.0;RPR=173.0;EPP=3.55824;EPPR=3.24576;DPRA=0.0;ODDS=108.505;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996885;PAIREDR=0.987952;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.97;Dels=0.0;FS=5.488;HaplotypeS [...]
+chr15 88625508 . C A 94.7171 REJECT NS=2;DP=102;DPB=169.423;AC=2;AN=2;AF=0.0;RO=40;AO=10;PRO=40.1524;PAO=13.1524;QR=1435;QA=134;PQR=1313.37;PQA=448.369;SRF=19;SRR=21;SAF=0;SAR=10;SRP=3.22745;SAP=24.725;AB=0.0980392;ABP=146.157;RUN=1;RPP=10.8276;RPPR=45.5712;RPL=2.0;RPR=8.0;EPP=10.8276;EPPR=3.22745;DPRA=0.0;ODDS=1.18901;GTI=0;TYPE=snp;CIGAR=1X25M;NUMALT=6;MEANALT=12.5;LEN=1;MQM=56.4;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr15 88625508 . C CA 94.7171 REJECT NS=2;DP=102;DPB=169.423;AC=2;AN=3;AF=0.25;RO=40;AO=8;PRO=40.1524;PAO=30.1524;QR=1435;QA=227;PQR=1313.37;PQA=1020.37;SRF=19;SRR=21;SAF=2;SAR=6;SRP=3.22745;SAP=7.35324;AB=0.0784314;ABP=160.463;RUN=1;RPP=7.35324;RPPR=45.5712;RPL=2.0;RPR=6.0;EPP=7.35324;EPPR=3.22745;DPRA=0.0;ODDS=1.18901;GTI=0;TYPE=ins;CIGAR=1M1I25M;NUMALT=6;MEANALT=12.5;LEN=1;MQM=58.75;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr15 88625508 . CA C 94.7171 REJECT NS=2;DP=102;DPB=169.423;AC=2;AN=3;AF=0.25;RO=40;AO=13;PRO=40.1524;PAO=19.6524;QR=1435;QA=406;PQR=1313.37;PQA=662.369;SRF=19;SRR=21;SAF=7;SAR=6;SRP=3.22745;SAP=3.17734;AB=0.127451;ABP=125.975;RUN=1;RPP=16.5402;RPPR=45.5712;RPL=2.0;RPR=11.0;EPP=4.51363;EPPR=3.22745;DPRA=0.0;ODDS=1.18901;GTI=0;TYPE=del;CIGAR=1M1D24M;NUMALT=6;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.416;FS= [...]
+chr15 88625508 . CAA C 94.7171 REJECT NS=2;DP=102;DPB=169.423;AC=2;AN=2;AF=0.0;RO=40;AO=6;PRO=40.1524;PAO=15.819;QR=1435;QA=163;PQR=1313.37;PQA=540.786;SRF=19;SRR=21;SAF=2;SAR=4;SRP=3.22745;SAP=4.45795;AB=0.0588235;ABP=175.451;RUN=1;RPP=8.80089;RPPR=45.5712;RPL=1.0;RPR=5.0;EPP=3.0103;EPPR=3.22745;DPRA=0.0;ODDS=1.18901;GTI=0;TYPE=del;CIGAR=1M2D23M;NUMALT=6;MEANALT=12.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr15 88625508 . CAAA C 94.7171 REJECT NS=2;DP=102;DPB=169.423;AC=2;AN=2;AF=0.0;RO=40;AO=5;PRO=40.1524;PAO=16.119;QR=1435;QA=128;PQR=1313.37;PQA=554.286;SRF=19;SRR=21;SAF=2;SAR=3;SRP=3.22745;SAP=3.44459;AB=0.0490196;ABP=183.2;RUN=1;RPP=3.44459;RPPR=45.5712;RPL=3.0;RPR=2.0;EPP=3.44459;EPPR=3.22745;DPRA=0.0;ODDS=1.18901;GTI=0;TYPE=del;CIGAR=1M3D22M;NUMALT=6;MEANALT=12.5;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=0.8;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr15 88625508 . CAAAA C 94.7171 REJECT NS=2;DP=102;DPB=169.423;AC=2;AN=2;AF=0.0;RO=40;AO=2;PRO=40.1524;PAO=14.9524;QR=1435;QA=53;PQR=1313.37;PQA=513.452;SRF=19;SRR=21;SAF=2;SAR=0;SRP=3.22745;SAP=7.35324;AB=0.0588235;ABP=60.4905;RUN=1;RPP=3.0103;RPPR=45.5712;RPL=1.0;RPR=1.0;EPP=3.0103;EPPR=3.22745;DPRA=0.0;ODDS=1.18901;GTI=0;TYPE=del;CIGAR=1M4D21M;NUMALT=6;MEANALT=13.0;LEN=4;MQM=50.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr15 88626015 . C T 10899.4 REJECT NS=2;DP=407;DPB=471.0;AC=2;AN=4;AF=0.5;RO=114;AO=357;PRO=0.0;PAO=0.0;QR=4399;QA=13617;PQR=0.0;PQA=0.0;SRF=52;SRR=62;SAF=165;SAR=192;SRP=4.9151;SAP=7.44448;AB=0.757962;ABP=275.247;RUN=1;RPP=6.22797;RPPR=3.08649;RPL=190.0;RPR=167.0;EPP=4.76816;EPPR=3.08649;DPRA=0.0;ODDS=186.752;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985994;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.9725;Dels=0.0;FS=0.997;HaplotypeSco [...]
+chr15 88626522 . G C 3152.05 REJECT NS=2;DP=123;DPB=145.0;AC=2;AN=4;AF=0.5;RO=37;AO=108;PRO=0.0;PAO=0.0;QR=1375;QA=4150;PQR=0.0;PQA=0.0;SRF=6;SRR=31;SAF=16;SAR=92;SRP=39.6906;SAP=119.144;AB=0.744828;ABP=78.5027;RUN=1;RPP=5.9056;RPPR=3.5385;RPL=60.0;RPR=48.0;EPP=8.15749;EPPR=3.06899;DPRA=0.0;ODDS=22.3044;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.963;MQMR=59.7838;PAIRED=0.990741;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.073;Dels=0.0;FS=0.0;HaplotypeScore=0.99 [...]
+chr15 88627317 . C T 511.257 REJECT NS=2;DP=173;DPB=249.864;AC=2;AN=2;AF=0.0;RO=88;AO=6;PRO=55.75;PAO=18.5833;QR=3150;QA=76;PQR=1952.67;PQA=620.667;SRF=51;SRR=37;SAF=0;SAR=6;SRP=7.84676;SAP=16.0391;AB=0.0346821;ABP=328.367;RUN=1;RPP=4.45795;RPPR=6.56362;RPL=4.0;RPR=2.0;EPP=4.45795;EPPR=7.84676;DPRA=0.0;ODDS=12.5663;GTI=0;TYPE=snp;CIGAR=1X21M;NUMALT=3;MEANALT=16.5;LEN=1;MQM=60.0;MQMR=59.7727;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr15 88627317 . C CT 511.257 REJECT NS=2;DP=173;DPB=249.864;AC=2;AN=2;AF=0.0;RO=88;AO=15;PRO=55.75;PAO=47.75;QR=3150;QA=530;PQR=1952.67;PQA=1645.67;SRF=51;SRR=37;SAF=12;SAR=3;SRP=7.84676;SAP=14.7363;AB=0.0867052;ABP=259.683;RUN=1;RPP=4.31318;RPPR=6.56362;RPL=9.0;RPR=6.0;EPP=4.31318;EPPR=7.84676;DPRA=0.0;ODDS=12.5663;GTI=0;TYPE=ins;CIGAR=1M1I21M;NUMALT=3;MEANALT=16.5;LEN=1;MQM=60.0;MQMR=59.7727;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr15 88627317 . CT C 511.257 REJECT NS=2;DP=173;DPB=249.864;AC=2;AN=4;AF=0.5;RO=88;AO=28;PRO=55.75;PAO=41.9167;QR=3150;QA=946;PQR=1952.67;PQA=1493.0;SRF=51;SRR=37;SAF=19;SAR=9;SRP=7.84676;SAP=10.7656;AB=0.16185;ABP=174.833;RUN=1;RPP=10.7656;RPPR=6.56362;RPL=19.0;RPR=9.0;EPP=4.25114;EPPR=7.84676;DPRA=0.0;ODDS=12.5663;GTI=0;TYPE=del;CIGAR=1M1D20M;NUMALT=3;MEANALT=16.5;LEN=1;MQM=60.7143;MQMR=59.7727;PAIRED=0.964286;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr15 88628979 . G C 9811.29 REJECT NS=2;DP=370;DPB=421.0;AC=2;AN=4;AF=0.5;RO=92;AO=329;PRO=0.0;PAO=0.0;QR=3500;QA=12280;PQR=0.0;PQA=0.0;SRF=47;SRR=45;SAF=182;SAR=147;SRP=3.10471;SAP=11.0956;AB=0.781473;ABP=292.724;RUN=1;RPP=3.33371;RPPR=12.4515;RPL=161.0;RPR=168.0;EPP=25.9857;EPPR=3.10471;DPRA=0.0;ODDS=125.053;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.98913;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.327;Dels=0.0;FS=1.116;HaplotypeScore [...]
+chr15 88631907 . G A 3325.35 PASS SOMATIC;NS=2;DP=467;DPB=467.0;AC=1;AN=3;AF=0.25;RO=344;AO=123;PRO=0.0;PAO=0.0;QR=13068;QA=4801;PQR=0.0;PQA=0.0;SRF=189;SRR=155;SAF=71;SAR=52;SRP=10.3075;SAP=9.38348;AB=0.360704;ABP=60.4811;RUN=1;RPP=9.38348;RPPR=15.2311;RPL=52.0;RPR=71.0;EPP=4.44029;EPPR=3.23755;DPRA=2.70635;ODDS=78.6231;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8455;MQMR=59.9419;PAIRED=0.99187;PAIREDR=0.991279;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.081;Dels= [...]
+chr15 88632886 . C G 8878.43 REJECT NS=2;DP=334;DPB=387.0;AC=2;AN=4;AF=0.5;RO=95;AO=291;PRO=0.0;PAO=0.0;QR=3607;QA=11106;PQR=0.0;PQA=0.0;SRF=53;SRR=42;SAF=148;SAR=143;SRP=5.77607;SAP=3.19685;AB=0.751938;ABP=216.37;RUN=1;RPP=3.07746;RPPR=3.21602;RPL=144.0;RPR=147.0;EPP=6.95775;EPPR=11.2619;DPRA=0.0;ODDS=144.211;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993127;PAIREDR=0.978947;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.217;Dels=0.0;FS=13.1795;Haplotyp [...]
+chr15 88632927 . G C 9035.92 REJECT NS=2;DP=328;DPB=381.0;AC=2;AN=4;AF=0.5;RO=86;AO=293;PRO=0.0;PAO=0.0;QR=3323;QA=11271;PQR=0.0;PQA=0.0;SRF=45;SRR=41;SAF=129;SAR=164;SRP=3.41429;SAP=12.089;AB=0.769029;ABP=242.528;RUN=1;RPP=3.90705;RPPR=4.62628;RPL=152.0;RPR=141.0;EPP=6.93081;EPPR=3.1113;DPRA=0.0;ODDS=130.112;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996587;PAIREDR=0.988372;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4625;Dels=0.0;FS=6.328;Haplotype [...]
+chr15 88635680 . T C 9936.37 REJECT NS=2;DP=365;DPB=414.0;AC=2;AN=4;AF=0.5;RO=89;AO=325;PRO=0.0;PAO=0.0;QR=3419;QA=12375;PQR=0.0;PQA=0.0;SRF=41;SRR=48;SAF=162;SAR=163;SRP=4.20583;SAP=3.01698;AB=0.785024;ABP=295.142;RUN=1;RPP=7.88108;RPPR=5.96253;RPL=176.0;RPR=149.0;EPP=8.6294;EPPR=3.0347;DPRA=0.0;ODDS=139.945;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.809;Dels=0.0;FS=0.687;HaplotypeScore=2.9326 [...]
+chr15 88636264 . G GT 232.966 REJECT NS=2;DP=179;DPB=217.261;AC=2;AN=2;AF=0.0;RO=115;AO=16;PRO=34.1667;PAO=25.1667;QR=4186;QA=479;PQR=1179.67;PQA=864.667;SRF=64;SRR=51;SAF=6;SAR=10;SRP=6.20142;SAP=5.18177;AB=0.0909091;ABP=194.889;RUN=1;RPP=22.5536;RPPR=31.7304;RPL=14.0;RPR=2.0;EPP=11.6962;EPPR=16.7755;DPRA=0.0;ODDS=3.65391;GTI=0;TYPE=ins;CIGAR=1M1I22M;NUMALT=2;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=59.9217;PAIRED=1.0;PAIREDR=0.982609;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO: [...]
+chr15 88636264 . GT G 232.966 REJECT NS=2;DP=179;DPB=217.261;AC=2;AN=3;AF=0.25;RO=115;AO=16;PRO=34.1667;PAO=28.6667;QR=4186;QA=566;PQR=1179.67;PQA=958.667;SRF=64;SRR=51;SAF=10;SAR=6;SRP=6.20142;SAP=5.18177;AB=0.106061;ABP=180.939;RUN=1;RPP=11.6962;RPPR=31.7304;RPL=12.0;RPR=4.0;EPP=5.18177;EPPR=16.7755;DPRA=0.0;ODDS=3.65391;GTI=0;TYPE=del;CIGAR=1M1D21M;NUMALT=2;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=59.9217;PAIRED=1.0;PAIREDR=0.982609;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum [...]
+chr15 88636305 . G T 2669.97 REJECT NS=2;DP=147;DPB=221.864;AC=2;AN=2;AF=0.0;RO=52;AO=23;PRO=35.3167;PAO=25.0167;QR=1801;QA=597;PQR=1161.17;PQA=683.367;SRF=27;SRR=25;SAF=0;SAR=23;SRP=3.17734;SAP=52.9542;AB=0.156463;ABP=153.699;RUN=1;RPP=5.3706;RPPR=31.2394;RPL=9.0;RPR=14.0;EPP=5.3706;EPPR=27.0635;DPRA=0.0;ODDS=69.3362;GTI=0;TYPE=snp;CIGAR=1X21M;NUMALT=6;MEANALT=17.5;LEN=1;MQM=57.6522;MQMR=59.8846;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-1.809;D [...]
+chr15 88636305 . G GT 2669.97 REJECT NS=2;DP=147;DPB=221.864;AC=2;AN=2;AF=0.0;RO=52;AO=14;PRO=35.3167;PAO=29.9833;QR=1801;QA=386;PQR=1161.17;PQA=958.5;SRF=27;SRR=25;SAF=7;SAR=7;SRP=3.17734;SAP=3.0103;AB=0.0952381;ABP=212.195;RUN=1;RPP=3.63072;RPPR=31.2394;RPL=6.0;RPR=8.0;EPP=25.3454;EPPR=27.0635;DPRA=0.0;ODDS=69.3362;GTI=0;TYPE=ins;CIGAR=1M1I21M;NUMALT=6;MEANALT=17.5;LEN=1;MQM=59.4286;MQMR=59.8846;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr15 88636305 . GT G 2669.97 REJECT NS=2;DP=147;DPB=221.864;AC=2;AN=2;AF=0.0;RO=52;AO=9;PRO=35.3167;PAO=26.15;QR=1801;QA=284;PQR=1161.17;PQA=835.333;SRF=27;SRR=25;SAF=6;SAR=3;SRP=3.17734;SAP=5.18177;AB=0.0612245;ABP=248.83;RUN=1;RPP=5.18177;RPPR=31.2394;RPL=3.0;RPR=6.0;EPP=9.04217;EPPR=27.0635;DPRA=0.0;ODDS=69.3362;GTI=0;TYPE=del;CIGAR=1M1D20M;NUMALT=6;MEANALT=17.5;LEN=1;MQM=60.0;MQMR=59.8846;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr15 88636305 . GTTTTTTTTTTTTTGTTGGG TTTTTTTTTTTTTTGTTGGT 2669.97 REJECT NS=2;DP=147;DPB=221.864;AC=2;AN=2;AF=0.0;RO=52;AO=2;PRO=35.3167;PAO=7.5;QR=1801;QA=28;PQR=1161.17;PQA=96.3333;SRF=27;SRR=25;SAF=0;SAR=2;SRP=3.17734;SAP=7.35324;AB=0.0689655;ABP=49.8093;RUN=1;RPP=7.35324;RPPR=31.2394;RPL=0.0;RPR=2.0;EPP=7.35324;EPPR=27.0635;DPRA=0.0;ODDS=69.3362;GTI=0;TYPE=complex;CIGAR=1X18M1X2M;NUMALT=6;MEANALT=12.0;LEN=22;MQM=50.0;MQMR=59.8846;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITM [...]
+chr15 88636319 . G T 2669.97 REJECT NS=2;DP=147;DPB=221.864;AC=2;AN=2;AF=0.0;RO=52;AO=7;PRO=35.3167;PAO=19.0667;QR=1801;QA=98;PQR=1161.17;PQA=547.667;SRF=27;SRR=25;SAF=7;SAR=0;SRP=3.17734;SAP=18.2106;AB=0.047619;ABP=264.311;RUN=1;RPP=3.32051;RPPR=31.2394;RPL=3.0;RPR=4.0;EPP=3.32051;EPPR=27.0635;DPRA=0.0;ODDS=69.3362;GTI=0;TYPE=snp;CIGAR=14M1X7M;NUMALT=6;MEANALT=17.5;LEN=1;MQM=59.0;MQMR=59.8846;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr15 88636319 . GTTGGGGA TTTGGGGG 2669.97 REJECT NS=2;DP=147;DPB=221.864;AC=2;AN=4;AF=0.5;RO=52;AO=8;PRO=35.3167;PAO=13.9667;QR=1801;QA=64;PQR=1161.17;PQA=428.633;SRF=27;SRR=25;SAF=8;SAR=0;SRP=3.17734;SAP=20.3821;AB=0.0544218;ABP=256.511;RUN=1;RPP=12.7819;RPPR=31.2394;RPL=7.0;RPR=1.0;EPP=12.7819;EPPR=27.0635;DPRA=0.0;ODDS=69.3362;GTI=0;TYPE=complex;CIGAR=14M1X6M1X;NUMALT=6;MEANALT=17.5;LEN=22;MQM=57.5;MQMR=59.8846;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP [...]
+chr15 88637734 . G A 520.529 REJECT NS=2;DP=82;DPB=89.75;AC=2;AN=2;AF=0.0;RO=58;AO=5;PRO=7.5;PAO=6.0;QR=2020;QA=56;PQR=146.0;PQA=142.0;SRF=31;SRR=27;SAF=5;SAR=0;SRP=3.60933;SAP=13.8677;AB=0.0609756;ABP=140.29;RUN=1;RPP=3.44459;RPPR=96.6082;RPL=2.0;RPR=3.0;EPP=3.44459;EPPR=3.0103;DPRA=0.0;ODDS=2.5537;GTI=0;TYPE=snp;CIGAR=1X3M;NUMALT=3;MEANALT=3.5;LEN=1;MQM=33.6;MQMR=58.9138;PAIRED=1.0;PAIREDR=0.913793;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-2.556;Dels=0.0;FS=13.341;H [...]
+chr15 88637734 . GAAT AAAA 520.529 REJECT NS=2;DP=82;DPB=89.75;AC=2;AN=3;AF=0.25;RO=58;AO=8;PRO=7.5;PAO=1.0;QR=2020;QA=173;PQR=146.0;PQA=37.0;SRF=31;SRR=27;SAF=8;SAR=0;SRP=3.60933;SAP=20.3821;AB=0.097561;ABP=118.363;RUN=1;RPP=4.09604;RPPR=96.6082;RPL=5.0;RPR=3.0;EPP=4.09604;EPPR=3.0103;DPRA=0.0;ODDS=2.5537;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=3;MEANALT=3.5;LEN=4;MQM=35.25;MQMR=58.9138;PAIRED=1.0;PAIREDR=0.913793;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr15 88637737 . T A 520.529 REJECT NS=2;DP=82;DPB=89.75;AC=2;AN=3;AF=0.25;RO=58;AO=10;PRO=7.5;PAO=2.5;QR=2020;QA=196;PQR=146.0;PQA=41.0;SRF=31;SRR=27;SAF=10;SAR=0;SRP=3.60933;SAP=24.725;AB=0.121951;ABP=104.805;RUN=1;RPP=6.48466;RPPR=96.6082;RPL=7.0;RPR=3.0;EPP=6.48466;EPPR=3.0103;DPRA=0.0;ODDS=2.5537;GTI=0;TYPE=snp;CIGAR=3M1X;NUMALT=3;MEANALT=3.5;LEN=1;MQM=38.4;MQMR=58.9138;PAIRED=1.0;PAIREDR=0.913793;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-3.673;Dels=0.0;FS=15.386 [...]
+chr15 88639672 . G A 9045.79 REJECT NS=2;DP=333;DPB=392.0;AC=2;AN=4;AF=0.5;RO=87;AO=303;PRO=0.0;PAO=0.0;QR=3190;QA=11308;PQR=0.0;PQA=0.0;SRF=49;SRR=38;SAF=148;SAR=155;SRP=6.03039;SAP=3.36146;AB=0.772959;ABP=256.696;RUN=1;RPP=5.59743;RPPR=3.03526;RPL=161.0;RPR=142.0;EPP=9.03739;EPPR=5.03202;DPRA=0.0;ODDS=115.452;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990099;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.5345;Dels=0.0;FS=4.6565;HaplotypeSc [...]
+chr15 88641838 . C A 3372.33 PASS SOMATIC;NS=2;DP=474;DPB=474.0;AC=1;AN=3;AF=0.25;RO=345;AO=128;PRO=0.0;PAO=0.0;QR=12976;QA=4867;PQR=0.0;PQA=0.0;SRF=186;SRR=159;SAF=63;SAR=65;SRP=7.59872;SAP=3.07816;AB=0.368876;ABP=54.8315;RUN=1;RPP=3.0103;RPPR=3.16765;RPL=64.0;RPR=64.0;EPP=18.2785;EPPR=6.94413;DPRA=2.73228;ODDS=80.1632;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994203;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.446;Dels=0.0;FS=3.61 [...]
+chr15 88642435 . A G 9380.73 REJECT NS=2;DP=361;DPB=407.0;AC=2;AN=4;AF=0.5;RO=99;AO=308;PRO=0.0;PAO=0.0;QR=3715;QA=11727;PQR=0.0;PQA=0.0;SRF=45;SRR=54;SAF=154;SAR=154;SRP=4.78696;SAP=3.0103;AB=0.756757;ABP=236.062;RUN=1;RPP=3.1231;RPPR=4.78696;RPL=152.0;RPR=156.0;EPP=5.83039;EPPR=5.66432;DPRA=0.0;ODDS=160.967;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993506;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.922;Dels=0.0;FS=2.7515;HaplotypeScore= [...]
+chr15 88646922 . A G 9706.73 REJECT NS=2;DP=338;DPB=392.0;AC=2;AN=4;AF=0.5;RO=76;AO=316;PRO=0.0;PAO=0.0;QR=2920;QA=12044;PQR=0.0;PQA=0.0;SRF=39;SRR=37;SAF=159;SAR=157;SRP=3.12459;SAP=3.03779;AB=0.806122;ABP=322.084;RUN=1;RPP=3.03779;RPPR=4.03889;RPL=159.0;RPR=157.0;EPP=5.759;EPPR=4.83891;DPRA=0.0;ODDS=94.428;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993671;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.18;Dels=0.0;FS=0.727;HaplotypeScore=3.9 [...]
+chr15 88650023 . G A 1444.48 REJECT NS=2;DP=61;DPB=71.0;AC=2;AN=4;AF=0.5;RO=20;AO=51;PRO=0.0;PAO=0.0;QR=725;QA=1979;PQR=0.0;PQA=0.0;SRF=4;SRR=16;SAF=8;SAR=43;SRP=18.6449;SAP=55.1682;AB=0.71831;ABP=32.4016;RUN=1;RPP=15.3153;RPPR=13.8677;RPL=34.0;RPR=17.0;EPP=29.6215;EPPR=13.8677;DPRA=0.0;ODDS=20.0239;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9804;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.481;Dels=0.0;FS=1.043;HaplotypeScore=1.9638;MLEAC= [...]
+chr15 88650170 . T TA 151.48 REJECT NS=2;DP=83;DPB=97.2857;AC=2;AN=2;AF=0.0;RO=50;AO=8;PRO=7.75;PAO=7.75;QR=1776;QA=266;PQR=265.5;PQA=265.5;SRF=46;SRR=4;SAF=6;SAR=2;SRP=79.6198;SAP=7.35324;AB=0.0963855;ABP=120.453;RUN=1;RPP=7.35324;RPPR=24.0302;RPL=2.0;RPR=6.0;EPP=7.35324;EPPR=17.0814;DPRA=0.0;ODDS=2.49659;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=3;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.875;PAIREDR=0.98;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr15 88650170 . TA T 151.48 REJECT NS=2;DP=83;DPB=97.2857;AC=2;AN=4;AF=0.5;RO=50;AO=11;PRO=7.75;PAO=8.75;QR=1776;QA=406;PQR=265.5;PQA=300.5;SRF=46;SRR=4;SAF=11;SAR=0;SRP=79.6198;SAP=26.8965;AB=0.13253;ABP=100.36;RUN=1;RPP=7.94546;RPPR=24.0302;RPL=3.0;RPR=8.0;EPP=7.94546;EPPR=17.0814;DPRA=0.0;ODDS=2.49659;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=3;MEANALT=7.5;LEN=1;MQM=60.9091;MQMR=60.0;PAIRED=0.909091;PAIREDR=0.98;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.714;FS=2.588;M [...]
+chr15 88650170 . TAA T 151.48 REJECT NS=2;DP=83;DPB=97.2857;AC=2;AN=2;AF=0.0;RO=50;AO=4;PRO=7.75;PAO=6.75;QR=1776;QA=144;PQR=265.5;PQA=232.5;SRF=46;SRR=4;SAF=3;SAR=1;SRP=79.6198;SAP=5.18177;AB=0.0481928;ABP=150.173;RUN=1;RPP=3.0103;RPPR=24.0302;RPL=2.0;RPR=2.0;EPP=5.18177;EPPR=17.0814;DPRA=0.0;ODDS=2.49659;GTI=0;TYPE=del;CIGAR=1M2D18M;NUMALT=3;MEANALT=7.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.98;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICO [...]
+chr15 88650278 . TATG T 3491.45 REJECT NS=2;DP=154;DPB=138.5;AC=2;AN=4;AF=0.5;RO=52;AO=127;PRO=10.5;PAO=9.5;QR=1973;QA=4492;PQR=348.0;PQA=309.0;SRF=27;SRR=25;SAF=65;SAR=62;SRP=3.17734;SAP=3.16418;AB=0.709497;ABP=71.2479;RUN=1;RPP=5.8999;RPPR=3.67845;RPL=57.0;RPR=70.0;EPP=6.8574;EPPR=4.51363;DPRA=0.0;ODDS=118.799;GTI=0;TYPE=del;CIGAR=1M3D4M;NUMALT=1;MEANALT=1.0;LEN=3;MQM=60.315;MQMR=60.0;PAIRED=0.992126;PAIREDR=0.980769;technology.ILLUMINA=1.0;MQ0=0;END=88650281;HOMLEN=3;HOMSEQ=ATG;SVLEN= [...]
+chr15 88650413 . T C 2003.0 REJECT NS=2;DP=87;DPB=97.0;AC=2;AN=4;AF=0.5;RO=29;AO=68;PRO=0.0;PAO=0.0;QR=1096;QA=2630;PQR=0.0;PQA=0.0;SRF=5;SRR=24;SAF=15;SAR=53;SRP=30.0414;SAP=49.1222;AB=0.701031;ABP=37.0599;RUN=1;RPP=4.1599;RPPR=3.08518;RPL=37.0;RPR=31.0;EPP=3.52123;EPPR=4.88226;DPRA=0.0;ODDS=56.4321;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.965517;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.792;Dels=0.0;FS=2.517;HaplotypeScore=0.9665;ML [...]
+chr15 88650510 . C T 1818.16 REJECT NS=2;DP=68;DPB=81.0;AC=2;AN=4;AF=0.5;RO=18;AO=63;PRO=0.0;PAO=0.0;QR=685;QA=2352;PQR=0.0;PQA=0.0;SRF=9;SRR=9;SAF=34;SAR=29;SRP=3.0103;SAP=3.872;AB=0.777778;ABP=57.2971;RUN=1;RPP=12.9715;RPPR=3.0103;RPL=23.0;RPR=40.0;EPP=21.2438;EPPR=15.074;DPRA=0.0;ODDS=5.06109;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.5275;Dels=0.0;FS=0.8715;HaplotypeScore=1.9663;MLEAC=1;ML [...]
+chr15 88650694 . G A 6558.55 REJECT NS=2;DP=254;DPB=289.0;AC=2;AN=4;AF=0.5;RO=71;AO=218;PRO=0.0;PAO=0.0;QR=2703;QA=8393;PQR=0.0;PQA=0.0;SRF=48;SRR=23;SAF=160;SAR=58;SRP=22.1254;SAP=106.643;AB=0.754325;ABP=165.375;RUN=1;RPP=43.8101;RPPR=8.17902;RPL=77.0;RPR=141.0;EPP=3.6478;EPPR=3.04088;DPRA=0.0;ODDS=162.986;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995413;PAIREDR=0.985915;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7405;Dels=0.0;FS=6.6395;HaplotypeSc [...]
+chr15 88650719 . A G 7904.77 REJECT NS=2;DP=305;DPB=348.0;AC=2;AN=4;AF=0.5;RO=87;AO=261;PRO=0.0;PAO=0.0;QR=3361;QA=9998;PQR=0.0;PQA=0.0;SRF=55;SRR=32;SAF=176;SAR=85;SRP=16.2139;SAP=71.9067;AB=0.75;ABP=191.928;RUN=1;RPP=15.6647;RPPR=3.23494;RPL=111.0;RPR=150.0;EPP=4.88226;EPPR=3.03526;DPRA=0.0;ODDS=166.428;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992337;PAIREDR=0.988506;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.491;Dels=0.0;FS=0.729;HaplotypeScore [...]
+chr15 88651194 . T C 9021.650000000001 REJECT NS=2;DP=342;DPB=398.0;AC=2;AN=4;AF=0.5;RO=98;AO=300;PRO=0.0;PAO=0.0;QR=3686;QA=11396;PQR=0.0;PQA=0.0;SRF=47;SRR=51;SAF=149;SAR=151;SRP=3.36483;SAP=3.03925;AB=0.753769;ABP=225.635;RUN=1;RPP=10.4223;RPPR=4.4284;RPL=134.0;RPR=166.0;EPP=3.03925;EPPR=10.1895;DPRA=0.0;ODDS=230.865;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8865;Dels=0.0;FS=0.6425;Haplotyp [...]
+chr15 88651207 . C G 8978.07 REJECT NS=2;DP=336;DPB=390.0;AC=2;AN=4;AF=0.5;RO=96;AO=294;PRO=0.0;PAO=0.0;QR=3679;QA=11235;PQR=0.0;PQA=0.0;SRF=46;SRR=50;SAF=142;SAR=152;SRP=3.37221;SAP=3.7489;AB=0.753846;ABP=221.293;RUN=1;RPP=8.00321;RPPR=3.10078;RPL=134.0;RPR=160.0;EPP=6.5851;EPPR=7.44372;DPRA=0.0;ODDS=222.419;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0565;Dels=0.0;FS=0.648;HaplotypeScore=4.823 [...]
+chr15 88651749 . C T 10577.9 REJECT NS=2;DP=375;DPB=432.0;AC=2;AN=4;AF=0.5;RO=88;AO=344;PRO=0.0;PAO=0.0;QR=3413;QA=13133;PQR=0.0;PQA=0.0;SRF=45;SRR=43;SAF=174;SAR=170;SRP=3.109;SAP=3.1113;AB=0.796296;ABP=332.431;RUN=1;RPP=3.91929;RPPR=3.89863;RPL=166.0;RPR=178.0;EPP=3.41429;EPPR=4.58955;DPRA=0.0;ODDS=104.054;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9302;MQMR=60.0;PAIRED=0.997093;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.956;Dels=0.0;FS=1.0995;HaplotypeSco [...]
+chr15 88651839 . G C 10691.6 REJECT NS=2;DP=398;DPB=464.0;AC=2;AN=4;AF=0.5;RO=116;AO=348;PRO=0.0;PAO=0.0;QR=4378;QA=13362;PQR=0.0;PQA=0.0;SRF=55;SRR=61;SAF=158;SAR=190;SRP=3.68421;SAP=9.39992;AB=0.75;ABP=254.901;RUN=1;RPP=3.03526;RPPR=3.30981;RPL=175.0;RPR=173.0;EPP=3.63429;EPPR=3.08518;DPRA=0.0;ODDS=197.285;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991379;PAIREDR=0.982759;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9715;Dels=0.0;FS=0.717;HaplotypeSc [...]
+chr15 88652423 . G C 9170.76 REJECT NS=2;DP=331;DPB=369.0;AC=2;AN=4;AF=0.5;RO=71;AO=297;PRO=0.0;PAO=0.0;QR=2655;QA=11373;PQR=0.0;PQA=0.0;SRF=30;SRR=41;SAF=138;SAR=159;SRP=6.71098;SAP=6.23461;AB=0.804878;ABP=300.926;RUN=1;RPP=4.24592;RPPR=3.04088;RPL=155.0;RPR=142.0;EPP=3.0761;EPPR=3.7749;DPRA=0.0;ODDS=82.4509;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996633;PAIREDR=0.985915;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.968;Dels=0.0;FS=0.0;HaplotypeScor [...]
+chr15 88652984 . A T 9253.98 REJECT NS=2;DP=362;DPB=413.0;AC=2;AN=4;AF=0.5;RO=107;AO=306;PRO=0.0;PAO=0.0;QR=3988;QA=11618;PQR=0.0;PQA=0.0;SRF=52;SRR=55;SAF=155;SAR=151;SRP=3.19295;SAP=3.12384;AB=0.74092;ABP=211.225;RUN=1;RPP=12.2071;RPPR=4.00471;RPL=171.0;RPR=135.0;EPP=9.39698;EPPR=4.00471;DPRA=0.0;ODDS=214.73;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993464;PAIREDR=0.990654;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.006;Dels=0.0;FS=1.0835;Haplotype [...]
+chr15 88653375 . A G 9860.4 REJECT NS=2;DP=359;DPB=413.0;AC=2;AN=4;AF=0.5;RO=90;AO=323;PRO=0.0;PAO=0.0;QR=3331;QA=12289;PQR=0.0;PQA=0.0;SRF=36;SRR=54;SAF=144;SAR=179;SRP=10.8276;SAP=11.2458;AB=0.782082;ABP=288.451;RUN=1;RPP=6.56667;RPPR=3.87889;RPL=150.0;RPR=173.0;EPP=3.82376;EPPR=7.73928;DPRA=0.0;ODDS=118.716;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.4065;Dels=0.0;FS=3.285;HaplotypeScore=3.84 [...]
+chr15 88653435 . T C 10456.1 REJECT NS=2;DP=392;DPB=451.0;AC=2;AN=4;AF=0.5;RO=105;AO=345;PRO=0.0;PAO=0.0;QR=4001;QA=13059;PQR=0.0;PQA=0.0;SRF=42;SRR=63;SAF=156;SAR=189;SRP=12.1305;SAP=9.8646;AB=0.764967;ABP=278.036;RUN=1;RPP=3.16765;RPPR=7.66346;RPL=170.0;RPR=175.0;EPP=4.42648;EPPR=3.52732;DPRA=0.0;ODDS=125.463;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994203;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.8235;Dels=0.0;FS=0.0;HaplotypeScore [...]
+chr15 88653528 . A C 10547.3 REJECT NS=2;DP=408;DPB=462.0;AC=2;AN=4;AF=0.5;RO=108;AO=354;PRO=0.0;PAO=0.0;QR=4046;QA=13196;PQR=0.0;PQA=0.0;SRF=56;SRR=52;SAF=179;SAR=175;SRP=3.332;SAP=3.10845;AB=0.766234;ABP=287.445;RUN=1;RPP=6.54354;RPPR=5.9056;RPL=189.0;RPR=165.0;EPP=7.15695;EPPR=5.9056;DPRA=0.0;ODDS=171.783;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991525;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.399;Dels=0.0;FS=2.594;HaplotypeScore=4. [...]
+chr15 88653595 . T C 8743.02 REJECT NS=2;DP=342;DPB=392.0;AC=2;AN=4;AF=0.5;RO=104;AO=288;PRO=0.0;PAO=0.0;QR=3979;QA=10980;PQR=0.0;PQA=0.0;SRF=57;SRR=47;SAF=144;SAR=144;SRP=5.09825;SAP=3.0103;AB=0.734694;ABP=190.555;RUN=1;RPP=3.13094;RPPR=3.09382;RPL=146.0;RPR=142.0;EPP=3.13094;EPPR=3.34437;DPRA=0.0;ODDS=234.803;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8125;MQMR=60.0;PAIRED=0.993056;PAIREDR=0.990385;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.244;Dels=0.0;FS=1.4165;Haplo [...]
+chr15 88653621 . A G 8424.82 REJECT NS=2;DP=333;DPB=380.0;AC=2;AN=4;AF=0.5;RO=105;AO=275;PRO=0.0;PAO=0.0;QR=4062;QA=10585;PQR=0.0;PQA=0.0;SRF=56;SRR=49;SAF=137;SAR=138;SRP=4.02365;SAP=3.0182;AB=0.723684;ABP=168.156;RUN=1;RPP=7.94546;RPPR=13.9504;RPL=150.0;RPR=125.0;EPP=3.20771;EPPR=3.52732;DPRA=0.0;ODDS=248.04;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992727;PAIREDR=0.990476;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0585;Dels=0.0;FS=3.661;Haplotype [...]
+chr15 88653811 . A G 8454.25 REJECT NS=2;DP=338;DPB=383.0;AC=2;AN=4;AF=0.5;RO=101;AO=281;PRO=0.0;PAO=0.0;QR=3877;QA=10632;PQR=0.0;PQA=0.0;SRF=55;SRR=46;SAF=146;SAR=135;SRP=4.75178;SAP=3.94535;AB=0.733681;ABP=184.671;RUN=1;RPP=12.4767;RPPR=3.54779;RPL=123.0;RPR=158.0;EPP=5.24359;EPPR=3.2038;DPRA=0.0;ODDS=194.641;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992883;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9935;Dels=0.0;FS=2.2235;HaplotypeSco [...]
+chr15 88653838 . A C 9201.79 REJECT NS=2;DP=364;DPB=414.0;AC=2;AN=4;AF=0.5;RO=112;AO=302;PRO=0.0;PAO=0.0;QR=4238;QA=11548;PQR=0.0;PQA=0.0;SRF=51;SRR=61;SAF=148;SAR=154;SRP=4.94911;SAP=3.26915;AB=0.729469;ABP=192.358;RUN=1;RPP=3.47048;RPPR=12.3942;RPL=155.0;RPR=147.0;EPP=4.0457;EPPR=3.32051;DPRA=0.0;ODDS=209.001;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993377;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.996;Dels=0.0;FS=2.2505;HaplotypeScor [...]
+chr15 88653850 . T G 9217.61 REJECT NS=2;DP=369;DPB=420.0;AC=2;AN=4;AF=0.5;RO=117;AO=302;PRO=0.0;PAO=0.0;QR=4454;QA=11588;PQR=0.0;PQA=0.0;SRF=55;SRR=62;SAF=151;SAR=151;SRP=3.91972;SAP=3.0103;AB=0.719048;ABP=178.052;RUN=1;RPP=5.33996;RPPR=11.1951;RPL=160.0;RPR=142.0;EPP=8.6475;EPPR=3.17734;DPRA=0.0;ODDS=246.025;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993377;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.808;Dels=0.0;FS=3.125;HaplotypeScore= [...]
+chr15 88654165 . T A 9602.01 REJECT NS=2;DP=378;DPB=435.0;AC=2;AN=4;AF=0.5;RO=110;AO=325;PRO=0.0;PAO=0.0;QR=3967;QA=12072;PQR=0.0;PQA=0.0;SRF=48;SRR=62;SAF=150;SAR=175;SRP=6.87947;SAP=7.18621;AB=0.747126;ABP=233.76;RUN=1;RPP=9.43118;RPPR=3.08926;RPL=178.0;RPR=147.0;EPP=9.43118;EPPR=9.40627;DPRA=0.0;ODDS=222.703;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996923;PAIREDR=0.990909;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.348;Dels=0.0;FS=2.33;HaplotypeS [...]
+chr15 88654227 . A G 11405.9 REJECT NS=2;DP=448;DPB=508.0;AC=2;AN=4;AF=0.5;RO=132;AO=376;PRO=0.0;PAO=0.0;QR=4981;QA=14326;PQR=0.0;PQA=0.0;SRF=59;SRR=73;SAF=184;SAR=192;SRP=6.23461;SAP=3.37991;AB=0.740157;ABP=257.5;RUN=1;RPP=41.8427;RPPR=10.9724;RPL=147.0;RPR=229.0;EPP=3.21821;EPPR=4.06314;DPRA=0.0;ODDS=315.338;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994681;PAIREDR=0.984848;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.342;Dels=0.0;FS=0.794;HaplotypeS [...]
+chr15 88654247 . A G 11215.3 REJECT NS=2;DP=442;DPB=503.0;AC=2;AN=4;AF=0.5;RO=134;AO=368;PRO=0.0;PAO=0.0;QR=5061;QA=14074;PQR=0.0;PQA=0.0;SRF=61;SRR=73;SAF=173;SAR=195;SRP=5.34382;SAP=5.86626;AB=0.73161;ABP=237.378;RUN=1;RPP=20.2169;RPPR=3.07512;RPL=157.0;RPR=211.0;EPP=3.10471;EPPR=4.04742;DPRA=0.0;ODDS=321.653;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994565;PAIREDR=0.977612;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.888;Dels=0.0;FS=0.3425;Haplotyp [...]
+chr15 88654525 . T C 10529.6 REJECT NS=2;DP=407;DPB=470.0;AC=2;AN=4;AF=0.5;RO=123;AO=346;PRO=0.0;PAO=0.0;QR=4613;QA=13198;PQR=0.0;PQA=0.0;SRF=50;SRR=73;SAF=162;SAR=184;SRP=12.3494;SAP=6.04785;AB=0.73617;ABP=230.71;RUN=1;RPP=3.11071;RPPR=3.16919;RPL=175.0;RPR=171.0;EPP=7.93063;EPPR=9.38348;DPRA=0.0;ODDS=196.771;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99711;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.087;Dels=0.0;FS=5.3825;HaplotypeScore= [...]
+chr15 88655122 . GT G 8186.365 REJECT NS=2;DP=99;DPB=211.943;AC=2;AN=3;AF=0.25;RO=13;AO=3;PRO=29.6667;PAO=37.9167;QR=466;QA=91;PQR=1059.5;PQA=1370.5;SRF=4;SRR=9;SAF=1;SAR=2;SRP=7.18621;SAP=3.73412;AB=0.030303;ABP=192.718;RUN=1;RPP=3.73412;RPPR=3.17734;RPL=1.0;RPR=2.0;EPP=9.52472;EPPR=3.17734;DPRA=0.0;ODDS=9.73954;GTI=0;TYPE=del;CIGAR=1M1D33M;NUMALT=5;MEANALT=16.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.923077;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.758;FS=0.5 [...]
+chr15 88655132 . TGTTTTTG GTTTTTGT 12746 REJECT NS=2;DP=99;DPB=211.943;AC=2;AN=2;AF=0.25;RO=13;AO=13;PRO=29.6667;PAO=40.5;QR=466;QA=399;PQR=1059.5;PQA=1380.08;SRF=4;SRR=9;SAF=7;SAR=6;SRP=7.18621;SAP=3.17734;AB=0.131313;ABP=119.897;RUN=1;RPP=4.51363;RPPR=3.17734;RPL=8.0;RPR=5.0;EPP=11.1951;EPPR=3.17734;DPRA=0.0;ODDS=9.73954;GTI=0;TYPE=complex;CIGAR=1M1D16M1I17M;NUMALT=5;MEANALT=16.5;LEN=35;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.923077;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO [...]
+chr15 88655132 . TGTTTTTG GTTTTTGTT 12746 REJECT NS=2;DP=99;DPB=211.943;AC=2;AN=3;AF=0.5;RO=13;AO=32;PRO=29.6667;PAO=39.5;QR=466;QA=827;PQR=1059.5;PQA=1411.58;SRF=4;SRR=9;SAF=9;SAR=23;SRP=7.18621;SAP=16.3106;AB=0.323232;ABP=29.8795;RUN=1;RPP=16.3106;RPPR=3.17734;RPL=23.0;RPR=9.0;EPP=4.09604;EPPR=3.17734;DPRA=0.0;ODDS=9.73954;GTI=0;TYPE=complex;CIGAR=1M1D16M2I17M;NUMALT=5;MEANALT=16.5;LEN=36;MQM=58.2812;MQMR=60.0;PAIRED=0.96875;PAIREDR=0.923077;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT [...]
+chr15 88655132 . TGTTTTTG GTTTTTGTTT 12746 REJECT NS=2;DP=99;DPB=211.943;AC=1;AN=3;AF=0.0;RO=13;AO=4;PRO=29.6667;PAO=39.5;QR=466;QA=132;PQR=1059.5;PQA=1410.08;SRF=4;SRR=9;SAF=3;SAR=1;SRP=7.18621;SAP=5.18177;AB=0.057971;ABP=120.112;RUN=1;RPP=3.0103;RPPR=3.17734;RPL=2.0;RPR=2.0;EPP=5.18177;EPPR=3.17734;DPRA=0.0;ODDS=9.73954;GTI=0;TYPE=complex;CIGAR=1M1D16M3I17M;NUMALT=5;MEANALT=24.0;LEN=37;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.923077;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO: [...]
+chr15 88655139 . G T 159.77 PASS SOMATIC;DP=178;AC=1;AN=4;AF=0.5;MQ0=1;ALERT;BaseQRankSum=1.484;Dels=0.01;FS=11.222;HaplotypeScore=86.0804;MLEAC=1;MLEAF=0.5;MQ=58.06;MQRankSum=-2.078;QD=0.9;ReadPosRankSum=0.783;SOR=2.49 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00690701 0/1:158,18:176:99.0:188,0,4386:18:10:176:.:1:.:.:.:.:-0.0142204
+chr15 88655139 . G GTT 7268.865 REJECT NS=2;DP=99;DPB=211.943;AC=2;AN=3;AF=0.25;RO=13;AO=2;PRO=29.6667;PAO=27.9167;QR=466;QA=67;PQR=1059.5;PQA=980.25;SRF=4;SRR=9;SAF=1;SAR=1;SRP=7.18621;SAP=3.0103;AB=0.0666667;ABP=51.9408;RUN=1;RPP=7.35324;RPPR=3.17734;RPL=2.0;RPR=0.0;EPP=3.0103;EPPR=3.17734;DPRA=0.0;ODDS=9.73954;GTI=0;TYPE=ins;CIGAR=18M2I17M;NUMALT=5;MEANALT=9.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.923077;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;ALERT;BaseQRankSum=0.58;F [...]
+chr15 88655327 . CA TG 2486.54 REJECT NS=2;DP=111;DPB=134.0;AC=2;AN=4;AF=0.5;RO=36;AO=96;PRO=0.0;PAO=4.0;QR=1305;QA=3337;PQR=0.0;PQA=145.0;SRF=27;SRR=9;SAF=72;SAR=24;SRP=22.5536;SAP=55.1256;AB=0.727273;ABP=62.2323;RUN=1;RPP=4.45795;RPPR=14.8328;RPL=44.0;RPR=52.0;EPP=6.26751;EPPR=27.1378;DPRA=0.0;ODDS=60.5356;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=1;MEANALT=1.0;LEN=2;MQM=40.2188;MQMR=52.9444;PAIRED=1.0;PAIREDR=0.972222;technology.ILLUMINA=1.0;MQ0=0;JOINED;BaseQRankSum=0.2175;Dels=0.0;FS=1.265;Hap [...]
+chr15 88655767 . C CCA 8973.17 REJECT NS=2;DP=356;DPB=575.25;AC=2;AN=4;AF=0.5;RO=102;AO=300;PRO=14.0;PAO=18.0;QR=3893;QA=11131;PQR=446.0;PQA=588.0;SRF=41;SRR=61;SAF=157;SAR=143;SRP=11.5259;SAP=4.429;AB=0.744417;ABP=212.124;RUN=1;RPP=7.17953;RPPR=3.35092;RPL=138.0;RPR=162.0;EPP=3.03925;EPPR=9.90792;DPRA=0.0;ODDS=150.424;GTI=0;TYPE=ins;CIGAR=1M2I3M;NUMALT=1;MEANALT=1.5;LEN=2;MQM=60.1667;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990196;technology.ILLUMINA=1.0;MQ0=0;END=88655767;HOMLEN=2;HOMSEQ=CA;SVLE [...]
+chr15 88655800 . A T 10472.5 REJECT NS=2;DP=393;DPB=450.0;AC=2;AN=4;AF=0.5;RO=108;AO=342;PRO=0.0;PAO=0.0;QR=3992;QA=13067;PQR=0.0;PQA=0.0;SRF=44;SRR=64;SAF=170;SAR=172;SRP=11.0528;SAP=3.0357;AB=0.76;ABP=267.235;RUN=1;RPP=3.0357;RPPR=3.73412;RPL=170.0;RPR=172.0;EPP=6.08338;EPPR=12.7417;DPRA=0.0;ODDS=155.573;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.2632;MQMR=59.7778;PAIRED=0.997076;PAIREDR=0.990741;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.172;Dels=0.0;FS=3.7385;Haploty [...]
+chr15 88656247 . C G 9830.8 REJECT NS=2;DP=348;DPB=400.0;AC=2;AN=4;AF=0.5;RO=83;AO=317;PRO=0.0;PAO=0.0;QR=3166;QA=12240;PQR=0.0;PQA=0.0;SRF=42;SRR=41;SAF=166;SAR=151;SRP=3.03646;SAP=4.55157;AB=0.7925;ABP=300.263;RUN=1;RPP=3.18155;RPPR=4.29225;RPL=156.0;RPR=161.0;EPP=33.7603;EPPR=4.29225;DPRA=0.0;ODDS=58.0227;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996845;PAIREDR=0.987952;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5095;Dels=0.0;FS=1.62;HaplotypeSco [...]
+chr15 88656542 . C T 153.782 REJECT NS=2;DP=31;DPB=89.2759;AC=2;AN=2;AF=0.0;RO=3;AO=7;PRO=24.2;PAO=11.3333;QR=101;QA=167;PQR=874.0;PQA=280.333;SRF=2;SRR=1;SAF=0;SAR=7;SRP=3.73412;SAP=18.2106;AB=0.225806;ABP=23.254;RUN=1;RPP=5.80219;RPPR=3.73412;RPL=2.0;RPR=5.0;EPP=5.80219;EPPR=3.73412;DPRA=0.0;ODDS=5.27356e-15;GTI=0;TYPE=snp;CIGAR=1X28M;NUMALT=5;MEANALT=9.5;LEN=1;MQM=43.1429;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr15 88656542 . C CT 153.782 REJECT NS=2;DP=31;DPB=89.2759;AC=2;AN=3;AF=0.25;RO=3;AO=2;PRO=24.2;PAO=27.2;QR=101;QA=29;PQR=874.0;PQA=940.5;SRF=2;SRR=1;SAF=0;SAR=2;SRP=3.73412;SAP=7.35324;AB=0.0952381;ABP=32.8939;RUN=1;RPP=7.35324;RPPR=3.73412;RPL=2.0;RPR=0.0;EPP=7.35324;EPPR=3.73412;DPRA=0.0;ODDS=5.27356e-15;GTI=0;TYPE=ins;CIGAR=1M1I28M;NUMALT=5;MEANALT=12.0;LEN=1;MQM=52.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr15 88656542 . C CTT 153.782 REJECT NS=2;DP=31;DPB=89.2759;AC=2;AN=3;AF=0.25;RO=3;AO=2;PRO=24.2;PAO=25.2;QR=101;QA=78;PQR=874.0;PQA=911.5;SRF=2;SRR=1;SAF=2;SAR=0;SRP=3.73412;SAP=7.35324;AB=0.0952381;ABP=32.8939;RUN=1;RPP=7.35324;RPPR=3.73412;RPL=2.0;RPR=0.0;EPP=7.35324;EPPR=3.73412;DPRA=0.0;ODDS=5.27356e-15;GTI=0;TYPE=ins;CIGAR=1M2I28M;NUMALT=5;MEANALT=12.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr15 88656542 . CT C 153.782 REJECT NS=2;DP=31;DPB=89.2759;AC=2;AN=2;AF=0.0;RO=3;AO=2;PRO=24.2;PAO=16.5333;QR=101;QA=31;PQR=874.0;PQA=562.333;SRF=2;SRR=1;SAF=1;SAR=1;SRP=3.73412;SAP=3.0103;AB=0.2;ABP=10.8276;RUN=1;RPP=7.35324;RPPR=3.73412;RPL=2.0;RPR=0.0;EPP=3.0103;EPPR=3.73412;DPRA=0.0;ODDS=5.27356e-15;GTI=0;TYPE=del;CIGAR=1M1D27M;NUMALT=5;MEANALT=7.0;LEN=1;MQM=51.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:C [...]
+chr15 88656542 . CTT C 153.782 REJECT NS=2;DP=31;DPB=89.2759;AC=2;AN=2;AF=0.0;RO=3;AO=3;PRO=24.2;PAO=15.5333;QR=101;QA=57;PQR=874.0;PQA=547.333;SRF=2;SRR=1;SAF=0;SAR=3;SRP=3.73412;SAP=9.52472;AB=0.0967742;ABP=46.79;RUN=1;RPP=3.73412;RPPR=3.73412;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=3.73412;DPRA=0.0;ODDS=5.27356e-15;GTI=0;TYPE=del;CIGAR=1M2D26M;NUMALT=5;MEANALT=9.5;LEN=2;MQM=53.3333;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr15 88657531 . T A 10924.8 REJECT NS=2;DP=407;DPB=463.0;AC=2;AN=4;AF=0.5;RO=106;AO=357;PRO=0.0;PAO=0.0;QR=4063;QA=13614;PQR=0.0;PQA=0.0;SRF=49;SRR=57;SAF=171;SAR=186;SRP=4.32138;SAP=4.37888;AB=0.771058;ABP=298.485;RUN=1;RPP=3.50299;RPPR=5.05886;RPL=183.0;RPR=174.0;EPP=3.74629;EPPR=3.0103;DPRA=0.0;ODDS=141.434;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9944;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990566;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.606;Dels=0.0;FS=2.961;HaplotypeSc [...]
+chr15 88659669 . T TA 529.718 REJECT NS=2;DP=331;DPB=382.111;AC=2;AN=2;AF=0.0;RO=237;AO=29;PRO=46.0;PAO=38.0;QR=8888;QA=1083;PQR=1513.0;PQA=1236.0;SRF=135;SRR=102;SAF=19;SAR=10;SRP=12.9881;SAP=9.07545;AB=0.0876133;ABP=491.946;RUN=1;RPP=3.68421;RPPR=44.14;RPL=13.0;RPR=16.0;EPP=3.68421;EPPR=7.85717;DPRA=0.0;ODDS=8.99451;GTI=0;TYPE=ins;CIGAR=1M1I17M;NUMALT=2;MEANALT=9.0;LEN=1;MQM=60.0;MQMR=59.9283;PAIRED=0.965517;PAIREDR=0.995781;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:Q [...]
+chr15 88659669 . TA T 529.718 REJECT NS=2;DP=331;DPB=382.111;AC=2;AN=4;AF=0.5;RO=237;AO=43;PRO=46.0;PAO=34.0;QR=8888;QA=1574;PQR=1513.0;PQA=1087.0;SRF=135;SRR=102;SAF=24;SAR=19;SRP=12.9881;SAP=4.27278;AB=0.129909;ABP=396.795;RUN=1;RPP=11.5447;RPPR=44.14;RPL=15.0;RPR=28.0;EPP=5.48477;EPPR=7.85717;DPRA=0.0;ODDS=8.99451;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=2;MEANALT=9.0;LEN=1;MQM=60.2326;MQMR=59.9283;PAIRED=1.0;PAIREDR=0.995781;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr15 88660829 . A G 15528.099999999999 REJECT NS=2;DP=407;DPB=462.0;AC=4;AN=4;AF=1.0;RO=0;AO=462;PRO=0.0;PAO=0.0;QR=0;QA=17744;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=197;SAR=265;SRP=0.0;SAP=24.7438;AB=0.0;ABP=0.0;RUN=1;RPP=3.31111;RPPR=0.0;RPL=235.0;RPR=227.0;EPP=7.24044;EPPR=0.0;DPRA=0.0;ODDS=71.6961;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993506;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=3 [...]
+chr15 88661739 . A G 9404.39 REJECT NS=2;DP=368;DPB=427.0;AC=2;AN=4;AF=0.5;RO=119;AO=308;PRO=0.0;PAO=0.0;QR=4563;QA=11857;PQR=0.0;PQA=0.0;SRF=65;SRR=54;SAF=149;SAR=159;SRP=5.21827;SAP=3.71532;AB=0.721311;ABP=184.666;RUN=1;RPP=4.81516;RPPR=8.28388;RPL=162.0;RPR=146.0;EPP=41.6174;EPPR=4.48836;DPRA=0.0;ODDS=216.241;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993506;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.637;Dels=0.0;FS=3.8345;HaplotypeSco [...]
+chr15 88662371 . G A 1820.73 REJECT NS=2;DP=352;DPB=401.0;AC=2;AN=4;AF=0.5;RO=311;AO=90;PRO=0.0;PAO=0.0;QR=11946;QA=3465;PQR=0.0;PQA=0.0;SRF=156;SRR=155;SAF=50;SAR=40;SRP=3.01728;SAP=5.42305;AB=0.224439;ABP=267.491;RUN=1;RPP=4.55446;RPPR=3.01728;RPL=49.0;RPR=41.0;EPP=4.55446;EPPR=6.08946;DPRA=0.0;ODDS=156.427;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990354;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.686;Dels=0.0;FS=5.4275;HaplotypeScore= [...]
+chr15 88667948 . T C 9960.89 REJECT NS=2;DP=369;DPB=424.0;AC=2;AN=4;AF=0.5;RO=97;AO=327;PRO=0.0;PAO=0.0;QR=3713;QA=12478;PQR=0.0;PQA=0.0;SRF=40;SRR=57;SAF=187;SAR=140;SRP=9.47994;SAP=17.6794;AB=0.771226;ABP=273.932;RUN=1;RPP=3.54819;RPPR=19.3299;RPL=168.0;RPR=159.0;EPP=4.50443;EPPR=6.79359;DPRA=0.0;ODDS=240.966;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8716;MQMR=60.0;PAIRED=0.993884;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.157;Dels=0.0;FS=10.4505;Haplotyp [...]
+chr15 88668501 . C T 10804.9 REJECT NS=2;DP=412;DPB=464.0;AC=2;AN=4;AF=0.5;RO=111;AO=353;PRO=0.0;PAO=0.0;QR=4257;QA=13487;PQR=0.0;PQA=0.0;SRF=54;SRR=57;SAF=180;SAR=173;SRP=3.18637;SAP=3.31172;AB=0.760776;ABP=277.084;RUN=1;RPP=6.85497;RPPR=3.18637;RPL=189.0;RPR=164.0;EPP=4.78808;EPPR=3.02986;DPRA=0.0;ODDS=226.406;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991501;PAIREDR=0.981982;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.611;Dels=0.0;FS=11.65;Haploty [...]
+chr15 88669163 . T C 10587.7 REJECT NS=2;DP=416;DPB=486.0;AC=2;AN=4;AF=0.5;RO=134;AO=352;PRO=0.0;PAO=0.0;QR=5018;QA=13321;PQR=0.0;PQA=0.0;SRF=78;SRR=56;SAF=154;SAR=198;SRP=10.8535;SAP=14.9534;AB=0.72428;ABP=215.35;RUN=1;RPP=4.21942;RPPR=3.59368;RPL=169.0;RPR=183.0;EPP=5.00904;EPPR=8.26073;DPRA=0.0;ODDS=233.435;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997159;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.1325;Dels=0.0;FS=8.666;HaplotypeScor [...]
+chr15 88669382 . G C 10602.5 REJECT NS=2;DP=414;DPB=473.0;AC=2;AN=4;AF=0.5;RO=124;AO=349;PRO=0.0;PAO=0.0;QR=4677;QA=13316;PQR=0.0;PQA=0.0;SRF=48;SRR=76;SAF=146;SAR=203;SRP=16.7396;SAP=23.2255;AB=0.737844;ABP=235.422;RUN=1;RPP=12.4739;RPPR=3.29049;RPL=155.0;RPR=194.0;EPP=3.0663;EPPR=3.0103;DPRA=0.0;ODDS=237.706;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994269;PAIREDR=0.991935;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.097;Dels=0.0;FS=1.679;HaplotypeS [...]
+chr15 88670113 . T A 9367.75 REJECT NS=2;DP=363;DPB=417.0;AC=2;AN=4;AF=0.5;RO=106;AO=309;PRO=0.0;PAO=0.0;QR=4081;QA=11743;PQR=0.0;PQA=0.0;SRF=53;SRR=53;SAF=150;SAR=159;SRP=3.0103;SAP=3.57952;AB=0.741007;ABP=213.393;RUN=1;RPP=10.6632;RPPR=5.96022;RPL=171.0;RPR=138.0;EPP=3.01733;EPPR=3.09224;DPRA=0.0;ODDS=179.949;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996764;PAIREDR=0.990566;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.443;Dels=0.0;FS=3.1245;Haploty [...]
+chr15 88670730 . C G 2545.82 PASS SOMATIC;NS=2;DP=423;DPB=423.0;AC=1;AN=3;AF=0.25;RO=322;AO=100;PRO=0.0;PAO=0.0;QR=12027;QA=3800;PQR=0.0;PQA=0.0;SRF=155;SRR=167;SAF=42;SAR=58;SRP=3.98139;SAP=8.56927;AB=0.332226;ABP=76.6023;RUN=1;RPP=5.18177;RPPR=4.33207;RPL=45.0;RPR=55.0;EPP=3.79203;EPPR=9.91585;DPRA=2.46721;ODDS=76.9836;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99;PAIREDR=0.987578;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.839;Dels=0.0;FS=4. [...]
+chr15 88670758 . T G 9590.74 REJECT NS=2;DP=367;DPB=431.0;AC=2;AN=4;AF=0.5;RO=115;AO=316;PRO=0.0;PAO=0.0;QR=4374;QA=12037;PQR=0.0;PQA=0.0;SRF=56;SRR=59;SAF=152;SAR=164;SRP=3.18024;SAP=3.99983;AB=0.733179;ABP=206.559;RUN=1;RPP=6.33623;RPPR=4.53977;RPL=169.0;RPR=147.0;EPP=5.23675;EPPR=14.8118;DPRA=0.0;ODDS=155.943;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993671;PAIREDR=0.991304;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.194;Dels=0.0;FS=2.6475;Haploty [...]
+chr15 88671372 . G T 7432.46 REJECT NS=2;DP=436;DPB=502.0;AC=2;AN=4;AF=0.5;RO=235;AO=266;PRO=0.0;PAO=0.0;QR=8940;QA=10161;PQR=0.0;PQA=0.0;SRF=143;SRR=92;SAF=140;SAR=126;SRP=27.0443;SAP=4.61033;AB=0.52988;ABP=6.90338;RUN=1;RPP=12.4472;RPPR=9.74648;RPL=116.0;RPR=150.0;EPP=4.61033;EPPR=5.08937;DPRA=0.0;ODDS=390.538;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992481;PAIREDR=0.991489;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6375;Dels=0.0;FS=7.9955;Haplot [...]
+chr15 88674252 . C A 3267.58 PASS SOMATIC;NS=2;DP=436;DPB=436.0;AC=1;AN=3;AF=0.25;RO=313;AO=122;PRO=0.0;PAO=0.0;QR=11762;QA=4707;PQR=0.0;PQA=0.0;SRF=142;SRR=171;SAF=56;SAR=66;SRP=8.84483;SAP=4.7902;AB=0.370821;ABP=50.6969;RUN=1;RPP=10.1299;RPPR=25.5506;RPL=51.0;RPR=71.0;EPP=16.9647;EPPR=4.18276;DPRA=3.07477;ODDS=67.0714;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.98722;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.232;Dels=0.0;FS=0.0;H [...]
+chr15 88674576 . T C 11135.2 REJECT NS=2;DP=406;DPB=461.0;AC=2;AN=4;AF=0.5;RO=97;AO=364;PRO=0.0;PAO=0.0;QR=3568;QA=13842;PQR=0.0;PQA=0.0;SRF=50;SRR=47;SAF=181;SAR=183;SRP=3.21178;SAP=3.03416;AB=0.789588;ABP=338.807;RUN=1;RPP=3.03416;RPPR=8.04722;RPL=183.0;RPR=181.0;EPP=6.44648;EPPR=6.79359;DPRA=0.0;ODDS=120.323;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991758;PAIREDR=0.989691;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.8225;Dels=0.0;FS=1.8285;Haploty [...]
+chr15 88674990 . G A 9532.06 REJECT NS=2;DP=355;DPB=405.0;AC=2;AN=4;AF=0.5;RO=89;AO=316;PRO=0.0;PAO=0.0;QR=3285;QA=11899;PQR=0.0;PQA=0.0;SRF=39;SRR=50;SAF=144;SAR=172;SRP=5.96253;SAP=8.39775;AB=0.780247;ABP=279.291;RUN=1;RPP=3.0103;RPPR=3.0347;RPL=158.0;RPR=158.0;EPP=10.047;EPPR=5.96253;DPRA=0.0;ODDS=99.9182;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996835;PAIREDR=0.977528;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.417;Dels=0.0;FS=3.7325;HaplotypeSc [...]
+chr15 88675488 . C G 10904.1 REJECT NS=2;DP=406;DPB=462.0;AC=2;AN=4;AF=0.5;RO=104;AO=358;PRO=0.0;PAO=0.0;QR=3910;QA=13586;PQR=0.0;PQA=0.0;SRF=58;SRR=46;SAF=186;SAR=172;SRP=6.01695;SAP=4.19915;AB=0.774892;ABP=306.246;RUN=1;RPP=3.03456;RPPR=3.34437;RPL=180.0;RPR=178.0;EPP=3.22866;EPPR=4.34659;DPRA=0.0;ODDS=129.992;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997207;PAIREDR=0.990385;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.046;Dels=0.0;FS=6.501;Haploty [...]
+chr15 88676794 . C T 9357.89 REJECT NS=2;DP=364;DPB=427.0;AC=2;AN=4;AF=0.5;RO=119;AO=307;PRO=0.0;PAO=0.0;QR=4555;QA=11770;PQR=0.0;PQA=0.0;SRF=63;SRR=56;SAF=138;SAR=169;SRP=3.90444;SAP=9.80765;AB=0.71897;ABP=180.842;RUN=1;RPP=3.58323;RPPR=3.17453;RPL=149.0;RPR=158.0;EPP=8.16666;EPPR=4.48836;DPRA=0.0;ODDS=203.074;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9739;MQMR=60.0;PAIRED=0.993485;PAIREDR=0.97479;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6325;Dels=0.0;FS=3.179;Haplot [...]
+chr15 88677388 . G C 10693.9 REJECT NS=2;DP=384;DPB=439.0;AC=2;AN=4;AF=0.5;RO=92;AO=344;PRO=0.0;PAO=0.0;QR=3474;QA=13282;PQR=0.0;PQA=0.0;SRF=53;SRR=39;SAF=174;SAR=170;SRP=7.63648;SAP=3.1113;AB=0.783599;ABP=309.692;RUN=1;RPP=6.64625;RPPR=3.38795;RPL=160.0;RPR=184.0;EPP=7.95924;EPPR=5.3706;DPRA=0.0;ODDS=119.18;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994186;PAIREDR=0.978261;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7805;Dels=0.0;FS=4.4935;HaplotypeS [...]
+chr15 88677816 . C G 6562.360000000001 REJECT NS=2;DP=416;DPB=478.0;AC=2;AN=4;AF=0.5;RO=238;AO=240;PRO=0.0;PAO=0.0;QR=9155;QA=9156;PQR=0.0;PQA=0.0;SRF=117;SRR=121;SAF=104;SAR=136;SRP=3.15628;SAP=12.2752;AB=0.502092;ABP=3.02847;RUN=1;RPP=5.94179;RPPR=3.92268;RPL=111.0;RPR=129.0;EPP=5.94179;EPPR=5.346;DPRA=0.0;ODDS=351.47;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991667;PAIREDR=0.983193;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.269;Dels=0.0;FS=3.110 [...]
+chr15 88679785 . G A 13990.55 REJECT NS=2;DP=367;DPB=415.0;AC=4;AN=4;AF=1.0;RO=0;AO=415;PRO=0.0;PAO=0.0;QR=0;QA=15960;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=169;SAR=246;SRP=0.0;SAP=34.0336;AB=0.0;ABP=0.0;RUN=1;RPP=7.4108;RPPR=0.0;RPL=222.0;RPR=193.0;EPP=3.14111;EPPR=0.0;DPRA=0.0;ODDS=64.2123;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99759;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8483;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.43;SOR=1.0 [...]
+chr15 88680684 . G A 1419.5 REJECT NS=1;DP=107;DPB=107.0;AC=1;AN=4;AF=0.5;RO=56;AO=51;PRO=0.0;PAO=0.0;QR=2146;QA=1957;PQR=0.0;PQA=0.0;SRF=33;SRR=23;SAF=29;SAR=22;SRP=6.88793;SAP=5.09662;AB=0.476636;ABP=3.51765;RUN=1;RPP=3.3935;RPPR=8.59409;RPL=24.0;RPR=27.0;EPP=4.07475;EPPR=3.16541;DPRA=0.0;ODDS=326.853;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.982143;technology.ILLUMINA=1.0;BaseQRankSum=-0.322;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0. [...]
+chr15 90035012 . T TA 286.187 REJECT NS=2;DP=235;DPB=277.235;AC=2;AN=2;AF=0.0;RO=180;AO=18;PRO=34.1667;PAO=30.1667;QR=6644;QA=650;PQR=1198.83;PQA=1050.83;SRF=155;SRR=25;SAF=14;SAR=4;SRP=206.887;SAP=15.074;AB=0.0765957;ABP=368.936;RUN=1;RPP=15.074;RPPR=40.8422;RPL=4.0;RPR=14.0;EPP=3.49285;EPPR=6.91895;DPRA=0.0;ODDS=14.7076;GTI=0;TYPE=ins;CIGAR=1M1I16M;NUMALT=2;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.944444;PAIREDR=0.988889;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO: [...]
+chr15 90035012 . TA T 286.187 REJECT NS=2;DP=235;DPB=277.235;AC=2;AN=4;AF=0.5;RO=180;AO=27;PRO=34.1667;PAO=29.6667;QR=6644;QA=1023;PQR=1198.83;PQA=1031.33;SRF=155;SRR=25;SAF=23;SAR=4;SRP=206.887;SAP=32.0437;AB=0.114894;ABP=305.732;RUN=1;RPP=9.52472;RPPR=40.8422;RPL=9.0;RPR=18.0;EPP=3.09072;EPPR=6.91895;DPRA=0.0;ODDS=14.7076;GTI=0;TYPE=del;CIGAR=1M1D15M;NUMALT=2;MEANALT=6.0;LEN=1;MQM=59.6296;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988889;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO: [...]
+chr15 91312823 . T C 2577.83 PASS SOMATIC;NS=2;DP=354;DPB=354.0;AC=1;AN=3;AF=0.25;RO=256;AO=98;PRO=0.0;PAO=0.0;QR=9939;QA=3790;PQR=0.0;PQA=0.0;SRF=85;SRR=171;SAF=39;SAR=59;SRP=65.7455;SAP=11.8735;AB=0.351254;ABP=56.6278;RUN=1;RPP=15.7732;RPPR=8.74434;RPL=61.0;RPR=37.0;EPP=5.22609;EPPR=3.55317;DPRA=3.72;ODDS=47.8061;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.426;Dels=0.0;FS=1.004;Haplotyp [...]
+chr15 91337479 . G A 2155.37 PASS SOMATIC;NS=2;DP=363;DPB=363.0;AC=1;AN=3;AF=0.25;RO=280;AO=83;PRO=0.0;PAO=0.0;QR=10691;QA=3239;PQR=0.0;PQA=0.0;SRF=139;SRR=141;SAF=43;SAR=40;SRP=3.04132;SAP=3.24576;AB=0.321705;ABP=74.2481;RUN=1;RPP=10.5712;RPPR=3.04132;RPL=33.0;RPR=50.0;EPP=4.29225;EPPR=10.9517;DPRA=2.45714;ODDS=66.5113;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9714;PAIRED=0.987952;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.714;Dels=0.0;FS=1 [...]
+chr15 91337623 . AT A . PASS SOMATIC;AC=1;AN=4 GT:AD:DP:MM:MQS:NQSBQ:NQSMM:REnd:RStart:SC:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:40,0:40:0.25,0.0:60.0,0.0:38.485,0.0:0.0,0.0:0,0:0,0:6,34,0,0:0:0:40:.:.:.:.:0:.:-0.00690701 0/1:69,30:99:0.15942,0.133333:60.0,61.0:38.4703,38.19:0.0,0.00333333:29,12:70,13:18,51,3,27:30:30:99:.:.:.:.:1:.:-0.0142204
+chr15 91341599 . T G 1725.26 PASS SOMATIC;NS=2;DP=251;DPB=251.0;AC=1;AN=3;AF=0.25;RO=185;AO=66;PRO=0.0;PAO=0.0;QR=6980;QA=2568;PQR=0.0;PQA=0.0;SRF=63;SRR=122;SAF=26;SAR=40;SRP=43.8692;SAP=9.45891;AB=0.358696;ABP=34.9215;RUN=1;RPP=32.6213;RPPR=174.862;RPL=48.0;RPR=18.0;EPP=4.19474;EPPR=5.65128;DPRA=2.74627;ODDS=42.7662;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994595;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.063;Dels=0.0;FS=3.727; [...]
+chr15 91346923 . C A 3138.1 PASS SOMATIC;NS=2;DP=410;DPB=410.0;AC=1;AN=3;AF=0.25;RO=292;AO=117;PRO=0.0;PAO=0.0;QR=10930;QA=4516;PQR=0.0;PQA=0.0;SRF=118;SRR=174;SAF=45;SAR=72;SRP=26.3313;SAP=16.5402;AB=0.370253;ABP=49.2159;RUN=1;RPP=3.91972;RPPR=41.5614;RPL=62.0;RPR=55.0;EPP=7.18621;EPPR=3.48624;DPRA=3.3617;ODDS=59.5597;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.253;Dels=0.0;FS=4.588;Hapl [...]
+chr15 91354505 . C T 2948.65 PASS SOMATIC;NS=2;DP=414;DPB=414.0;AC=1;AN=3;AF=0.25;RO=302;AO=112;PRO=0.0;PAO=0.0;QR=11389;QA=4257;PQR=0.0;PQA=0.0;SRF=153;SRR=149;SAF=62;SAR=50;SRP=3.12534;SAP=5.80219;AB=0.366013;ABP=50.7259;RUN=1;RPP=9.29206;RPPR=5.33996;RPL=47.0;RPR=65.0;EPP=4.94911;EPPR=4.0457;DPRA=2.83333;ODDS=68.3131;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.684;Dels=0.0;FS=6.309;Hap [...]
+chr15 93510603 . A G 8283.715 REJECT NS=2;DP=379;DPB=431.0;AC=3;AN=4;AF=0.75;RO=133;AO=298;PRO=0.0;PAO=0.0;QR=5140;QA=11365;PQR=0.0;PQA=0.0;SRF=69;SRR=64;SAF=159;SAR=139;SRP=3.41847;SAP=5.92503;AB=0.594512;ABP=28.4589;RUN=1;RPP=4.43852;RPPR=3.41847;RPL=142.0;RPR=156.0;EPP=10.472;EPPR=13.2146;DPRA=0.0;ODDS=65.2298;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996644;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.427;Dels=0.0;FS=0.426;HaplotypeSco [...]
+chr15 93521604 . A G 6512.305 REJECT NS=2;DP=289;DPB=327.0;AC=3;AN=4;AF=0.75;RO=89;AO=238;PRO=0.0;PAO=0.0;QR=3458;QA=8849;PQR=0.0;PQA=0.0;SRF=28;SRR=61;SAF=78;SAR=160;SRP=29.5803;SAP=64.359;AB=0.646825;ABP=50.1967;RUN=1;RPP=13.5575;RPPR=4.20583;RPL=136.0;RPR=102.0;EPP=22.3163;EPPR=10.0615;DPRA=0.0;ODDS=47.777;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995798;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-3.49;Dels=0.0;FS=0.5405;HaplotypeScore= [...]
+chr15 93536197 . C T 6757.55 REJECT NS=2;DP=401;DPB=457.0;AC=2;AN=4;AF=0.5;RO=215;AO=242;PRO=0.0;PAO=0.0;QR=8267;QA=9232;PQR=0.0;PQA=0.0;SRF=103;SRR=112;SAF=126;SAR=116;SRP=3.82839;SAP=3.9076;AB=0.52954;ABP=6.4742;RUN=1;RPP=3.15387;RPPR=3.50519;RPL=123.0;RPR=119.0;EPP=3.0103;EPPR=5.28277;DPRA=0.0;ODDS=301.287;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983471;PAIREDR=0.995349;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.402;Dels=0.0;FS=1.5235;HaplotypeS [...]
+chr15 93567864 . A C 7446.17 REJECT NS=2;DP=419;DPB=482.0;AC=2;AN=4;AF=0.5;RO=220;AO=261;PRO=0.0;PAO=0.0;QR=8309;QA=9934;PQR=0.0;PQA=0.0;SRF=90;SRR=130;SAF=101;SAR=160;SRP=18.8028;SAP=31.9716;AB=0.541494;ABP=10.2185;RUN=1;RPP=6.01375;RPPR=3.36563;RPL=140.0;RPR=121.0;EPP=21.3888;EPPR=3.04978;DPRA=0.0;ODDS=404.991;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992337;PAIREDR=0.990909;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.4515;Dels=0.0;FS=6.819;Haploty [...]
+chr15 99093865 . T C 13647.599999999999 REJECT NS=2;DP=364;DPB=410.0;AC=4;AN=4;AF=1.0;RO=0;AO=410;PRO=0.0;PAO=0.0;QR=0;QA=15452;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=193;SAR=217;SRP=0.0;SAP=6.06095;AB=0.0;ABP=0.0;RUN=1;RPP=7.16258;RPPR=0.0;RPL=219.0;RPR=191.0;EPP=6.59058;EPPR=0.0;DPRA=0.0;ODDS=59.8315;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.980488;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9552;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=2 [...]
+chr15 99100484 . A G 9708.435000000001 REJECT NS=2;DP=393;DPB=447.0;AC=3;AN=4;AF=0.75;RO=115;AO=332;PRO=0.0;PAO=0.0;QR=4454;QA=12904;PQR=0.0;PQA=0.0;SRF=52;SRR=63;SAF=180;SAR=152;SRP=5.29507;SAP=8.13811;AB=0.662757;ABP=81.4699;RUN=1;RPP=3.66436;RPPR=4.53977;RPL=161.0;RPR=171.0;EPP=5.12945;EPPR=3.48236;DPRA=0.0;ODDS=67.1043;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991304;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.322;Dels=0.0;FS=3.0085;H [...]
+chr15 99251356 . C T 857.673 REJECT NS=2;DP=232;DPB=264.0;AC=2;AN=4;AF=0.5;RO=213;AO=51;PRO=0.0;PAO=0.0;QR=8193;QA=1867;PQR=0.0;PQA=0.0;SRF=74;SRR=139;SAF=17;SAR=34;SRP=46.0829;SAP=15.3153;AB=0.193182;ABP=218.874;RUN=1;RPP=43.9277;RPPR=48.7743;RPL=41.0;RPR=10.0;EPP=4.07475;EPPR=3.50984;DPRA=0.0;ODDS=27.6656;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.6395;Dels=0.0;FS=2.2205;HaplotypeScore=3.890 [...]
+chr15 99456253 . T C 4796.985000000001 REJECT NS=2;DP=135;DPB=159.0;AC=4;AN=4;AF=1.0;RO=1;AO=158;PRO=0.0;PAO=0.0;QR=34;QA=5945;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=136;SAR=22;SRP=5.18177;SAP=181.621;AB=0.0;ABP=0.0;RUN=1;RPP=43.0863;RPPR=5.18177;RPL=52.0;RPR=106.0;EPP=5.70403;EPPR=5.18177;DPRA=0.0;ODDS=33.0244;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993671;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.0;MQ [...]
+chr15 99467934 . A C 5447.82 REJECT NS=2;DP=237;DPB=274.0;AC=3;AN=4;AF=0.75;RO=73;AO=201;PRO=0.0;PAO=0.0;QR=2806;QA=7614;PQR=0.0;PQA=0.0;SRF=20;SRR=53;SAF=59;SAR=142;SRP=35.4039;SAP=77.4345;AB=0.635;ABP=34.6704;RUN=1;RPP=54.445;RPPR=31.5964;RPL=135.0;RPR=66.0;EPP=4.83607;EPPR=6.60959;DPRA=0.0;ODDS=47.1494;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.698;Dels=0.0;FS=0.6315;HaplotypeScore=1.9664;M [...]
+chr15 99478225 . G A 2382.33 PASS SOMATIC;NS=2;DP=386;DPB=386.0;AC=1;AN=3;AF=0.25;RO=294;AO=92;PRO=0.0;PAO=0.0;QR=11155;QA=3526;PQR=0.0;PQA=0.0;SRF=136;SRR=158;SAF=42;SAR=50;SRP=6.5851;SAP=4.52089;AB=0.340741;ABP=62.4926;RUN=1;RPP=7.63648;RPPR=8.00321;RPL=53.0;RPR=39.0;EPP=3.86001;EPPR=3.27619;DPRA=2.32759;ODDS=73.254;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986395;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.278;Dels=0.0;FS=0.0;H [...]
+chr15 99604346 . T C 14412.15 REJECT NS=2;DP=380;DPB=429.0;AC=4;AN=4;AF=1.0;RO=0;AO=429;PRO=0.0;PAO=0.0;QR=0;QA=16463;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=184;SAR=245;SRP=0.0;SAP=21.8449;AB=0.0;ABP=0.0;RUN=1;RPP=3.62277;RPPR=0.0;RPL=220.0;RPR=209.0;EPP=46.789;EPPR=0.0;DPRA=0.0;ODDS=65.4855;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0233;MQMR=0.0;PAIRED=0.990676;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.0;MQ=60.015;QD=29.39;S [...]
+chr15 99604404 . A G 9516.52 REJECT NS=2;DP=259;DPB=296.0;AC=4;AN=4;AF=1.0;RO=0;AO=295;PRO=0.0;PAO=0.0;QR=0;QA=11181;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=69;SAR=226;SRP=0.0;SAP=184.45;AB=0.0;ABP=0.0;RUN=1;RPP=137.163;RPPR=0.0;RPL=215.0;RPR=80.0;EPP=6.25647;EPPR=0.0;DPRA=0.0;ODDS=49.7963;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0339;MQMR=0.0;PAIRED=0.99661;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9243;MLEAC=2;MLEAF=1.0;MQ=60.025;QD=28.635;SOR= [...]
+chr15 99605041 . A G 14224.3 REJECT NS=2;DP=375;DPB=428.0;AC=4;AN=4;AF=1.0;RO=0;AO=428;PRO=0.0;PAO=0.0;QR=0;QA=16340;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=218;SAR=210;SRP=0.0;SAP=3.33501;AB=0.0;ABP=0.0;RUN=1;RPP=4.65412;RPPR=0.0;RPL=205.0;RPR=223.0;EPP=37.1247;EPPR=0.0;DPRA=0.0;ODDS=70.4243;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992991;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.525;SOR=0. [...]
+chr15 99605101 . A G 10067.785 REJECT NS=2;DP=271;DPB=312.0;AC=4;AN=4;AF=1.0;RO=1;AO=311;PRO=0.0;PAO=0.0;QR=34;QA=11757;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=102;SAR=209;SRP=5.18177;SAP=82.9498;AB=0.0;ABP=0.0;RUN=1;RPP=74.236;RPPR=5.18177;RPL=206.0;RPR=105.0;EPP=8.10034;EPPR=5.18177;DPRA=0.0;ODDS=50.4325;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993569;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.887;Dels=0.0;FS=2.3335;HaplotypeScore=4.8376;MLEA [...]
+chr15 99606243 . A G 13691.15 REJECT NS=2;DP=362;DPB=415.0;AC=4;AN=4;AF=1.0;RO=0;AO=415;PRO=0.0;PAO=0.0;QR=0;QA=15848;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=229;SAR=186;SRP=0.0;SAP=12.6851;AB=0.0;ABP=0.0;RUN=1;RPP=15.5734;RPPR=0.0;RPL=183.0;RPR=232.0;EPP=3.64343;EPPR=0.0;DPRA=0.0;ODDS=69.1737;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9639;MQMR=0.0;PAIRED=0.995181;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8464;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.235;S [...]
+chr15 99606489 . G A 14874.05 REJECT NS=2;DP=389;DPB=451.0;AC=4;AN=4;AF=1.0;RO=0;AO=451;PRO=0.0;PAO=0.0;QR=0;QA=17425;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=178;SAR=273;SRP=0.0;SAP=46.4638;AB=0.0;ABP=0.0;RUN=1;RPP=11.9129;RPPR=0.0;RPL=247.0;RPR=204.0;EPP=6.52029;EPPR=0.0;DPRA=0.0;ODDS=80.9822;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991131;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8546;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.22;SOR=1 [...]
+chr15 100514417 . CC TG 4828.945 REJECT NS=2;DP=302;DPB=346.0;AC=2;AN=4;AF=0.5;RO=179;AO=163;PRO=3.0;PAO=3.0;QR=6856;QA=6258;PQR=0.0;PQA=119.0;SRF=106;SRR=73;SAF=97;SAR=66;SRP=16.2211;SAP=15.8127;AB=0.475219;ABP=4.83991;RUN=1;RPP=46.2932;RPPR=23.4027;RPL=53.0;RPR=110.0;EPP=32.4384;EPPR=8.36013;DPRA=0.0;ODDS=259.684;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=1;MEANALT=1.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=0.993865;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;JOINED;BaseQRankSum=1.635;Dels=0.0;FS=0.483;Hap [...]
+chr15 100514494 . T C 5870.17 REJECT NS=2;DP=369;DPB=421.0;AC=2;AN=4;AF=0.5;RO=213;AO=208;PRO=0.0;PAO=0.0;QR=8037;QA=7872;PQR=0.0;PQA=0.0;SRF=96;SRR=117;SAF=94;SAR=114;SRP=7.50617;SAP=7.18621;AB=0.494062;ABP=3.13925;RUN=1;RPP=3.67845;RPPR=38.4981;RPL=108.0;RPR=100.0;EPP=9.02361;EPPR=4.73321;DPRA=0.0;ODDS=294.206;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.65;Dels=0.0;FS=0.5795;HaplotypeScore=6.7 [...]
+chr15 102005895 . A AG 7256.605 REJECT NS=2;DP=308;DPB=414.375;AC=2;AN=4;AF=0.5;RO=89;AO=257;PRO=29.0;PAO=34.0;QR=3337;QA=9160;PQR=959.5;PQA=1143.5;SRF=58;SRR=31;SAF=140;SAR=117;SRP=20.7969;SAP=7.47998;AB=0.73639;ABP=172.404;RUN=1;RPP=3.01875;RPPR=7.13366;RPL=129.0;RPR=128.0;EPP=4.03267;EPPR=3.0347;DPRA=0.0;ODDS=66.1807;GTI=0;TYPE=ins;CIGAR=1M1I7M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988327;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.019;FS=5.9455;MLEAC=1;M [...]
+chr15 102005913 . A C 8963.54 REJECT NS=2;DP=341;DPB=397.0;AC=2;AN=4;AF=0.5;RO=98;AO=298;PRO=0.0;PAO=0.0;QR=3800;QA=11257;PQR=0.0;PQA=0.0;SRF=58;SRR=40;SAF=145;SAR=153;SRP=10.1895;SAP=3.47666;AB=0.75063;ABP=219.616;RUN=1;RPP=17.1176;RPPR=5.22609;RPL=127.0;RPR=171.0;EPP=15.8643;EPPR=17.989;DPRA=0.0;ODDS=83.4466;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.1342;MQMR=60.0;PAIRED=0.986577;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.095;Dels=0.0;FS=7.481;HaplotypeSc [...]
+chr16 338332 . A AC 625.094 REJECT NS=2;DP=160;DPB=175.143;AC=2;AN=4;AF=0.5;RO=121;AO=36;PRO=9.0;PAO=10.0;QR=4488;QA=1276;PQR=313.5;PQA=327.5;SRF=14;SRR=107;SAF=4;SAR=32;SRP=158.226;SAP=50.3001;AB=0.225;ABP=108.11;RUN=1;RPP=18.4519;RPPR=46.0988;RPL=26.0;RPR=10.0;EPP=18.4519;EPPR=14.2266;DPRA=0.0;ODDS=34.68;GTI=0;TYPE=ins;CIGAR=1M1I6M;NUMALT=1;MEANALT=2.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.63;FS=4.576;MLEAC=1;MLEAF=0.5;MQ=60.42;MQRankSu [...]
+chr16 359953 . A G 1205.45 REJECT NS=2;DP=235;DPB=271.0;AC=2;AN=4;AF=0.5;RO=205;AO=66;PRO=0.0;PAO=0.0;QR=7824;QA=2489;PQR=0.0;PQA=0.0;SRF=136;SRR=69;SAF=45;SAR=21;SRP=50.5602;SAP=21.9613;AB=0.243542;ABP=157.826;RUN=1;RPP=6.30041;RPPR=94.6253;RPL=28.0;RPR=38.0;EPP=3.53672;EPPR=3.52933;DPRA=0.0;ODDS=148.154;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984848;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1135;Dels=0.0;FS=0.4765;HaplotypeScore=6. [...]
+chr16 396264 . A G 1704.275 REJECT NS=2;DP=337;DPB=383.0;AC=2;AN=4;AF=0.5;RO=295;AO=88;PRO=0.0;PAO=0.0;QR=11231;QA=3366;PQR=0.0;PQA=0.0;SRF=173;SRR=122;SAF=50;SAR=38;SRP=22.1561;SAP=6.56362;AB=0.229765;ABP=245.949;RUN=1;RPP=3.40511;RPPR=5.13761;RPL=42.0;RPR=46.0;EPP=4.58955;EPPR=4.66651;DPRA=0.0;ODDS=169.06;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.965909;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7355;Dels=0.0;FS=2.9495;HaplotypeScore=2 [...]
+chr16 397044 . G T 1776.7150000000001 REJECT NS=2;DP=283;DPB=328.0;AC=2;AN=4;AF=0.5;RO=248;AO=80;PRO=0.0;PAO=0.0;QR=9530;QA=3071;PQR=0.0;PQA=0.0;SRF=103;SRR=145;SAF=35;SAR=45;SRP=18.4558;SAP=5.72464;AB=0.243902;ABP=189.863;RUN=1;RPP=34.3881;RPPR=64.7922;RPL=57.0;RPR=23.0;EPP=3.44459;EPPR=7.24817;DPRA=0.0;ODDS=63.799;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.9875;PAIREDR=0.995968;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.318;Dels=0.0;FS=1.438;Haplo [...]
+chr16 2105400 . C T 2766.8 PASS SOMATIC;NS=2;DP=368;DPB=368.0;AC=1;AN=3;AF=0.25;RO=262;AO=106;PRO=0.0;PAO=0.0;QR=9912;QA=4053;PQR=0.0;PQA=0.0;SRF=173;SRR=89;SAF=78;SAR=28;SRP=61.4909;SAP=54.2243;AB=0.386861;ABP=33.4743;RUN=1;RPP=29.5596;RPPR=53.4349;RPL=35.0;RPR=71.0;EPP=8.25461;EPPR=29.0017;DPRA=2.91489;ODDS=59.4939;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992366;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.292;Dels=0.0;FS=6.471;H [...]
+chr16 2138218 . A C 2981.37 PASS SOMATIC;NS=2;DP=430;DPB=430.0;AC=1;AN=3;AF=0.25;RO=316;AO=114;PRO=0.0;PAO=0.0;QR=11991;QA=4357;PQR=0.0;PQA=0.0;SRF=145;SRR=171;SAF=59;SAR=55;SRP=7.6556;SAP=3.31507;AB=0.349693;ABP=66.9821;RUN=1;RPP=3.31507;RPPR=4.35716;RPL=55.0;RPR=59.0;EPP=4.9151;EPPR=3.12025;DPRA=3.13462;ODDS=65.879;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991228;PAIREDR=0.993671;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.803;Dels=0.0;FS=0. [...]
+chr16 2138422 . C G 1883.0 PASS SOMATIC;NS=2;DP=328;DPB=328.0;AC=1;AN=3;AF=0.25;RO=249;AO=79;PRO=0.0;PAO=0.0;QR=9540;QA=2962;PQR=0.0;PQA=0.0;SRF=138;SRR=111;SAF=41;SAR=38;SRP=9.36774;SAP=3.25768;AB=0.303846;ABP=89.9026;RUN=1;RPP=29.4253;RPPR=60.2273;RPL=24.0;RPR=55.0;EPP=3.03779;EPPR=5.5306;DPRA=3.82353;ODDS=42.5392;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987952;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.996;Dels=0.0;FS=3.023;H [...]
+chr16 2222286 . C T 2812.06 PASS SOMATIC;NS=2;DP=402;DPB=402.0;AC=1;AN=3;AF=0.25;RO=293;AO=109;PRO=0.0;PAO=0.0;QR=11198;QA=4073;PQR=0.0;PQA=0.0;SRF=140;SRR=153;SAF=46;SAR=63;SRP=4.26279;SAP=8.76769;AB=0.37457;ABP=42.7759;RUN=1;RPP=3.98647;RPPR=8.41304;RPL=51.0;RPR=58.0;EPP=7.4927;EPPR=4.67781;DPRA=2.62162;ODDS=70.1393;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.023;Dels=0.0;FS=4.879;Hapl [...]
+chr16 2223860 . T TC 148.73 PASS DP=80;AC=1;AN=4;AF=0.5;BaseQRankSum=-2.788;FS=131.562;MLEAC=1;MLEAF=0.5;MQ=59.01;MQRankSum=0.788;QD=1.86;ReadPosRankSum=-1.045;SOR=6.438;ClippingRankSum=1.134 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:52,24:76:99.0:186,0,4985:24:32:76:1:.:.:.:.:.:-0.0183821 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.631719
+chr16 2223864 . G C 509.75 PASS DP=182;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-6.607;Dels=0.0;FS=199.2505;HaplotypeScore=89.065;MLEAC=1;MLEAF=0.5;MQ=59.265;MQRankSum=-0.51;QD=4.635;ReadPosRankSum=-1.001;SOR=7.7465;ClippingRankSum=-1.219 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:52,27:79:99.0:660,0,5200:27:34:79:1:.:.:.:.:.:-0.0183821 0/1:196,90:286:99.0:425,0,6123:90:31:286:.:1:.:.:.:.:-0.631719
+chr16 2223864 . GCCCA CCCCC 246.535 REJECT NS=2;DP=341;DPB=384.444;AC=2;AN=4;AF=0.5;RO=199;AO=66;PRO=59.6667;PAO=11.6667;QR=7242;QA=1455;PQR=1908.33;PQA=320.333;SRF=25;SRR=174;SAF=66;SAR=0;SRP=245.266;SAP=146.327;AB=0.193548;ABP=281.169;RUN=1;RPP=113.69;RPPR=12.1872;RPL=62.0;RPR=4.0;EPP=113.69;EPPR=8.78271;DPRA=0.0;ODDS=4.20892;GTI=0;TYPE=complex;CIGAR=4M1X3M1X;NUMALT=2;MEANALT=10.5;LEN=9;MQM=57.6515;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984925;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP [...]
+chr16 2223864 . GCCCA CCCCCC 246.535 REJECT NS=2;DP=341;DPB=384.444;AC=2;AN=2;AF=0.0;RO=199;AO=34;PRO=59.6667;PAO=11.6667;QR=7242;QA=584;PQR=1908.33;PQA=320.333;SRF=25;SRR=174;SAF=34;SAR=0;SRP=245.266;SAP=76.8404;AB=0.0997067;ABP=477.608;RUN=1;RPP=15.5282;RPPR=12.1872;RPL=24.0;RPR=10.0;EPP=15.5282;EPPR=8.78271;DPRA=0.0;ODDS=4.20892;GTI=0;TYPE=complex;CIGAR=1M1I3M1X3M1X;NUMALT=2;MEANALT=10.5;LEN=10;MQM=56.5;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984925;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT [...]
+chr16 2223868 . A C 635.27 PASS DP=184;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-7.272;Dels=0.0;FS=203.2055;HaplotypeScore=88.0318;MLEAC=1;MLEAF=0.5;MQ=59.275;MQRankSum=0.307;QD=4.665;ReadPosRankSum=-0.8145;SOR=7.7505;ClippingRankSum=0.395 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:54,26:80:99.0:575,0,4571:26:33:80:1:.:.:.:.:.:-0.0183821 0/1:199,88:289:99.0:752,0,6373:88:31:287:.:1:.:.:.:.:-0.631719
+chr16 2223872 . T C 814.662 REJECT NS=2;DP=333;DPB=383.0;AC=2;AN=4;AF=0.5;RO=233;AO=139;PRO=12.5;PAO=4.5;QR=8192;QA=2739;PQR=195.0;PQA=82.0;SRF=34;SRR=199;SAF=139;SAR=0;SRP=256.737;SAP=304.845;AB=0.369681;ABP=58.4752;RUN=1;RPP=216.861;RPPR=7.94038;RPL=128.0;RPR=11.0;EPP=216.861;EPPR=3.01962;DPRA=0.0;ODDS=61.4969;GTI=0;TYPE=snp;CIGAR=3M1X;NUMALT=1;MEANALT=3.0;LEN=1;MQM=57.777;MQMR=59.9785;PAIRED=1.0;PAIREDR=0.982833;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-6.985;Dels=0.0;FS=227.2305;Ha [...]
+chr16 2237549 . C T 3968.46 REJECT NS=1;DP=119;DPB=119.0;AC=2;AN=4;AF=1.0;RO=0;AO=119;PRO=0.0;PAO=0.0;QR=0;QA=4491;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=52;SAR=67;SRP=0.0;SAP=7.11603;AB=0.0;ABP=0.0;RUN=1;RPP=18.3566;RPPR=0.0;RPL=45.0;RPR=74.0;EPP=22.882;EPPR=0.0;DPRA=0.0;ODDS=78.8434;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991597;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.25;SOR=1.035 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr16 2496724 . T G 12965.05 REJECT NS=2;DP=345;DPB=396.0;AC=4;AN=4;AF=1.0;RO=0;AO=393;PRO=0.0;PAO=0.0;QR=0;QA=15033;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=212;SAR=181;SRP=0.0;SAP=8.32019;AB=0.0;ABP=0.0;RUN=1;RPP=15.2159;RPPR=0.0;RPL=173.0;RPR=220.0;EPP=8.32019;EPPR=0.0;DPRA=0.0;ODDS=66.0814;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992366;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8239;MLEAC=2;MLEAF=1.0;MQ=59.975;QD=29.885;SOR [...]
+chr16 2496760 . T C 13750.7 REJECT NS=2;DP=360;DPB=414.0;AC=4;AN=4;AF=1.0;RO=0;AO=414;PRO=0.0;PAO=0.0;QR=0;QA=15983;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=206;SAR=208;SRP=0.0;SAP=3.03128;AB=0.0;ABP=0.0;RUN=1;RPP=14.1089;RPPR=0.0;RPL=230.0;RPR=184.0;EPP=6.55599;EPPR=0.0;DPRA=0.0;ODDS=70.4749;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995169;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9637;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.825;SOR=0. [...]
+chr16 2607730 . C T 1036.71 REJECT NS=2;DP=196;DPB=196.0;AC=2;AN=4;AF=0.5;RO=119;AO=77;PRO=0.0;PAO=0.0;QR=4396;QA=2797;PQR=0.0;PQA=0.0;SRF=118;SRR=1;SAF=77;SAR=0;SRP=252.803;SAP=170.214;AB=0.392857;ABP=22.5536;RUN=1;RPP=5.29458;RPPR=5.21827;RPL=34.0;RPR=43.0;EPP=5.29458;EPPR=6.09416;DPRA=0.0;ODDS=86.0986;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=27.9091;MQMR=26.9664;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=334;BaseQRankSum=-1.9475;Dels=0.0;FS=1.694;HaplotypeScore=0 [...]
+chr16 2642822 . C T 1960.42 REJECT NS=2;DP=413;DPB=466.0;AC=2;AN=4;AF=0.5;RO=359;AO=106;PRO=0.0;PAO=0.0;QR=13715;QA=3932;PQR=0.0;PQA=0.0;SRF=196;SRR=163;SAF=58;SAR=48;SRP=9.5973;SAP=5.05886;AB=0.227468;ABP=303.643;RUN=1;RPP=5.05886;RPPR=4.37125;RPL=48.0;RPR=58.0;EPP=21.4473;EPPR=8.82307;DPRA=0.0;ODDS=179.179;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991643;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4575;Dels=0.0;FS=1.87;HaplotypeScore=5. [...]
+chr16 2750455 . A G 877.782 REJECT NS=1;DP=87;DPB=87.0;AC=1;AN=4;AF=0.5;RO=51;AO=36;PRO=0.0;PAO=0.0;QR=1751;QA=1290;PQR=0.0;PQA=0.0;SRF=32;SRR=19;SAF=19;SAR=17;SRP=10.206;SAP=3.25157;AB=0.413793;ABP=8.62618;RUN=1;RPP=6.8707;RPPR=6.45911;RPL=14.0;RPR=22.0;EPP=5.18177;EPPR=3.05288;DPRA=0.0;ODDS=202.117;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=0.938;FS=4.475;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.371;QD [...]
+chr16 2750618 . C G 929.976 REJECT NS=2;DP=244;DPB=283.0;AC=2;AN=4;AF=0.5;RO=230;AO=52;PRO=0.0;PAO=0.0;QR=8837;QA=1974;PQR=0.0;PQA=0.0;SRF=137;SRR=93;SAF=33;SAR=19;SRP=21.2884;SAP=11.1951;AB=0.183746;ABP=248.862;RUN=1;RPP=23.2217;RPPR=82.9205;RPL=15.0;RPR=37.0;EPP=5.68288;EPPR=4.86077;DPRA=0.0;ODDS=16.1139;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986957;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1745;Dels=0.0;FS=2.3285;HaplotypeScore=3 [...]
+chr16 2750639 . T TGA 1020.54 REJECT NS=2;DP=371;DPB=411.0;AC=2;AN=4;AF=0.5;RO=307;AO=63;PRO=8.0;PAO=8.0;QR=11626;QA=2327;PQR=208.0;PQA=208.0;SRF=179;SRR=128;SAF=42;SAR=21;SRP=21.4077;SAP=18.2106;AB=0.169811;ABP=354.338;RUN=1;RPP=3.32051;RPPR=3.01737;RPL=30.0;RPR=33.0;EPP=5.80219;EPPR=4.60177;DPRA=0.0;ODDS=19.3472;GTI=0;TYPE=ins;CIGAR=1M2I3M;NUMALT=1;MEANALT=1.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986971;technology.ILLUMINA=1.0;END=2750639;HOMLEN=3;HOMSEQ=GAG;SVLEN=2;SVTYPE=INS [...]
+chr16 2750696 . G A 3092.13 PASS SOMATIC;NS=2;DP=419;DPB=419.0;AC=1;AN=3;AF=0.25;RO=301;AO=118;PRO=0.0;PAO=0.0;QR=11415;QA=4533;PQR=0.0;PQA=0.0;SRF=133;SRR=168;SAF=53;SAR=65;SRP=11.8477;SAP=5.66023;AB=0.354545;ABP=63.6536;RUN=1;RPP=7.72129;RPPR=3.01751;RPL=51.0;RPR=67.0;EPP=3.08391;EPPR=52.7089;DPRA=0.0;ODDS=49.1579;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993355;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.501;Dels=0.0;FS=0.0;Hapl [...]
+chr16 2752154 . A G 1407.55 REJECT NS=1;DP=94;DPB=94.0;AC=1;AN=4;AF=0.5;RO=44;AO=50;PRO=0.0;PAO=0.0;QR=1663;QA=1929;PQR=0.0;PQA=0.0;SRF=28;SRR=16;SAF=30;SAR=20;SRP=10.1169;SAP=7.35324;AB=0.531915;ABP=3.84193;RUN=1;RPP=3.18402;RPPR=4.78696;RPL=24.0;RPR=26.0;EPP=24.0302;EPPR=3.20771;DPRA=0.0;ODDS=272.982;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.98;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=1.148;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=1.894;QD [...]
+chr16 2753180 . T C 2334.55 REJECT NS=2;DP=355;DPB=410.0;AC=2;AN=4;AF=0.5;RO=302;AO=107;PRO=0.0;PAO=0.0;QR=11633;QA=4158;PQR=0.0;PQA=0.0;SRF=127;SRR=175;SAF=50;SAR=57;SRP=19.5768;SAP=4.00471;AB=0.260976;ABP=206.472;RUN=1;RPP=6.44001;RPPR=5.33996;RPL=47.0;RPR=60.0;EPP=20.0777;EPPR=19.5768;DPRA=0.0;ODDS=156.023;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990654;PAIREDR=0.993377;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.7845;Dels=0.0;FS=1.039;HaplotypeS [...]
+chr16 3777836 . T C 7592.05 REJECT NS=2;DP=532;DPB=615.0;AC=2;AN=4;AF=0.5;RO=334;AO=281;PRO=0.0;PAO=0.0;QR=12636;QA=10660;PQR=0.0;PQA=0.0;SRF=170;SRR=164;SAF=145;SAR=136;SRP=3.24435;SAP=3.63624;AB=0.456911;ABP=12.9285;RUN=1;RPP=11.4257;RPPR=9.66775;RPL=124.0;RPR=157.0;EPP=3.07985;EPPR=3.42639;DPRA=0.0;ODDS=489.147;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992883;PAIREDR=0.991018;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.5965;Dels=0.0;FS=0.846;Haplo [...]
+chr16 3808052 . T TA 429.677 REJECT NS=2;DP=210;DPB=238.444;AC=2;AN=3;AF=0.25;RO=139;AO=29;PRO=27.1667;PAO=19.1667;QR=5199;QA=977;PQR=985.833;PQA=691.833;SRF=16;SRR=123;SAF=5;SAR=24;SRP=181.868;SAP=30.0414;AB=0.138095;ABP=241.914;RUN=1;RPP=3.68421;RPPR=4.27569;RPL=13.0;RPR=16.0;EPP=15.6647;EPPR=11.2744;DPRA=0.0;ODDS=6.98576;GTI=0;TYPE=ins;CIGAR=1M1I17M;NUMALT=2;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr16 3808052 . TA T 429.677 REJECT NS=2;DP=210;DPB=238.444;AC=2;AN=3;AF=0.25;RO=139;AO=29;PRO=27.1667;PAO=15.6667;QR=5199;QA=1070;PQR=985.833;PQA=550.333;SRF=16;SRR=123;SAF=8;SAR=21;SRP=181.868;SAP=15.6647;AB=0.138095;ABP=241.914;RUN=1;RPP=15.6647;RPPR=4.27569;RPL=21.0;RPR=8.0;EPP=3.68421;EPPR=11.2744;DPRA=0.0;ODDS=6.98576;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=2;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr16 6000642 . G C 1654.96 REJECT NS=2;DP=375;DPB=425.0;AC=2;AN=4;AF=0.5;RO=339;AO=86;PRO=0.0;PAO=0.0;QR=12967;QA=3267;PQR=0.0;PQA=0.0;SRF=179;SRR=160;SAF=43;SAR=43;SRP=5.32269;SAP=3.0103;AB=0.202353;ABP=330.054;RUN=1;RPP=17.5541;RPPR=15.9815;RPL=55.0;RPR=31.0;EPP=3.1113;EPPR=7.01375;DPRA=0.0;ODDS=99.0331;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988372;PAIREDR=0.988201;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.5905;Dels=0.0;FS=3.957;HaplotypeScor [...]
+chr16 8988386 . C CG 4285.59 REJECT NS=2;DP=203;DPB=263.267;AC=2;AN=2;AF=0.5;RO=24;AO=67;PRO=25.8333;PAO=25.8333;QR=899;QA=2399;PQR=862.833;PQA=862.833;SRF=12;SRR=12;SAF=46;SAR=21;SRP=3.0103;SAP=23.2666;AB=0.29386;ABP=87.1644;RUN=1;RPP=20.1552;RPPR=39.2015;RPL=22.0;RPR=45.0;EPP=10.3026;EPPR=4.45795;DPRA=0.0;ODDS=68.0639;GTI=0;TYPE=ins;CIGAR=1M1I14M;NUMALT=2;MEANALT=7.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.677;FS=3. [...]
+chr16 8988386 . CG C 4285.59 REJECT NS=2;DP=203;DPB=263.267;AC=2;AN=2;AF=0.5;RO=24;AO=121;PRO=25.8333;PAO=24.3333;QR=899;QA=4400;PQR=862.833;PQA=806.333;SRF=12;SRR=12;SAF=74;SAR=47;SRP=3.0103;SAP=16.093;AB=0.530702;ABP=4.877;RUN=1;RPP=9.48883;RPPR=39.2015;RPL=51.0;RPR=70.0;EPP=20.2565;EPPR=4.45795;DPRA=0.0;ODDS=68.0639;GTI=0;TYPE=del;CIGAR=1M1D13M;NUMALT=2;MEANALT=7.0;LEN=1;MQM=60.4959;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.677;FS= [...]
+chr16 8995927 . G A 3706.52 REJECT NS=2;DP=279;DPB=314.0;AC=2;AN=4;AF=0.5;RO=178;AO=136;PRO=0.0;PAO=0.0;QR=6817;QA=5291;PQR=0.0;PQA=0.0;SRF=111;SRR=67;SAF=88;SAR=48;SRP=26.6281;SAP=28.557;AB=0.433121;ABP=15.2093;RUN=1;RPP=17.3803;RPPR=10.0371;RPL=53.0;RPR=83.0;EPP=4.60697;EPPR=33.5085;DPRA=0.0;ODDS=230.007;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992647;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.0535;Dels=0.0;FS=1.6855;HaplotypeScore=8. [...]
+chr16 9004564 . C A 11291.0 REJECT NS=2;DP=307;DPB=354.0;AC=4;AN=4;AF=1.0;RO=1;AO=353;PRO=0.0;PAO=0.0;QR=14;QA=13300;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=196;SAR=157;SRP=5.18177;SAP=12.3667;AB=0.0;ABP=0.0;RUN=1;RPP=256.507;RPPR=5.18177;RPL=75.0;RPR=278.0;EPP=7.49473;EPPR=5.18177;DPRA=0.0;ODDS=60.8682;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994334;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.694;Dels=0.0;FS=1.8965;HaplotypeScore=7.7654;MLEAC=2 [...]
+chr16 9010446 . A AC 8724.28 REJECT NS=2;DP=249;DPB=381.0;AC=4;AN=4;AF=1.0;RO=0;AO=281;PRO=7.5;PAO=7.5;QR=0;QA=9930;PQR=264.5;PQA=264.5;SRF=0;SRR=0;SAF=78;SAR=203;SRP=0.0;SAP=123.755;AB=0.0;ABP=0.0;RUN=1;RPP=48.8276;RPPR=0.0;RPL=179.0;RPR=102.0;EPP=4.74902;EPPR=0.0;DPRA=0.0;ODDS=53.5706;GTI=0;TYPE=ins;CIGAR=1M1I2M;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0356;MQMR=0.0;PAIRED=0.989324;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=9010446;HOMLEN=0;SVLEN=1;SVTYPE=INS;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60 [...]
+chr16 9017061 . T A 179.395 REJECT NS=2;DP=6;DPB=6.0;AC=4;AN=4;AF=1.0;RO=0;AO=6;PRO=0.0;PAO=0.0;QR=0;QA=225;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=2;SAR=4;SRP=0.0;SAP=4.45795;AB=0.0;ABP=0.0;RUN=1;RPP=16.0391;RPPR=0.0;RPL=0.0;RPR=6.0;EPP=4.45795;EPPR=0.0;DPRA=0.0;ODDS=5.01053;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.92;SOR=1.022 GT:GQ:DP:RO:QR:AO:QA: [...]
+chr16 9017061 . T TACAACGATGTGGGGGTTTGTAGTTGCATCATTTAA 2964.73 PASS DP=31;AC=4;AN=4;AF=1.0;END=9017061;HOMLEN=2;HOMSEQ=AC;SVLEN=35;SVTYPE=INS;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.43;SOR=1.765 GT:AD:GMIMUT:GMIMAF:GMICOV:DP:GQ:PL:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:0,41:41:99:42:30:99.0:3002,200,0:1:.:.:1:.:.:-0.00057019 1/1:5,167:167:97:172:.:.:.:.:.:.:1:.:.:-0.0160207
+chr16 9030444 . C G 13402.25 REJECT NS=2;DP=356;DPB=402.0;AC=4;AN=4;AF=1.0;RO=0;AO=402;PRO=0.0;PAO=0.0;QR=0;QA=15241;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=193;SAR=209;SRP=0.0;SAP=4.39313;AB=0.0;ABP=0.0;RUN=1;RPP=14.4402;RPPR=0.0;RPL=224.0;RPR=178.0;EPP=57.027;EPPR=0.0;DPRA=0.0;ODDS=60.7554;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992537;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.495;SOR=0.819 [...]
+chr16 9916204 . C G 8972.685000000001 REJECT NS=2;DP=365;DPB=425.0;AC=3;AN=4;AF=0.75;RO=104;AO=321;PRO=0.0;PAO=0.0;QR=3971;QA=12284;PQR=0.0;PQA=0.0;SRF=51;SRR=53;SAF=170;SAR=151;SRP=3.09382;SAP=5.45236;AB=0.661238;ABP=72.3347;RUN=1;RPP=3.34177;RPPR=15.0369;RPL=164.0;RPR=157.0;EPP=3.17942;EPPR=3.09382;DPRA=0.0;ODDS=74.5627;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993769;PAIREDR=0.971154;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.736;Dels=0.0;FS=2.01 [...]
+chr16 9943666 . C T 8537.93 REJECT NS=2;DP=374;DPB=432.0;AC=3;AN=4;AF=0.75;RO=116;AO=316;PRO=0.0;PAO=0.0;QR=4384;QA=11791;PQR=0.0;PQA=0.0;SRF=63;SRR=53;SAF=161;SAR=155;SRP=4.88226;SAP=3.25768;AB=0.632911;ABP=51.4974;RUN=1;RPP=10.047;RPPR=7.80251;RPL=142.0;RPR=174.0;EPP=3.69747;EPPR=12.0706;DPRA=0.0;ODDS=73.2417;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990506;PAIREDR=0.991379;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.156;Dels=0.0;FS=1.601;Haplotyp [...]
+chr16 10528356 . C G 3658.79 REJECT NS=2;DP=233;DPB=269.0;AC=2;AN=4;AF=0.5;RO=135;AO=134;PRO=0.0;PAO=0.0;QR=5118;QA=5087;PQR=0.0;PQA=0.0;SRF=95;SRR=40;SAF=94;SAR=40;SRP=51.6674;SAP=50.2641;AB=0.498141;ABP=3.01837;RUN=1;RPP=73.5994;RPPR=55.2704;RPL=34.0;RPR=100.0;EPP=4.6308;EPPR=3.15506;DPRA=0.0;ODDS=208.027;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992537;PAIREDR=0.985185;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.629;Dels=0.0;FS=0.2835;HaplotypeSco [...]
+chr16 11348706 . C G 5542.54 REJECT NS=2;DP=369;DPB=412.0;AC=2;AN=4;AF=0.5;RO=214;AO=197;PRO=0.0;PAO=0.0;QR=8096;QA=7552;PQR=0.0;PQA=0.0;SRF=134;SRR=80;SAF=129;SAR=68;SRP=32.5991;SAP=44.0258;AB=0.478155;ABP=4.71796;RUN=1;RPP=3.55041;RPPR=20.9097;RPL=95.0;RPR=102.0;EPP=38.8231;EPPR=9.86972;DPRA=0.0;ODDS=257.092;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.985981;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1875;Dels=0.0;FS=3.1665;HaplotypeScor [...]
+chr16 19509305 . C G 7407.47 REJECT NS=2;DP=279;DPB=320.0;AC=2;AN=4;AF=0.5;RO=75;AO=245;PRO=0.0;PAO=0.0;QR=2866;QA=9377;PQR=0.0;PQA=0.0;SRF=13;SRR=62;SAF=96;SAR=149;SRP=72.5264;SAP=27.9069;AB=0.765625;ABP=199.121;RUN=1;RPP=76.4061;RPPR=13.4623;RPL=168.0;RPR=77.0;EPP=3.23188;EPPR=3.03925;DPRA=0.0;ODDS=117.858;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3895;Dels=0.0;FS=24.783;HaplotypeScore=12.6 [...]
+chr16 21008081 . A G 1243.925 REJECT NS=2;DP=226;DPB=257.0;AC=2;AN=4;AF=0.5;RO=197;AO=60;PRO=0.0;PAO=0.0;QR=7558;QA=2279;PQR=0.0;PQA=0.0;SRF=107;SRR=90;SAF=40;SAR=20;SRP=6.19586;SAP=17.4868;AB=0.233463;ABP=161.595;RUN=1;RPP=20.5268;RPPR=90.3211;RPL=19.0;RPR=41.0;EPP=6.62942;EPPR=19.7758;DPRA=0.0;ODDS=78.7762;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8985;PAIRED=1.0;PAIREDR=0.994924;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.147;Dels=0.0;FS=6.1295;HaplotypeScor [...]
+chr16 23517300 . C T 1422.855 REJECT NS=2;DP=362;DPB=411.0;AC=2;AN=4;AF=0.5;RO=332;AO=79;PRO=0.0;PAO=0.0;QR=12619;QA=3079;PQR=0.0;PQA=0.0;SRF=155;SRR=177;SAF=34;SAR=45;SRP=6.17594;SAP=6.33623;AB=0.192214;ABP=341.195;RUN=1;RPP=3.03779;RPPR=4.29225;RPL=39.0;RPR=40.0;EPP=3.03779;EPPR=4.68469;DPRA=0.0;ODDS=98.6873;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.974684;PAIREDR=0.990964;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6815;Dels=0.0;FS=2.9525;Haplotyp [...]
+chr16 23518214 . T TC 11856.2 REJECT NS=2;DP=353;DPB=464.182;AC=4;AN=4;AF=1.0;RO=1;AO=373;PRO=28.0;PAO=54.0;QR=39;QA=13529;PQR=919.5;PQA=1829.5;SRF=1;SRR=0;SAF=198;SAR=175;SRP=5.18177;SAP=6.08995;AB=0.0;ABP=0.0;RUN=1;RPP=4.32017;RPPR=5.18177;RPL=194.0;RPR=179.0;EPP=12.7965;EPPR=5.18177;DPRA=0.0;ODDS=57.4381;GTI=0;TYPE=ins;CIGAR=1M1I10M;NUMALT=1;MEANALT=4.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991957;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.613;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60 [...]
+chr16 23750116 . G A 9602.935000000001 REJECT NS=2;DP=391;DPB=443.0;AC=3;AN=4;AF=0.75;RO=112;AO=331;PRO=0.0;PAO=0.0;QR=4324;QA=12666;PQR=0.0;PQA=0.0;SRF=60;SRR=52;SAF=180;SAR=151;SRP=4.25114;SAP=8.52755;AB=0.674487;ABP=93.1869;RUN=1;RPP=11.0467;RPPR=4.25114;RPL=148.0;RPR=183.0;EPP=39.9122;EPPR=5.80219;DPRA=0.0;ODDS=56.3246;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987915;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.5145;Dels=0.0;FS=2.828; [...]
+chr16 27003637 . C T 1916.405 REJECT NS=2;DP=375;DPB=425.0;AC=2;AN=4;AF=0.5;RO=329;AO=96;PRO=0.0;PAO=0.0;QR=12643;QA=3710;PQR=0.0;PQA=0.0;SRF=148;SRR=181;SAF=43;SAR=53;SRP=10.1979;SAP=5.27225;AB=0.225882;ABP=280.392;RUN=1;RPP=16.0391;RPPR=11.0956;RPL=60.0;RPR=36.0;EPP=13.9581;EPPR=12.046;DPRA=0.0;ODDS=137.264;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993921;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0345;Dels=0.0;FS=2.3555;HaplotypeScore [...]
+chr16 27003656 . A G 12577.349999999999 REJECT NS=2;DP=338;DPB=380.0;AC=4;AN=4;AF=1.0;RO=0;AO=380;PRO=0.0;PAO=0.0;QR=0;QA=14312;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=151;SAR=229;SRP=0.0;SAP=37.7767;AB=0.0;ABP=0.0;RUN=1;RPP=53.5027;RPPR=0.0;RPL=237.0;RPR=143.0;EPP=14.0734;EPPR=0.0;DPRA=0.0;ODDS=55.3922;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994737;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9574;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=2 [...]
+chr16 31191482 . A G 3012.14 REJECT NS=1;DP=89;DPB=89.0;AC=2;AN=4;AF=1.0;RO=0;AO=89;PRO=0.0;PAO=0.0;QR=0;QA=3434;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=56;SAR=33;SRP=0.0;SAP=15.9171;AB=0.0;ABP=0.0;RUN=1;RPP=29.5803;RPPR=0.0;RPL=28.0;RPR=61.0;EPP=10.0615;EPPR=0.0;DPRA=0.0;ODDS=60.1186;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.82;SOR=1.338 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:A [...]
+chr16 31193942 . C A 12236.3 REJECT NS=2;DP=456;DPB=517.0;AC=2;AN=4;AF=0.5;RO=119;AO=398;PRO=0.0;PAO=0.0;QR=4470;QA=15255;PQR=0.0;PQA=0.0;SRF=51;SRR=68;SAF=188;SAR=210;SRP=8.28388;SAP=5.65098;AB=0.769826;ABP=329.953;RUN=1;RPP=11.7398;RPPR=5.21827;RPL=179.0;RPR=219.0;EPP=11.7398;EPPR=6.09416;DPRA=0.0;ODDS=177.926;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.995;MQMR=60.0;PAIRED=0.997487;PAIREDR=0.983193;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.548;Dels=0.0;FS=2.0705;Haplo [...]
+chr16 31195279 . C T 1782.82 REJECT NS=2;DP=370;DPB=423.0;AC=2;AN=4;AF=0.5;RO=334;AO=88;PRO=0.0;PAO=0.0;QR=12868;QA=3317;PQR=0.0;PQA=0.0;SRF=163;SRR=171;SAF=41;SAR=47;SRP=3.42639;SAP=3.89863;AB=0.208038;ABP=316.2;RUN=1;RPP=5.47788;RPPR=3.03631;RPL=39.0;RPR=49.0;EPP=3.40511;EPPR=29.6401;DPRA=0.0;ODDS=73.6773;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.977273;PAIREDR=0.994012;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0435;Dels=0.0;FS=0.712;HaplotypeSco [...]
+chr16 31195759 . CT C 45.74 PASS DP=18;AC=1;AN=4;AF=0.5;BaseQRankSum=0.736;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.07;MQRankSum=-0.736;QD=2.54;ReadPosRankSum=-0.736;SOR=0.941;ClippingRankSum=0.736 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:3,5:8:33.0:80,0,33:5:63:8:1:.:.:.:.:.:-1.32166 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0160207
+chr16 31195965 . C G 714.591 REJECT NS=2;DP=142;DPB=167.0;AC=2;AN=4;AF=0.5;RO=128;AO=39;PRO=0.0;PAO=0.0;QR=4840;QA=1468;PQR=0.0;PQA=0.0;SRF=123;SRR=5;SAF=38;SAR=1;SRP=239.226;SAP=79.2345;AB=0.233533;ABP=106.006;RUN=1;RPP=4.40227;RPPR=35.8538;RPL=17.0;RPR=22.0;EPP=5.73856;EPPR=38.9075;DPRA=0.0;ODDS=32.9485;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=55.9744;MQMR=52.9766;PAIRED=1.0;PAIREDR=0.992188;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.486;Dels=0.0;FS=0.0;HaplotypeScore= [...]
+chr16 31196105 . T C 9328.25 REJECT NS=2;DP=346;DPB=404.0;AC=2;AN=4;AF=0.5;RO=99;AO=305;PRO=0.0;PAO=0.0;QR=3720;QA=11683;PQR=0.0;PQA=0.0;SRF=51;SRR=48;SAF=175;SAR=130;SRP=3.20771;SAP=17.4275;AB=0.75495;ABP=231.101;RUN=1;RPP=7.46004;RPPR=16.7191;RPL=140.0;RPR=165.0;EPP=8.20047;EPPR=3.55865;DPRA=0.0;ODDS=158.303;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0328;MQMR=60.0;PAIRED=0.993443;PAIREDR=0.969697;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.833;Dels=0.0;FS=2.6295;Haplot [...]
+chr16 31196141 . GTCTTTTTACTT G 6380.57 REJECT NS=2;DP=322;DPB=186.538;AC=2;AN=4;AF=0.5;RO=108;AO=246;PRO=79.5;PAO=8.5;QR=4047;QA=8370;PQR=2846.0;PQA=214.0;SRF=57;SRR=51;SAF=117;SAR=129;SRP=3.73412;SAP=4.28141;AB=0.694915;ABP=119.828;RUN=1;RPP=18.5813;RPPR=3.09072;RPL=102.0;RPR=144.0;EPP=23.348;EPPR=3.0103;DPRA=0.0;ODDS=218.795;GTI=0;TYPE=del;CIGAR=1M11D1M;NUMALT=1;MEANALT=1.0;LEN=11;MQM=60.2439;MQMR=60.0;PAIRED=0.99187;PAIREDR=0.972222;technology.ILLUMINA=1.0;MQ0=0;END=31196152;HOMLEN=6 [...]
+chr16 31196224 . G T 407.549 REJECT NS=2;DP=291;DPB=382.333;AC=2;AN=2;AF=0.0;RO=195;AO=15;PRO=75.8333;PAO=23.5;QR=7214;QA=313;PQR=2613.17;PQA=720.0;SRF=81;SRR=114;SAF=0;SAR=15;SRP=15.1371;SAP=35.5824;AB=0.0515464;ABP=511.336;RUN=1;RPP=35.5824;RPPR=3.02144;RPL=0.0;RPR=15.0;EPP=35.5824;EPPR=5.51585;DPRA=0.0;ODDS=31.315;GTI=0;TYPE=snp;CIGAR=1X20M;NUMALT=3;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=60.2051;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr16 31196224 . G GT 407.549 REJECT NS=2;DP=291;DPB=382.333;AC=2;AN=4;AF=0.5;RO=195;AO=41;PRO=75.8333;PAO=47.8333;QR=7214;QA=1198;PQR=2613.17;PQA=1545.17;SRF=81;SRR=114;SAF=18;SAR=23;SRP=15.1371;SAP=4.33437;AB=0.140893;ABP=328.962;RUN=1;RPP=3.06326;RPPR=3.02144;RPL=20.0;RPR=21.0;EPP=5.60547;EPPR=5.51585;DPRA=0.0;ODDS=31.315;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=3;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=60.2051;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.435;FS [...]
+chr16 31196224 . GT G 407.549 REJECT NS=2;DP=291;DPB=382.333;AC=2;AN=2;AF=0.0;RO=195;AO=14;PRO=75.8333;PAO=41.8333;QR=7214;QA=496;PQR=2613.17;PQA=1396.67;SRF=81;SRR=114;SAF=5;SAR=9;SRP=15.1371;SAP=5.49198;AB=0.04811;ABP=519.157;RUN=1;RPP=5.49198;RPPR=3.02144;RPL=9.0;RPR=5.0;EPP=3.63072;EPPR=5.51585;DPRA=0.0;ODDS=31.315;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=3;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=60.2051;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr16 31199399 . G T 14125.65 REJECT NS=2;DP=369;DPB=415.0;AC=4;AN=4;AF=1.0;RO=0;AO=415;PRO=0.0;PAO=0.0;QR=0;QA=15979;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=236;SAR=179;SRP=0.0;SAP=20.0106;AB=0.0;ABP=0.0;RUN=1;RPP=3.14111;RPPR=0.0;RPL=210.0;RPR=205.0;EPP=3.64343;EPPR=0.0;DPRA=0.0;ODDS=61.7165;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99759;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=10.7143;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.56;SOR=1 [...]
+chr16 31202698 . A AT 800.113 REJECT NS=2;DP=268;DPB=344.522;AC=2;AN=3;AF=0.25;RO=121;AO=38;PRO=65.8333;PAO=62.8333;QR=4278;QA=1238;PQR=2273.33;PQA=2140.33;SRF=92;SRR=29;SAF=24;SAR=14;SRP=74.2382;SAP=8.7247;AB=0.141791;ABP=301.701;RUN=1;RPP=3.9246;RPPR=24.9942;RPL=17.0;RPR=21.0;EPP=6.66752;EPPR=6.04318;DPRA=0.0;ODDS=3.66782;GTI=0;TYPE=ins;CIGAR=1M1I22M;NUMALT=2;MEANALT=21.0;LEN=1;MQM=60.0;MQMR=59.9835;PAIRED=1.0;PAIREDR=0.991736;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSu [...]
+chr16 31202698 . AT A 800.113 REJECT NS=2;DP=268;DPB=344.522;AC=2;AN=3;AF=0.25;RO=121;AO=47;PRO=65.8333;PAO=50.3333;QR=4278;QA=1567;PQR=2273.33;PQA=1726.33;SRF=92;SRR=29;SAF=31;SAR=16;SRP=74.2382;SAP=13.4056;AB=0.175373;ABP=248.322;RUN=1;RPP=4.16534;RPPR=24.9942;RPL=21.0;RPR=26.0;EPP=10.8184;EPPR=6.04318;DPRA=0.0;ODDS=3.66782;GTI=0;TYPE=del;CIGAR=1M1D21M;NUMALT=2;MEANALT=21.0;LEN=1;MQM=59.7447;MQMR=59.9835;PAIRED=0.978723;PAIREDR=0.991736;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRa [...]
+chr16 31526823 . G A 8698.255000000001 REJECT NS=2;DP=360;DPB=420.0;AC=3;AN=4;AF=0.75;RO=109;AO=311;PRO=0.0;PAO=0.0;QR=4182;QA=12061;PQR=0.0;PQA=0.0;SRF=44;SRR=65;SAF=122;SAR=189;SRP=11.7958;SAP=34.3535;AB=0.640264;ABP=54.7888;RUN=1;RPP=24.1315;RPPR=11.7958;RPL=183.0;RPR=128.0;EPP=36.2527;EPPR=5.42083;DPRA=0.0;ODDS=73.9752;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9871;MQMR=60.0;PAIRED=0.993569;PAIREDR=0.990826;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.06;Dels=0.0;FS= [...]
+chr16 33601187 . C T 3770.58 REJECT NS=2;DP=370;DPB=416.0;AC=2;AN=4;AF=0.5;RO=271;AO=144;PRO=0.0;PAO=0.0;QR=10439;QA=5548;PQR=0.0;PQA=0.0;SRF=130;SRR=141;SAF=82;SAR=62;SRP=3.97985;SAP=9.04217;AB=0.346154;ABP=88.5329;RUN=1;RPP=5.18177;RPPR=16.4798;RPL=66.0;RPR=78.0;EPP=32.2045;EPPR=19.2362;DPRA=0.0;ODDS=110.416;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99631;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.2005;Dels=0.0;FS=5.804;HaplotypeScore= [...]
+chr16 33601195 . C T 4015.9300000000003 REJECT NS=2;DP=384;DPB=433.0;AC=2;AN=4;AF=0.5;RO=270;AO=162;PRO=0.0;PAO=0.0;QR=10159;QA=6175;PQR=0.0;PQA=0.0;SRF=129;SRR=141;SAF=79;SAR=83;SRP=4.16842;SAP=3.22477;AB=0.374134;ABP=62.5929;RUN=1;RPP=5.63751;RPPR=5.06918;RPL=74.0;RPR=88.0;EPP=39.2551;EPPR=10.2485;DPRA=0.0;ODDS=308.973;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993827;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4275;Dels=0.0;FS=0.0;Haplo [...]
+chr16 46582406 . A G 889.0385 REJECT NS=2;DP=248;DPB=282.0;AC=2;AN=4;AF=0.5;RO=231;AO=51;PRO=0.0;PAO=0.0;QR=8944;QA=1976;PQR=0.0;PQA=0.0;SRF=146;SRR=85;SAF=32;SAR=19;SRP=37.9889;SAP=10.206;AB=0.180851;ABP=252.499;RUN=1;RPP=10.206;RPPR=58.7448;RPL=19.0;RPR=32.0;EPP=3.05288;EPPR=8.8855;DPRA=0.0;ODDS=61.6599;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995671;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.178;Dels=0.0;FS=5.5445;HaplotypeScore=5.93 [...]
+chr16 50827601 . A G 8906.244999999999 REJECT NS=2;DP=239;DPB=275.0;AC=4;AN=4;AF=1.0;RO=0;AO=275;PRO=0.0;PAO=0.0;QR=0;QA=10464;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=75;SAR=200;SRP=0.0;SAP=126.389;AB=0.0;ABP=0.0;RUN=1;RPP=134.412;RPPR=0.0;RPL=202.0;RPR=73.0;EPP=4.78696;EPPR=0.0;DPRA=0.0;ODDS=48.5964;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.985455;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.07 [...]
+chr16 51057736 . G T 15049.349999999999 REJECT NS=2;DP=396;DPB=455.0;AC=4;AN=4;AF=1.0;RO=0;AO=454;PRO=0.0;PAO=0.0;QR=0;QA=17483;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=200;SAR=254;SRP=0.0;SAP=16.9575;AB=0.0;ABP=0.0;RUN=1;RPP=3.0103;RPPR=0.0;RPL=227.0;RPR=227.0;EPP=30.6368;EPPR=0.0;DPRA=0.0;ODDS=76.0856;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991189;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.8909;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26 [...]
+chr16 51098427 . G C 1721.695 REJECT NS=2;DP=364;DPB=426.0;AC=2;AN=4;AF=0.5;RO=336;AO=90;PRO=0.0;PAO=0.0;QR=12877;QA=3487;PQR=0.0;PQA=0.0;SRF=131;SRR=205;SAF=37;SAR=53;SRP=38.4001;SAP=9.18693;AB=0.211268;ABP=311.482;RUN=1;RPP=9.18693;RPPR=72.911;RPL=53.0;RPR=37.0;EPP=19.3205;EPPR=7.3791;DPRA=0.0;ODDS=149.214;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988889;PAIREDR=0.988095;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5605;Dels=0.0;FS=2.481;HaplotypeSc [...]
+chr16 56855496 . C G 5257.87 REJECT NS=2;DP=338;DPB=383.0;AC=2;AN=4;AF=0.5;RO=196;AO=187;PRO=0.0;PAO=0.0;QR=7419;QA=7114;PQR=0.0;PQA=0.0;SRF=93;SRR=103;SAF=84;SAR=103;SRP=4.11819;SAP=7.20229;AB=0.488251;ABP=3.46954;RUN=1;RPP=5.62303;RPPR=10.4997;RPL=101.0;RPR=86.0;EPP=40.7382;EPPR=20.7366;DPRA=0.0;ODDS=259.846;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994652;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6175;Dels=0.0;FS=0.848;HaplotypeScore [...]
+chr16 56864618 . C T 1478.38 PASS SOMATIC;NS=2;DP=269;DPB=269.0;AC=1;AN=3;AF=0.25;RO=207;AO=62;PRO=0.0;PAO=0.0;QR=7960;QA=2385;PQR=0.0;PQA=0.0;SRF=63;SRR=144;SAF=11;SAR=51;SRP=71.8365;SAP=59.0483;AB=0.306931;ABP=68.4125;RUN=1;RPP=14.358;RPPR=42.0444;RPL=40.0;RPR=22.0;EPP=3.57068;EPPR=9.56668;DPRA=3.01493;ODDS=42.7712;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983871;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.281;Dels=0.0;FS=11.198; [...]
+chr16 56868700 . A G 2387.96 PASS SOMATIC;NS=2;DP=373;DPB=373.0;AC=1;AN=3;AF=0.25;RO=279;AO=94;PRO=0.0;PAO=0.0;QR=10791;QA=3558;PQR=0.0;PQA=0.0;SRF=136;SRR=143;SAF=42;SAR=52;SRP=3.39167;SAP=5.32038;AB=0.338129;ABP=66.2798;RUN=1;RPP=8.9241;RPPR=4.76149;RPL=55.0;RPR=39.0;EPP=3.0103;EPPR=16.0936;DPRA=2.92632;ODDS=60.2774;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.957447;PAIREDR=0.992832;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.697;Dels=0.0;FS= [...]
+chr16 56873495 . C T 2571.56 PASS SOMATIC;NS=2;DP=411;DPB=411.0;AC=1;AN=3;AF=0.25;RO=306;AO=104;PRO=0.0;PAO=0.0;QR=11591;QA=3824;PQR=0.0;PQA=0.0;SRF=162;SRR=144;SAF=52;SAR=52;SRP=5.30951;SAP=3.0103;AB=0.346667;ABP=64.2748;RUN=1;RPP=4.34659;RPPR=11.2136;RPL=56.0;RPR=48.0;EPP=8.35546;EPPR=11.2136;DPRA=2.7027;ODDS=70.2523;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0962;MQMR=59.9967;PAIRED=0.990385;PAIREDR=0.993464;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.596;Dels=0 [...]
+chr16 56876467 . C T 1360.34 REJECT NS=2;DP=262;DPB=363.238;AC=2;AN=2;AF=0.0;RO=82;AO=36;PRO=57.7167;PAO=12.2167;QR=2909;QA=438;PQR=2049.62;PQA=347.95;SRF=54;SRR=28;SAF=0;SAR=36;SRP=20.9117;SAP=81.1833;AB=0.137405;ABP=302.209;RUN=1;RPP=37.7539;RPPR=111.478;RPL=6.0;RPR=30.0;EPP=37.7539;EPPR=54.2782;DPRA=0.0;ODDS=9.27647;GTI=0;TYPE=snp;CIGAR=1X20M;NUMALT=4;MEANALT=17.0;LEN=1;MQM=59.3611;MQMR=59.7927;PAIRED=1.0;PAIREDR=0.987805;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr16 56876467 . C CT 1360.34 REJECT NS=2;DP=262;DPB=363.238;AC=2;AN=3;AF=0.25;RO=82;AO=25;PRO=57.7167;PAO=46.7167;QR=2909;QA=741;PQR=2049.62;PQA=1626.62;SRF=54;SRR=28;SAF=15;SAR=10;SRP=20.9117;SAP=5.18177;AB=0.0954198;ABP=375.509;RUN=1;RPP=28.1125;RPPR=111.478;RPL=21.0;RPR=4.0;EPP=5.18177;EPPR=54.2782;DPRA=0.0;ODDS=9.27647;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=4;MEANALT=17.0;LEN=1;MQM=60.0;MQMR=59.7927;PAIRED=0.96;PAIREDR=0.987805;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:A [...]
+chr16 56876467 . CT C 1360.34 REJECT NS=2;DP=262;DPB=363.238;AC=2;AN=3;AF=0.25;RO=82;AO=60;PRO=57.7167;PAO=48.05;QR=2909;QA=1903;PQR=2049.62;PQA=1638.62;SRF=54;SRR=28;SAF=37;SAR=23;SRP=20.9117;SAP=10.1038;AB=0.229008;ABP=170.131;RUN=1;RPP=79.5909;RPPR=111.478;RPL=53.0;RPR=7.0;EPP=31.3842;EPPR=54.2782;DPRA=0.0;ODDS=9.27647;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=4;MEANALT=17.0;LEN=1;MQM=60.0;MQMR=59.7927;PAIRED=0.983333;PAIREDR=0.987805;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR [...]
+chr16 56876467 . CTT C 1360.34 REJECT NS=2;DP=262;DPB=363.238;AC=2;AN=2;AF=0.0;RO=82;AO=15;PRO=57.7167;PAO=31.3;QR=2909;QA=415;PQR=2049.62;PQA=1097.2;SRF=54;SRR=28;SAF=8;SAR=7;SRP=20.9117;SAP=3.15506;AB=0.0572519;ABP=449.107;RUN=1;RPP=10.1038;RPPR=111.478;RPL=11.0;RPR=4.0;EPP=3.15506;EPPR=54.2782;DPRA=0.0;ODDS=9.27647;GTI=0;TYPE=del;CIGAR=1M2D18M;NUMALT=4;MEANALT=17.0;LEN=2;MQM=60.0;MQMR=59.7927;PAIRED=1.0;PAIREDR=0.987805;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.29 [...]
+chr16 57052730 . C G 5770.465 REJECT NS=2;DP=407;DPB=468.0;AC=2;AN=4;AF=0.5;RO=258;AO=210;PRO=0.0;PAO=0.0;QR=9800;QA=7996;PQR=0.0;PQA=0.0;SRF=139;SRR=119;SAF=125;SAR=85;SRP=6.37692;SAP=19.5549;AB=0.448718;ABP=13.7006;RUN=1;RPP=5.03701;RPPR=3.0103;RPL=98.0;RPR=112.0;EPP=23.0292;EPPR=27.553;DPRA=0.0;ODDS=319.641;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995238;PAIREDR=0.996124;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.549;Dels=0.0;FS=3.826;Haplotype [...]
+chr16 67117201 . A AT 345.665 REJECT NS=2;DP=99;DPB=147.0;AC=2;AN=3;AF=0.25;RO=52;AO=19;PRO=35.5833;PAO=26.5833;QR=1908;QA=618;PQR=1270.0;PQA=946.0;SRF=13;SRR=39;SAF=7;SAR=12;SRP=31.2394;SAP=5.8675;AB=0.191919;ABP=84.627;RUN=1;RPP=5.8675;RPPR=16.5402;RPL=12.0;RPR=7.0;EPP=3.12459;EPPR=5.68288;DPRA=0.0;ODDS=2.82244;GTI=1;TYPE=ins;CIGAR=1M1I21M;NUMALT=3;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr16 67117201 . AT A 345.665 REJECT NS=2;DP=99;DPB=147.0;AC=2;AN=3;AF=0.25;RO=52;AO=14;PRO=35.5833;PAO=22.9167;QR=1908;QA=456;PQR=1270.0;PQA=783.0;SRF=13;SRR=39;SAF=1;SAR=13;SRP=31.2394;SAP=25.3454;AB=0.141414;ABP=113.58;RUN=1;RPP=3.63072;RPPR=16.5402;RPL=8.0;RPR=6.0;EPP=3.0103;EPPR=5.68288;DPRA=0.0;ODDS=2.82244;GTI=1;TYPE=del;CIGAR=1M1D20M;NUMALT=3;MEANALT=7.5;LEN=1;MQM=58.5714;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr16 67117217 . G T 345.665 REJECT NS=2;DP=99;DPB=147.0;AC=2;AN=2;AF=0.0;RO=52;AO=4;PRO=35.5833;PAO=18.9167;QR=1908;QA=56;PQR=1270.0;PQA=666.0;SRF=13;SRR=39;SAF=4;SAR=0;SRP=31.2394;SAP=11.6962;AB=0.040404;ABP=184.646;RUN=1;RPP=11.6962;RPPR=16.5402;RPL=4.0;RPR=0.0;EPP=11.6962;EPPR=5.68288;DPRA=0.0;ODDS=2.82244;GTI=1;TYPE=snp;CIGAR=16M1X5M;NUMALT=3;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr16 67118943 . ATTAT A 1412.18 REJECT NS=2;DP=353;DPB=362.091;AC=2;AN=4;AF=0.5;RO=275;AO=77;PRO=53.5;PAO=21.5;QR=10560;QA=2852;PQR=1894.5;PQA=724.5;SRF=93;SRR=182;SAF=18;SAR=59;SRP=65.5566;SAP=50.4161;AB=0.21813;ABP=246.615;RUN=1;RPP=13.1908;RPPR=3.08137;RPL=48.0;RPR=29.0;EPP=3.26411;EPPR=13.8203;DPRA=0.0;ODDS=63.2848;GTI=0;TYPE=del;CIGAR=1M4D6M;NUMALT=1;MEANALT=1.5;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;END=67118947;HOMLEN=3;HOMSEQ=TTA;SVLEN=-4;SVTYPE= [...]
+chr16 67120715 . T A 3042.225 REJECT NS=2;DP=507;DPB=582.0;AC=2;AN=4;AF=0.5;RO=429;AO=153;PRO=0.0;PAO=0.0;QR=16177;QA=5722;PQR=0.0;PQA=0.0;SRF=221;SRR=208;SAF=79;SAR=74;SRP=3.86573;SAP=3.36512;AB=0.262887;ABP=287.227;RUN=1;RPP=4.72761;RPPR=4.14918;RPL=82.0;RPR=71.0;EPP=6.20364;EPPR=11.519;DPRA=0.0;ODDS=302.44;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997669;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.48;Dels=0.0;FS=1.405;HaplotypeScore=11 [...]
+chr16 67120890 . TT GA 18544.949999999997 REJECT NS=2;DP=487;DPB=554.0;AC=4;AN=4;AF=1.0;RO=0;AO=545;PRO=0.0;PAO=12.0;QR=0;QA=20530;PQR=0.0;PQA=443.0;SRF=0;SRR=0;SAF=288;SAR=257;SRP=0.0;SAP=6.83926;AB=0.0;ABP=0.0;RUN=1;RPP=3.90678;RPPR=0.0;RPL=265.0;RPR=280.0;EPP=3.10991;EPPR=0.0;DPRA=0.0;ODDS=86.5717;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=1;MEANALT=2.5;LEN=2;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;JOINED;BaseQRankSum=-1.065;Dels=0.0;FS=0.0;HaplotypeScore=6.9231;MLE [...]
+chr16 67123241 . C G 3148.105 REJECT NS=2;DP=589;DPB=673.0;AC=2;AN=4;AF=0.5;RO=525;AO=148;PRO=0.0;PAO=0.0;QR=20031;QA=5649;PQR=0.0;PQA=0.0;SRF=269;SRR=256;SAF=70;SAR=78;SRP=3.70931;SAP=3.94932;AB=0.219911;ABP=461.598;RUN=1;RPP=4.47751;RPPR=3.21297;RPL=69.0;RPR=79.0;EPP=10.1116;EPPR=8.67267;DPRA=0.0;ODDS=168.289;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993243;PAIREDR=0.998095;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.2715;Dels=0.0;FS=3.06;Haplotype [...]
+chr16 67123926 . C T 2778.13 REJECT NS=2;DP=574;DPB=660.0;AC=2;AN=4;AF=0.5;RO=518;AO=141;PRO=0.0;PAO=0.0;QR=19560;QA=5366;PQR=0.0;PQA=0.0;SRF=286;SRR=232;SAF=67;SAR=74;SRP=15.2343;SAP=3.76493;AB=0.213636;ABP=473.114;RUN=1;RPP=4.87376;RPPR=4.68711;RPL=65.0;RPR=76.0;EPP=4.87376;EPPR=7.30294;DPRA=0.0;ODDS=208.504;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990347;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.605;Dels=0.0;FS=7.1745;HaplotypeScore [...]
+chr16 67126356 . T G 2271.02 REJECT NS=2;DP=446;DPB=512.0;AC=2;AN=4;AF=0.5;RO=396;AO=116;PRO=0.0;PAO=0.0;QR=15143;QA=4424;PQR=0.0;PQA=0.0;SRF=190;SRR=206;SAF=58;SAR=58;SRP=4.41408;SAP=3.0103;AB=0.226562;ABP=335.517;RUN=1;RPP=4.20835;RPPR=3.20771;RPL=62.0;RPR=54.0;EPP=4.20835;EPPR=9.34924;DPRA=0.0;ODDS=213.366;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991379;PAIREDR=0.979798;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5815;Dels=0.0;FS=1.228;HaplotypeS [...]
+chr16 67126740 . C T 23.79 LowQual SOMATIC;DP=8;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-0.322;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=1;MLEAF=0.5;MQ=57.66;MQRankSum=0.684;QD=2.97;ReadPosRankSum=-0.684;SOR=1.27 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:0.00488421 0/1:5,3:8:52.0:52,0,105:3:38:8:.:1:.:.:.:.:-0.0352835
+chr16 67128020 . C T 284.631 REJECT NS=2;DP=127;DPB=224.621;AC=2;AN=2;AF=0.0;RO=37;AO=10;PRO=99.25;PAO=22.0833;QR=1253;QA=80;PQR=3423.58;PQA=664.25;SRF=11;SRR=26;SAF=0;SAR=10;SRP=16.2152;SAP=24.725;AB=0.0787402;ABP=198.768;RUN=1;RPP=3.87889;RPPR=3.06899;RPL=4.0;RPR=6.0;EPP=3.87889;EPPR=10.1116;DPRA=0.0;ODDS=27.7528;GTI=0;TYPE=snp;CIGAR=1X28M;NUMALT=3;MEANALT=20.5;LEN=1;MQM=52.4;MQMR=57.3784;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr16 67128020 . CT C 284.631 REJECT NS=2;DP=127;DPB=224.621;AC=2;AN=4;AF=0.5;RO=37;AO=25;PRO=99.25;PAO=66.75;QR=1253;QA=552;PQR=3423.58;PQA=2193.08;SRF=11;SRR=26;SAF=10;SAR=15;SRP=16.2152;SAP=5.18177;AB=0.19685;ABP=104.386;RUN=1;RPP=3.79203;RPPR=3.06899;RPL=14.0;RPR=11.0;EPP=5.18177;EPPR=10.1116;DPRA=0.0;ODDS=27.7528;GTI=0;TYPE=del;CIGAR=1M1D27M;NUMALT=3;MEANALT=20.5;LEN=1;MQM=59.08;MQMR=57.3784;PAIRED=0.96;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.144;FS=5.31 [...]
+chr16 67128020 . CTT C 284.631 REJECT NS=2;DP=127;DPB=224.621;AC=2;AN=2;AF=0.0;RO=37;AO=10;PRO=99.25;PAO=55.9167;QR=1253;QA=276;PQR=3423.58;PQA=1858.08;SRF=11;SRR=26;SAF=6;SAR=4;SRP=16.2152;SAP=3.87889;AB=0.0787402;ABP=198.768;RUN=1;RPP=10.8276;RPPR=3.06899;RPL=8.0;RPR=2.0;EPP=3.87889;EPPR=10.1116;DPRA=0.0;ODDS=27.7528;GTI=0;TYPE=del;CIGAR=1M2D26M;NUMALT=3;MEANALT=20.5;LEN=2;MQM=59.7;MQMR=57.3784;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr16 67128081 . G T 1649.5900000000001 REJECT NS=2;DP=215;DPB=254.0;AC=2;AN=4;AF=0.5;RO=172;AO=82;PRO=0.0;PAO=0.0;QR=5898;QA=2959;PQR=0.0;PQA=0.0;SRF=92;SRR=80;SAF=49;SAR=33;SRP=4.82828;SAP=9.78953;AB=0.322835;ABP=72.258;RUN=1;RPP=23.7717;RPPR=48.4597;RPL=27.0;RPR=55.0;EPP=69.2137;EPPR=42.6018;DPRA=0.0;ODDS=167.682;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.7561;MQMR=60.1744;PAIRED=1.0;PAIREDR=0.994186;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.296;Dels=0.0;FS=1.0585;Ha [...]
+chr16 67129657 . A G 81.8066 REJECT;LowQual NS=2;DP=13;DPB=15.0;AC=3;AN=4;AF=0.5;RO=10;AO=5;PRO=0.0;PAO=0.0;QR=351;QA=182;PQR=0.0;PQA=0.0;SRF=0;SRR=10;SAF=1;SAR=4;SRP=24.725;SAP=6.91895;AB=0.333333;ABP=6.62942;RUN=1;RPP=3.44459;RPPR=10.8276;RPL=3.0;RPR=2.0;EPP=6.91895;EPPR=10.8276;DPRA=0.0;ODDS=3.34536;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.8;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.118;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=1;ML [...]
+chr16 67130213 . C CA 51.1969 REJECT NS=2;DP=185;DPB=288.929;AC=2;AN=3;AF=0.25;RO=144;AO=17;PRO=79.0;PAO=68.0;QR=5375;QA=600;PQR=2789.67;PQA=2383.67;SRF=120;SRR=24;SAF=16;SAR=1;SRP=141.985;SAP=31.7504;AB=0.0918919;ABP=270.641;RUN=1;RPP=9.26925;RPPR=18.4519;RPL=5.0;RPR=12.0;EPP=6.20364;EPPR=3.0103;DPRA=0.0;ODDS=0.00337105;GTI=0;TYPE=ins;CIGAR=1M1I27M;NUMALT=2;MEANALT=7.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr16 67130213 . CA C 51.1969 REJECT NS=2;DP=185;DPB=288.929;AC=2;AN=3;AF=0.25;RO=144;AO=13;PRO=79.0;PAO=67.0;QR=5375;QA=471;PQR=2789.67;PQA=2352.67;SRF=120;SRR=24;SAF=10;SAR=3;SRP=141.985;SAP=11.1951;AB=0.0702703;ABP=299.751;RUN=1;RPP=11.1951;RPPR=18.4519;RPL=3.0;RPR=10.0;EPP=3.17734;EPPR=3.0103;DPRA=0.0;ODDS=0.00337105;GTI=0;TYPE=del;CIGAR=1M1D26M;NUMALT=2;MEANALT=7.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr16 67131448 . C CA 20.3618 REJECT NS=2;DP=100;DPB=213.56;AC=2;AN=3;AF=0.25;RO=30;AO=7;PRO=76.3333;PAO=75.3333;QR=1046;QA=183;PQR=2514.83;PQA=2482.83;SRF=22;SRR=8;SAF=3;SAR=4;SRP=17.1973;SAP=3.32051;AB=0.07;ABP=163.612;RUN=1;RPP=10.7656;RPPR=31.9633;RPL=1.0;RPR=6.0;EPP=3.32051;EPPR=7.64277;DPRA=0.0;ODDS=0.914949;GTI=1;TYPE=ins;CIGAR=1M1I24M;NUMALT=3;MEANALT=18.0;LEN=1;MQM=60.0;MQMR=59.8;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr16 67131448 . CA C 20.3618 REJECT NS=2;DP=100;DPB=213.56;AC=2;AN=3;AF=0.25;RO=30;AO=20;PRO=76.3333;PAO=38.8333;QR=1046;QA=620;PQR=2514.83;PQA=1223.83;SRF=22;SRR=8;SAF=14;SAR=6;SRP=17.1973;SAP=9.95901;AB=0.2;ABP=81.1833;RUN=1;RPP=46.4397;RPPR=31.9633;RPL=0.0;RPR=20.0;EPP=9.95901;EPPR=7.64277;DPRA=0.0;ODDS=0.914949;GTI=1;TYPE=del;CIGAR=1M1D23M;NUMALT=3;MEANALT=18.0;LEN=1;MQM=60.0;MQMR=59.8;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr16 67131448 . CAA C 20.3618 REJECT NS=2;DP=100;DPB=213.56;AC=2;AN=2;AF=0.0;RO=30;AO=7;PRO=76.3333;PAO=35.5;QR=1046;QA=198;PQR=2514.83;PQA=1124.5;SRF=22;SRR=8;SAF=4;SAR=3;SRP=17.1973;SAP=3.32051;AB=0.07;ABP=163.612;RUN=1;RPP=18.2106;RPPR=31.9633;RPL=0.0;RPR=7.0;EPP=3.32051;EPPR=7.64277;DPRA=0.0;ODDS=0.914949;GTI=1;TYPE=del;CIGAR=1M2D22M;NUMALT=3;MEANALT=18.0;LEN=2;MQM=60.0;MQMR=59.8;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr16 67131601 . T C 2715.955 REJECT NS=2;DP=477;DPB=547.0;AC=2;AN=4;AF=0.5;RO=413;AO=134;PRO=0.0;PAO=0.0;QR=15587;QA=5030;PQR=0.0;PQA=0.0;SRF=234;SRR=179;SAF=82;SAR=52;SRP=18.9152;SAP=17.5948;AB=0.244973;ABP=312.022;RUN=1;RPP=5.34382;RPPR=7.43211;RPL=61.0;RPR=73.0;EPP=3.26958;EPPR=12.732;DPRA=0.0;ODDS=205.509;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.954;PAIRED=0.992537;PAIREDR=0.997579;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.213;Dels=0.0;FS=1.669;Haplotyp [...]
+chr16 67132017 . TTTTGTTTG T 612.137 REJECT NS=2;DP=134;DPB=246.953;AC=2;AN=4;AF=0.5;RO=91;AO=32;PRO=140.5;PAO=96.5;QR=3466;QA=1094;PQR=5209.5;PQA=3574.5;SRF=10;SRR=81;SAF=4;SAR=28;SRP=123.3;SAP=42.0968;AB=0.238806;ABP=82.4149;RUN=1;RPP=4.09604;RPPR=4.17955;RPL=14.0;RPR=18.0;EPP=4.09604;EPPR=3.60686;DPRA=0.0;ODDS=39.241;GTI=0;TYPE=del;CIGAR=1M8D34M;NUMALT=1;MEANALT=6.0;LEN=8;MQM=60.625;MQMR=60.0;PAIRED=1.0;PAIREDR=0.978022;technology.ILLUMINA=1.0;END=67132025;HOMLEN=27;HOMSEQ=TTTGTTTGTTT [...]
+chr16 68857441 . T C 6049.280000000001 REJECT NS=2;DP=361;DPB=408.0;AC=2;AN=4;AF=0.5;RO=196;AO=212;PRO=0.0;PAO=0.0;QR=7440;QA=8109;PQR=0.0;PQA=0.0;SRF=94;SRR=102;SAF=87;SAR=125;SRP=3.71935;SAP=17.8009;AB=0.519608;ABP=4.37279;RUN=1;RPP=3.05127;RPPR=5.84651;RPL=107.0;RPR=105.0;EPP=26.6097;EPPR=4.60567;DPRA=0.0;ODDS=267.434;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995283;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.55;Dels=0.0;FS=5.178;Haplo [...]
+chr16 72821381 . A G 237.8 REJECT NS=2;DP=412;DPB=412.0;AC=2;AN=4;AF=0.5;RO=274;AO=135;PRO=0.0;PAO=0.0;QR=7574;QA=2345;PQR=0.0;PQA=0.0;SRF=190;SRR=84;SAF=3;SAR=132;SRP=92.0565;SAP=270.68;AB=0.32767;ABP=109.286;RUN=1;RPP=173.656;RPPR=3.2956;RPL=16.0;RPR=119.0;EPP=180.347;EPPR=4.56362;DPRA=0.0;ODDS=26.0322;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=57.563;MQMR=59.9818;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=1;BaseQRankSum=-9.004;Dels=0.0;FS=143.031;HaplotypeScore=69. [...]
+chr16 72821625 . C T 3878.54 REJECT NS=2;DP=256;DPB=295.0;AC=2;AN=4;AF=0.5;RO=148;AO=147;PRO=0.0;PAO=0.0;QR=5438;QA=5548;PQR=0.0;PQA=0.0;SRF=59;SRR=89;SAF=72;SAR=75;SRP=16.2152;SAP=3.14325;AB=0.498305;ABP=3.01766;RUN=1;RPP=4.20683;RPPR=7.76406;RPL=69.0;RPR=78.0;EPP=4.20683;EPPR=6.76636;DPRA=0.0;ODDS=193.979;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993243;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4465;Dels=0.0;FS=4.9445;HaplotypeScore=8 [...]
+chr16 72822012 . TGCTGCTGCTGCTGTAGTTGCC T 1577.71 REJECT NS=2;DP=178;DPB=166.609;AC=2;AN=4;AF=0.5;RO=95;AO=81;PRO=122.0;PAO=6.0;QR=3640;QA=2710;PQR=4475.5;PQA=146.5;SRF=54;SRR=41;SAF=48;SAR=33;SRP=6.87324;SAP=9.04217;AB=0.455056;ABP=6.13332;RUN=1;RPP=12.6881;RPPR=3.03316;RPL=31.0;RPR=50.0;EPP=3.03711;EPPR=8.15326;DPRA=0.0;ODDS=66.8749;GTI=0;TYPE=del;CIGAR=1M21D1M;NUMALT=1;MEANALT=1.5;LEN=21;MQM=62.0988;MQMR=60.0;PAIRED=1.0;PAIREDR=0.978947;technology.ILLUMINA=1.0;MQ0=0;END=72822033;HOMLE [...]
+chr16 72827758 . T C 12914.15 REJECT NS=2;DP=346;DPB=399.0;AC=4;AN=4;AF=1.0;RO=1;AO=397;PRO=0.0;PAO=0.0;QR=14;QA=15028;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=226;SAR=171;SRP=5.18177;SAP=19.5562;AB=0.0;ABP=0.0;RUN=1;RPP=9.71069;RPPR=5.18177;RPL=181.0;RPR=216.0;EPP=20.7814;EPPR=5.18177;DPRA=0.0;ODDS=68.3794;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987406;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.664;Dels=0.0;FS=1.9055;HaplotypeScore=2.966;MLEAC [...]
+chr16 72830425 . C T 1749.14 PASS SOMATIC;NS=2;DP=280;DPB=280.0;AC=2;AN=3;AF=0.25;RO=189;AO=75;PRO=0.0;PAO=0.0;QR=6471;QA=2612;PQR=0.0;PQA=0.0;SRF=130;SRR=59;SAF=47;SAR=28;SRP=60.9277;SAP=13.4623;AB=0.348837;ABP=45.6823;RUN=1;RPP=3.03925;RPPR=11.386;RPL=38.0;RPR=37.0;EPP=13.4623;EPPR=5.59539;DPRA=3.30769;ODDS=34.8041;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=2;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994709;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;VT=SNP;BaseQRankSum=-1.705; [...]
+chr16 72830425 . C G 1749.14 REJECT NS=2;DP=280;DPB=280.0;AC=2;AN=2;AF=0.0;RO=189;AO=15;PRO=0.0;PAO=0.0;QR=6471;QA=109;PQR=0.0;PQA=0.0;SRF=130;SRR=59;SAF=0;SAR=15;SRP=60.9277;SAP=35.5824;AB=0.0604651;ABP=363.788;RUN=1;RPP=35.5824;RPPR=11.386;RPL=0.0;RPR=15.0;EPP=35.5824;EPPR=5.59539;DPRA=0.0;ODDS=34.8041;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=2;MEANALT=2.0;LEN=1;MQM=59.8;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994709;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:C [...]
+chr16 72832135 . T A 10873.5 REJECT NS=2;DP=285;DPB=328.0;AC=4;AN=4;AF=1.0;RO=0;AO=328;PRO=0.0;PAO=0.0;QR=0;QA=12646;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=171;SAR=157;SRP=0.0;SAP=4.30789;AB=0.0;ABP=0.0;RUN=1;RPP=3.67233;RPPR=0.0;RPL=159.0;RPR=169.0;EPP=3.11623;EPPR=0.0;DPRA=0.0;ODDS=57.3757;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996951;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.9326;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.995;SOR=1 [...]
+chr16 72991660 . C G 13698.25 REJECT NS=2;DP=367;DPB=424.0;AC=4;AN=4;AF=1.0;RO=0;AO=424;PRO=0.0;PAO=0.0;QR=0;QA=16051;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=205;SAR=219;SRP=0.0;SAP=4.01409;AB=0.0;ABP=0.0;RUN=1;RPP=28.1051;RPPR=0.0;RPL=247.0;RPR=177.0;EPP=9.64763;EPPR=0.0;DPRA=0.0;ODDS=74.7814;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9929;MQMR=0.0;PAIRED=0.995283;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.709;MLEAC=2;MLEAF=1.0;MQ=59.995;QD=22.465; [...]
+chr16 72991715 . A G 11901.75 REJECT NS=2;DP=319;DPB=368.0;AC=4;AN=4;AF=1.0;RO=0;AO=368;PRO=0.0;PAO=0.0;QR=0;QA=13979;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=186;SAR=182;SRP=0.0;SAP=3.10471;AB=0.0;ABP=0.0;RUN=1;RPP=5.3706;RPPR=0.0;RPL=174.0;RPR=194.0;EPP=12.4515;EPPR=0.0;DPRA=0.0;ODDS=68.5236;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9918;MQMR=0.0;PAIRED=0.991848;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.02;FS=0.0;HaplotypeScore=20.3487;MLEAC=2;MLEAF=1.0;MQ=59.995;QD=31.1; [...]
+chr16 72993860 . G A 1858.62 PASS SOMATIC;NS=2;DP=302;DPB=302.0;AC=1;AN=3;AF=0.25;RO=229;AO=73;PRO=0.0;PAO=0.0;QR=8597;QA=2774;PQR=0.0;PQA=0.0;SRF=139;SRR=90;SAF=45;SAR=28;SRP=25.7776;SAP=11.607;AB=0.347619;ABP=45.3644;RUN=1;RPP=11.607;RPPR=4.61283;RPL=28.0;RPR=45.0;EPP=4.46786;EPPR=4.61283;DPRA=2.28261;ODDS=57.4986;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.448;Dels=0.0;FS=4.198;Haploty [...]
+chr16 75007460 . CA C . PASS SOMATIC;AC=1;AN=4 GT:AD:DP:MM:MQS:NQSBQ:NQSMM:REnd:RStart:SC:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:53,0:53:0.0943396,0.0:60.0,0.0:38.6096,0.0:0.0,0.0:0,0:0,0:41,12,0,0:0:0:53:.:.:.:.:0:.:-8.39515e-05 0/1:105,69:174:0.104762,1.05797:60.0,60.1449:38.4902,38.1686:0.00292969,0.101173:66,17:34,17:73,32,50,19:69:40:174:.:.:.:.:1:.:-0.0352835
+chr16 75007466 . G A 2020.32 PASS SOMATIC;NS=2;DP=249;DPB=249.0;AC=1;AN=4;AF=0.25;RO=173;AO=76;PRO=0.0;PAO=0.0;QR=6717;QA=2928;PQR=0.0;PQA=0.0;SRF=123;SRR=50;SAF=54;SAR=22;SRP=69.8992;SAP=32.268;AB=0.397906;ABP=20.3025;RUN=1;RPP=16.8392;RPPR=77.4303;RPL=27.0;RPR=49.0;EPP=5.8675;EPPR=3.02285;DPRA=3.2931;ODDS=37.2239;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.1316;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.317;Dels=0.0;FS=0.595;HaplotypeSc [...]
+chr16 76501609 . C A 2764.01 PASS SOMATIC;NS=2;DP=391;DPB=391.0;AC=1;AN=3;AF=0.25;RO=287;AO=103;PRO=0.0;PAO=0.0;QR=10826;QA=4021;PQR=0.0;PQA=0.0;SRF=183;SRR=104;SAF=64;SAR=39;SRP=50.2304;SAP=16.1867;AB=0.363958;ABP=48.5038;RUN=1;RPP=4.04333;RPPR=9.3734;RPL=48.0;RPR=55.0;EPP=23.2703;EPPR=10.2813;DPRA=2.62037;ODDS=67.6678;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990291;PAIREDR=0.993031;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.718;Dels=0.0;FS [...]
+chr16 76501643 . C T 3193.99 PASS SOMATIC;NS=2;DP=435;DPB=435.0;AC=1;AN=3;AF=0.25;RO=317;AO=118;PRO=0.0;PAO=0.0;QR=12008;QA=4598;PQR=0.0;PQA=0.0;SRF=165;SRR=152;SAF=54;SAR=64;SRP=4.16796;SAP=4.85053;AB=0.37224;ABP=47.9536;RUN=1;RPP=3.0103;RPPR=4.98997;RPL=59.0;RPR=59.0;EPP=38.6372;EPPR=72.8879;DPRA=2.68644;ODDS=74.5704;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991525;PAIREDR=0.996845;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.754;Dels=0.0;FS= [...]
+chr16 89805261 . A G 10249.335 REJECT NS=2;DP=426;DPB=499.0;AC=3;AN=4;AF=0.75;RO=126;AO=373;PRO=0.0;PAO=0.0;QR=4824;QA=14209;PQR=0.0;PQA=0.0;SRF=72;SRR=54;SAF=208;SAR=165;SRP=8.59409;SAP=13.7745;AB=0.644068;ABP=66.8295;RUN=1;RPP=5.11191;RPPR=14.6604;RPL=177.0;RPR=196.0;EPP=5.57764;EPPR=4.73369;DPRA=0.0;ODDS=91.2547;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994638;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.813;Dels=0.0;FS=0.4265;Haplotype [...]
+chr16 89805977 . G A 4408.18 REJECT NS=2;DP=284;DPB=325.0;AC=2;AN=4;AF=0.5;RO=168;AO=157;PRO=0.0;PAO=0.0;QR=6415;QA=6045;PQR=0.0;PQA=0.0;SRF=47;SRR=121;SAF=46;SAR=111;SRP=73.79;SAP=61.4464;AB=0.483077;ABP=3.81876;RUN=1;RPP=33.5631;RPPR=16.2459;RPL=102.0;RPR=55.0;EPP=3.68802;EPPR=4.30284;DPRA=0.0;ODDS=233.986;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987261;PAIREDR=0.994048;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.021;Dels=0.0;FS=0.5475;HaplotypeSc [...]
+chr16 89806347 . A T 6140.765 REJECT NS=2;DP=366;DPB=414.0;AC=2;AN=4;AF=0.5;RO=199;AO=215;PRO=0.0;PAO=0.0;QR=7563;QA=8406;PQR=0.0;PQA=0.0;SRF=121;SRR=78;SAF=127;SAR=88;SRP=23.1864;SAP=18.3722;AB=0.519324;ABP=4.35305;RUN=1;RPP=3.50519;RPPR=5.46548;RPL=111.0;RPR=104.0;EPP=3.2628;EPPR=3.2831;DPRA=0.0;ODDS=233.95;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994975;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.127;Dels=0.0;FS=1.836;HaplotypeScore=5 [...]
+chr16 89815217 . C T 2937.08 REJECT NS=2;DP=167;DPB=189.0;AC=2;AN=4;AF=0.5;RO=82;AO=107;PRO=0.0;PAO=0.0;QR=3132;QA=4050;PQR=0.0;PQA=0.0;SRF=26;SRR=56;SAF=44;SAR=63;SRP=26.8435;SAP=10.3365;AB=0.566138;ABP=10.1911;RUN=1;RPP=123.334;RPPR=140.29;RPL=92.0;RPR=15.0;EPP=3.51765;EPPR=30.1272;DPRA=0.0;ODDS=100.109;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990654;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.443;Dels=0.0;FS=2.63;HaplotypeScore=0.0;M [...]
+chr16 89831510 . C A 1246.77 REJECT NS=2;DP=192;DPB=221.0;AC=2;AN=4;AF=0.5;RO=163;AO=57;PRO=0.0;PAO=0.0;QR=6204;QA=2219;PQR=0.0;PQA=0.0;SRF=55;SRR=108;SAF=23;SAR=34;SRP=40.4316;SAP=7.61992;AB=0.257919;ABP=115.504;RUN=1;RPP=87.1644;RPPR=191.662;RPL=52.0;RPR=5.0;EPP=9.44853;EPPR=8.88527;DPRA=0.0;ODDS=72.8679;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993865;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0835;Dels=0.0;FS=2.107;HaplotypeScore=5.9 [...]
+chr16 89836323 . C T 5465.605 REJECT NS=2;DP=352;DPB=401.0;AC=2;AN=4;AF=0.5;RO=205;AO=196;PRO=0.0;PAO=0.0;QR=7875;QA=7413;PQR=0.0;PQA=0.0;SRF=86;SRR=119;SAF=96;SAR=100;SRP=14.5456;SAP=3.18756;AB=0.488778;ABP=3.44893;RUN=1;RPP=24.4591;RPPR=26.4092;RPL=120.0;RPR=76.0;EPP=9.39177;EPPR=7.68161;DPRA=0.0;ODDS=282.297;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995122;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.7915;Dels=0.0;FS=4.5975;HaplotypeSc [...]
+chr16 89838078 . A G 4110.435 REJECT NS=2;DP=271;DPB=315.0;AC=2;AN=4;AF=0.5;RO=160;AO=155;PRO=0.0;PAO=0.0;QR=6103;QA=5945;PQR=0.0;PQA=0.0;SRF=116;SRR=44;SAF=105;SAR=50;SRP=73.366;SAP=45.389;AB=0.492063;ABP=3.18264;RUN=1;RPP=26.5603;RPPR=10.8276;RPL=57.0;RPR=98.0;EPP=3.36054;EPPR=20.5992;DPRA=0.0;ODDS=233.272;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1685;Dels=0.0;FS=3.7;HaplotypeScore=1.9664; [...]
+chr16 89845194 . A G 4672.25 REJECT NS=2;DP=328;DPB=390.0;AC=2;AN=4;AF=0.5;RO=207;AO=183;PRO=0.0;PAO=0.0;QR=7943;QA=6806;PQR=0.0;PQA=0.0;SRF=123;SRR=84;SAF=125;SAR=58;SRP=18.9659;SAP=56.2766;AB=0.469231;ABP=6.2174;RUN=1;RPP=17.5461;RPPR=11.8326;RPL=74.0;RPR=109.0;EPP=3.30695;EPPR=6.79726;DPRA=0.0;ODDS=328.802;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.978142;PAIREDR=0.937198;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.453;Dels=0.0;FS=5.938;HaplotypeS [...]
+chr16 89849480 . C T 9735.085 REJECT NS=2;DP=387;DPB=444.0;AC=3;AN=4;AF=0.75;RO=106;AO=337;PRO=0.0;PAO=0.0;QR=4084;QA=13063;PQR=0.0;PQA=0.0;SRF=50;SRR=56;SAF=114;SAR=223;SRP=3.74778;SAP=79.566;AB=0.683735;ABP=100.36;RUN=1;RPP=9.20254;RPPR=5.05886;RPL=184.0;RPR=153.0;EPP=8.42932;EPPR=3.09224;DPRA=0.0;ODDS=69.8401;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997033;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.281;Dels=0.0;FS=5.712;HaplotypeSco [...]
+chr16 89857964 . T C 3483.0150000000003 REJECT NS=2;DP=221;DPB=259.0;AC=2;AN=4;AF=0.5;RO=128;AO=131;PRO=0.0;PAO=0.0;QR=4843;QA=5046;PQR=0.0;PQA=0.0;SRF=39;SRR=89;SAF=37;SAR=94;SRP=45.4219;SAP=56.8661;AB=0.505792;ABP=3.08576;RUN=1;RPP=53.1531;RPPR=27.5072;RPL=93.0;RPR=38.0;EPP=3.4247;EPPR=4.09604;DPRA=0.0;ODDS=221.011;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.5885;Dels=0.0;FS=1.0865;HaplotypeSc [...]
+chr16 89866043 . T C 6019.1900000000005 REJECT NS=2;DP=359;DPB=419.0;AC=2;AN=4;AF=0.5;RO=196;AO=223;PRO=0.0;PAO=0.0;QR=7488;QA=8448;PQR=0.0;PQA=0.0;SRF=97;SRR=99;SAF=101;SAR=122;SRP=3.05462;SAP=7.30456;AB=0.53222;ABP=6.78835;RUN=1;RPP=3.09794;RPPR=4.11819;RPL=113.0;RPR=110.0;EPP=21.015;EPPR=7.44188;DPRA=0.0;ODDS=334.383;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991031;PAIREDR=0.984694;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.026;Dels=0.0;FS=1.7155 [...]
+chr16 89869761 . T C 6301.22 REJECT NS=2;DP=261;DPB=295.0;AC=3;AN=4;AF=0.75;RO=72;AO=222;PRO=0.0;PAO=0.0;QR=2741;QA=8446;PQR=0.0;PQA=0.0;SRF=15;SRR=57;SAF=47;SAR=175;SRP=56.2114;SAP=163.269;AB=0.681223;ABP=68.3346;RUN=1;RPP=48.2395;RPPR=20.3821;RPL=145.0;RPR=77.0;EPP=3.04943;EPPR=6.02623;DPRA=0.0;ODDS=42.1818;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986486;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.466;Dels=0.0;FS=0.318;HaplotypeScore= [...]
+chr16 89882807 . G T 1433.63 REJECT NS=1;DP=99;DPB=99.0;AC=1;AN=4;AF=0.5;RO=43;AO=55;PRO=0.0;PAO=0.0;QR=1616;QA=1955;PQR=0.0;PQA=0.0;SRF=23;SRR=20;SAF=29;SAR=26;SRP=3.46479;SAP=3.36563;AB=0.555556;ABP=5.66432;RUN=1;RPP=17.2631;RPPR=11.5447;RPL=18.0;RPR=37.0;EPP=3.99733;EPPR=5.48477;DPRA=0.0;ODDS=260.361;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.963636;PAIREDR=0.976744;technology.ILLUMINA=1.0;BaseQRankSum=-1.237;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankS [...]
+chr16 89882826 . C T 1695.79 REJECT NS=1;DP=103;DPB=103.0;AC=1;AN=4;AF=0.5;RO=43;AO=60;PRO=0.0;PAO=0.0;QR=1587;QA=2266;PQR=0.0;PQA=0.0;SRF=21;SRR=22;SAF=27;SAR=33;SRP=3.0608;SAP=4.31318;AB=0.582524;ABP=9.10307;RUN=1;RPP=14.7363;RPPR=14.3727;RPL=21.0;RPR=39.0;EPP=5.32654;EPPR=4.27278;DPRA=0.0;ODDS=250.867;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.966667;PAIREDR=0.976744;technology.ILLUMINA=1.0;BaseQRankSum=0.867;FS=1.619;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRan [...]
+chr17 1249777 . A G 8559.67 REJECT NS=2;DP=560;DPB=645.0;AC=2;AN=4;AF=0.5;RO=339;AO=306;PRO=0.0;PAO=0.0;QR=12706;QA=11762;PQR=0.0;PQA=0.0;SRF=193;SRR=146;SAF=155;SAR=151;SRP=17.1601;SAP=3.12384;AB=0.474419;ABP=6.67655;RUN=1;RPP=3.03869;RPPR=3.78537;RPL=154.0;RPR=152.0;EPP=3.46446;EPPR=5.32269;DPRA=0.0;ODDS=513.499;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996732;PAIREDR=0.99115;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.5175;Dels=0.0;FS=9.115;Haplot [...]
+chr17 1250465 . CAA C 14.4429 REJECT SOMATIC;NS=1;DP=6;DPB=9.48;AC=1;AN=4;AF=0.5;RO=1;AO=3;PRO=3.0;PAO=4.0;QR=33;QA=32;PQR=103.5;PQA=138.5;SRF=1;SRR=0;SAF=1;SAR=2;SRP=5.18177;SAP=3.73412;AB=0.5;ABP=3.0103;RUN=1;RPP=9.52472;RPPR=5.18177;RPL=3.0;RPR=0.0;EPP=3.73412;EPPR=5.18177;DPRA=0.0;ODDS=1.05638;GTI=0;TYPE=del;CIGAR=1M2D22M;NUMALT=1;MEANALT=3.0;LEN=2;MQM=27.3333;MQMR=60.0;PAIRED=0.666667;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:Call [...]
+chr17 1250625 . C CA 223.229 REJECT NS=2;DP=60;DPB=75.0;AC=2;AN=4;AF=0.5;RO=31;AO=14;PRO=11.8333;PAO=10.8333;QR=1077;QA=508;PQR=429.5;PQA=392.5;SRF=30;SRR=1;SAF=14;SAR=0;SRP=61.9202;SAP=33.4109;AB=0.233333;ABP=40.0701;RUN=1;RPP=18.5208;RPPR=14.8483;RPL=2.0;RPR=12.0;EPP=18.5208;EPPR=11.486;DPRA=0.0;ODDS=13.9072;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=2;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.967742;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.244;FS=0.0;MLEAC=1; [...]
+chr17 1250625 . CA C 223.229 REJECT NS=2;DP=60;DPB=75.0;AC=2;AN=2;AF=0.0;RO=31;AO=9;PRO=11.8333;PAO=10.3333;QR=1077;QA=311;PQR=429.5;PQA=374.0;SRF=30;SRR=1;SAF=9;SAR=0;SRP=61.9202;SAP=22.5536;AB=0.15;ABP=66.8516;RUN=1;RPP=22.5536;RPPR=14.8483;RPL=0.0;RPR=9.0;EPP=22.5536;EPPR=11.486;DPRA=0.0;ODDS=13.9072;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=2;MEANALT=5.0;LEN=1;MQM=57.7778;MQMR=60.0;PAIRED=1.0;PAIREDR=0.967742;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr17 1252321 . C G 286.932 REJECT NS=2;DP=24;DPB=24.0;AC=2;AN=4;AF=0.5;RO=11;AO=13;PRO=0.0;PAO=0.0;QR=335;QA=446;PQR=0.0;PQA=0.0;SRF=3;SRR=8;SAF=6;SAR=7;SRP=7.94546;SAP=3.17734;AB=0.541667;ABP=3.37221;RUN=1;RPP=11.1951;RPPR=3.20771;RPL=10.0;RPR=3.0;EPP=4.51363;EPPR=4.78696;DPRA=0.0;ODDS=11.1899;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.358;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=1.231;QD=9.15;R [...]
+chr17 1252330 . GA G 57.7769 REJECT NS=2;DP=18;DPB=23.1111;AC=2;AN=4;AF=0.5;RO=8;AO=5;PRO=7.5;PAO=3.5;QR=275;QA=163;PQR=237.0;PQA=119.0;SRF=6;SRR=2;SAF=2;SAR=3;SRP=7.35324;SAP=3.44459;AB=0.277778;ABP=10.7311;RUN=1;RPP=6.91895;RPPR=7.35324;RPL=4.0;RPR=1.0;EPP=6.91895;EPPR=7.35324;DPRA=0.0;ODDS=5.04299;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=1;MEANALT=3.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:Ca [...]
+chr17 1252536 . C T 2149.6 REJECT NS=2;DP=159;DPB=179.0;AC=2;AN=4;AF=0.5;RO=92;AO=87;PRO=0.0;PAO=0.0;QR=3487;QA=3246;PQR=0.0;PQA=0.0;SRF=92;SRR=0;SAF=86;SAR=1;SRP=202.786;SAP=183.342;AB=0.486034;ABP=3.31358;RUN=1;RPP=3.63429;RPPR=6.40913;RPL=41.0;RPR=46.0;EPP=3.23494;EPPR=6.40913;DPRA=0.0;ODDS=110.078;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.965517;PAIREDR=0.978261;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.452;Dels=0.0;FS=1.6175;HaplotypeScore=4. [...]
+chr17 1252843 . T G 6887.51 REJECT NS=2;DP=469;DPB=542.0;AC=2;AN=4;AF=0.5;RO=288;AO=253;PRO=0.0;PAO=0.0;QR=10829;QA=9507;PQR=0.0;PQA=0.0;SRF=108;SRR=180;SAF=96;SAR=157;SRP=42.0968;SAP=34.9473;AB=0.46679;ABP=8.2026;RUN=1;RPP=4.46081;RPPR=11.7263;RPL=120.0;RPR=133.0;EPP=8.37461;EPPR=13.8978;DPRA=0.0;ODDS=399.294;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.1581;MQMR=59.9861;PAIRED=1.0;PAIREDR=0.986111;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8155;Dels=0.0;FS=2.913;Haplotyp [...]
+chr17 1252911 . A AT 2480.26 REJECT NS=2;DP=221;DPB=299.35;AC=2;AN=2;AF=0.0;RO=84;AO=16;PRO=49.9167;PAO=42.9167;QR=3110;QA=457;PQR=1752.0;PQA=1501.0;SRF=18;SRR=66;SAF=1;SAR=15;SRP=62.5707;SAP=29.6108;AB=0.0723982;ABP=353.993;RUN=1;RPP=16.582;RPPR=13.3506;RPL=13.0;RPR=3.0;EPP=11.6962;EPPR=6.73282;DPRA=0.0;ODDS=145.271;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=3;MEANALT=7.0;LEN=1;MQM=56.875;MQMR=59.5238;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr17 1252911 . AT A 1943.9950000000001 REJECT NS=2;DP=221;DPB=299.35;AC=2;AN=4;AF=0.5;RO=84;AO=90;PRO=49.9167;PAO=47.4167;QR=3110;QA=3087;PQR=1752.0;PQA=1699.5;SRF=18;SRR=66;SAF=21;SAR=69;SRP=62.5707;SAP=58.6;AB=0.40724;ABP=19.5272;RUN=1;RPP=9.18693;RPPR=13.3506;RPL=53.0;RPR=37.0;EPP=3.10681;EPPR=6.73282;DPRA=0.0;ODDS=145.271;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=3;MEANALT=7.0;LEN=1;MQM=58.9444;MQMR=59.5238;PAIRED=0.988889;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQR [...]
+chr17 1252911 . ATT A 2480.26 PASS SOMATIC;NS=2;DP=221;DPB=299.35;AC=2;AN=2;AF=0.0;RO=84;AO=23;PRO=49.9167;PAO=31.75;QR=3110;QA=764;PQR=1752.0;PQA=1134.5;SRF=18;SRR=66;SAF=5;SAR=18;SRP=62.5707;SAP=18.9659;AB=0.104072;ABP=303.921;RUN=1;RPP=3.86001;RPPR=13.3506;RPL=10.0;RPR=13.0;EPP=18.9659;EPPR=6.73282;DPRA=0.0;ODDS=145.271;GTI=0;TYPE=del;CIGAR=1M2D17M;NUMALT=3;MEANALT=7.0;LEN=2;MQM=59.6087;MQMR=59.5238;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr17 1253070 . G T 1218.89 REJECT NS=2;DP=105;DPB=121.0;AC=2;AN=4;AF=0.5;RO=70;AO=51;PRO=0.0;PAO=0.0;QR=2584;QA=1913;PQR=0.0;PQA=0.0;SRF=32;SRR=38;SAF=11;SAR=40;SRP=4.12706;SAP=38.8183;AB=0.421488;ABP=9.48883;RUN=1;RPP=43.9277;RPPR=3.13438;RPL=41.0;RPR=10.0;EPP=29.6215;EPPR=47.8047;DPRA=0.0;ODDS=90.4597;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=57.2549;MQMR=59.5714;PAIRED=1.0;PAIREDR=0.985714;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5765;Dels=0.0;FS=9.9675;HaplotypeScor [...]
+chr17 1253130 . A G 1169.1100000000001 REJECT NS=2;DP=98;DPB=114.0;AC=2;AN=4;AF=0.5;RO=65;AO=49;PRO=0.0;PAO=0.0;QR=2429;QA=1813;PQR=0.0;PQA=0.0;SRF=49;SRR=16;SAF=33;SAR=16;SRP=39.3908;SAP=15.8176;AB=0.429825;ABP=7.88659;RUN=1;RPP=10.4997;RPPR=5.71629;RPL=18.0;RPR=31.0;EPP=4.11819;EPPR=3.04371;DPRA=0.0;ODDS=83.1113;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=46.3061;MQMR=58.5231;PAIRED=0.979592;PAIREDR=0.953846;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1775;Dels=0.0;FS=1.67 [...]
+chr17 1253252 . A AT 572.47 REJECT NS=2;DP=135;DPB=174.118;AC=2;AN=3;AF=0.25;RO=62;AO=19;PRO=16.1;PAO=13.4333;QR=2301;QA=667;PQR=586.45;PQA=485.117;SRF=25;SRR=37;SAF=11;SAR=8;SRP=8.05372;SAP=4.03889;AB=0.140741;ABP=154.354;RUN=1;RPP=4.03889;RPPR=14.358;RPL=11.0;RPR=8.0;EPP=3.12459;EPPR=11.9764;DPRA=0.0;ODDS=1.28206;GTI=0;TYPE=ins;CIGAR=1M1I16M;NUMALT=4;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=59.8548;PAIRED=1.0;PAIREDR=0.967742;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr17 1253252 . A ATT 572.47 REJECT NS=2;DP=135;DPB=174.118;AC=2;AN=3;AF=0.25;RO=62;AO=27;PRO=16.1;PAO=10.9333;QR=2301;QA=844;PQR=586.45;PQA=390.617;SRF=25;SRR=37;SAF=8;SAR=19;SRP=8.05372;SAP=12.7417;AB=0.2;ABP=108.544;RUN=1;RPP=9.52472;RPPR=14.358;RPL=18.0;RPR=9.0;EPP=3.09072;EPPR=11.9764;DPRA=0.0;ODDS=1.28206;GTI=0;TYPE=ins;CIGAR=1M2I16M;NUMALT=4;MEANALT=9.5;LEN=2;MQM=58.8148;MQMR=59.8548;PAIRED=0.962963;PAIREDR=0.967742;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-1.8 [...]
+chr17 1253252 . A ATTT 572.47 REJECT NS=2;DP=135;DPB=174.118;AC=2;AN=2;AF=0.0;RO=62;AO=7;PRO=16.1;PAO=10.9333;QR=2301;QA=240;PQR=586.45;PQA=390.617;SRF=25;SRR=37;SAF=3;SAR=4;SRP=8.05372;SAP=3.32051;AB=0.0518519;ABP=238.511;RUN=1;RPP=5.80219;RPPR=14.358;RPL=5.0;RPR=2.0;EPP=3.32051;EPPR=11.9764;DPRA=0.0;ODDS=1.28206;GTI=0;TYPE=ins;CIGAR=1M3I16M;NUMALT=4;MEANALT=9.5;LEN=3;MQM=60.0;MQMR=59.8548;PAIRED=0.857143;PAIREDR=0.967742;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr17 1253252 . AT A 572.47 REJECT NS=2;DP=135;DPB=174.118;AC=2;AN=2;AF=0.0;RO=62;AO=8;PRO=16.1;PAO=7.6;QR=2301;QA=305;PQR=586.45;PQA=275.2;SRF=25;SRR=37;SAF=4;SAR=4;SRP=8.05372;SAP=3.0103;AB=0.0592593;ABP=230.79;RUN=1;RPP=12.7819;RPPR=14.358;RPL=7.0;RPR=1.0;EPP=4.09604;EPPR=11.9764;DPRA=0.0;ODDS=1.28206;GTI=0;TYPE=del;CIGAR=1M1D15M;NUMALT=4;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=59.8548;PAIRED=0.875;PAIREDR=0.967742;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr17 1253540 . C A 12554.6 REJECT NS=2;DP=334;DPB=372.0;AC=4;AN=4;AF=1.0;RO=0;AO=372;PRO=0.0;PAO=0.0;QR=0;QA=14301;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=273;SAR=99;SRP=0.0;SAP=179.74;AB=0.0;ABP=0.0;RUN=1;RPP=34.9753;RPPR=0.0;RPL=149.0;RPR=223.0;EPP=33.2708;EPPR=0.0;DPRA=0.0;ODDS=51.7513;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.086;MQMR=0.0;PAIRED=0.991935;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8795;MLEAC=2;MLEAF=1.0;MQ=59.125;QD=32.575;SOR= [...]
+chr17 1253963 . T C 729.859 REJECT NS=2;DP=47;DPB=58.0;AC=2;AN=4;AF=0.5;RO=27;AO=31;PRO=0.0;PAO=0.0;QR=992;QA=1132;PQR=0.0;PQA=0.0;SRF=1;SRR=26;SAF=0;SAR=31;SRP=53.2759;SAP=70.3259;AB=0.534483;ABP=3.60933;RUN=1;RPP=3.64073;RPPR=6.95112;RPL=17.0;RPR=14.0;EPP=3.64073;EPPR=9.52472;DPRA=0.0;ODDS=36.6947;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.6129;MQMR=55.7037;PAIRED=0.935484;PAIREDR=0.962963;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9995;Dels=0.0;FS=0.0;HaplotypeScore=2 [...]
+chr17 1254672 . C CA 281.935 REJECT NS=2;DP=299;DPB=440.897;AC=2;AN=3;AF=0.25;RO=208;AO=24;PRO=85.0833;PAO=67.0833;QR=7515;QA=797;PQR=3006.42;PQA=2365.42;SRF=132;SRR=76;SAF=17;SAR=7;SRP=35.7494;SAP=12.0581;AB=0.0802676;ABP=460.552;RUN=1;RPP=4.45795;RPPR=57.1301;RPL=10.0;RPR=14.0;EPP=3.37221;EPPR=7.18621;DPRA=0.0;ODDS=1.34147;GTI=0;TYPE=ins;CIGAR=1M1I28M;NUMALT=3;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr17 1254672 . CA C 281.935 REJECT NS=2;DP=299;DPB=440.897;AC=2;AN=3;AF=0.25;RO=208;AO=32;PRO=85.0833;PAO=55.0833;QR=7515;QA=1130;PQR=3006.42;PQA=1964.92;SRF=132;SRR=76;SAF=25;SAR=7;SRP=35.7494;SAP=24.9965;AB=0.107023;ABP=404.079;RUN=1;RPP=3.28173;RPPR=57.1301;RPL=15.0;RPR=17.0;EPP=7.35324;EPPR=7.18621;DPRA=0.0;ODDS=1.34147;GTI=0;TYPE=del;CIGAR=1M1D27M;NUMALT=3;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.053;FS=0 [...]
+chr17 1254672 . CAA C 281.935 REJECT NS=2;DP=299;DPB=440.897;AC=2;AN=2;AF=0.0;RO=208;AO=10;PRO=85.0833;PAO=49.75;QR=7515;QA=346;PQR=3006.42;PQA=1765.25;SRF=132;SRR=76;SAF=7;SAR=3;SRP=35.7494;SAP=6.48466;AB=0.0334448;ABP=568.327;RUN=1;RPP=6.48466;RPPR=57.1301;RPL=3.0;RPR=7.0;EPP=3.87889;EPPR=7.18621;DPRA=0.0;ODDS=1.34147;GTI=0;TYPE=del;CIGAR=1M2D26M;NUMALT=3;MEANALT=12.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr17 1254875 . A G 8592.755000000001 REJECT NS=2;DP=533;DPB=614.0;AC=2;AN=4;AF=0.5;RO=307;AO=307;PRO=0.0;PAO=0.0;QR=11722;QA=11784;PQR=0.0;PQA=0.0;SRF=107;SRR=200;SAF=108;SAR=199;SRP=64.1864;SAP=61.5835;AB=0.5;ABP=3.0103;RUN=1;RPP=3.01737;RPPR=6.75202;RPL=154.0;RPR=153.0;EPP=3.18713;EPPR=3.01737;DPRA=0.0;ODDS=533.288;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990228;PAIREDR=0.993485;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5015;Dels=0.0;FS=1.7215; [...]
+chr17 1255246 . A AT 628.5585 REJECT NS=2;DP=120;DPB=154.7;AC=2;AN=4;AF=0.5;RO=49;AO=33;PRO=13.7833;PAO=13.1167;QR=1788;QA=1122;PQR=460.017;PQA=434.017;SRF=44;SRR=5;SAF=30;SAR=3;SRP=70.4146;SAP=50.9801;AB=0.255814;ABP=69.821;RUN=1;RPP=3.0761;RPPR=8.37251;RPL=17.0;RPR=16.0;EPP=4.65535;EPPR=15.8176;DPRA=0.0;ODDS=12.0828;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=5;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.689;FS=1.5 [...]
+chr17 1255246 . A ATT 770.387 REJECT NS=2;DP=129;DPB=154.7;AC=2;AN=2;AF=0.0;RO=49;AO=4;PRO=13.7833;PAO=13.1167;QR=1788;QA=140;PQR=460.017;PQA=434.017;SRF=44;SRR=5;SAF=4;SAR=0;SRP=70.4146;SAP=11.6962;AB=0.0310078;ABP=249.464;RUN=1;RPP=5.18177;RPPR=8.37251;RPL=1.0;RPR=3.0;EPP=5.18177;EPPR=15.8176;DPRA=0.0;ODDS=12.0828;GTI=0;TYPE=ins;CIGAR=1M2I19M;NUMALT=5;MEANALT=11.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr17 1255246 . AT A 770.387 REJECT NS=2;DP=129;DPB=154.7;AC=2;AN=2;AF=0.0;RO=49;AO=18;PRO=13.7833;PAO=11.5333;QR=1788;QA=654;PQR=460.017;PQA=373.767;SRF=44;SRR=5;SAF=17;SAR=1;SRP=70.4146;SAP=33.8935;AB=0.139535;ABP=148.6;RUN=1;RPP=4.9405;RPPR=8.37251;RPL=7.0;RPR=11.0;EPP=7.35324;EPPR=15.8176;DPRA=0.0;ODDS=12.0828;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=5;MEANALT=11.5;LEN=1;MQM=59.8333;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr17 1255246 . ATT A 770.387 REJECT NS=2;DP=129;DPB=154.7;AC=2;AN=2;AF=0.0;RO=49;AO=3;PRO=13.7833;PAO=11.3333;QR=1788;QA=119;PQR=460.017;PQA=366.967;SRF=44;SRR=5;SAF=2;SAR=1;SRP=70.4146;SAP=3.73412;AB=0.0232558;ABP=257.679;RUN=1;RPP=3.73412;RPPR=8.37251;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=15.8176;DPRA=0.0;ODDS=12.0828;GTI=0;TYPE=del;CIGAR=1M2D17M;NUMALT=5;MEANALT=11.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr17 1255261 . A TT 770.387 REJECT NS=2;DP=129;DPB=154.7;AC=2;AN=2;AF=0.0;RO=49;AO=2;PRO=13.7833;PAO=8.11667;QR=1788;QA=62;PQR=460.017;PQA=268.217;SRF=44;SRR=5;SAF=1;SAR=1;SRP=70.4146;SAP=3.0103;AB=0.0540541;ABP=66.922;RUN=1;RPP=3.0103;RPPR=8.37251;RPL=1.0;RPR=1.0;EPP=7.35324;EPPR=15.8176;DPRA=0.0;ODDS=12.0828;GTI=0;TYPE=complex;CIGAR=1M1I14M1X4M;NUMALT=5;MEANALT=7.0;LEN=21;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr17 1255502 . G C 9392.11 REJECT NS=2;DP=573;DPB=658.0;AC=2;AN=4;AF=0.5;RO=327;AO=331;PRO=0.0;PAO=0.0;QR=12547;QA=12771;PQR=0.0;PQA=0.0;SRF=181;SRR=146;SAF=157;SAR=174;SRP=11.145;SAP=4.90624;AB=0.50304;ABP=3.0631;RUN=1;RPP=8.52755;RPPR=3.81381;RPL=151.0;RPR=180.0;EPP=6.48072;EPPR=3.07007;DPRA=0.0;ODDS=548.538;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996979;PAIREDR=0.990826;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.654;Dels=0.0;FS=4.5855;Haplotyp [...]
+chr17 1255823 . C CT 818.918 REJECT NS=2;DP=266;DPB=365.381;AC=2;AN=2;AF=0.0;RO=119;AO=24;PRO=74.3333;PAO=54.3333;QR=4273;QA=585;PQR=2657.75;PQA=1951.75;SRF=38;SRR=81;SAF=4;SAR=20;SRP=36.7502;SAP=26.1727;AB=0.0902256;ABP=390.969;RUN=1;RPP=8.80089;RPPR=8.28388;RPL=16.0;RPR=8.0;EPP=8.80089;EPPR=7.11603;DPRA=0.0;ODDS=40.9424;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=3;MEANALT=17.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr17 1255823 . CT C 818.918 REJECT NS=2;DP=266;DPB=365.381;AC=2;AN=4;AF=0.5;RO=119;AO=56;PRO=74.3333;PAO=49.8333;QR=4273;QA=1583;PQR=2657.75;PQA=1791.25;SRF=38;SRR=81;SAF=13;SAR=43;SRP=36.7502;SAP=37.909;AB=0.210526;ABP=196.614;RUN=1;RPP=15.5738;RPPR=8.28388;RPL=37.0;RPR=19.0;EPP=3.63072;EPPR=7.11603;DPRA=0.0;ODDS=40.9424;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=3;MEANALT=17.0;LEN=1;MQM=60.3214;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.735;FS= [...]
+chr17 1255823 . CTT C 818.918 REJECT NS=2;DP=266;DPB=365.381;AC=2;AN=2;AF=0.0;RO=119;AO=19;PRO=74.3333;PAO=40.5;QR=4273;QA=467;PQR=2657.75;PQA=1452.25;SRF=38;SRR=81;SAF=5;SAR=14;SRP=36.7502;SAP=12.2676;AB=0.0714286;ABP=427.378;RUN=1;RPP=5.8675;RPPR=8.28388;RPL=12.0;RPR=7.0;EPP=5.8675;EPPR=7.11603;DPRA=0.0;ODDS=40.9424;GTI=0;TYPE=del;CIGAR=1M2D18M;NUMALT=3;MEANALT=17.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.377;FS=0.0 [...]
+chr17 1256745 . G A 67.9303 REJECT NS=2;DP=7;DPB=19.94;AC=2;AN=4;AF=0.5;RO=3;AO=2;PRO=18.5;PAO=14.5;QR=106;QA=79;PQR=648.5;PQA=463.5;SRF=2;SRR=1;SAF=1;SAR=1;SRP=3.73412;SAP=3.0103;AB=0.5;ABP=3.0103;RUN=1;RPP=3.0103;RPPR=3.73412;RPL=1.0;RPR=1.0;EPP=7.35324;EPPR=9.52472;DPRA=0.0;ODDS=7.77175;GTI=0;TYPE=snp;CIGAR=14M1X35M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallS [...]
+chr17 1257057 . C CA 2177.43 REJECT NS=2;DP=280;DPB=357.864;AC=2;AN=2;AF=0.0;RO=71;AO=19;PRO=44.2167;PAO=45.2167;QR=2515;QA=636;PQR=1548.97;PQA=1544.97;SRF=44;SRR=27;SAF=15;SAR=4;SRP=11.8491;SAP=16.8392;AB=0.0678571;ABP=457.189;RUN=1;RPP=16.8392;RPPR=28.7315;RPL=4.0;RPR=15.0;EPP=4.03889;EPPR=8.17902;DPRA=0.0;ODDS=63.3611;GTI=0;TYPE=ins;CIGAR=1M1I21M;NUMALT=4;MEANALT=19.0;LEN=1;MQM=59.8421;MQMR=60.0;PAIRED=1.0;PAIREDR=0.971831;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr17 1257057 . CA C 2177.43 REJECT NS=2;DP=280;DPB=357.864;AC=2;AN=2;AF=0.0;RO=71;AO=29;PRO=44.2167;PAO=31.2167;QR=2515;QA=950;PQR=1548.97;PQA=1046.97;SRF=44;SRR=27;SAF=22;SAR=7;SRP=11.8491;SAP=19.8579;AB=0.103571;ABP=385.22;RUN=1;RPP=12.0706;RPPR=28.7315;RPL=9.0;RPR=20.0;EPP=3.68421;EPPR=8.17902;DPRA=0.0;ODDS=63.3611;GTI=0;TYPE=del;CIGAR=1M1D20M;NUMALT=4;MEANALT=19.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.971831;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr17 1257057 . CAA C 2177.43 REJECT NS=2;DP=275;DPB=357.864;AC=2;AN=4;AF=0.5;RO=71;AO=96;PRO=44.2167;PAO=33.55;QR=2515;QA=3103;PQR=1548.97;PQA=1155.3;SRF=44;SRR=27;SAF=67;SAR=29;SRP=11.8491;SAP=35.6729;AB=0.342857;ABP=63.067;RUN=1;RPP=39.2015;RPPR=28.7315;RPL=28.0;RPR=68.0;EPP=3.8246;EPPR=8.17902;DPRA=0.0;ODDS=63.3611;GTI=0;TYPE=del;CIGAR=1M2D19M;NUMALT=4;MEANALT=19.0;LEN=2;MQM=60.1042;MQMR=60.0;PAIRED=0.989583;PAIREDR=0.971831;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSu [...]
+chr17 1257057 . CAAA C 2177.43 REJECT NS=2;DP=280;DPB=357.864;AC=2;AN=2;AF=0.0;RO=71;AO=16;PRO=44.2167;PAO=29.8;QR=2515;QA=530;PQR=1548.97;PQA=1000.8;SRF=44;SRR=27;SAF=11;SAR=5;SRP=11.8491;SAP=7.89611;AB=0.0571429;ABP=479.99;RUN=1;RPP=3.0103;RPPR=28.7315;RPL=8.0;RPR=8.0;EPP=3.55317;EPPR=8.17902;DPRA=0.0;ODDS=63.3611;GTI=0;TYPE=del;CIGAR=1M3D18M;NUMALT=4;MEANALT=19.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.971831;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr17 1265304 . TA T 684.881 REJECT NS=1;DP=56;DPB=71.7037;AC=1;AN=3;AF=0.0;RO=16;AO=7;PRO=9.25;PAO=5.75;QR=598;QA=246;PQR=323.0;PQA=200.0;SRF=5;SRR=11;SAF=1;SAR=6;SRP=7.89611;SAP=10.7656;AB=0.125;ABP=71.4117;RUN=1;RPP=5.80219;RPPR=16.582;RPL=5.0;RPR=2.0;EPP=3.32051;EPPR=5.18177;DPRA=0.0;ODDS=47.6871;GTI=0;TYPE=del;CIGAR=1M1D25M;NUMALT=3;MEANALT=10.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=1.892;FS=3.148;MLEAC=1;MLEAF=0.5;MQ= [...]
+chr17 1265317 . ATTTTTTTT TTTTTTTA 684.881 REJECT NS=1;DP=56;DPB=71.7037;AC=1;AN=3;AF=0.0;RO=16;AO=4;PRO=9.25;PAO=4.75;QR=598;QA=147;PQR=323.0;PQA=160.0;SRF=5;SRR=11;SAF=1;SAR=3;SRP=7.89611;SAP=5.18177;AB=0.0714286;ABP=92.3509;RUN=1;RPP=3.0103;RPPR=16.582;RPL=2.0;RPR=2.0;EPP=5.18177;EPPR=5.18177;DPRA=0.0;ODDS=47.6871;GTI=0;TYPE=complex;CIGAR=1M1D19M1X5M;NUMALT=3;MEANALT=10.0;LEN=26;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr17 1265325 . T A 684.881 REJECT NS=1;DP=56;DPB=71.7037;AC=1;AN=4;AF=0.5;RO=16;AO=20;PRO=9.25;PAO=13.25;QR=598;QA=791;PQR=323.0;PQA=461.0;SRF=5;SRR=11;SAF=3;SAR=17;SRP=7.89611;SAP=24.2907;AB=0.357143;ABP=12.937;RUN=1;RPP=9.95901;RPPR=16.582;RPL=14.0;RPR=6.0;EPP=3.44459;EPPR=5.18177;DPRA=0.0;ODDS=47.6871;GTI=0;TYPE=snp;CIGAR=21M1X5M;NUMALT=3;MEANALT=10.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV [...]
+chr17 4531882 . T C 6228.13 REJECT NS=2;DP=386;DPB=449.0;AC=2;AN=4;AF=0.5;RO=221;AO=227;PRO=0.0;PAO=0.0;QR=8448;QA=8647;PQR=0.0;PQA=0.0;SRF=96;SRR=125;SAF=94;SAR=133;SRP=11.2737;SAP=17.5601;AB=0.505568;ABP=3.13121;RUN=1;RPP=3.01987;RPPR=3.49176;RPL=113.0;RPR=114.0;EPP=19.0907;EPPR=16.4616;DPRA=0.0;ODDS=390.349;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991189;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.207;Dels=0.0;FS=5.325;HaplotypeScore= [...]
+chr17 5031541 . A G 18061.8 REJECT NS=2;DP=476;DPB=543.0;AC=4;AN=4;AF=1.0;RO=0;AO=542;PRO=0.0;PAO=0.0;QR=0;QA=20657;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=260;SAR=282;SRP=0.0;SAP=4.9494;AB=0.0;ABP=0.0;RUN=1;RPP=6.15132;RPPR=0.0;RPL=285.0;RPR=257.0;EPP=10.7667;EPPR=0.0;DPRA=0.0;ODDS=87.7152;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9354;MQMR=0.0;PAIRED=0.99631;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8568;MLEAC=2;MLEAF=1.0;MQ=59.925;QD=26.575;SOR [...]
+chr17 5032026 . A G 4077.3 REJECT NS=2;DP=119;DPB=137.0;AC=4;AN=4;AF=1.0;RO=0;AO=137;PRO=0.0;PAO=0.0;QR=0;QA=5111;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=121;SAR=16;SRP=0.0;SAP=177.758;AB=0.0;ABP=0.0;RUN=1;RPP=4.92817;RPPR=0.0;RPL=63.0;RPR=74.0;EPP=3.15295;EPPR=0.0;DPRA=0.0;ODDS=28.0858;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=46.3139;MQMR=0.0;PAIRED=0.992701;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=2;Dels=0.0;FS=0.0;HaplotypeScore=2.9242;MLEAC=2;MLEAF=1.0;MQ=46.295;QD=31.065;SOR=4. [...]
+chr17 5032168 . G A 9833.585 REJECT NS=2;DP=263;DPB=305.0;AC=4;AN=4;AF=1.0;RO=0;AO=304;PRO=0.0;PAO=0.0;QR=0;QA=11477;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=190;SAR=114;SRP=0.0;SAP=44.2683;AB=0.0;ABP=0.0;RUN=1;RPP=3.26745;RPPR=0.0;RPL=155.0;RPR=149.0;EPP=3.26745;EPPR=0.0;DPRA=0.0;ODDS=55.4035;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9243;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.0;SOR=1.4755 G [...]
+chr17 5032410 . G A 15180.15 REJECT NS=2;DP=407;DPB=461.0;AC=4;AN=4;AF=1.0;RO=0;AO=461;PRO=0.0;PAO=0.0;QR=0;QA=17351;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=254;SAR=207;SRP=0.0;SAP=13.4155;AB=0.0;ABP=0.0;RUN=1;RPP=9.45877;RPPR=0.0;RPL=212.0;RPR=249.0;EPP=12.5488;EPPR=0.0;DPRA=0.0;ODDS=71.0687;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9436;MQMR=0.0;PAIRED=0.991323;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8989;MLEAC=2;MLEAF=1.0;MQ=59.93;QD=27.535;S [...]
+chr17 5036191 . G A 1081.05 REJECT NS=2;DP=233;DPB=265.0;AC=2;AN=4;AF=0.5;RO=186;AO=79;PRO=0.0;PAO=0.0;QR=6941;QA=2986;PQR=0.0;PQA=0.0;SRF=122;SRR=64;SAF=59;SAR=20;SRP=42.2836;SAP=44.818;AB=0.298113;ABP=96.8261;RUN=1;RPP=80.2213;RPPR=53.8648;RPL=13.0;RPR=66.0;EPP=7.6556;EPPR=32.1968;DPRA=0.0;ODDS=89.0255;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=32.557;MQMR=60.0;PAIRED=0.860759;PAIREDR=0.989247;technology.ILLUMINA=1.0;MQ0=7;BaseQRankSum=0.089;Dels=0.0;FS=4.7765;HaplotypeScor [...]
+chr17 5036205 . A C 1248.55 REJECT NS=2;DP=263;DPB=303.0;AC=2;AN=4;AF=0.5;RO=214;AO=88;PRO=0.0;PAO=0.0;QR=8191;QA=3404;PQR=0.0;PQA=0.0;SRF=134;SRR=80;SAF=60;SAR=28;SRP=32.5991;SAP=28.2783;AB=0.290429;ABP=118.6;RUN=1;RPP=74.965;RPPR=49.9303;RPL=17.0;RPR=71.0;EPP=3.109;EPPR=13.4009;DPRA=0.0;ODDS=114.574;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=33.25;MQMR=60.0;PAIRED=0.840909;PAIREDR=0.990654;technology.ILLUMINA=1.0;MQ0=6;BaseQRankSum=-0.082;Dels=0.0;FS=2.3815;HaplotypeScore=1 [...]
+chr17 5036210 . TC GT 962.77 PASS DP=148;AC=2;AN=4;AF=0.5;MQ0=6;JOINED;BaseQRankSum=-0.9505;Dels=0.0;FS=3.505;HaplotypeScore=1.9243;MLEAC=1;MLEAF=0.5;MQ=54.94;MQRankSum=-8.9875;QD=7.74;ReadPosRankSum=2.198;SOR=1.0955;ClippingRankSum=-0.704 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:53,22:75:99.0:797,0,2262:22:29:75:1:.:.:.:.:.:-0.0664495 0/1:158,63:221:99.0:1185,0,6045:63:29:221:.:1:.:.:.:.:-0.107524
+chr17 5036210 . TCGGC GTGGT 1423.48 REJECT NS=2;DP=295;DPB=309.2;AC=2;AN=4;AF=0.5;RO=207;AO=87;PRO=21.0;PAO=4.0;QR=7846;QA=3163;PQR=694.0;PQA=148.0;SRF=124;SRR=83;SAF=59;SAR=28;SRP=20.6443;SAP=26.9963;AB=0.294915;ABP=110.782;RUN=1;RPP=18.61;RPPR=32.4773;RPL=31.0;RPR=56.0;EPP=4.23331;EPPR=3.27256;DPRA=0.0;ODDS=128.76;GTI=0;TYPE=complex;CIGAR=2X2M1X;NUMALT=1;MEANALT=1.5;LEN=5;MQM=33.1724;MQMR=60.0;PAIRED=0.83908;PAIREDR=0.990338;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr17 5036214 . C T 1000.77 PASS DP=156;AC=2;AN=4;AF=0.5;MQ0=6;BaseQRankSum=-3.0875;Dels=0.0;FS=2.376;HaplotypeScore=2.8909;MLEAC=1;MLEAF=0.5;MQ=55.035;MQRankSum=-9.174;QD=7.745;ReadPosRankSum=1.995;SOR=1.0095;ClippingRankSum=-0.877 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:56,24:80:99.0:866,0,2283:24:30:80:1:.:.:.:.:.:-0.0664495 0/1:166,66:232:99.0:1192,0,6450:66:28:232:.:1:.:.:.:.:-0.107524
+chr17 5036224 . C G 1998.18 REJECT NS=2;DP=324;DPB=371.0;AC=2;AN=4;AF=0.5;RO=249;AO=121;PRO=0.0;PAO=0.0;QR=9207;QA=4494;PQR=0.0;PQA=0.0;SRF=139;SRR=110;SAF=74;SAR=47;SRP=10.3445;SAP=16.093;AB=0.326146;ABP=100.41;RUN=1;RPP=24.9942;RPPR=39.8556;RPL=43.0;RPR=78.0;EPP=5.18177;EPPR=3.22832;DPRA=0.0;ODDS=163.548;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=38.4132;MQMR=60.0;PAIRED=0.809917;PAIREDR=0.991968;technology.ILLUMINA=1.0;MQ0=6;BaseQRankSum=1.2825;Dels=0.0;FS=3.011;HaplotypeS [...]
+chr17 5036274 . C A 3051.325 REJECT NS=2;DP=357;DPB=403.0;AC=2;AN=4;AF=0.5;RO=262;AO=140;PRO=0.0;PAO=0.0;QR=9960;QA=5295;PQR=0.0;PQA=0.0;SRF=132;SRR=130;SAF=73;SAR=67;SRP=3.04345;SAP=3.56868;AB=0.347395;ABP=84.5294;RUN=1;RPP=6.98099;RPPR=32.8473;RPL=78.0;RPR=62.0;EPP=4.56135;EPPR=11.4973;DPRA=0.0;ODDS=173.186;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=44.8071;MQMR=60.0;PAIRED=0.771429;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=5;BaseQRankSum=0.4545;Dels=0.0;FS=0.458;HaplotypeSco [...]
+chr17 5036281 . G C 2922.45 REJECT NS=2;DP=344;DPB=391.0;AC=2;AN=4;AF=0.5;RO=254;AO=137;PRO=0.0;PAO=0.0;QR=9749;QA=5078;PQR=0.0;PQA=0.0;SRF=123;SRR=131;SAF=65;SAR=72;SRP=3.55744;SAP=3.78696;AB=0.350384;ABP=79.034;RUN=1;RPP=7.591;RPPR=42.5414;RPL=77.0;RPR=60.0;EPP=5.68898;EPPR=12.8931;DPRA=0.0;ODDS=189.36;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=46.1241;MQMR=60.0;PAIRED=0.759124;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=3;BaseQRankSum=-0.6695;Dels=0.0;FS=0.2335;HaplotypeScore= [...]
+chr17 5036329 . A G 1823.8 REJECT NS=2;DP=167;DPB=190.0;AC=2;AN=4;AF=0.5;RO=112;AO=78;PRO=0.0;PAO=0.0;QR=4354;QA=2955;PQR=0.0;PQA=0.0;SRF=43;SRR=69;SAF=31;SAR=47;SRP=16.1167;SAP=10.1372;AB=0.410526;ABP=16.222;RUN=1;RPP=61.9184;RPPR=114.996;RPL=62.0;RPR=16.0;EPP=3.45573;EPPR=3.70827;DPRA=0.0;ODDS=106.287;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=47.5897;MQMR=60.0;PAIRED=0.717949;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3185;Dels=0.0;FS=0.5945;HaplotypeScore=2 [...]
+chr17 5036740 . C G 866.709 REJECT NS=2;DP=311;DPB=355.0;AC=2;AN=4;AF=0.5;RO=278;AO=77;PRO=0.0;PAO=0.0;QR=10438;QA=2954;PQR=0.0;PQA=0.0;SRF=191;SRR=87;SAF=54;SAR=23;SRP=87.4946;SAP=30.1114;AB=0.216901;ABP=250.136;RUN=1;RPP=65.3062;RPPR=43.5028;RPL=15.0;RPR=62.0;EPP=3.71532;EPPR=29.2867;DPRA=0.0;ODDS=65.0842;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=35.8831;MQMR=59.946;PAIRED=0.818182;PAIREDR=0.996403;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.4095;Dels=0.0;FS=8.0625;Haplot [...]
+chr17 5036748 . G T 1011.12 REJECT NS=2;DP=328;DPB=375.0;AC=2;AN=4;AF=0.5;RO=289;AO=85;PRO=0.0;PAO=0.0;QR=11071;QA=3246;PQR=0.0;PQA=0.0;SRF=193;SRR=96;SAF=56;SAR=29;SRP=73.7071;SAP=21.6339;AB=0.226667;ABP=246.36;RUN=1;RPP=59.443;RPPR=54.7725;RPL=19.0;RPR=66.0;EPP=4.26209;EPPR=30.9689;DPRA=0.0;ODDS=66.7623;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=35.3294;MQMR=59.9377;PAIRED=0.823529;PAIREDR=0.99654;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0095;Dels=0.0;FS=7.851;Haplotype [...]
+chr17 5036761 . A C 950.836 REJECT NS=2;DP=418;DPB=418.0;AC=2;AN=4;AF=0.5;RO=327;AO=90;PRO=0.0;PAO=0.0;QR=12525;QA=3418;PQR=0.0;PQA=0.0;SRF=199;SRR=128;SAF=58;SAR=32;SRP=36.4855;SAP=19.3205;AB=0.215311;ABP=297.271;RUN=1;RPP=34.2795;RPPR=50.9886;RPL=27.0;RPR=63.0;EPP=21.9262;EPPR=26.1262;DPRA=0.0;ODDS=64.4012;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=34.2;MQMR=58.7492;PAIRED=0.833333;PAIREDR=0.990826;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.377;Dels=0.0;FS=1.21;Haplotype [...]
+chr17 5036784 . C T 1107.17 REJECT NS=2;DP=467;DPB=474.0;AC=2;AN=3;AF=0.25;RO=372;AO=34;PRO=9.5;PAO=4.0;QR=14078;QA=947;PQR=259.0;PQA=48.0;SRF=202;SRR=170;SAF=19;SAR=15;SRP=8.98769;SAP=4.03217;AB=0.0728051;ABP=743.268;RUN=1;RPP=5.30951;RPPR=28.4375;RPL=20.0;RPR=14.0;EPP=19.3602;EPPR=4.15441;DPRA=0.0;ODDS=33.0394;GTI=0;TYPE=snp;CIGAR=1X2M;NUMALT=2;MEANALT=3.0;LEN=1;MQM=33.0882;MQMR=57.9409;PAIRED=0.735294;PAIREDR=0.989247;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.992;FS=23 [...]
+chr17 5036784 . CGG TGT 1107.17 REJECT NS=2;DP=467;DPB=474.0;AC=2;AN=3;AF=0.25;RO=372;AO=59;PRO=9.5;PAO=1.5;QR=14078;QA=2198;PQR=259.0;PQA=58.0;SRF=202;SRR=170;SAF=31;SAR=28;SRP=8.98769;SAP=3.34154;AB=0.126338;ABP=569.365;RUN=1;RPP=4.81373;RPPR=28.4375;RPL=33.0;RPR=26.0;EPP=16.2968;EPPR=4.15441;DPRA=0.0;ODDS=33.0394;GTI=0;TYPE=complex;CIGAR=1X1M1X;NUMALT=2;MEANALT=3.0;LEN=3;MQM=32.7458;MQMR=57.9409;PAIRED=0.898305;PAIREDR=0.989247;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;JOINED;Ba [...]
+chr17 5036823 . T C 396.069 REJECT NS=2;DP=426;DPB=426.0;AC=2;AN=4;AF=0.5;RO=351;AO=75;PRO=0.0;PAO=0.0;QR=13027;QA=2829;PQR=0.0;PQA=0.0;SRF=169;SRR=182;SAF=23;SAR=52;SRP=4.05582;SAP=27.3597;AB=0.176056;ABP=391.306;RUN=1;RPP=21.1059;RPPR=43.6001;RPL=50.0;RPR=25.0;EPP=3.73412;EPPR=5.73856;DPRA=0.0;ODDS=31.7889;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=28.76;MQMR=54.3105;PAIRED=0.813333;PAIREDR=0.988604;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.053;Dels=0.0;FS=15.283;Haploty [...]
+chr17 5036834 . G A 202.76999999999998 PASS DP=188;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-0.0395;Dels=0.0;FS=20.192;HaplotypeScore=5.8956;MLEAC=1;MLEAF=0.5;MQ=52.315;MQRankSum=-6.159;QD=0.915;ReadPosRankSum=0.146;SOR=3.1885;ClippingRankSum=0.631 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:80,8:88:83.0:83,0,3401:8:9:88:1:.:.:.:.:.:-0.0664495 0/1:250,39:289:99.0:379,0,9848:39:13:289:.:1:.:.:.:.:-0.107524
+chr17 5036834 . GGAAG AGAAA 304.109 REJECT NS=2;DP=359;DPB=378.4;AC=2;AN=4;AF=0.5;RO=308;AO=49;PRO=30.0;PAO=10.0;QR=11685;QA=1820;PQR=1011.0;PQA=272.0;SRF=145;SRR=163;SAF=11;SAR=38;SRP=5.29458;SAP=35.3165;AB=0.13649;ABP=415.052;RUN=1;RPP=10.4997;RPPR=88.3181;RPL=31.0;RPR=18.0;EPP=4.11819;EPPR=12.1474;DPRA=0.0;ODDS=26.8134;GTI=0;TYPE=complex;CIGAR=1X3M1X;NUMALT=1;MEANALT=2.0;LEN=5;MQM=25.5714;MQMR=52.6818;PAIRED=0.979592;PAIREDR=0.987013;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr17 5036838 . G A 98.77000000000001 PASS DP=178;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.1025;Dels=0.0;FS=16.7785;HaplotypeScore=4.9291;MLEAC=1;MLEAF=0.5;MQ=51.93;MQRankSum=-6.346;QD=0.65;ReadPosRankSum=1.001;SOR=3.1105;ClippingRankSum=-1.034 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:72,8:80:95.0:95,0,3277:8:10:80:1:.:.:.:.:.:-0.0664495 0/1:245,31:276:99.0:159,0,9663:31:11:276:.:1:.:.:.:.:-0.107524
+chr17 5036843 . C A 56.8097 REJECT;LowQual NS=2;DP=310;DPB=356.0;AC=2;AN=4;AF=0.375;RO=307;AO=49;PRO=0.0;PAO=0.0;QR=11789;QA=1790;PQR=0.0;PQA=0.0;SRF=134;SRR=173;SAF=9;SAR=40;SRP=13.7686;SAP=45.5977;AB=0.217391;ABP=66.8327;RUN=1;RPP=6.59988;RPPR=69.562;RPL=29.0;RPR=20.0;EPP=4.11819;EPPR=8.16666;DPRA=0.0;ODDS=13.0809;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=26.0612;MQMR=52.5016;PAIRED=1.0;PAIREDR=0.990228;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.809;Dels=0.0;FS=20.9915;H [...]
+chr17 5058808 . G A 14376.5 REJECT NS=2;DP=376;DPB=431.0;AC=4;AN=4;AF=1.0;RO=0;AO=431;PRO=0.0;PAO=0.0;QR=0;QA=16605;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=249;SAR=182;SRP=0.0;SAP=25.6269;AB=0.0;ABP=0.0;RUN=1;RPP=3.01534;RPPR=0.0;RPL=215.0;RPR=216.0;EPP=3.05564;EPPR=0.0;DPRA=0.0;ODDS=72.2785;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.7285;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.7768;MLEAC=2;MLEAF=1.0;MQ=59.76;QD=29.725;SOR=1.0 [...]
+chr17 5066305 . A T 12101.2 REJECT NS=2;DP=321;DPB=368.0;AC=4;AN=4;AF=1.0;RO=0;AO=368;PRO=0.0;PAO=0.0;QR=0;QA=14094;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=121;SAR=247;SRP=0.0;SAP=96.6905;AB=0.0;ABP=0.0;RUN=1;RPP=13.4192;RPPR=0.0;RPL=205.0;RPR=163.0;EPP=14.4341;EPPR=0.0;DPRA=0.0;ODDS=61.136;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.4049;MQMR=0.0;PAIRED=0.98913;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.7956;MLEAC=2;MLEAF=1.0;MQ=59.495;QD=25.99;SOR= [...]
+chr17 5072316 . C T 8670.445 REJECT NS=2;DP=235;DPB=267.0;AC=4;AN=4;AF=1.0;RO=0;AO=267;PRO=0.0;PAO=0.0;QR=0;QA=10111;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=76;SAR=191;SRP=0.0;SAP=110.567;AB=0.0;ABP=0.0;RUN=1;RPP=31.3208;RPPR=0.0;RPL=163.0;RPR=104.0;EPP=11.867;EPPR=0.0;DPRA=0.0;ODDS=44.5676;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=55.9551;MQMR=0.0;PAIRED=0.985019;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=2;Dels=0.0;FS=0.0;HaplotypeScore=2.8995;MLEAC=2;MLEAF=1.0;MQ=56.355;QD=31.885;SO [...]
+chr17 6005356 . G A 3710.3900000000003 REJECT NS=2;DP=221;DPB=251.0;AC=2;AN=4;AF=0.5;RO=121;AO=130;PRO=0.0;PAO=0.0;QR=4578;QA=4999;PQR=0.0;PQA=0.0;SRF=75;SRR=46;SAF=69;SAR=61;SRP=18.1029;SAP=4.07933;AB=0.517928;ABP=3.71105;RUN=1;RPP=48.1769;RPPR=39.3511;RPL=39.0;RPR=91.0;EPP=4.68066;EPPR=12.5038;DPRA=0.0;ODDS=186.085;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.326;Dels=0.0;FS=5.9765;HaplotypeSco [...]
+chr17 7472884 . G A 13693.9 REJECT NS=2;DP=361;DPB=407.0;AC=4;AN=4;AF=1.0;RO=1;AO=406;PRO=0.0;PAO=0.0;QR=2;QA=15557;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=173;SAR=233;SRP=5.18177;SAP=22.2647;AB=0.0;ABP=0.0;RUN=1;RPP=10.7335;RPPR=5.18177;RPL=222.0;RPR=184.0;EPP=5.14968;EPPR=5.18177;DPRA=0.0;ODDS=60.8883;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.980296;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30. [...]
+chr17 7473457 . C A 13289.5 REJECT NS=2;DP=352;DPB=400.0;AC=4;AN=4;AF=1.0;RO=0;AO=400;PRO=0.0;PAO=0.0;QR=0;QA=15254;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=195;SAR=205;SRP=0.0;SAP=3.55317;AB=0.0;ABP=0.0;RUN=1;RPP=3.03201;RPPR=0.0;RPL=199.0;RPR=201.0;EPP=3.79203;EPPR=0.0;DPRA=0.0;ODDS=63.5695;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.8288;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.12;SOR=0.79 G [...]
+chr17 7474277 . C T 13581.2 REJECT NS=2;DP=367;DPB=422.0;AC=4;AN=4;AF=1.0;RO=0;AO=420;PRO=0.0;PAO=0.0;QR=0;QA=15832;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=198;SAR=222;SRP=0.0;SAP=5.98832;AB=0.0;ABP=0.0;RUN=1;RPP=3.19643;RPPR=0.0;RPL=207.0;RPR=213.0;EPP=31.3222;EPPR=0.0;DPRA=0.0;ODDS=72.297;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997619;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8378;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.15;SOR=0.81 [...]
+chr17 7578115 . T C 4111.915 REJECT NS=2;DP=252;DPB=290.0;AC=2;AN=4;AF=0.5;RO=142;AO=148;PRO=0.0;PAO=0.0;QR=5448;QA=5717;PQR=0.0;PQA=0.0;SRF=98;SRR=44;SAF=102;SAR=46;SRP=47.6019;SAP=49.022;AB=0.510345;ABP=3.27986;RUN=1;RPP=36.8148;RPPR=77.9414;RPL=50.0;RPR=98.0;EPP=6.76636;EPPR=3.07147;DPRA=0.0;ODDS=211.809;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992958;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.5225;Dels=0.0;FS=5.083;HaplotypeScore=4. [...]
+chr17 7579472 . G C 6696.665000000001 REJECT NS=2;DP=411;DPB=473.0;AC=2;AN=4;AF=0.5;RO=224;AO=247;PRO=0.0;PAO=0.0;QR=8604;QA=9320;PQR=0.0;PQA=0.0;SRF=109;SRR=115;SAF=118;SAR=129;SRP=3.35929;SAP=4.07406;AB=0.522199;ABP=5.03487;RUN=1;RPP=11.4588;RPPR=4.40625;RPL=108.0;RPR=139.0;EPP=16.382;EPPR=3.97971;DPRA=0.0;ODDS=348.109;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991071;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.2145;Dels=0.0;FS=2.074;Ha [...]
+chr17 7579643 . CCCCCAGCCCTCCAGGT C 1000.74 REJECT NS=2;DP=347;DPB=320.667;AC=2;AN=4;AF=0.5;RO=242;AO=87;PRO=85.1667;PAO=3.66667;QR=9078;QA=2641;PQR=3059.5;PQA=110.0;SRF=136;SRR=106;SAF=45;SAR=42;SRP=11.086;SAP=3.23494;AB=0.25072;ABP=190.301;RUN=1;RPP=73.1214;RPPR=35.3132;RPL=17.0;RPR=70.0;EPP=3.23494;EPPR=4.30242;DPRA=0.0;ODDS=63.3287;GTI=0;TYPE=del;CIGAR=1M16D1M;NUMALT=2;MEANALT=4.0;LEN=16;MQM=60.9195;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995868;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;END=7 [...]
+chr17 7579651 . CCTCCAGGT C 1000.74 REJECT NS=2;DP=347;DPB=320.667;AC=2;AN=2;AF=0.0;RO=242;AO=14;PRO=85.1667;PAO=22.1667;QR=9078;QA=411;PQR=3059.5;PQA=765.5;SRF=136;SRR=106;SAF=6;SAR=8;SRP=11.086;SAP=3.63072;AB=0.0403458;ABP=639.815;RUN=1;RPP=25.3454;RPPR=35.3132;RPL=1.0;RPR=13.0;EPP=3.0103;EPPR=4.30242;DPRA=0.0;ODDS=63.3287;GTI=0;TYPE=del;CIGAR=9M8D1M;NUMALT=2;MEANALT=4.0;LEN=8;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995868;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr17 7580256 . A AT 2090.4 REJECT NS=2;DP=263;DPB=345.125;AC=2;AN=2;AF=0.0;RO=82;AO=16;PRO=54.25;PAO=47.25;QR=2773;QA=403;PQR=1924.83;PQA=1675.83;SRF=20;SRR=62;SAF=2;SAR=14;SRP=49.7234;SAP=22.5536;AB=0.0608365;ABP=443.588;RUN=1;RPP=3.0103;RPPR=3.11623;RPL=8.0;RPR=8.0;EPP=5.18177;EPPR=26.8435;DPRA=0.0;ODDS=147.474;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=3;MEANALT=19.0;LEN=1;MQM=57.5;MQMR=59.7439;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr17 7580256 . AT A 1768.065 REJECT NS=2;DP=263;DPB=345.125;AC=2;AN=4;AF=0.5;RO=82;AO=88;PRO=54.25;PAO=53.25;QR=2773;QA=2565;PQR=1924.83;PQA=1843.83;SRF=20;SRR=62;SAF=28;SAR=60;SRP=49.7234;SAP=28.2783;AB=0.334601;ABP=65.5041;RUN=1;RPP=7.84676;RPPR=3.11623;RPL=51.0;RPR=37.0;EPP=11.0053;EPPR=26.8435;DPRA=0.0;ODDS=147.474;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=3;MEANALT=19.0;LEN=1;MQM=59.3409;MQMR=59.7439;PAIRED=0.965909;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum [...]
+chr17 7580256 . ATT A 2090.4 REJECT NS=2;DP=263;DPB=345.125;AC=2;AN=2;AF=0.0;RO=82;AO=28;PRO=54.25;PAO=35.25;QR=2773;QA=870;PQR=1924.83;PQA=1228.5;SRF=20;SRR=62;SAF=7;SAR=21;SRP=49.7234;SAP=18.2106;AB=0.106464;ABP=356.795;RUN=1;RPP=10.7656;RPPR=3.11623;RPL=19.0;RPR=9.0;EPP=4.25114;EPPR=26.8435;DPRA=0.0;ODDS=147.474;GTI=0;TYPE=del;CIGAR=1M2D21M;NUMALT=3;MEANALT=19.0;LEN=2;MQM=59.8929;MQMR=59.7439;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr17 7582141 . C T 451.142 REJECT NS=2;DP=201;DPB=228.444;AC=2;AN=2;AF=0.0;RO=115;AO=13;PRO=16.3;PAO=9.96667;QR=4224;QA=260;PQR=558.483;PQA=317.233;SRF=73;SRR=42;SAF=1;SAR=12;SRP=21.1563;SAP=23.2217;AB=0.0646766;ABP=333.863;RUN=1;RPP=31.2394;RPPR=16.7755;RPL=0.0;RPR=13.0;EPP=23.2217;EPPR=18.8904;DPRA=0.0;ODDS=20.9453;GTI=0;TYPE=snp;CIGAR=1X17M;NUMALT=4;MEANALT=8.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr17 7582141 . C CT 451.142 REJECT NS=2;DP=201;DPB=228.444;AC=2;AN=2;AF=0.0;RO=115;AO=18;PRO=16.3;PAO=15.3;QR=4224;QA=573;PQR=558.483;PQA=525.483;SRF=73;SRR=42;SAF=13;SAR=5;SRP=21.1563;SAP=10.7311;AB=0.0895522;ABP=297.131;RUN=1;RPP=15.074;RPPR=16.7755;RPL=4.0;RPR=14.0;EPP=3.0103;EPPR=18.8904;DPRA=0.0;ODDS=20.9453;GTI=0;TYPE=ins;CIGAR=1M1I17M;NUMALT=4;MEANALT=8.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.888889;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr17 7582141 . CT C 371.43600000000004 REJECT NS=2;DP=186;DPB=228.444;AC=2;AN=4;AF=0.5;RO=115;AO=35;PRO=16.3;PAO=12.6333;QR=4224;QA=1079;PQR=558.483;PQA=421.15;SRF=73;SRR=42;SAF=20;SAR=15;SRP=21.1563;SAP=4.56135;AB=0.174129;ABP=188.407;RUN=1;RPP=10.5174;RPPR=16.7755;RPL=12.0;RPR=23.0;EPP=25.4075;EPPR=18.8904;DPRA=0.0;ODDS=20.9453;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=4;MEANALT=8.5;LEN=1;MQM=60.5714;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankS [...]
+chr17 7582141 . CTT C 451.142 REJECT NS=2;DP=201;DPB=228.444;AC=2;AN=2;AF=0.0;RO=115;AO=10;PRO=16.3;PAO=11.8;QR=4224;QA=303;PQR=558.483;PQA=389.65;SRF=73;SRR=42;SAF=5;SAR=5;SRP=21.1563;SAP=3.0103;AB=0.0497512;ABP=356.939;RUN=1;RPP=3.0103;RPPR=16.7755;RPL=5.0;RPR=5.0;EPP=10.8276;EPPR=18.8904;DPRA=0.0;ODDS=20.9453;GTI=0;TYPE=del;CIGAR=1M2D15M;NUMALT=4;MEANALT=8.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr17 7582240 . G T 216.711 REJECT NS=2;DP=100;DPB=146.238;AC=2;AN=2;AF=0.0;RO=50;AO=8;PRO=25.3833;PAO=10.8;QR=1750;QA=124;PQR=874.617;PQA=214.2;SRF=15;SRR=35;SAF=0;SAR=8;SRP=20.3821;SAP=20.3821;AB=0.08;ABP=156.229;RUN=1;RPP=7.35324;RPPR=14.1282;RPL=6.0;RPR=2.0;EPP=7.35324;EPPR=7.35324;DPRA=0.0;ODDS=15.0499;GTI=0;TYPE=snp;CIGAR=1X20M;NUMALT=4;MEANALT=8.5;LEN=1;MQM=45.75;MQMR=59.02;PAIRED=1.0;PAIREDR=0.98;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMIC [...]
+chr17 7582240 . G GT 216.711 REJECT NS=2;DP=100;DPB=146.238;AC=2;AN=4;AF=0.5;RO=50;AO=16;PRO=25.3833;PAO=19.8833;QR=1750;QA=469;PQR=874.617;PQA=655.617;SRF=15;SRR=35;SAF=9;SAR=7;SRP=20.3821;SAP=3.55317;AB=0.16;ABP=103.419;RUN=1;RPP=3.55317;RPPR=14.1282;RPL=9.0;RPR=7.0;EPP=5.18177;EPPR=7.35324;DPRA=0.0;ODDS=15.0499;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=4;MEANALT=8.5;LEN=1;MQM=59.1875;MQMR=59.02;PAIRED=1.0;PAIREDR=0.98;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr17 7582240 . G GTT 216.711 REJECT NS=2;DP=100;DPB=146.238;AC=2;AN=2;AF=0.0;RO=50;AO=4;PRO=25.3833;PAO=17.8833;QR=1750;QA=119;PQR=874.617;PQA=600.617;SRF=15;SRR=35;SAF=2;SAR=2;SRP=20.3821;SAP=3.0103;AB=0.0533333;ABP=132.98;RUN=1;RPP=3.0103;RPPR=14.1282;RPL=2.0;RPR=2.0;EPP=3.0103;EPPR=7.35324;DPRA=0.0;ODDS=15.0499;GTI=0;TYPE=ins;CIGAR=1M2I20M;NUMALT=4;MEANALT=11.0;LEN=2;MQM=56.0;MQMR=59.02;PAIRED=0.75;PAIREDR=0.98;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr17 7582240 . GT G 216.711 REJECT NS=2;DP=100;DPB=146.238;AC=2;AN=2;AF=0.0;RO=50;AO=10;PRO=25.3833;PAO=14.05;QR=1750;QA=278;PQR=874.617;PQA=475.95;SRF=15;SRR=35;SAF=3;SAR=7;SRP=20.3821;SAP=6.48466;AB=0.1;ABP=141.985;RUN=1;RPP=3.0103;RPPR=14.1282;RPL=5.0;RPR=5.0;EPP=3.87889;EPPR=7.35324;DPRA=0.0;ODDS=15.0499;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=4;MEANALT=8.5;LEN=1;MQM=59.7;MQMR=59.02;PAIRED=1.0;PAIREDR=0.98;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr17 7582606 . T TTTTTA 555.396 REJECT NS=2;DP=56;DPB=194.24;AC=2;AN=4;AF=0.5;RO=32;AO=21;PRO=135.5;PAO=131.5;QR=1215;QA=738;PQR=4934.0;PQA=4784.0;SRF=8;SRR=24;SAF=3;SAR=18;SRP=20.3821;SAP=26.2761;AB=0.375;ABP=10.6105;RUN=1;RPP=3.94093;RPPR=9.79615;RPL=12.0;RPR=9.0;EPP=3.1137;EPPR=3.28173;DPRA=0.0;ODDS=30.1367;GTI=0;TYPE=ins;CIGAR=1M5I49M;NUMALT=1;MEANALT=2.5;LEN=5;MQM=60.4762;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;END=7582606;HOMLEN=44;HOMSEQ=TTTTATTTTATTTTATTTTATTTTA [...]
+chr17 7583227 . G A 2352.025 REJECT NS=2;DP=489;DPB=557.0;AC=2;AN=4;AF=0.5;RO=441;AO=116;PRO=0.0;PAO=0.0;QR=16959;QA=4384;PQR=0.0;PQA=0.0;SRF=225;SRR=216;SAF=51;SAR=65;SRP=3.40914;SAP=6.67934;AB=0.208259;ABP=414.791;RUN=1;RPP=3.68421;RPPR=5.61508;RPL=61.0;RPR=55.0;EPP=10.4981;EPPR=7.74224;DPRA=0.0;ODDS=83.2783;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997732;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.936;Dels=0.0;FS=3.882;HaplotypeScore [...]
+chr17 7583814 . C T 426.859 REJECT NS=2;DP=176;DPB=243.238;AC=2;AN=2;AF=0.0;RO=87;AO=22;PRO=50.0833;PAO=1.25;QR=3128;QA=328;PQR=1796.22;PQA=31.55;SRF=35;SRR=52;SAF=0;SAR=22;SRP=10.2236;SAP=50.7827;AB=0.125;ABP=217.986;RUN=1;RPP=17.2236;RPPR=121.842;RPL=17.0;RPR=5.0;EPP=17.2236;EPPR=6.03039;DPRA=0.0;ODDS=43.0416;GTI=0;TYPE=snp;CIGAR=1X20M;NUMALT=4;MEANALT=12.5;LEN=1;MQM=58.9545;MQMR=59.1954;PAIRED=1.0;PAIREDR=0.965517;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr17 7583814 . C CT 426.859 REJECT NS=2;DP=176;DPB=243.238;AC=2;AN=2;AF=0.0;RO=87;AO=10;PRO=50.0833;PAO=33.0833;QR=3128;QA=362;PQR=1796.22;PQA=1185.22;SRF=35;SRR=52;SAF=7;SAR=3;SRP=10.2236;SAP=6.48466;AB=0.0568182;ABP=303.266;RUN=1;RPP=10.8276;RPPR=121.842;RPL=8.0;RPR=2.0;EPP=3.0103;EPPR=6.03039;DPRA=0.0;ODDS=43.0416;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=4;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=59.1954;PAIRED=0.8;PAIREDR=0.965517;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr17 7583814 . CT C 426.859 REJECT NS=2;DP=176;DPB=243.238;AC=2;AN=4;AF=0.5;RO=87;AO=29;PRO=50.0833;PAO=30.0833;QR=3128;QA=960;PQR=1796.22;PQA=1060.22;SRF=35;SRR=52;SAF=12;SAR=17;SRP=10.2236;SAP=4.88226;AB=0.164773;ABP=174.803;RUN=1;RPP=65.983;RPPR=121.842;RPL=29.0;RPR=0.0;EPP=4.88226;EPPR=6.03039;DPRA=0.0;ODDS=43.0416;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=4;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=59.1954;PAIRED=1.0;PAIREDR=0.965517;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-1.501;F [...]
+chr17 7583814 . CTT C 426.859 REJECT NS=2;DP=176;DPB=243.238;AC=2;AN=2;AF=0.0;RO=87;AO=9;PRO=50.0833;PAO=23.5;QR=3128;QA=295;PQR=1796.22;PQA=831.8;SRF=35;SRR=52;SAF=3;SAR=6;SRP=10.2236;SAP=5.18177;AB=0.0511364;ABP=311.014;RUN=1;RPP=22.5536;RPPR=121.842;RPL=9.0;RPR=0.0;EPP=5.18177;EPPR=6.03039;DPRA=0.0;ODDS=43.0416;GTI=0;TYPE=del;CIGAR=1M2D18M;NUMALT=4;MEANALT=12.5;LEN=2;MQM=60.0;MQMR=59.1954;PAIRED=1.0;PAIREDR=0.965517;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr17 7585116 . CT C 43.3047 REJECT NS=2;DP=10;DPB=13.3333;AC=2;AN=4;AF=0.5;RO=5;AO=4;PRO=3.5;PAO=2.5;QR=176;QA=129;PQR=124.5;PQA=90.5;SRF=5;SRR=0;SAF=4;SAR=0;SRP=13.8677;SAP=11.6962;AB=0.4;ABP=3.87889;RUN=1;RPP=5.18177;RPPR=3.44459;RPL=1.0;RPR=3.0;EPP=5.18177;EPPR=3.44459;DPRA=0.0;ODDS=3.01415;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=56.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:C [...]
+chr17 7585525 . C T 38.8631 REJECT NS=2;DP=54;DPB=127.759;AC=2;AN=2;AF=0.0;RO=7;AO=19;PRO=39.5167;PAO=19.1;QR=236;QA=354;PQR=1423.48;PQA=451.15;SRF=2;SRR=5;SAF=0;SAR=19;SRP=5.80219;SAP=44.2683;AB=0.351852;ABP=13.3047;RUN=1;RPP=28.7251;RPPR=10.7656;RPL=2.0;RPR=17.0;EPP=28.7251;EPPR=3.32051;DPRA=0.0;ODDS=4.40876;GTI=0;TYPE=snp;CIGAR=1X28M;NUMALT=4;MEANALT=10.5;LEN=1;MQM=50.0526;MQMR=52.1429;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr17 7585525 . C CT 38.8631 REJECT NS=2;DP=54;DPB=127.759;AC=2;AN=4;AF=0.5;RO=7;AO=4;PRO=39.5167;PAO=39.0167;QR=236;QA=83;PQR=1423.48;PQA=1339.48;SRF=2;SRR=5;SAF=2;SAR=2;SRP=5.80219;SAP=3.0103;AB=0.0740741;ABP=88.0998;RUN=1;RPP=3.0103;RPPR=10.7656;RPL=2.0;RPR=2.0;EPP=3.0103;EPPR=3.32051;DPRA=0.0;ODDS=4.40876;GTI=0;TYPE=ins;CIGAR=1M1I28M;NUMALT=4;MEANALT=10.5;LEN=1;MQM=60.0;MQMR=52.1429;PAIRED=0.75;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr17 7585525 . CT C 38.8631 REJECT NS=2;DP=54;DPB=127.759;AC=2;AN=2;AF=0.0;RO=7;AO=4;PRO=39.5167;PAO=29.85;QR=236;QA=110;PQR=1423.48;PQA=1070.15;SRF=2;SRR=5;SAF=2;SAR=2;SRP=5.80219;SAP=3.0103;AB=0.0740741;ABP=88.0998;RUN=1;RPP=11.6962;RPPR=10.7656;RPL=4.0;RPR=0.0;EPP=3.0103;EPPR=3.32051;DPRA=0.0;ODDS=4.40876;GTI=0;TYPE=del;CIGAR=1M1D27M;NUMALT=4;MEANALT=10.5;LEN=1;MQM=50.0;MQMR=52.1429;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr17 7585548 . G T 38.8631 REJECT NS=2;DP=54;DPB=127.759;AC=2;AN=2;AF=0.0;RO=7;AO=5;PRO=39.5167;PAO=31.5167;QR=236;QA=34;PQR=1423.48;PQA=1085.73;SRF=2;SRR=5;SAF=5;SAR=0;SRP=5.80219;SAP=13.8677;AB=0.128205;ABP=49.8362;RUN=1;RPP=6.91895;RPPR=10.7656;RPL=4.0;RPR=1.0;EPP=6.91895;EPPR=3.32051;DPRA=0.0;ODDS=4.40876;GTI=0;TYPE=snp;CIGAR=23M1X5M;NUMALT=4;MEANALT=12.0;LEN=1;MQM=60.0;MQMR=52.1429;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr17 7586422 . A AT 79.806 REJECT NS=2;DP=27;DPB=30.1364;AC=2;AN=3;AF=0.25;RO=12;AO=4;PRO=4.33333;PAO=3.33333;QR=422;QA=104;PQR=127.667;PQA=113.667;SRF=0;SRR=12;SAF=0;SAR=4;SRP=29.068;SAP=11.6962;AB=0.210526;ABP=16.8392;RUN=1;RPP=3.0103;RPPR=5.9056;RPL=2.0;RPR=2.0;EPP=3.0103;EPPR=5.9056;DPRA=0.0;ODDS=6.4298;GTI=0;TYPE=ins;CIGAR=1M1I21M;NUMALT=2;MEANALT=6.0;LEN=1;MQM=58.0;MQMR=59.5;PAIRED=0.75;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr17 7586422 . AT A 79.806 REJECT NS=2;DP=27;DPB=30.1364;AC=2;AN=3;AF=0.25;RO=12;AO=5;PRO=4.33333;PAO=3.33333;QR=422;QA=186;PQR=127.667;PQA=113.667;SRF=0;SRR=12;SAF=0;SAR=5;SRP=29.068;SAP=13.8677;AB=0.185185;ABP=26.2531;RUN=1;RPP=13.8677;RPPR=5.9056;RPL=5.0;RPR=0.0;EPP=13.8677;EPPR=5.9056;DPRA=0.0;ODDS=6.4298;GTI=0;TYPE=del;CIGAR=1M1D20M;NUMALT=2;MEANALT=4.5;LEN=1;MQM=60.0;MQMR=59.5;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr17 7587687 . A G 1566.75 PASS SOMATIC;NS=2;DP=233;DPB=233.0;AC=1;AN=3;AF=0.25;RO=169;AO=64;PRO=0.0;PAO=0.0;QR=6484;QA=2412;PQR=0.0;PQA=0.0;SRF=127;SRR=42;SAF=52;SAR=12;SRP=95.844;SAP=57.2971;AB=0.353591;ABP=36.7101;RUN=1;RPP=9.66043;RPPR=12.3772;RPL=25.0;RPR=39.0;EPP=3.14602;EPPR=3.02315;DPRA=3.48077;ODDS=33.4792;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994083;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.23;Dels=0.0;FS=3.392;Hap [...]
+chr17 7587999 . T TA 1306.82 REJECT NS=2;DP=338;DPB=458.136;AC=2;AN=2;AF=0.0;RO=129;AO=16;PRO=79.0167;PAO=65.0167;QR=4758;QA=514;PQR=2786.62;PQA=2301.62;SRF=42;SRR=87;SAF=3;SAR=13;SRP=37.0974;SAP=16.582;AB=0.0473373;ABP=604.572;RUN=1;RPP=3.55317;RPPR=17.167;RPL=9.0;RPR=7.0;EPP=11.6962;EPPR=11.915;DPRA=0.0;ODDS=23.7268;GTI=0;TYPE=ins;CIGAR=1M1I21M;NUMALT=4;MEANALT=27.5;LEN=1;MQM=59.8125;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr17 7587999 . TA T 1306.82 REJECT NS=2;DP=338;DPB=458.136;AC=2;AN=4;AF=0.5;RO=129;AO=72;PRO=79.0167;PAO=40.0167;QR=4758;QA=2408;PQR=2786.62;PQA=1392.62;SRF=42;SRR=87;SAF=25;SAR=47;SRP=37.0974;SAP=17.6074;AB=0.213018;ABP=244.802;RUN=1;RPP=7.35324;RPPR=17.167;RPL=30.0;RPR=42.0;EPP=8.92153;EPPR=11.915;DPRA=0.0;ODDS=23.7268;GTI=0;TYPE=del;CIGAR=1M1D20M;NUMALT=4;MEANALT=27.5;LEN=1;MQM=60.1389;MQMR=60.0;PAIRED=0.986111;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:Q [...]
+chr17 7587999 . TAA T 1306.82 REJECT NS=2;DP=338;DPB=458.136;AC=2;AN=2;AF=0.0;RO=129;AO=38;PRO=79.0167;PAO=35.35;QR=4758;QA=1191;PQR=2786.62;PQA=1190.95;SRF=42;SRR=87;SAF=14;SAR=24;SRP=37.0974;SAP=8.7247;AB=0.112426;ABP=444.012;RUN=1;RPP=5.06748;RPPR=17.167;RPL=22.0;RPR=16.0;EPP=3.23888;EPPR=11.915;DPRA=0.0;ODDS=23.7268;GTI=0;TYPE=del;CIGAR=1M2D19M;NUMALT=4;MEANALT=27.5;LEN=2;MQM=59.4737;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.231;F [...]
+chr17 7587999 . TAAA T 1306.82 REJECT NS=2;DP=338;DPB=458.136;AC=2;AN=2;AF=0.0;RO=129;AO=20;PRO=79.0167;PAO=31.6;QR=4758;QA=615;PQR=2786.62;PQA=1078.2;SRF=42;SRR=87;SAF=8;SAR=12;SRP=37.0974;SAP=4.74748;AB=0.0591716;ABP=573.529;RUN=1;RPP=3.0103;RPPR=17.167;RPL=10.0;RPR=10.0;EPP=3.0103;EPPR=11.915;DPRA=0.0;ODDS=23.7268;GTI=0;TYPE=del;CIGAR=1M3D18M;NUMALT=4;MEANALT=27.5;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr17 7589621 . C CT 381.092 REJECT NS=2;DP=502;DPB=617.5;AC=2;AN=3;AF=0.25;RO=378;AO=49;PRO=105.333;PAO=65.3333;QR=13938;QA=1609;PQR=3778.0;PQA=2335.0;SRF=196;SRR=182;SAF=23;SAR=26;SRP=4.13625;SAP=3.40914;AB=0.0976096;ABP=709.024;RUN=1;RPP=15.8176;RPPR=8.89281;RPL=33.0;RPR=16.0;EPP=3.05462;EPPR=10.4553;DPRA=0.0;ODDS=1.78242;GTI=1;TYPE=ins;CIGAR=1M1I17M;NUMALT=2;MEANALT=12.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992063;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:Q [...]
+chr17 7589621 . CT C 381.092 REJECT NS=2;DP=502;DPB=617.5;AC=2;AN=3;AF=0.25;RO=378;AO=48;PRO=105.333;PAO=61.3333;QR=13938;QA=1684;PQR=3778.0;PQA=2192.0;SRF=196;SRR=182;SAF=22;SAR=26;SRP=4.13625;SAP=3.73412;AB=0.0956175;ABP=716.032;RUN=1;RPP=5.9056;RPPR=8.89281;RPL=28.0;RPR=20.0;EPP=5.9056;EPPR=10.4553;DPRA=0.0;ODDS=1.78242;GTI=1;TYPE=del;CIGAR=1M1D16M;NUMALT=2;MEANALT=12.0;LEN=1;MQM=60.2083;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992063;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO: [...]
+chr17 8108331 . A G 14011.55 REJECT NS=2;DP=369;DPB=420.0;AC=4;AN=4;AF=1.0;RO=0;AO=420;PRO=0.0;PAO=0.0;QR=0;QA=16047;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=186;SAR=234;SRP=0.0;SAP=14.9224;AB=0.0;ABP=0.0;RUN=1;RPP=4.02365;RPPR=0.0;RPL=217.0;RPR=203.0;EPP=3.03098;EPPR=0.0;DPRA=0.0;ODDS=66.6584;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995238;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9329;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=34.895;SOR=0 [...]
+chr17 8108339 . G A 13773.75 REJECT NS=2;DP=364;DPB=412.0;AC=4;AN=4;AF=1.0;RO=0;AO=412;PRO=0.0;PAO=0.0;QR=0;QA=15768;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=175;SAR=237;SRP=0.0;SAP=23.2703;AB=0.0;ABP=0.0;RUN=1;RPP=4.71796;RPPR=0.0;RPL=215.0;RPR=197.0;EPP=3.76926;EPPR=0.0;DPRA=0.0;ODDS=64.2145;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997573;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9664;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.365;SOR=1 [...]
+chr17 9001373 . G A 9722.83 REJECT NS=2;DP=378;DPB=432.0;AC=2;AN=4;AF=0.5;RO=115;AO=317;PRO=0.0;PAO=0.0;QR=4447;QA=12283;PQR=0.0;PQA=0.0;SRF=56;SRR=59;SAF=201;SAR=116;SRP=3.18024;SAP=52.5021;AB=0.733796;ABP=208.114;RUN=1;RPP=10.47;RPPR=21.1563;RPL=142.0;RPR=175.0;EPP=37.5415;EPPR=12.9991;DPRA=0.0;ODDS=311.596;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993691;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.586;Dels=0.0;FS=11.952;HaplotypeScore= [...]
+chr17 9001410 . A G 15800.9 REJECT NS=2;DP=411;DPB=470.0;AC=4;AN=4;AF=1.0;RO=1;AO=469;PRO=0.0;PAO=0.0;QR=34;QA=18180;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=230;SAR=239;SRP=5.18177;SAP=3.38533;AB=0.0;ABP=0.0;RUN=1;RPP=5.90405;RPPR=5.18177;RPL=247.0;RPR=222.0;EPP=13.238;EPPR=5.18177;DPRA=0.0;ODDS=71.6978;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995736;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.276;Dels=0.0;FS=0.0;HaplotypeScore=7.8147;MLEAC=2;ML [...]
+chr17 10503956 . A T 10008.085 REJECT NS=2;DP=267;DPB=307.0;AC=4;AN=4;AF=1.0;RO=1;AO=306;PRO=0.0;PAO=0.0;QR=36;QA=11675;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=201;SAR=105;SRP=5.18177;SAP=68.4099;AB=0.0;ABP=0.0;RUN=1;RPP=92.0265;RPPR=5.18177;RPL=97.0;RPR=209.0;EPP=15.5282;EPPR=5.18177;DPRA=0.0;ODDS=48.2009;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993464;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.687;Dels=0.0;FS=0.0;HaplotypeScore=3.9327;MLEAC=2 [...]
+chr17 16062134 . G C 1699.21 REJECT NS=2;DP=337;DPB=392.0;AC=2;AN=4;AF=0.5;RO=309;AO=83;PRO=0.0;PAO=0.0;QR=11567;QA=3130;PQR=0.0;PQA=0.0;SRF=133;SRR=176;SAF=34;SAR=49;SRP=16.004;SAP=8.89682;AB=0.211735;ABP=285.944;RUN=1;RPP=6.17594;RPPR=3.01733;RPL=47.0;RPR=36.0;EPP=3.66436;EPPR=19.8831;DPRA=0.0;ODDS=44.5618;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990291;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.066;Dels=0.0;FS=5.2105;HaplotypeScore=3 [...]
+chr17 16068252 . C A 71.77 PASS DP=38;AC=1;AN=4;AF=0.5;BaseQRankSum=-0.907;FS=5.058;MLEAC=1;MLEAF=0.5;MQ=57.25;MQRankSum=-3.584;QD=1.89;ReadPosRankSum=-0.777;SOR=1.911;ClippingRankSum=-0.993 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:33,5:38:99.0:100,0,1332:5:13:38:1:.:.:.:.:.:0.000295696 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.107524
+chr17 16068278 . A G 179.1665 REJECT NS=2;DP=252;DPB=274.0;AC=2;AN=4;AF=0.5;RO=222;AO=52;PRO=0.0;PAO=0.0;QR=8473;QA=1961;PQR=0.0;PQA=0.0;SRF=150;SRR=72;SAF=52;SAR=0;SRP=62.5204;SAP=115.927;AB=0.189781;ABP=232.045;RUN=1;RPP=35.7494;RPPR=6.92286;RPL=12.0;RPR=40.0;EPP=35.7494;EPPR=3.1668;DPRA=0.0;ODDS=2.19874;GTI=1;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=25.4808;MQMR=59.6982;PAIRED=1.0;PAIREDR=0.990991;technology.ILLUMINA=1.0;MQ0=12;BaseQRankSum=0.6525;Dels=0.0;FS=25.333;HaplotypeS [...]
+chr17 16068287 . A T 348.3275 REJECT NS=2;DP=259;DPB=282.0;AC=2;AN=4;AF=0.5;RO=220;AO=62;PRO=0.0;PAO=0.0;QR=8376;QA=2355;PQR=0.0;PQA=0.0;SRF=145;SRR=75;SAF=61;SAR=1;SRP=51.3749;SAP=129.096;AB=0.219858;ABP=195.24;RUN=1;RPP=43.4978;RPPR=3.642;RPL=14.0;RPR=48.0;EPP=38.8746;EPPR=4.94488;DPRA=0.0;ODDS=37.7935;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=25.7903;MQMR=59.0545;PAIRED=1.0;PAIREDR=0.990909;technology.ILLUMINA=1.0;MQ0=12;BaseQRankSum=-0.594;Dels=0.0;FS=36.5845;HaplotypeSc [...]
+chr17 16068340 . C T 1094.77 PASS DP=155;AC=2;AN=4;AF=0.5;MQ0=5;BaseQRankSum=3.2145;Dels=0.0;FS=58.959;HaplotypeScore=4.9151;MLEAC=1;MLEAF=0.5;MQ=49.85;MQRankSum=-9.4605;QD=9.575;ReadPosRankSum=2.262;SOR=5.2485;ClippingRankSum=3.365 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:41,26:67:99.0:968,0,1618:26:39:67:1:.:.:.:.:.:0.000295696 0/1:171,73:244:99.0:1278,0,6699:73:30:244:.:1:.:.:.:.:-0.107524
+chr17 16068340 . CTCG TTCA 1591.94 REJECT NS=2;DP=300;DPB=309.75;AC=2;AN=4;AF=0.5;RO=203;AO=96;PRO=14.0;PAO=8.0;QR=7726;QA=3666;PQR=351.0;PQA=280.0;SRF=123;SRR=80;SAF=92;SAR=4;SRP=22.7889;SAP=178.176;AB=0.32;ABP=87.4371;RUN=1;RPP=4.45795;RPPR=3.27772;RPL=52.0;RPR=44.0;EPP=6.26751;EPPR=4.81808;DPRA=0.0;ODDS=144.994;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=1;MEANALT=1.5;LEN=4;MQM=27.8542;MQMR=56.1823;PAIRED=0.989583;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr17 16068343 . G A 1174.77 PASS DP=158;AC=2;AN=4;AF=0.5;MQ0=6;BaseQRankSum=1.7815;Dels=0.0;FS=52.103;HaplotypeScore=5.9237;MLEAC=1;MLEAF=0.5;MQ=49.51;MQRankSum=-9.631;QD=10.03;ReadPosRankSum=1.5635;SOR=4.785;ClippingRankSum=-0.748 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:40,27:67:99.0:1002,0,1618:27:40:67:1:.:.:.:.:.:0.000295696 0/1:170,79:249:99.0:1404,0,6578:79:32:249:.:1:.:.:.:.:-0.107524
+chr17 16068362 . C T 1479.14 REJECT NS=2;DP=289;DPB=320.0;AC=2;AN=4;AF=0.5;RO=208;AO=111;PRO=0.0;PAO=0.0;QR=8024;QA=4108;PQR=0.0;PQA=0.0;SRF=124;SRR=84;SAF=99;SAR=12;SRP=19.7139;SAP=151.081;AB=0.346875;ABP=68.1816;RUN=1;RPP=5.3774;RPPR=4.51363;RPL=50.0;RPR=61.0;EPP=4.59489;EPPR=11.1951;DPRA=0.0;ODDS=112.731;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=27.8468;MQMR=54.5529;PAIRED=0.990991;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=10;BaseQRankSum=-1.859;Dels=0.0;FS=45.4815;Haplotyp [...]
+chr17 16068377 . C G 1778.09 REJECT NS=2;DP=309;DPB=347.0;AC=2;AN=4;AF=0.5;RO=218;AO=129;PRO=0.0;PAO=0.0;QR=8290;QA=4967;PQR=0.0;PQA=0.0;SRF=121;SRR=97;SAF=100;SAR=29;SRP=8.74777;SAP=87.8661;AB=0.371758;ABP=52.5787;RUN=1;RPP=10.4337;RPPR=13.2102;RPL=54.0;RPR=75.0;EPP=13.531;EPPR=4.96263;DPRA=0.0;ODDS=131.604;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=26.7054;MQMR=54.0183;PAIRED=0.984496;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=9;BaseQRankSum=1.477;Dels=0.0;FS=25.0175;Haplotype [...]
+chr17 16068383 . G A 2201.54 REJECT NS=2;DP=326;DPB=368.0;AC=2;AN=4;AF=0.5;RO=218;AO=150;PRO=0.0;PAO=0.0;QR=8370;QA=5716;PQR=0.0;PQA=0.0;SRF=116;SRR=102;SAF=105;SAR=45;SRP=4.96263;SAP=55.1256;AB=0.407609;ABP=30.2953;RUN=1;RPP=26.1727;RPPR=13.2102;RPL=55.0;RPR=95.0;EPP=19.7451;EPPR=6.99465;DPRA=0.0;ODDS=157.107;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=27.54;MQMR=54.7936;PAIRED=0.966667;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=10;BaseQRankSum=1.0405;Dels=0.0;FS=17.116;Haplotyp [...]
+chr17 16068396 . G A 2791.605 REJECT NS=2;DP=375;DPB=429.0;AC=2;AN=4;AF=0.5;RO=248;AO=181;PRO=0.0;PAO=0.0;QR=9605;QA=6904;PQR=0.0;PQA=0.0;SRF=123;SRR=125;SAF=102;SAR=79;SRP=3.04532;SAP=9.35676;AB=0.421911;ABP=25.7323;RUN=1;RPP=74.141;RPPR=18.4558;RPL=52.0;RPR=129.0;EPP=47.6515;EPPR=11.9764;DPRA=0.0;ODDS=194.032;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=29.5801;MQMR=55.7258;PAIRED=0.944751;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=12;BaseQRankSum=0.344;Dels=0.0;FS=5.851;Haploty [...]
+chr17 16068463 . C T 183.136 REJECT NS=2;DP=435;DPB=435.0;AC=1;AN=4;AF=0.25;RO=400;AO=35;PRO=0.0;PAO=0.0;QR=15283;QA=1341;PQR=0.0;PQA=0.0;SRF=124;SRR=276;SAF=5;SAR=30;SRP=128.435;SAP=41.7866;AB=0.156522;ABP=120.855;RUN=1;RPP=6.05036;RPPR=128.435;RPL=21.0;RPR=14.0;EPP=3.56868;EPPR=3.79203;DPRA=0.0;ODDS=42.1685;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=40.9429;MQMR=46.9875;PAIRED=0.942857;PAIREDR=0.9625;technology.ILLUMINA=1.0;BaseQRankSum=1.238;FS=2.62;MLEAC=1;MLEAF=0.5;MQ=49 [...]
+chr17 16097825 . T G 263.77 PASS SOMATIC;DP=324;AC=1;AN=4;AF=0.5;MQ0=5;BaseQRankSum=-0.308;Dels=0.0;FS=56.793;HaplotypeScore=11.6376;MLEAC=1;MLEAF=0.5;MQ=57.98;MQRankSum=-6.358;QD=0.81;ReadPosRankSum=-5.074;SOR=4.697 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:0.000295696 0/1:288,36:324:99.0:292,0,11082:36:11:324:.:1:.:.:.:.:-0.107524
+chr17 16097870 . C A 855.482 REJECT NS=2;DP=402;DPB=448.0;AC=2;AN=4;AF=0.5;RO=363;AO=85;PRO=0.0;PAO=0.0;QR=13791;QA=3279;PQR=0.0;PQA=0.0;SRF=127;SRR=236;SAF=68;SAR=17;SRP=74.0827;SAP=69.4574;AB=0.189732;ABP=377.609;RUN=1;RPP=3.64897;RPPR=46.2304;RPL=40.0;RPR=45.0;EPP=7.3277;EPPR=19.8138;DPRA=0.0;ODDS=35.7661;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=36.2588;MQMR=57.4077;PAIRED=0.988235;PAIREDR=0.997245;technology.ILLUMINA=1.0;MQ0=7;BaseQRankSum=0.3265;Dels=0.0;FS=58.754;Hapl [...]
+chr17 17017170 . G T 1578.43 REJECT NS=1;DP=135;DPB=135.0;AC=1;AN=4;AF=0.5;RO=70;AO=65;PRO=0.0;PAO=0.0;QR=2453;QA=2414;PQR=0.0;PQA=0.0;SRF=17;SRR=53;SAF=18;SAR=47;SRP=43.2136;SAP=31.1058;AB=0.481481;ABP=3.41242;RUN=1;RPP=96.8513;RPPR=38.8706;RPL=59.0;RPR=6.0;EPP=39.3908;EPPR=43.2136;DPRA=0.0;ODDS=363.447;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.6154;MQMR=59.4286;PAIRED=0.984615;PAIREDR=0.985714;technology.ILLUMINA=1.0;BaseQRankSum=0.065;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;M [...]
+chr17 17017198 . TC T 615.873 REJECT NS=1;DP=66;DPB=70.3333;AC=1;AN=3;AF=0.0;RO=33;AO=4;PRO=5.33333;PAO=2.33333;QR=1117;QA=160;PQR=173.0;PQA=70.0;SRF=14;SRR=19;SAF=4;SAR=0;SRP=4.65535;SAP=11.6962;AB=0.0606061;ABP=113.69;RUN=1;RPP=3.0103;RPPR=58.3499;RPL=2.0;RPR=2.0;EPP=3.0103;EPPR=4.65535;DPRA=0.0;ODDS=116.733;GTI=0;TYPE=del;CIGAR=1M1D1M;NUMALT=2;MEANALT=3.0;LEN=1;MQM=60.0;MQMR=57.1515;PAIRED=1.0;PAIREDR=0.969697;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr17 17017199 . C T 615.873 REJECT NS=1;DP=66;DPB=70.3333;AC=1;AN=4;AF=0.5;RO=33;AO=28;PRO=5.33333;PAO=2.33333;QR=1117;QA=840;PQR=173.0;PQA=70.0;SRF=14;SRR=19;SAF=6;SAR=22;SRP=4.65535;SAP=22.8638;AB=0.424242;ABP=6.30041;RUN=1;RPP=10.7656;RPPR=58.3499;RPL=19.0;RPR=9.0;EPP=3.32051;EPPR=4.65535;DPRA=0.0;ODDS=116.733;GTI=0;TYPE=snp;CIGAR=1M1X1M;NUMALT=2;MEANALT=3.0;LEN=1;MQM=53.9286;MQMR=57.1515;PAIRED=1.0;PAIREDR=0.969697;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr17 17017873 . C G 814.641 REJECT NS=2;DP=246;DPB=281.0;AC=2;AN=4;AF=0.5;RO=233;AO=48;PRO=0.0;PAO=0.0;QR=8844;QA=1838;PQR=0.0;PQA=0.0;SRF=140;SRR=93;SAF=30;SAR=18;SRP=23.5973;SAP=9.52472;AB=0.170819;ABP=267.489;RUN=1;RPP=21.1059;RPPR=134.985;RPL=14.0;RPR=34.0;EPP=5.9056;EPPR=8.83507;DPRA=0.0;ODDS=17.1517;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.982833;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.0965;Dels=0.0;FS=4.96;HaplotypeScore=3.86 [...]
+chr17 17017961 . G A 2903.95 PASS SOMATIC;NS=2;DP=423;DPB=423.0;AC=1;AN=3;AF=0.25;RO=309;AO=114;PRO=0.0;PAO=0.0;QR=11689;QA=4273;PQR=0.0;PQA=0.0;SRF=137;SRR=172;SAF=54;SAR=60;SRP=11.6189;SAP=3.69603;AB=0.352941;ABP=63.6838;RUN=1;RPP=13.982;RPPR=5.04122;RPL=69.0;RPR=45.0;EPP=4.22937;EPPR=5.5472;DPRA=3.23;ODDS=63.3891;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993528;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.238;Dels=0.0;FS=0.433;Ha [...]
+chr17 17018177 . G A 2239.25 REJECT NS=2;DP=412;DPB=472.0;AC=2;AN=4;AF=0.5;RO=364;AO=108;PRO=0.0;PAO=0.0;QR=14056;QA=4243;PQR=0.0;PQA=0.0;SRF=131;SRR=233;SAF=39;SAR=69;SRP=65.0762;SAP=21.1059;AB=0.228814;ABP=304.514;RUN=1;RPP=4.2971;RPPR=8.37933;RPL=50.0;RPR=58.0;EPP=3.09072;EPPR=21.7184;DPRA=0.0;ODDS=168.756;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997253;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.354;Dels=0.0;FS=1.4065;HaplotypeScore= [...]
+chr17 17122327 . G A 1536.275 REJECT NS=2;DP=217;DPB=255.0;AC=2;AN=4;AF=0.5;RO=184;AO=71;PRO=0.0;PAO=0.0;QR=7134;QA=2735;PQR=0.0;PQA=0.0;SRF=157;SRR=27;SAF=67;SAR=4;SRP=202.455;SAP=124.399;AB=0.278431;ABP=111.746;RUN=1;RPP=4.50892;RPPR=12.2627;RPL=32.0;RPR=39.0;EPP=3.04088;EPPR=3.43515;DPRA=0.0;ODDS=103.882;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0365;Dels=0.0;FS=3.038;HaplotypeScore=4.9317; [...]
+chr17 17127471 . G A 1396.365 REJECT NS=2;DP=301;DPB=345.0;AC=2;AN=4;AF=0.5;RO=270;AO=75;PRO=0.0;PAO=0.0;QR=10374;QA=2831;PQR=0.0;PQA=0.0;SRF=86;SRR=184;SAF=19;SAR=56;SRP=80.2504;SAP=42.6469;AB=0.217391;ABP=242.344;RUN=1;RPP=18.3264;RPPR=44.7026;RPL=49.0;RPR=26.0;EPP=3.03925;EPPR=4.16842;DPRA=0.0;ODDS=115.839;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.973333;PAIREDR=0.996296;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.311;Dels=0.0;FS=4.25;HaplotypeSc [...]
+chr17 17238410 . G T 67.0144 REJECT NS=2;DP=275;DPB=313.125;AC=2;AN=2;AF=0.0;RO=204;AO=15;PRO=29.4167;PAO=7.08333;QR=7524;QA=230;PQR=1051.5;PQA=251.167;SRF=42;SRR=162;SAF=0;SAR=15;SRP=156.291;SAP=35.5824;AB=0.0322581;ABP=120.83;RUN=1;RPP=14.7363;RPPR=55.1682;RPL=3.0;RPR=12.0;EPP=14.7363;EPPR=3.05288;DPRA=0.0;ODDS=6.24554;GTI=0;TYPE=snp;CIGAR=1X15M;NUMALT=3;MEANALT=9.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995098;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr17 17238410 . G GT 67.0144 REJECT NS=2;DP=275;DPB=313.125;AC=2;AN=3;AF=0.25;RO=204;AO=25;PRO=29.4167;PAO=28.4167;QR=7524;QA=752;PQR=1051.5;PQA=1013.5;SRF=42;SRR=162;SAF=11;SAR=14;SRP=156.291;SAP=3.79203;AB=0.145161;ABP=70.8163;RUN=1;RPP=17.6895;RPPR=55.1682;RPL=19.0;RPR=6.0;EPP=10.0459;EPPR=3.05288;DPRA=0.0;ODDS=6.24554;GTI=0;TYPE=ins;CIGAR=1M1I15M;NUMALT=3;MEANALT=9.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995098;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.158;FS [...]
+chr17 17238410 . GT G 67.0144 REJECT NS=2;DP=275;DPB=313.125;AC=2;AN=2;AF=0.0;RO=204;AO=18;PRO=29.4167;PAO=25.0833;QR=7524;QA=591;PQR=1051.5;PQA=890.833;SRF=42;SRR=162;SAF=6;SAR=12;SRP=156.291;SAP=7.35324;AB=0.112903;ABP=83.705;RUN=1;RPP=15.074;RPPR=55.1682;RPL=14.0;RPR=4.0;EPP=3.49285;EPPR=3.05288;DPRA=0.0;ODDS=6.24554;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=3;MEANALT=9.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995098;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr17 29508775 . G A 2412.72 PASS SOMATIC;NS=2;DP=395;DPB=395.0;AC=1;AN=3;AF=0.25;RO=287;AO=101;PRO=0.0;PAO=0.0;QR=10166;QA=3621;PQR=0.0;PQA=0.0;SRF=126;SRR=161;SAF=42;SAR=59;SRP=12.2788;SAP=9.22372;AB=0.348276;ABP=60.9961;RUN=1;RPP=18.6836;RPPR=31.1638;RPL=64.0;RPR=37.0;EPP=4.06379;EPPR=3.07839;DPRA=2.7619;ODDS=64.9677;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.099;MQMR=59.9303;PAIRED=0.990099;PAIREDR=0.996516;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.213;Dels=0 [...]
+chr17 29508819 . A AT 671.459 REJECT NS=2;DP=151;DPB=202.552;AC=2;AN=2;AF=0.0;RO=60;AO=27;PRO=42.1667;PAO=29.1667;QR=2222;QA=611;PQR=1525.0;PQA=1004.0;SRF=6;SRR=54;SAF=1;SAR=26;SRP=86.3948;SAP=53.2759;AB=0.178808;ABP=138.317;RUN=1;RPP=3.73412;RPPR=3.58936;RPL=15.0;RPR=12.0;EPP=3.09072;EPPR=8.22183;DPRA=0.0;ODDS=33.6645;GTI=0;TYPE=ins;CIGAR=1M1I28M;NUMALT=3;MEANALT=14.0;LEN=1;MQM=59.7407;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr17 29508819 . AT A 671.459 REJECT NS=2;DP=151;DPB=202.552;AC=2;AN=4;AF=0.5;RO=60;AO=32;PRO=42.1667;PAO=24.6667;QR=2222;QA=1058;PQR=1525.0;PQA=802.5;SRF=6;SRR=54;SAF=5;SAR=27;SRP=86.3948;SAP=35.8538;AB=0.211921;ABP=111.857;RUN=1;RPP=7.35324;RPPR=3.58936;RPL=20.0;RPR=12.0;EPP=3.28173;EPPR=8.22183;DPRA=0.0;ODDS=33.6645;GTI=0;TYPE=del;CIGAR=1M1D27M;NUMALT=3;MEANALT=14.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.936;FS=1.56;MLE [...]
+chr17 29508819 . ATT A 671.459 REJECT NS=2;DP=151;DPB=202.552;AC=2;AN=2;AF=0.0;RO=60;AO=7;PRO=42.1667;PAO=17.0;QR=2222;QA=166;PQR=1525.0;PQA=606.5;SRF=6;SRR=54;SAF=0;SAR=7;SRP=86.3948;SAP=18.2106;AB=0.0463576;ABP=272.92;RUN=1;RPP=5.80219;RPPR=3.58936;RPL=2.0;RPR=5.0;EPP=5.80219;EPPR=8.22183;DPRA=0.0;ODDS=33.6645;GTI=0;TYPE=del;CIGAR=1M2D26M;NUMALT=3;MEANALT=14.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr17 29545987 . A AT . PASS SOMATIC;AC=1;AN=4 GT:AD:DP:MM:MQS:NQSBQ:NQSMM:REnd:RStart:SC:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:60,0:60:0.7,0.0:60.0,0.0:37.445,0.0:0.00676819,0.0:0,0:0,0:39,21,0,0:0:0:60:.:.:.:.:0:.:-0.00997748 0/1:97,55:152:0.185567,0.0909091:60.0,60.0:38.0663,39.044:0.00320856,0.0:78,11:21,11:64,33,42,13:55:36:152:.:.:.:.:1:.:-0.0533013
+chr17 29546175 . T C 1214.57 PASS SOMATIC;NS=2;DP=188;DPB=188.0;AC=1;AN=3;AF=0.25;RO=139;AO=49;PRO=0.0;PAO=0.0;QR=5320;QA=1897;PQR=0.0;PQA=0.0;SRF=33;SRR=106;SAF=8;SAR=41;SRP=86.2605;SAP=51.2702;AB=0.35;ABP=30.3709;RUN=1;RPP=15.8176;RPPR=86.2605;RPL=33.0;RPR=16.0;EPP=4.11819;EPPR=14.3988;DPRA=2.91667;ODDS=30.9864;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.4898;MQMR=60.0;PAIRED=0.979592;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.507;Dels=0.0;FS=6.788;Ha [...]
+chr17 29553485 . G A 8573.28 REJECT NS=2;DP=386;DPB=440.0;AC=3;AN=4;AF=0.75;RO=127;AO=313;PRO=0.0;PAO=0.0;QR=4807;QA=11705;PQR=0.0;PQA=0.0;SRF=79;SRR=48;SAF=197;SAR=116;SRP=19.4417;SAP=48.528;AB=0.61747;ABP=42.8032;RUN=1;RPP=10.5654;RPPR=3.0274;RPL=140.0;RPR=173.0;EPP=13.5624;EPPR=7.95168;DPRA=0.0;ODDS=68.2316;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9393;MQMR=60.0;PAIRED=0.99361;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.361;Dels=0.0;FS=0.976;HaplotypeSco [...]
+chr17 29559932 . C A 6551.675 REJECT NS=2;DP=266;DPB=302.0;AC=3;AN=4;AF=0.75;RO=75;AO=227;PRO=0.0;PAO=0.0;QR=2837;QA=8708;PQR=0.0;PQA=0.0;SRF=39;SRR=36;SAF=105;SAR=122;SRP=3.27088;SAP=5.77486;AB=0.675325;ABP=64.6858;RUN=1;RPP=29.8811;RPPR=38.4777;RPL=140.0;RPR=87.0;EPP=12.2032;EPPR=15.7786;DPRA=0.0;ODDS=45.3298;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986667;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.05;Dels=0.0;FS=1.221;HaplotypeScore [...]
+chr17 29653293 . T C 1230.29 PASS SOMATIC;NS=2;DP=227;DPB=227.0;AC=1;AN=3;AF=0.25;RO=174;AO=53;PRO=0.0;PAO=0.0;QR=6705;QA=2029;PQR=0.0;PQA=0.0;SRF=58;SRR=116;SAF=18;SAR=35;SRP=44.9921;SAP=14.851;AB=0.297753;ABP=66.2514;RUN=1;RPP=53.2;RPPR=104.096;RPL=44.0;RPR=9.0;EPP=3.05127;EPPR=7.05373;DPRA=3.63265;ODDS=31.5647;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994253;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.032;Dels=0.0;FS=1.369;Hapl [...]
+chr17 29800531 . C T 4800.525 REJECT NS=2;DP=216;DPB=244.0;AC=3;AN=4;AF=0.75;RO=67;AO=176;PRO=0.0;PAO=0.0;QR=2635;QA=6523;PQR=0.0;PQA=0.0;SRF=55;SRR=12;SAF=135;SAR=41;SRP=62.9365;SAP=112.028;AB=0.645503;ABP=37.7653;RUN=1;RPP=33.8551;RPPR=3.30199;RPL=63.0;RPR=113.0;EPP=15.6443;EPPR=17.3031;DPRA=0.0;ODDS=34.6957;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988636;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-3.856;Dels=0.0;FS=1.695;HaplotypeScore [...]
+chr17 29800551 . T C 5741.225 REJECT NS=2;DP=248;DPB=288.0;AC=3;AN=4;AF=0.75;RO=74;AO=214;PRO=0.0;PAO=0.0;QR=2849;QA=8107;PQR=0.0;PQA=0.0;SRF=55;SRR=19;SAF=146;SAR=68;SRP=41.0404;SAP=64.7451;AB=0.645933;ABP=41.6708;RUN=1;RPP=100.463;RPPR=10.5224;RPL=58.0;RPR=156.0;EPP=3.37559;EPPR=8.76177;DPRA=0.0;ODDS=50.2718;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990654;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.511;Dels=0.0;FS=2.3285;HaplotypeScore [...]
+chr17 29800656 . C T 8596.075 REJECT NS=2;DP=408;DPB=461.0;AC=3;AN=4;AF=0.75;RO=144;AO=317;PRO=0.0;PAO=0.0;QR=5536;QA=11757;PQR=0.0;PQA=0.0;SRF=72;SRR=72;SAF=185;SAR=132;SRP=3.0103;SAP=22.2521;AB=0.594366;ABP=30.4687;RUN=1;RPP=8.004;RPPR=9.04217;RPL=145.0;RPR=172.0;EPP=3.01715;EPPR=3.25157;DPRA=0.0;ODDS=67.0298;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990536;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.542;Dels=0.0;FS=4.8965;HaplotypeSco [...]
+chr17 29800755 . T C 9245.585 REJECT NS=2;DP=405;DPB=463.0;AC=3;AN=4;AF=0.75;RO=130;AO=333;PRO=0.0;PAO=0.0;QR=4901;QA=12503;PQR=0.0;PQA=0.0;SRF=46;SRR=84;SAF=125;SAR=208;SRP=27.1303;SAP=47.933;AB=0.627507;ABP=52.2946;RUN=1;RPP=5.36436;RPPR=3.07711;RPL=176.0;RPR=157.0;EPP=15.0675;EPPR=11.0949;DPRA=0.0;ODDS=71.92;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990991;PAIREDR=0.992308;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.822;Dels=0.0;FS=0.0;HaplotypeSc [...]
+chr17 29803805 . T C 7988.71 REJECT NS=2;DP=347;DPB=397.0;AC=3;AN=4;AF=0.75;RO=109;AO=288;PRO=0.0;PAO=0.0;QR=4154;QA=10935;PQR=0.0;PQA=0.0;SRF=56;SRR=53;SAF=160;SAR=128;SRP=3.1896;SAP=10.7311;AB=0.632997;ABP=48.6405;RUN=1;RPP=20.3821;RPPR=3.98647;RPL=120.0;RPR=168.0;EPP=33.8935;EPPR=7.4927;DPRA=0.0;ODDS=63.3175;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989583;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.369;Dels=0.0;FS=3.2545;HaplotypeScor [...]
+chr17 30293149 . C CT 860.88 REJECT NS=2;DP=232;DPB=327.762;AC=2;AN=4;AF=0.5;RO=93;AO=45;PRO=57.75;PAO=54.75;QR=3289;QA=1691;PQR=2036.25;PQA=1931.25;SRF=68;SRR=25;SAF=41;SAR=4;SRP=46.1829;SAP=69.0713;AB=0.188285;ABP=204.721;RUN=1;RPP=3.05855;RPPR=5.83555;RPL=23.0;RPR=22.0;EPP=4.21667;EPPR=11.4393;DPRA=0.0;ODDS=47.4907;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=3;MEANALT=18.5;LEN=1;MQM=59.9111;MQMR=59.871;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=2.366;F [...]
+chr17 30293149 . CT C 1070.03 REJECT NS=2;DP=239;DPB=327.762;AC=2;AN=2;AF=0.0;RO=93;AO=36;PRO=57.75;PAO=38.25;QR=3289;QA=1157;PQR=2036.25;PQA=1310.75;SRF=68;SRR=25;SAF=23;SAR=13;SRP=46.1829;SAP=9.04217;AB=0.150628;ABP=256.4;RUN=1;RPP=5.18177;RPPR=5.83555;RPL=15.0;RPR=21.0;EPP=3.9754;EPPR=11.4393;DPRA=0.0;ODDS=47.4907;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=3;MEANALT=18.5;LEN=1;MQM=57.7778;MQMR=59.871;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr17 30293149 . CTT C 1070.03 REJECT NS=2;DP=239;DPB=327.762;AC=2;AN=2;AF=0.0;RO=93;AO=9;PRO=57.75;PAO=35.25;QR=3289;QA=301;PQR=2036.25;PQA=1197.75;SRF=68;SRR=25;SAF=7;SAR=2;SRP=46.1829;SAP=9.04217;AB=0.0535714;ABP=293.832;RUN=1;RPP=9.04217;RPPR=5.83555;RPL=2.0;RPR=7.0;EPP=3.25157;EPPR=11.4393;DPRA=0.0;ODDS=47.4907;GTI=0;TYPE=del;CIGAR=1M2D18M;NUMALT=3;MEANALT=26.0;LEN=2;MQM=54.0;MQMR=59.871;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr17 30302736 . A AT 187.626 REJECT NS=2;DP=190;DPB=226.647;AC=2;AN=2;AF=0.0;RO=152;AO=13;PRO=31.1667;PAO=19.1667;QR=5733;QA=498;PQR=1111.83;PQA=681.833;SRF=41;SRR=111;SAF=2;SAR=11;SRP=73.0117;SAP=16.5402;AB=0.0684211;ABP=310.399;RUN=1;RPP=3.17734;RPPR=61.5258;RPL=7.0;RPR=6.0;EPP=4.51363;EPPR=4.4389;DPRA=0.0;ODDS=10.1493;GTI=0;TYPE=ins;CIGAR=1M1I16M;NUMALT=2;MEANALT=4.5;LEN=1;MQM=60.0;MQMR=58.8355;PAIRED=1.0;PAIREDR=0.993421;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr17 30302736 . AT A 187.626 REJECT NS=2;DP=190;DPB=226.647;AC=2;AN=4;AF=0.5;RO=152;AO=20;PRO=31.1667;PAO=19.6667;QR=5733;QA=726;PQR=1111.83;PQA=713.333;SRF=41;SRR=111;SAF=3;SAR=17;SRP=73.0117;SAP=24.2907;AB=0.105263;ABP=260.158;RUN=1;RPP=6.91895;RPPR=61.5258;RPL=13.0;RPR=7.0;EPP=3.0103;EPPR=4.4389;DPRA=0.0;ODDS=10.1493;GTI=0;TYPE=del;CIGAR=1M1D15M;NUMALT=2;MEANALT=4.5;LEN=1;MQM=57.4;MQMR=58.8355;PAIRED=1.0;PAIREDR=0.993421;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr17 30321567 . T G 2925.88 REJECT NS=2;DP=211;DPB=231.0;AC=2;AN=4;AF=0.5;RO=113;AO=116;PRO=0.0;PAO=0.0;QR=4216;QA=4156;PQR=0.0;PQA=0.0;SRF=93;SRR=20;SAF=91;SAR=25;SRP=105.415;SAP=84.5528;AB=0.502165;ABP=3.0197;RUN=1;RPP=49.8093;RPPR=21.4774;RPL=33.0;RPR=83.0;EPP=7.80251;EPPR=9.94748;DPRA=0.0;ODDS=114.672;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=59.9381;PAIRED=0.982759;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.435;Dels=0.0;FS=5.606;HaplotypeScore= [...]
+chr17 30321762 . G C 3378.4 REJECT NS=2;DP=230;DPB=255.0;AC=2;AN=4;AF=0.5;RO=132;AO=122;PRO=0.0;PAO=0.0;QR=4969;QA=4651;PQR=0.0;PQA=0.0;SRF=35;SRR=97;SAF=40;SAR=82;SRP=66.2462;SAP=34.4077;AB=0.478431;ABP=4.04068;RUN=1;RPP=31.4886;RPPR=44.1367;RPL=81.0;RPR=41.0;EPP=4.14943;EPPR=5.37918;DPRA=0.0;ODDS=145.272;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991803;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1605;Dels=0.0;FS=2.4265;HaplotypeScore=1. [...]
+chr17 33433487 . C T 2863.24 REJECT NS=1;DP=87;DPB=87.0;AC=2;AN=4;AF=1.0;RO=0;AO=87;PRO=0.0;PAO=0.0;QR=0;QA=3344;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=12;SAR=75;SRP=0.0;SAP=102.074;AB=0.0;ABP=0.0;RUN=1;RPP=7.22845;RPPR=0.0;RPL=50.0;RPR=37.0;EPP=5.03202;EPPR=0.0;DPRA=0.0;ODDS=58.8694;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.977011;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.89;SOR=3.528 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr17 33445549 . G A 5453.355 REJECT NS=2;DP=349;DPB=404.0;AC=2;AN=4;AF=0.5;RO=205;AO=199;PRO=0.0;PAO=0.0;QR=7828;QA=7655;PQR=0.0;PQA=0.0;SRF=111;SRR=94;SAF=114;SAR=85;SRP=6.07155;SAP=12.1872;AB=0.492574;ABP=3.2038;RUN=1;RPP=3.54498;RPPR=4.80044;RPL=96.0;RPR=103.0;EPP=16.3774;EPPR=8.61376;DPRA=0.0;ODDS=330.425;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995122;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8705;Dels=0.0;FS=4.8805;HaplotypeScor [...]
+chr17 37745821 . A AAAAT 6488.67 REJECT NS=2;DP=175;DPB=334.25;AC=4;AN=4;AF=1.0;RO=3;AO=184;PRO=47.0;PAO=72.0;QR=116;QA=6647;PQR=1591.0;PQA=2476.0;SRF=2;SRR=1;SAF=144;SAR=40;SRP=3.73412;SAP=130.655;AB=0.0;ABP=0.0;RUN=1;RPP=20.0516;RPPR=3.73412;RPL=73.0;RPR=111.0;EPP=16.6528;EPPR=9.52472;DPRA=0.0;ODDS=41.112;GTI=0;TYPE=ins;CIGAR=1M4I11M;NUMALT=1;MEANALT=3.0;LEN=4;MQM=59.837;MQMR=60.0;PAIRED=0.98913;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=37745821;HOMLEN=10;HOMSEQ=AAATAAATAA;SVLEN=4; [...]
+chr17 37745828 . A ATAAG . PASS SOMATIC;AC=1;AN=4;END=37745828;HOMLEN=7;HOMSEQ=TAAGTAA;SVLEN=4;SVTYPE=INS GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:-0.00997748 0/1:42,27:27:39:69:.:.:.:1:.:.:-0.0533013
+chr17 37745979 . A G 13150.2 REJECT NS=2;DP=351;DPB=408.0;AC=4;AN=4;AF=1.0;RO=1;AO=407;PRO=0.0;PAO=0.0;QR=16;QA=15554;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=153;SAR=254;SRP=5.18177;SAP=57.4358;AB=0.0;ABP=0.0;RUN=1;RPP=3.27173;RPPR=5.18177;RPL=207.0;RPR=200.0;EPP=8.13754;EPPR=5.18177;DPRA=0.0;ODDS=73.6;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990172;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.701;Dels=0.0;FS=2.2165;HaplotypeScore=2.8909;MLEAC=2; [...]
+chr17 37749811 . T C 6045.945 REJECT NS=2;DP=389;DPB=445.0;AC=2;AN=4;AF=0.5;RO=224;AO=221;PRO=0.0;PAO=0.0;QR=8563;QA=8413;PQR=0.0;PQA=0.0;SRF=112;SRR=112;SAF=112;SAR=109;SRP=3.0103;SAP=3.09873;AB=0.496629;ABP=3.05422;RUN=1;RPP=3.25594;RPPR=3.16541;RPL=113.0;RPR=108.0;EPP=8.20808;EPPR=21.778;DPRA=0.0;ODDS=341.958;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.434;Dels=0.0;FS=3.1155;HaplotypeScore=2. [...]
+chr17 37855834 . C A 1966.24 REJECT NS=2;DP=378;DPB=427.0;AC=2;AN=4;AF=0.5;RO=330;AO=97;PRO=0.0;PAO=0.0;QR=12545;QA=3736;PQR=0.0;PQA=0.0;SRF=154;SRR=176;SAF=45;SAR=52;SRP=6.19513;SAP=4.10723;AB=0.227166;ABP=279.092;RUN=1;RPP=8.04722;RPPR=5.14229;RPL=56.0;RPR=41.0;EPP=5.71904;EPPR=61.1531;DPRA=0.0;ODDS=151.622;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8727;PAIRED=0.989691;PAIREDR=0.99697;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.326;Dels=0.0;FS=1.4655;Haplotyp [...]
+chr17 37868715 . C T 4252.88 REJECT NS=2;DP=236;DPB=269.0;AC=2;AN=4;AF=0.5;RO=121;AO=148;PRO=0.0;PAO=0.0;QR=4549;QA=5696;PQR=0.0;PQA=0.0;SRF=43;SRR=78;SAF=55;SAR=93;SRP=24.9942;SAP=24.1968;AB=0.550186;ABP=8.89507;RUN=1;RPP=24.1968;RPPR=27.5784;RPL=93.0;RPR=55.0;EPP=3.0103;EPPR=6.04318;DPRA=0.0;ODDS=172.376;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986486;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1705;Dels=0.0;FS=1.0775;HaplotypeScore=2. [...]
+chr17 37884037 . C G 6368.82 REJECT NS=2;DP=373;DPB=429.0;AC=2;AN=4;AF=0.5;RO=199;AO=228;PRO=0.0;PAO=0.0;QR=7548;QA=8620;PQR=0.0;PQA=0.0;SRF=106;SRR=93;SAF=110;SAR=118;SRP=4.85441;SAP=3.61984;AB=0.531469;ABP=6.70028;RUN=1;RPP=3.0484;RPPR=3.54498;RPL=115.0;RPR=113.0;EPP=11.5819;EPPR=21.3532;DPRA=0.0;ODDS=356.366;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995614;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.622;Dels=0.0;FS=1.874;HaplotypeScore [...]
+chr17 37922259 . G A 5160.405000000001 REJECT NS=2;DP=368;DPB=414.0;AC=2;AN=4;AF=0.5;RO=225;AO=189;PRO=0.0;PAO=0.0;QR=8740;QA=7205;PQR=0.0;PQA=0.0;SRF=103;SRR=122;SAF=93;SAR=96;SRP=6.49431;SAP=3.1137;AB=0.456522;ABP=9.80795;RUN=1;RPP=3.57327;RPPR=3.09716;RPL=91.0;RPR=98.0;EPP=12.6728;EPPR=9.04217;DPRA=0.0;ODDS=289.376;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991111;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.0305;Dels=0.0;FS=0.933;Haplo [...]
+chr17 37976469 . C T 5991.735000000001 REJECT NS=2;DP=387;DPB=444.0;AC=2;AN=4;AF=0.5;RO=227;AO=217;PRO=0.0;PAO=0.0;QR=8711;QA=8194;PQR=0.0;PQA=0.0;SRF=111;SRR=116;SAF=110;SAR=107;SRP=3.24945;SAP=3.10036;AB=0.488739;ABP=3.49937;RUN=1;RPP=9.26454;RPPR=4.62695;RPL=121.0;RPR=96.0;EPP=21.5128;EPPR=9.98388;DPRA=0.0;ODDS=329.524;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995392;PAIREDR=0.986784;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.165;Dels=0.0;FS=5.1 [...]
+chr17 38020419 . T C 3910.98 REJECT NS=2;DP=263;DPB=300.0;AC=2;AN=4;AF=0.5;RO=154;AO=146;PRO=0.0;PAO=0.0;QR=5779;QA=5475;PQR=0.0;PQA=0.0;SRF=40;SRR=114;SAF=29;SAR=117;SRP=80.2245;SAP=118.188;AB=0.486667;ABP=3.47355;RUN=1;RPP=5.92543;RPPR=7.57885;RPL=80.0;RPR=66.0;EPP=22.2858;EPPR=27.8835;DPRA=0.0;ODDS=214.208;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993151;PAIREDR=0.993506;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7475;Dels=0.0;FS=3.8765;Haplotype [...]
+chr17 38548371 . T TA 462.103 REJECT NS=2;DP=344;DPB=388.438;AC=2;AN=2;AF=0.0;RO=270;AO=20;PRO=39.1667;PAO=32.1667;QR=10114;QA=652;PQR=1358.83;PQA=1096.83;SRF=145;SRR=125;SAF=16;SAR=4;SRP=6.2273;SAP=18.6449;AB=0.0581395;ABP=586.379;RUN=1;RPP=6.91895;RPPR=3.04247;RPL=7.0;RPR=13.0;EPP=3.44459;EPPR=3.52502;DPRA=0.0;ODDS=28.2737;GTI=0;TYPE=ins;CIGAR=1M1I15M;NUMALT=2;MEANALT=6.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr17 38548371 . TA T 462.103 REJECT NS=2;DP=344;DPB=388.438;AC=2;AN=4;AF=0.5;RO=270;AO=44;PRO=39.1667;PAO=28.6667;QR=10114;QA=1554;PQR=1358.83;PQA=962.333;SRF=145;SRR=125;SAF=22;SAR=22;SRP=6.2273;SAP=3.0103;AB=0.127907;ABP=416.701;RUN=1;RPP=4.78696;RPPR=3.04247;RPL=25.0;RPR=19.0;EPP=7.94546;EPPR=3.52502;DPRA=0.0;ODDS=28.2737;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=2;MEANALT=6.5;LEN=1;MQM=60.9091;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr17 38556770 . T C 11178.45 REJECT NS=2;DP=297;DPB=346.0;AC=4;AN=4;AF=1.0;RO=0;AO=346;PRO=0.0;PAO=0.0;QR=0;QA=13225;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=215;SAR=131;SRP=0.0;SAP=47.2933;AB=0.0;ABP=0.0;RUN=1;RPP=14.081;RPPR=0.0;RPL=152.0;RPR=194.0;EPP=3.41196;EPPR=0.0;DPRA=0.0;ODDS=63.6118;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.985549;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8323;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.43;SOR=1. [...]
+chr17 38670513 . A G 2957.94 PASS SOMATIC;NS=2;DP=384;DPB=384.0;AC=1;AN=3;AF=0.25;RO=273;AO=110;PRO=0.0;PAO=0.0;QR=10604;QA=4246;PQR=0.0;PQA=0.0;SRF=143;SRR=130;SAF=58;SAR=52;SRP=4.35454;SAP=3.72096;AB=0.369128;ABP=47.3433;RUN=1;RPP=3.08926;RPPR=7.98162;RPL=54.0;RPR=56.0;EPP=3.72096;EPPR=4.35454;DPRA=3.46512;ODDS=54.0193;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996337;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.797;Dels=0.0;FS=0.0 [...]
+chr17 40475650 . G GA 2704.08 PASS SOMATIC;NS=2;DP=289;DPB=334.857;AC=1;AN=4;AF=0.25;RO=195;AO=91;PRO=46.5;PAO=32.5;QR=7422;QA=3432;PQR=1656.0;PQA=1153.0;SRF=74;SRR=121;SAF=34;SAR=57;SRP=27.6092;SAP=15.6335;AB=0.423256;ABP=14.0091;RUN=1;RPP=20.4059;RPPR=19.9478;RPL=59.0;RPR=32.0;EPP=3.03416;EPPR=34.2906;DPRA=2.90541;ODDS=52.1743;GTI=0;TYPE=ins;CIGAR=1M1I13M;NUMALT=1;MEANALT=3.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=40475650;HOMLEN=3;HOMSEQ=AAA; [...]
+chr17 40854534 . G GT 2396.18 PASS SOMATIC;NS=2;DP=343;DPB=381.333;AC=1;AN=4;AF=0.25;RO=244;AO=96;PRO=4.0;PAO=6.0;QR=9180;QA=3479;PQR=88.0;PQA=162.0;SRF=148;SRR=96;SAF=63;SAR=33;SRP=27.0745;SAP=23.3679;AB=0.360902;ABP=47.7132;RUN=1;RPP=10.339;RPPR=6.57009;RPL=39.0;RPR=57.0;EPP=3.37221;EPPR=17.2495;DPRA=3.45455;ODDS=48.3925;GTI=0;TYPE=ins;CIGAR=1M1I2M;NUMALT=1;MEANALT=3.0;LEN=1;MQM=60.4167;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=40854534;HOMLEN=1;HOMSEQ=T;SVLEN= [...]
+chr17 41096398 . C T 13293.8 REJECT NS=2;DP=348;DPB=402.0;AC=4;AN=4;AF=1.0;RO=0;AO=402;PRO=0.0;PAO=0.0;QR=0;QA=15433;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=227;SAR=175;SRP=0.0;SAP=17.6164;AB=0.0;ABP=0.0;RUN=1;RPP=13.4679;RPPR=0.0;RPL=179.0;RPR=223.0;EPP=10.8103;EPPR=0.0;DPRA=0.0;ODDS=69.1705;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99005;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8656;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.85;SOR=0.9 [...]
+chr17 41098108 . G A 13221.4 REJECT NS=2;DP=347;DPB=401.0;AC=4;AN=4;AF=1.0;RO=0;AO=400;PRO=0.0;PAO=0.0;QR=0;QA=15480;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=163;SAR=237;SRP=0.0;SAP=32.7378;AB=0.0;ABP=0.0;RUN=1;RPP=9.28586;RPPR=0.0;RPL=217.0;RPR=183.0;EPP=71.1077;EPPR=0.0;DPRA=0.0;ODDS=71.6997;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.9925;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8325;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.755;SOR=1.1 [...]
+chr17 41098676 . C CT 12275.3 REJECT NS=2;DP=336;DPB=471.4;AC=4;AN=4;AF=1.0;RO=2;AO=372;PRO=10.0;PAO=18.0;QR=78;QA=13633;PQR=273.5;PQA=537.5;SRF=1;SRR=1;SAF=212;SAR=160;SRP=3.0103;SAP=18.7943;AB=0.0;ABP=0.0;RUN=1;RPP=56.8068;RPPR=3.0103;RPL=138.0;RPR=234.0;EPP=56.8068;EPPR=7.35324;DPRA=0.0;ODDS=56.6651;GTI=0;TYPE=ins;CIGAR=1M1I4M;NUMALT=1;MEANALT=2.5;LEN=1;MQM=60.1237;MQMR=60.0;PAIRED=0.991935;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=41098676;HOMLEN=0;SVLEN=1;SVTYPE=INS;BaseQRankSum [...]
+chr17 41103938 . T C 13277.2 REJECT NS=2;DP=353;DPB=400.0;AC=4;AN=4;AF=1.0;RO=0;AO=400;PRO=0.0;PAO=0.0;QR=0;QA=15211;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=190;SAR=210;SRP=0.0;SAP=5.18177;AB=0.0;ABP=0.0;RUN=1;RPP=4.07432;RPPR=0.0;RPL=193.0;RPR=207.0;EPP=3.20573;EPPR=0.0;DPRA=0.0;ODDS=62.3428;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9663;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.785;SOR=0.8295 [...]
+chr17 41104750 . C A 15246.3 REJECT NS=2;DP=402;DPB=463.0;AC=4;AN=4;AF=1.0;RO=0;AO=462;PRO=0.0;PAO=0.0;QR=0;QA=17837;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=233;SAR=229;SRP=0.0;SAP=3.0855;AB=0.0;ABP=0.0;RUN=1;RPP=39.4083;RPPR=0.0;RPL=187.0;RPR=275.0;EPP=132.528;EPPR=0.0;DPRA=0.0;ODDS=79.2078;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.989177;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9663;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.74;SOR=0.8 [...]
+chr17 41223094 . T C 1555.745 REJECT NS=2;DP=394;DPB=435.0;AC=2;AN=4;AF=0.5;RO=344;AO=91;PRO=0.0;PAO=0.0;QR=13043;QA=3426;PQR=0.0;PQA=0.0;SRF=158;SRR=186;SAF=50;SAR=41;SRP=7.95924;SAP=4.94315;AB=0.209195;ABP=322.536;RUN=1;RPP=5.89764;RPPR=4.24753;RPL=51.0;RPR=40.0;EPP=3.03416;EPPR=3.64154;DPRA=0.0;ODDS=208.572;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997093;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2165;Dels=0.0;FS=4.944;HaplotypeScore [...]
+chr17 41231221 . A C 2594.895 REJECT NS=2;DP=473;DPB=539.0;AC=2;AN=4;AF=0.5;RO=413;AO=126;PRO=0.0;PAO=0.0;QR=16105;QA=4795;PQR=0.0;PQA=0.0;SRF=243;SRR=170;SAF=76;SAR=50;SRP=31.0291;SAP=14.6604;AB=0.233766;ABP=334.851;RUN=1;RPP=53.2644;RPPR=171.476;RPL=36.0;RPR=90.0;EPP=8.59409;EPPR=7.43211;DPRA=0.0;ODDS=124.282;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984127;PAIREDR=0.990315;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.443;Dels=0.0;FS=1.8545;Haploty [...]
+chr17 41231516 . C T 604.547 REJECT NS=2;DP=174;DPB=174.0;AC=1;AN=4;AF=0.25;RO=143;AO=31;PRO=0.0;PAO=0.0;QR=5439;QA=1191;PQR=0.0;PQA=0.0;SRF=53;SRR=90;SAF=6;SAR=25;SRP=23.7987;SAP=28.2974;AB=0.469388;ABP=3.40914;RUN=1;RPP=4.76149;RPPR=14.0803;RPL=18.0;RPR=13.0;EPP=4.76149;EPPR=15.781;DPRA=0.0;ODDS=19.0958;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.2903;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986014;technology.ILLUMINA=1.0;BaseQRankSum=0.907;FS=2.851;MLEAC=1;MLEAF=0.5;MQ=59.62;MQRan [...]
+chr17 41234470 . A G 1569.1 REJECT NS=2;DP=358;DPB=404.0;AC=2;AN=4;AF=0.5;RO=319;AO=85;PRO=0.0;PAO=0.0;QR=12025;QA=3162;PQR=0.0;PQA=0.0;SRF=195;SRR=124;SAF=53;SAR=32;SRP=37.325;SAP=14.2764;AB=0.210396;ABP=297.32;RUN=1;RPP=3.24022;RPPR=3.07156;RPL=44.0;RPR=41.0;EPP=6.10145;EPPR=10.4233;DPRA=0.0;ODDS=89.732;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99373;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.439;Dels=0.0;FS=4.0355;HaplotypeScore=2.93 [...]
+chr17 41244000 . T C 1865.37 REJECT NS=2;DP=339;DPB=391.0;AC=2;AN=4;AF=0.5;RO=305;AO=85;PRO=0.0;PAO=0.0;QR=11649;QA=3318;PQR=0.0;PQA=0.0;SRF=135;SRR=170;SAF=43;SAR=42;SRP=11.7318;SAP=3.03585;AB=0.217391;ABP=274.256;RUN=1;RPP=12.2327;RPPR=4.21351;RPL=52.0;RPR=33.0;EPP=3.24022;EPPR=3.58699;DPRA=0.0;ODDS=53.0838;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988235;PAIREDR=0.990164;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.375;Dels=0.0;FS=2.1905;HaplotypeS [...]
+chr17 41244435 . T C 1963.0349999999999 REJECT NS=2;DP=369;DPB=425.0;AC=2;AN=4;AF=0.5;RO=328;AO=97;PRO=0.0;PAO=0.0;QR=12553;QA=3596;PQR=0.0;PQA=0.0;SRF=162;SRR=166;SAF=43;SAR=54;SRP=3.11623;SAP=5.71904;AB=0.228235;ABP=275.65;RUN=1;RPP=4.10723;RPPR=3.434;RPL=45.0;RPR=52.0;EPP=3.03269;EPPR=15.8273;DPRA=0.0;ODDS=102.42;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989691;PAIREDR=0.993902;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.407;Dels=0.0;FS=2.622;Hap [...]
+chr17 41244936 . G A 1705.2649999999999 REJECT NS=2;DP=334;DPB=383.0;AC=2;AN=4;AF=0.5;RO=299;AO=84;PRO=0.0;PAO=0.0;QR=11358;QA=3201;PQR=0.0;PQA=0.0;SRF=145;SRR=154;SAF=39;SAR=45;SRP=3.59856;SAP=3.94093;AB=0.219321;ABP=265.089;RUN=1;RPP=3.0103;RPPR=3.01756;RPL=42.0;RPR=42.0;EPP=3.1137;EPPR=8.30463;DPRA=0.0;ODDS=90.6178;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.5;MQMR=60.0;PAIRED=0.97619;PAIREDR=0.989967;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0405;Dels=0.0;FS=3.6235;H [...]
+chr17 41245237 . A G 1753.59 REJECT NS=2;DP=350;DPB=404.0;AC=2;AN=4;AF=0.5;RO=310;AO=94;PRO=0.0;PAO=0.0;QR=12017;QA=3575;PQR=0.0;PQA=0.0;SRF=159;SRR=151;SAF=57;SAR=37;SRP=3.4586;SAP=12.2506;AB=0.232673;ABP=253.783;RUN=1;RPP=6.33681;RPPR=6.4006;RPL=41.0;RPR=53.0;EPP=5.32038;EPPR=3.4586;DPRA=0.0;ODDS=202.941;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.978723;PAIREDR=0.996774;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.5705;Dels=0.0;FS=6.57;HaplotypeScore [...]
+chr17 41245466 . G A 2247.92 REJECT NS=2;DP=396;DPB=451.0;AC=2;AN=4;AF=0.5;RO=336;AO=114;PRO=0.0;PAO=0.0;QR=12640;QA=4352;PQR=0.0;PQA=0.0;SRF=177;SRR=159;SAF=58;SAR=56;SRP=5.10422;SAP=3.08649;AB=0.252772;ABP=242.445;RUN=1;RPP=3.31507;RPPR=3.24296;RPL=55.0;RPR=59.0;EPP=3.31507;EPPR=3.94093;DPRA=0.0;ODDS=260.734;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994048;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.446;Dels=0.0;FS=1.216;HaplotypeScore= [...]
+chr17 41251931 . G A 1647.36 PASS SOMATIC;NS=2;DP=256;DPB=256.0;AC=1;AN=3;AF=0.25;RO=192;AO=64;PRO=0.0;PAO=0.0;QR=7322;QA=2501;PQR=0.0;PQA=0.0;SRF=66;SRR=126;SAF=21;SAR=43;SRP=43.7254;SAP=19.4321;AB=0.353591;ABP=36.7101;RUN=1;RPP=46.9826;RPPR=155.194;RPL=50.0;RPR=14.0;EPP=4.23175;EPPR=29.068;DPRA=2.41333;ODDS=47.7786;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994792;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.079;Dels=0.0;FS=0.6;Hap [...]
+chr17 41277187 . G C 1566.75 REJECT NS=2;DP=378;DPB=429.0;AC=2;AN=4;AF=0.5;RO=339;AO=89;PRO=0.0;PAO=0.0;QR=12181;QA=3157;PQR=0.0;PQA=0.0;SRF=183;SRR=156;SAF=36;SAR=53;SRP=7.67993;SAP=10.0615;AB=0.207459;ABP=321.903;RUN=1;RPP=3.22989;RPPR=3.32417;RPL=46.0;RPR=43.0;EPP=3.22989;EPPR=3.06795;DPRA=0.0;ODDS=112.518;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99705;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.308;Dels=0.0;FS=7.047;HaplotypeScore=1 [...]
+chr17 41371844 . A G 2405.795 REJECT NS=2;DP=390;DPB=450.0;AC=2;AN=4;AF=0.5;RO=338;AO=111;PRO=0.0;PAO=0.0;QR=12145;QA=4173;PQR=0.0;PQA=0.0;SRF=234;SRR=104;SAF=70;SAR=41;SRP=111.584;SAP=19.4626;AB=0.246667;ABP=253.859;RUN=1;RPP=3.18637;RPPR=3.24158;RPL=57.0;RPR=54.0;EPP=11.6375;EPPR=46.2085;DPRA=0.0;ODDS=110.956;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.955;MQMR=59.9349;PAIRED=1.0;PAIREDR=0.988166;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.0545;Dels=0.0;FS=2.4665;Haploty [...]
+chr17 41371958 . T C 2018.5049999999999 REJECT NS=2;DP=411;DPB=469.0;AC=2;AN=4;AF=0.5;RO=365;AO=104;PRO=0.0;PAO=0.0;QR=13925;QA=3983;PQR=0.0;PQA=0.0;SRF=165;SRR=200;SAF=39;SAR=65;SRP=10.2981;SAP=17.1249;AB=0.221748;ABP=318.411;RUN=1;RPP=4.34659;RPPR=5.15798;RPL=48.0;RPR=56.0;EPP=3.76196;EPPR=28.1458;DPRA=0.0;ODDS=147.657;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990385;PAIREDR=0.983562;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7495;Dels=0.0;FS=2.78 [...]
+chr17 41375503 . T A 228.29 REJECT NS=2;DP=243;DPB=243.0;AC=1;AN=4;AF=0.25;RO=215;AO=28;PRO=0.0;PAO=0.0;QR=7807;QA=1068;PQR=0.0;PQA=0.0;SRF=189;SRR=26;SAF=27;SAR=1;SRP=271.354;SAP=55.4358;AB=0.213333;ABP=56.5443;RUN=1;RPP=34.0313;RPPR=27.2601;RPL=24.0;RPR=4.0;EPP=40.5458;EPPR=3.2628;DPRA=0.0;ODDS=41.7467;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=51.5357;MQMR=59.4512;PAIRED=1.0;PAIREDR=0.995349;technology.ILLUMINA=1.0;BaseQRankSum=0.913;FS=6.181;MLEAC=1;MLEAF=0.5;MQ=58.3;MQRa [...]
+chr17 41375505 . ACACT TCACA 505.215 REJECT NS=2;DP=199;DPB=223.6;AC=2;AN=4;AF=0.5;RO=168;AO=25;PRO=30.0;PAO=8.0;QR=6150;QA=899;PQR=1000.0;PQA=265.0;SRF=152;SRR=16;SAF=18;SAR=7;SRP=242.079;SAP=13.5202;AB=0.125628;ABP=245.266;RUN=1;RPP=57.2971;RPPR=4.87156;RPL=0.0;RPR=25.0;EPP=13.5202;EPPR=6.31921;DPRA=0.0;ODDS=21.9781;GTI=0;TYPE=complex;CIGAR=1X3M1X;NUMALT=1;MEANALT=3.5;LEN=5;MQM=57.92;MQMR=59.7024;PAIRED=0.96;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMIC [...]
+chr17 41375509 . T TCTCACA 229.73 PASS DP=69;AC=1;AN=4;AF=0.5;BaseQRankSum=0.01;FS=4.207;MLEAC=1;MLEAF=0.5;MQ=58.45;MQRankSum=0.166;QD=3.33;ReadPosRankSum=-0.44;SOR=0.175;ClippingRankSum=-0.656 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:45,12:57:99.0:267,0,1722:12:21:57:1:.:.:.:.:.:-0.00997748 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0533013
+chr17 41375555 . T G 1746.2150000000001 REJECT NS=2;DP=321;DPB=378.0;AC=2;AN=4;AF=0.5;RO=282;AO=94;PRO=0.0;PAO=0.0;QR=10540;QA=3428;PQR=0.0;PQA=0.0;SRF=181;SRR=101;SAF=61;SAR=33;SRP=52.2919;SAP=21.1213;AB=0.248677;ABP=210.392;RUN=1;RPP=14.1911;RPPR=40.7416;RPL=36.0;RPR=58.0;EPP=3.37991;EPPR=30.7312;DPRA=0.0;ODDS=154.494;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.0638;MQMR=60.0;PAIRED=0.978723;PAIREDR=0.996454;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7505;Dels=0.0;FS=0. [...]
+chr17 41375597 . A G 1898.335 REJECT NS=2;DP=413;DPB=477.0;AC=2;AN=4;AF=0.5;RO=365;AO=110;PRO=0.0;PAO=0.0;QR=13689;QA=4154;PQR=0.0;PQA=0.0;SRF=190;SRR=175;SAF=61;SAR=49;SRP=4.34888;SAP=5.85295;AB=0.230608;ABP=303.689;RUN=1;RPP=3.72096;RPPR=3.73016;RPL=52.0;RPR=58.0;EPP=23.2247;EPPR=21.0067;DPRA=0.0;ODDS=248.786;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.954545;PAIREDR=0.994521;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0925;Dels=0.0;FS=4.598;Haplotyp [...]
+chr17 43131480 . A T 5817.115 REJECT NS=2;DP=360;DPB=410.0;AC=2;AN=4;AF=0.5;RO=207;AO=203;PRO=0.0;PAO=0.0;QR=7875;QA=7783;PQR=0.0;PQA=0.0;SRF=104;SRR=103;SAF=105;SAR=98;SRP=3.02079;SAP=3.53445;AB=0.495122;ABP=3.09504;RUN=1;RPP=7.72764;RPPR=5.3706;RPL=112.0;RPR=91.0;EPP=6.10171;EPPR=20.6443;DPRA=0.0;ODDS=301.08;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.697;Dels=0.0;FS=0.43;HaplotypeScore=1.9652 [...]
+chr17 46505696 . A G 5344.985000000001 REJECT NS=2;DP=347;DPB=401.0;AC=2;AN=4;AF=0.5;RO=208;AO=193;PRO=0.0;PAO=0.0;QR=8082;QA=7422;PQR=0.0;PQA=0.0;SRF=91;SRR=117;SAF=82;SAR=111;SRP=10.0676;SAP=12.4725;AB=0.481297;ABP=4.22871;RUN=1;RPP=3.56161;RPPR=3.17734;RPL=100.0;RPR=93.0;EPP=10.0423;EPPR=12.4061;DPRA=0.0;ODDS=330.97;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994819;PAIREDR=0.980769;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0155;Dels=0.0;FS=2.3725 [...]
+chr17 46805590 . G A 11146.6 REJECT NS=2;DP=425;DPB=491.0;AC=2;AN=4;AF=0.5;RO=114;AO=375;PRO=0.0;PAO=0.0;QR=4401;QA=13938;PQR=0.0;PQA=0.0;SRF=54;SRR=60;SAF=192;SAR=183;SRP=3.69603;SAP=3.47934;AB=0.763747;ABP=299.679;RUN=1;RPP=4.31318;RPPR=3.69603;RPL=180.0;RPR=195.0;EPP=3.98891;EPPR=12.2295;DPRA=0.0;ODDS=171.897;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997333;PAIREDR=0.991228;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-2.507;Dels=0.0;FS=2.9075;Haplot [...]
+chr17 48263021 . C T 6198.535 REJECT NS=2;DP=269;DPB=305.0;AC=3;AN=4;AF=0.75;RO=79;AO=226;PRO=0.0;PAO=0.0;QR=2969;QA=8337;PQR=0.0;PQA=0.0;SRF=33;SRR=46;SAF=99;SAR=127;SRP=7.6556;SAP=10.5432;AB=0.660944;ABP=55.4332;RUN=1;RPP=35.3326;RPPR=15.1321;RPL=142.0;RPR=84.0;EPP=5.47002;EPPR=3.03779;DPRA=0.0;ODDS=45.8779;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995575;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.39;Dels=0.0;FS=0.0;HaplotypeScore=11. [...]
+chr17 48265426 . A G 9098.635 REJECT NS=2;DP=373;DPB=432.0;AC=3;AN=4;AF=0.75;RO=106;AO=326;PRO=0.0;PAO=0.0;QR=4070;QA=12432;PQR=0.0;PQA=0.0;SRF=47;SRR=59;SAF=141;SAR=185;SRP=5.96022;SAP=15.9059;AB=0.66242;ABP=74.9593;RUN=1;RPP=4.71551;RPPR=5.96022;RPL=155.0;RPR=171.0;EPP=5.16845;EPPR=3.74778;DPRA=0.0;ODDS=74.5642;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996933;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.965;Dels=0.0;FS=0.0;HaplotypeScore [...]
+chr17 48265495 . T C 9485.91 REJECT NS=2;DP=256;DPB=296.4;AC=4;AN=4;AF=1.0;RO=0;AO=271;PRO=3.5;PAO=14.0;QR=0;QA=10035;PQR=92.0;PQA=400.5;SRF=0;SRR=0;SAF=75;SAR=196;SRP=0.0;SAP=120.326;AB=0.0;ABP=0.0;RUN=1;RPP=16.4798;RPPR=0.0;RPL=156.0;RPR=115.0;EPP=4.81318;EPPR=0.0;DPRA=0.0;ODDS=24.1717;GTI=0;TYPE=snp;CIGAR=1X4M;NUMALT=2;MEANALT=2.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=13.5144;MLEAC=2;MLEAF=1.0;MQ=6 [...]
+chr17 48265495 . TGGGA CGGGG 9940.05 REJECT NS=2;DP=285;DPB=296.4;AC=0;AN=4;AF=0.0;RO=0;AO=13;PRO=3.5;PAO=10.5;QR=0;QA=110;PQR=92.0;PQA=308.5;SRF=0;SRR=0;SAF=13;SAR=0;SRP=0.0;SAP=31.2394;AB=0.0;ABP=0.0;RUN=1;RPP=31.2394;RPPR=0.0;RPL=13.0;RPR=0.0;EPP=31.2394;EPPR=0.0;DPRA=0.0;ODDS=24.1717;GTI=0;TYPE=complex;CIGAR=1X3M1X;NUMALT=2;MEANALT=2.5;LEN=5;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:Ca [...]
+chr17 48265542 . G T 1020.72 PASS SOMATIC;NS=2;DP=203;DPB=203.0;AC=1;AN=3;AF=0.25;RO=156;AO=47;PRO=0.0;PAO=0.0;QR=5927;QA=1694;PQR=0.0;PQA=0.0;SRF=36;SRR=120;SAF=8;SAR=39;SRP=101.228;SAP=47.41;AB=0.313333;ABP=48.4085;RUN=1;RPP=5.27418;RPPR=27.5646;RPL=27.0;RPR=20.0;EPP=4.16534;EPPR=3.06598;DPRA=2.83019;ODDS=34.1071;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.401;Dels=0.0;FS=5.255;Haplotyp [...]
+chr17 48266160 . CAG C 17.5267 REJECT NS=2;DP=275;DPB=344.238;AC=2;AN=3;AF=0.25;RO=229;AO=23;PRO=64.8333;PAO=43.8333;QR=8617;QA=838;PQR=2307.0;PQA=1545.0;SRF=96;SRR=133;SAF=5;SAR=18;SRP=15.9917;SAP=18.9659;AB=0.0882353;ABP=303.44;RUN=1;RPP=3.86001;RPPR=14.6263;RPL=10.0;RPR=13.0;EPP=3.86001;EPPR=3.01978;DPRA=0.0;ODDS=4.01767;GTI=0;TYPE=del;CIGAR=1M2D18M;NUMALT=2;MEANALT=6.5;LEN=2;MQM=60.4348;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991266;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO: [...]
+chr17 48266160 . CAGAG C 17.5267 REJECT NS=2;DP=275;DPB=344.238;AC=2;AN=2;AF=0.0;RO=229;AO=10;PRO=64.8333;PAO=38.3333;QR=8617;QA=385;PQR=2307.0;PQA=1340.0;SRF=96;SRR=133;SAF=3;SAR=7;SRP=15.9917;SAP=6.48466;AB=0.0294118;ABP=395.408;RUN=1;RPP=6.48466;RPPR=14.6263;RPL=7.0;RPR=3.0;EPP=10.8276;EPPR=3.01978;DPRA=0.0;ODDS=4.01767;GTI=0;TYPE=del;CIGAR=1M4D16M;NUMALT=2;MEANALT=6.5;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991266;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr17 48266669 . G C 12015.05 REJECT NS=2;DP=318;DPB=364.0;AC=4;AN=4;AF=1.0;RO=0;AO=364;PRO=0.0;PAO=0.0;QR=0;QA=13870;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=163;SAR=201;SRP=0.0;SAP=11.6246;AB=0.0;ABP=0.0;RUN=1;RPP=4.53749;RPPR=0.0;RPL=190.0;RPR=174.0;EPP=7.04303;EPPR=0.0;DPRA=0.0;ODDS=61.7044;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994505;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.9571;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.825;SOR= [...]
+chr17 48267291 . G C 4750.965 REJECT NS=2;DP=308;DPB=355.0;AC=2;AN=4;AF=0.5;RO=182;AO=172;PRO=0.0;PAO=0.0;QR=6892;QA=6503;PQR=0.0;PQA=0.0;SRF=89;SRR=93;SAF=82;SAR=90;SRP=3.2012;SAP=3.81829;AB=0.484507;ABP=3.75044;RUN=1;RPP=3.46479;RPPR=3.0103;RPL=89.0;RPR=83.0;EPP=7.10075;EPPR=3.05802;DPRA=0.0;ODDS=276.777;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.479;Dels=0.0;FS=1.3365;HaplotypeScore=0.9999;M [...]
+chr17 48268223 . A G 13445.599999999999 REJECT NS=2;DP=356;DPB=405.0;AC=4;AN=4;AF=1.0;RO=0;AO=405;PRO=0.0;PAO=0.0;QR=0;QA=15485;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=226;SAR=179;SRP=0.0;SAP=14.8542;AB=0.0;ABP=0.0;RUN=1;RPP=12.924;RPPR=0.0;RPL=181.0;RPR=224.0;EPP=47.4102;EPPR=0.0;DPRA=0.0;ODDS=64.8127;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997531;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31 [...]
+chr17 48269302 . G A 8828.635 REJECT NS=2;DP=376;DPB=437.0;AC=3;AN=4;AF=0.75;RO=114;AO=323;PRO=0.0;PAO=0.0;QR=4309;QA=12209;PQR=0.0;PQA=0.0;SRF=54;SRR=60;SAF=168;SAR=155;SRP=3.69603;SAP=4.14646;AB=0.638095;ABP=55.1877;RUN=1;RPP=6.56667;RPPR=10.6295;RPL=173.0;RPR=150.0;EPP=9.47093;EPPR=3.0103;DPRA=0.0;ODDS=77.0752;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993808;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.278;Dels=0.0;FS=0.6965;HaplotypeSc [...]
+chr17 48269426 . C T 6494.555 REJECT NS=2;DP=289;DPB=328.0;AC=3;AN=4;AF=0.75;RO=94;AO=234;PRO=0.0;PAO=0.0;QR=3510;QA=8869;PQR=0.0;PQA=0.0;SRF=41;SRR=53;SAF=69;SAR=165;SRP=6.33681;SAP=88.5329;AB=0.625498;ABP=37.3472;RUN=1;RPP=45.9201;RPPR=16.3163;RPL=151.0;RPR=83.0;EPP=3.34437;EPPR=14.1911;DPRA=0.0;ODDS=49.0087;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995726;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.259;Dels=0.0;FS=6.9875;HaplotypeScore [...]
+chr17 48273464 . T C 2538.935 REJECT NS=2;DP=180;DPB=213.0;AC=2;AN=4;AF=0.5;RO=113;AO=99;PRO=0.0;PAO=0.0;QR=4336;QA=3800;PQR=0.0;PQA=0.0;SRF=65;SRR=48;SAF=59;SAR=40;SRP=8.56389;SAP=10.9285;AB=0.464789;ABP=5.30411;RUN=1;RPP=51.4626;RPPR=49.1493;RPL=26.0;RPR=73.0;EPP=3.03223;EPPR=6.2579;DPRA=0.0;ODDS=196.523;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.229;Dels=0.0;FS=1.7125;HaplotypeScore=5.8371;M [...]
+chr17 48276971 . G C 10505.2 REJECT NS=2;DP=391;DPB=454.0;AC=2;AN=4;AF=0.5;RO=105;AO=349;PRO=0.0;PAO=0.0;QR=3992;QA=13156;PQR=0.0;PQA=0.0;SRF=52;SRR=53;SAF=164;SAR=185;SRP=3.03098;SAP=5.75419;AB=0.768722;ABP=287.77;RUN=1;RPP=32.6332;RPPR=4.02365;RPL=209.0;RPR=140.0;EPP=6.30173;EPPR=3.03098;DPRA=0.0;ODDS=119.794;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994269;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.332;Dels=0.0;FS=1.034;HaplotypeScor [...]
+chr17 56432362 . C G 1748.555 REJECT NS=2;DP=286;DPB=329.0;AC=2;AN=4;AF=0.5;RO=238;AO=91;PRO=0.0;PAO=0.0;QR=9026;QA=3461;PQR=0.0;PQA=0.0;SRF=86;SRR=152;SAF=37;SAR=54;SRP=42.7537;SAP=9.90651;AB=0.276596;ABP=145.634;RUN=1;RPP=11.6246;RPPR=73.6653;RPL=55.0;RPR=36.0;EPP=4.17955;EPPR=3.15628;DPRA=0.0;ODDS=233.636;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.754;Dels=0.0;FS=1.4505;HaplotypeScore=5.877; [...]
+chr17 56436211 . T A 3426.11 REJECT NS=2;DP=218;DPB=253.0;AC=2;AN=4;AF=0.5;RO=129;AO=124;PRO=0.0;PAO=0.0;QR=4896;QA=4718;PQR=0.0;PQA=0.0;SRF=46;SRR=83;SAF=44;SAR=80;SRP=26.0548;SAP=25.7057;AB=0.490119;ABP=3.22487;RUN=1;RPP=54.0749;RPPR=31.3068;RPL=89.0;RPR=35.0;EPP=4.76149;EPPR=3.02713;DPRA=0.0;ODDS=175.553;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984496;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.5885;Dels=0.0;FS=3.0295;HaplotypeScore= [...]
+chr17 56438301 . G A 3981.52 REJECT NS=2;DP=300;DPB=343.0;AC=2;AN=4;AF=0.5;RO=196;AO=147;PRO=0.0;PAO=0.0;QR=7457;QA=5646;PQR=0.0;PQA=0.0;SRF=56;SRR=140;SAF=34;SAR=113;SRP=81.1833;SAP=95.2019;AB=0.428571;ABP=18.2106;RUN=1;RPP=17.2061;RPPR=24.4591;RPL=89.0;RPR=58.0;EPP=3.02507;EPPR=5.84651;DPRA=0.0;ODDS=219.899;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994898;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.591;Dels=0.0;FS=5.681;HaplotypeScore=3 [...]
+chr17 56448297 . C T 2441.95 PASS SOMATIC;NS=2;DP=338;DPB=338.0;AC=1;AN=3;AF=0.25;RO=245;AO=93;PRO=0.0;PAO=0.0;QR=9115;QA=3548;PQR=0.0;PQA=0.0;SRF=150;SRR=95;SAF=55;SAR=38;SRP=29.8213;SAP=9.75821;AB=0.367589;ABP=41.5389;RUN=1;RPP=3.22044;RPPR=3.01916;RPL=45.0;RPR=48.0;EPP=9.75821;EPPR=8.54977;DPRA=2.97647;ODDS=53.0343;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989247;PAIREDR=0.995918;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.523;Dels=0.0;FS=0 [...]
+chr17 56492800 . T C 3125.05 PASS SOMATIC;NS=2;DP=429;DPB=429.0;AC=1;AN=3;AF=0.25;RO=313;AO=116;PRO=0.0;PAO=0.0;QR=12045;QA=4508;PQR=0.0;PQA=0.0;SRF=130;SRR=183;SAF=56;SAR=60;SRP=22.4981;SAP=3.30981;AB=0.363636;ABP=54.5334;RUN=1;RPP=15.6647;RPPR=27.1601;RPL=71.0;RPR=45.0;EPP=3.08518;EPPR=5.01527;DPRA=2.9;ODDS=69.6542;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991379;PAIREDR=0.98722;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.268;Dels=0.0;FS=3.8 [...]
+chr17 56769979 . C T 956.133 REJECT NS=2;DP=208;DPB=240.0;AC=2;AN=4;AF=0.5;RO=189;AO=50;PRO=0.0;PAO=0.0;QR=7191;QA=1903;PQR=0.0;PQA=0.0;SRF=119;SRR=70;SAF=32;SAR=18;SRP=30.596;SAP=11.5225;AB=0.208333;ABP=180.347;RUN=1;RPP=47.4821;RPPR=115.617;RPL=9.0;RPR=41.0;EPP=5.78978;EPPR=7.15793;DPRA=0.0;ODDS=41.5342;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989418;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0425;Dels=0.0;FS=0.972;HaplotypeScore=1.96 [...]
+chr17 59760996 . A G 13648.3 REJECT NS=2;DP=362;DPB=417.0;AC=4;AN=4;AF=1.0;RO=0;AO=417;PRO=0.0;PAO=0.0;QR=0;QA=15852;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=215;SAR=202;SRP=0.0;SAP=3.89035;AB=0.0;ABP=0.0;RUN=1;RPP=3.05717;RPPR=0.0;RPL=210.0;RPR=207.0;EPP=3.01551;EPPR=0.0;DPRA=0.0;ODDS=72.8313;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992806;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9217;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.565;SOR=0 [...]
+chr17 59763114 . A T 2685.4700000000003 REJECT NS=2;DP=217;DPB=245.0;AC=2;AN=4;AF=0.5;RO=141;AO=103;PRO=0.0;PAO=0.0;QR=5372;QA=3965;PQR=0.0;PQA=0.0;SRF=108;SRR=33;SAF=73;SAR=30;SRP=89.6382;SAP=41.9914;AB=0.420408;ABP=16.4912;RUN=1;RPP=20.7405;RPPR=21.8759;RPL=37.0;RPR=66.0;EPP=5.56125;EPPR=3.76493;DPRA=0.0;ODDS=157.753;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=59.8156;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.5945;Dels=0.0;FS=2.863;Haploty [...]
+chr17 59763347 . A G 14914.65 REJECT NS=2;DP=400;DPB=456.0;AC=4;AN=4;AF=1.0;RO=0;AO=455;PRO=0.0;PAO=0.0;QR=0;QA=17128;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=220;SAR=235;SRP=0.0;SAP=4.0841;AB=0.0;ABP=0.0;RUN=1;RPP=3.12961;RPPR=0.0;RPL=225.0;RPR=230.0;EPP=5.11496;EPPR=0.0;DPRA=0.0;ODDS=71.0043;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.986813;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=9.681;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.41;SOR=0.7 [...]
+chr17 59763465 . T C 11896.5 REJECT NS=2;DP=315;DPB=354.0;AC=4;AN=4;AF=1.0;RO=0;AO=354;PRO=0.0;PAO=0.0;QR=0;QA=13477;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=147;SAR=207;SRP=0.0;SAP=25.0931;AB=0.0;ABP=0.0;RUN=1;RPP=15.9901;RPPR=0.0;RPL=154.0;RPR=200.0;EPP=6.54354;EPPR=0.0;DPRA=0.0;ODDS=51.7333;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.988701;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8659;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=25.995;SOR=1 [...]
+chr17 59924512 . C T 2427.31 PASS SOMATIC;NS=2;DP=407;DPB=407.0;AC=1;AN=3;AF=0.25;RO=309;AO=98;PRO=0.0;PAO=0.0;QR=11748;QA=3695;PQR=0.0;PQA=0.0;SRF=177;SRR=132;SAF=54;SAR=44;SRP=17.2408;SAP=5.22609;AB=0.316129;ABP=94.044;RUN=1;RPP=4.4284;RPPR=3.86062;RPL=53.0;RPR=45.0;EPP=4.4284;EPPR=17.2408;DPRA=3.19588;ODDS=60.5078;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987055;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.693;Dels=0.0;FS=1.476; [...]
+chr17 61502459 . TTTGTATCTGCTG T 5437.22 REJECT NS=2;DP=331;DPB=206.786;AC=3;AN=4;AF=0.5;RO=137;AO=216;PRO=69.0;PAO=5.0;QR=5194;QA=7380;PQR=2453.5;PQA=95.5;SRF=81;SRR=56;SAF=117;SAR=99;SRP=12.9167;SAP=6.26751;AB=0.610169;ABP=40.3302;RUN=1;RPP=4.45795;RPPR=3.02615;RPL=102.0;RPR=114.0;EPP=12.0581;EPPR=6.57659;DPRA=0.0;ODDS=71.0127;GTI=0;TYPE=del;CIGAR=1M12D1M;NUMALT=1;MEANALT=1.5;LEN=12;MQM=60.3704;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992701;technology.ILLUMINA=1.0;MQ0=0;END=61502471;HOMLEN=8;HO [...]
+chr17 62007498 . A G 9237.71 REJECT NS=2;DP=356;DPB=409.0;AC=2;AN=4;AF=0.5;RO=107;AO=302;PRO=0.0;PAO=0.0;QR=3998;QA=11618;PQR=0.0;PQA=0.0;SRF=69;SRR=38;SAF=173;SAR=129;SRP=22.513;SAP=16.9307;AB=0.738386;ABP=204.894;RUN=1;RPP=7.15192;RPPR=5.46589;RPL=139.0;RPR=163.0;EPP=27.1985;EPPR=3.51765;DPRA=0.0;ODDS=191.64;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.1395;Dels=0.0;FS=6.014;HaplotypeScore=11.7 [...]
+chr17 63532517 . G A 5910.4400000000005 REJECT NS=2;DP=381;DPB=436.0;AC=2;AN=4;AF=0.5;RO=223;AO=213;PRO=0.0;PAO=0.0;QR=8639;QA=8103;PQR=0.0;PQA=0.0;SRF=119;SRR=104;SAF=106;SAR=107;SRP=5.20125;SAP=3.02049;AB=0.488532;ABP=3.50834;RUN=1;RPP=3.50984;RPPR=6.52555;RPL=110.0;RPR=103.0;EPP=3.02049;EPPR=3.48744;DPRA=0.0;ODDS=352.183;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995305;PAIREDR=0.991031;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.6245;Dels=0.0;FS= [...]
+chr17 63533768 . G A 5434.015 REJECT NS=2;DP=328;DPB=374.0;AC=2;AN=4;AF=0.5;RO=179;AO=195;PRO=0.0;PAO=0.0;QR=6902;QA=7368;PQR=0.0;PQA=0.0;SRF=79;SRR=100;SAF=91;SAR=104;SRP=8.36013;SAP=4.89224;AB=0.52139;ABP=4.49666;RUN=1;RPP=3.55595;RPPR=3.02243;RPL=94.0;RPR=101.0;EPP=4.89224;EPPR=5.7398;DPRA=0.0;ODDS=295.547;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.8495;Dels=0.0;FS=0.612;HaplotypeScore=5.99 [...]
+chr17 63533789 . T C 11612.95 REJECT NS=2;DP=308;DPB=352.0;AC=4;AN=4;AF=1.0;RO=0;AO=352;PRO=0.0;PAO=0.0;QR=0;QA=13337;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=166;SAR=186;SRP=0.0;SAP=5.47788;AB=0.0;ABP=0.0;RUN=1;RPP=3.89863;RPPR=0.0;RPL=170.0;RPR=182.0;EPP=4.58955;EPPR=0.0;DPRA=0.0;ODDS=58.5657;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.465;SOR=0.7895 G [...]
+chr17 63534221 . C T 924.681 REJECT NS=2;DP=169;DPB=194.0;AC=2;AN=4;AF=0.5;RO=149;AO=45;PRO=0.0;PAO=0.0;QR=5671;QA=1758;PQR=0.0;PQA=0.0;SRF=113;SRR=36;SAF=38;SAR=7;SRP=89.4174;SAP=49.3833;AB=0.231959;ABP=124.075;RUN=1;RPP=6.91895;RPPR=25.1768;RPL=18.0;RPR=27.0;EPP=3.44459;EPPR=4.77371;DPRA=0.0;ODDS=70.5303;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.973154;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.5385;Dels=0.0;FS=4.9875;HaplotypeScore=7. [...]
+chr17 63534250 . T C 8332.135 REJECT NS=2;DP=225;DPB=262.0;AC=4;AN=4;AF=1.0;RO=0;AO=262;PRO=0.0;PAO=0.0;QR=0;QA=9893;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=184;SAR=78;SRP=0.0;SAP=96.135;AB=0.0;ABP=0.0;RUN=1;RPP=43.6218;RPPR=0.0;RPL=96.0;RPR=166.0;EPP=3.83911;EPPR=0.0;DPRA=0.0;ODDS=48.3173;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.980916;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8463;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=34.68;SOR=1.779 [...]
+chr17 63545622 . T C 3573.04 REJECT NS=2;DP=201;DPB=228.0;AC=2;AN=4;AF=0.5;RO=102;AO=126;PRO=0.0;PAO=0.0;QR=3976;QA=4808;PQR=0.0;PQA=0.0;SRF=76;SRR=26;SAF=86;SAR=40;SRP=56.2327;SAP=39.4772;AB=0.552632;ABP=8.49612;RUN=1;RPP=33.4109;RPPR=22.1704;RPL=42.0;RPR=84.0;EPP=3.63072;EPPR=3.7767;DPRA=0.0;ODDS=143.352;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2675;Dels=0.0;FS=5.695;HaplotypeScore=3.9661;M [...]
+chr17 63554591 . G A 5181.14 REJECT NS=2;DP=318;DPB=354.0;AC=2;AN=4;AF=0.5;RO=171;AO=183;PRO=0.0;PAO=0.0;QR=6424;QA=7017;PQR=0.0;PQA=0.0;SRF=82;SRR=89;SAF=93;SAR=90;SRP=3.63253;SAP=3.11709;AB=0.516949;ABP=3.89361;RUN=1;RPP=3.02217;RPPR=5.15638;RPL=91.0;RPR=92.0;EPP=3.30695;EPPR=5.15638;DPRA=0.0;ODDS=154.381;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.988304;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9345;Dels=0.0;FS=1.606;HaplotypeScore=2. [...]
+chr17 64550701 . AGGTG A 3855.98 REJECT NS=2;DP=307;DPB=293.1;AC=2;AN=4;AF=0.5;RO=169;AO=152;PRO=40.0;PAO=24.0;QR=6380;QA=5457;PQR=1380.5;PQA=804.5;SRF=52;SRR=117;SAF=49;SAR=103;SRP=57.2971;SAP=44.6683;AB=0.470588;ABP=5.43724;RUN=1;RPP=35.9253;RPPR=54.0078;RPL=100.0;RPR=52.0;EPP=9.92473;EPPR=4.05106;DPRA=0.0;ODDS=175.539;GTI=0;TYPE=del;CIGAR=1M4D5M;NUMALT=1;MEANALT=2.0;LEN=4;MQM=60.1974;MQMR=60.0;PAIRED=0.960526;PAIREDR=0.982249;technology.ILLUMINA=1.0;MQ0=0;END=64550705;HOMLEN=4;HOMSEQ= [...]
+chr17 64685078 . G A 8022.780000000001 REJECT NS=2;DP=333;DPB=390.0;AC=3;AN=4;AF=0.75;RO=98;AO=292;PRO=0.0;PAO=0.0;QR=3712;QA=11200;PQR=0.0;PQA=0.0;SRF=56;SRR=42;SAF=173;SAR=119;SRP=7.35324;SAP=24.6953;AB=0.646209;ABP=54.4436;RUN=1;RPP=8.84055;RPPR=3.80798;RPL=132.0;RPR=160.0;EPP=4.46786;EPPR=5.22609;DPRA=0.0;ODDS=71.4998;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989726;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.227;Dels=0.0;FS=0.232;Hap [...]
+chr17 64685390 . G C 16464.25 REJECT NS=2;DP=434;DPB=509.0;AC=4;AN=4;AF=1.0;RO=0;AO=507;PRO=0.0;PAO=0.0;QR=0;QA=19555;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=271;SAR=236;SRP=0.0;SAP=8.25695;AB=0.0;ABP=0.0;RUN=1;RPP=3.04885;RPPR=0.0;RPL=255.0;RPR=252.0;EPP=5.276;EPPR=0.0;DPRA=0.0;ODDS=96.0225;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.990138;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.84;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.065;SOR=0.81 [...]
+chr17 64686048 . G A 15513.8 REJECT NS=2;DP=415;DPB=478.0;AC=4;AN=4;AF=1.0;RO=0;AO=477;PRO=0.0;PAO=0.0;QR=0;QA=17977;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=233;SAR=244;SRP=0.0;SAP=3.56113;AB=0.0;ABP=0.0;RUN=1;RPP=7.38511;RPPR=0.0;RPL=223.0;RPR=254.0;EPP=3.77965;EPPR=0.0;DPRA=0.0;ODDS=81.6706;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997904;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=9.7563;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.61;SOR=0. [...]
+chr17 64686545 . C T 2521.67 PASS SOMATIC;NS=2;DP=402;DPB=402.0;AC=1;AN=3;AF=0.25;RO=304;AO=98;PRO=0.0;PAO=0.0;QR=11692;QA=3761;PQR=0.0;PQA=0.0;SRF=104;SRR=200;SAF=40;SAR=58;SRP=68.8402;SAP=10.1895;AB=0.34386;ABP=63.362;RUN=1;RPP=13.7347;RPPR=3.26745;RPL=38.0;RPR=60.0;EPP=22.9524;EPPR=3.7246;DPRA=2.4359;ODDS=73.9923;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9605;PAIRED=1.0;PAIREDR=0.996711;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.745;Dels=0.0;FS=3.587 [...]
+chr17 64686679 . A G 1172.59 PASS SOMATIC;NS=2;DP=197;DPB=197.0;AC=1;AN=3;AF=0.25;RO=149;AO=48;PRO=0.0;PAO=0.0;QR=5753;QA=1861;PQR=0.0;PQA=0.0;SRF=35;SRR=114;SAF=12;SAR=36;SRP=93.9644;SAP=29.068;AB=0.315789;ABP=47.8112;RUN=1;RPP=4.6389;RPPR=8.27138;RPL=27.0;RPR=21.0;EPP=17.6677;EPPR=20.863;DPRA=3.37778;ODDS=29.1113;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986577;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.39;Dels=0.0;FS=1.693;Hapl [...]
+chr17 64686818 . T C 1137.005 REJECT NS=2;DP=35;DPB=42.0;AC=4;AN=4;AF=1.0;RO=0;AO=41;PRO=0.0;PAO=0.0;QR=0;QA=1501;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=0;SAR=41;SRP=0.0;SAP=92.0407;AB=0.0;ABP=0.0;RUN=1;RPP=5.60547;RPPR=0.0;RPL=24.0;RPR=17.0;EPP=5.60547;EPPR=0.0;DPRA=0.0;ODDS=13.1179;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.655;SOR=6.0435 GT:GQ:D [...]
+chr17 64686866 . T A 1072.955 REJECT NS=2;DP=31;DPB=38.0;AC=4;AN=4;AF=1.0;RO=0;AO=38;PRO=0.0;PAO=0.0;QR=0;QA=1417;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=1;SAR=37;SRP=0.0;SAP=77.0689;AB=0.0;ABP=0.0;RUN=1;RPP=3.0103;RPPR=0.0;RPL=19.0;RPR=19.0;EPP=3.23888;EPPR=0.0;DPRA=0.0;ODDS=13.1172;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.175;SOR=5.1755 GT:GQ:DP:RO [...]
+chr17 64687199 . C T 683.157 PASS SOMATIC;NS=2;DP=120;DPB=120.0;AC=1;AN=3;AF=0.25;RO=90;AO=30;PRO=0.0;PAO=0.0;QR=3398;QA=1149;PQR=0.0;PQA=0.0;SRF=90;SRR=0;SAF=30;SAR=0;SRP=198.443;SAP=68.1545;AB=0.361446;ABP=16.8502;RUN=1;RPP=3.29983;RPPR=19.3205;RPL=14.0;RPR=16.0;EPP=3.29983;EPPR=19.3205;DPRA=2.24324;ODDS=24.0806;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.294;Dels=0.0;FS=0.0;HaplotypeS [...]
+chr17 64687216 . G A 873.639 PASS SOMATIC;NS=2;DP=132;DPB=132.0;AC=1;AN=3;AF=0.25;RO=94;AO=38;PRO=0.0;PAO=0.0;QR=3585;QA=1404;PQR=0.0;PQA=0.0;SRF=94;SRR=0;SAF=37;SAR=1;SRP=207.129;SAP=77.0689;AB=0.404255;ABP=10.4949;RUN=1;RPP=3.0103;RPPR=10.4949;RPL=19.0;RPR=19.0;EPP=3.23888;EPPR=10.4949;DPRA=2.47368;ODDS=24.7466;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.767;Dels=0.0;FS=3.933;HaplotypeS [...]
+chr17 64687446 . A G 2607.68 PASS SOMATIC;NS=2;DP=439;DPB=439.0;AC=1;AN=3;AF=0.25;RO=330;AO=108;PRO=0.0;PAO=0.0;QR=12205;QA=3934;PQR=0.0;PQA=0.0;SRF=202;SRR=128;SAF=68;SAR=40;SRP=39.0436;SAP=18.7736;AB=0.338558;ABP=75.2271;RUN=1;RPP=3.332;RPPR=5.64239;RPL=52.0;RPR=56.0;EPP=5.9056;EPPR=3.11558;DPRA=2.65833;ODDS=75.7896;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990741;PAIREDR=0.99697;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.413;Dels=0.0;FS=2 [...]
+chr17 64687878 . CA C 2943.49 PASS SOMATIC;NS=2;DP=416;DPB=389.0;AC=1;AN=4;AF=0.25;RO=294;AO=118;PRO=19.0;PAO=9.0;QR=11191;QA=4296;PQR=434.5;PQA=93.5;SRF=147;SRR=147;SAF=61;SAR=57;SRP=3.0103;SAP=3.30474;AB=0.371069;ABP=48.9253;RUN=1;RPP=3.30474;RPPR=13.6756;RPL=57.0;RPR=61.0;EPP=3.67278;EPPR=3.12848;DPRA=3.2449;ODDS=64.62;GTI=0;TYPE=del;CIGAR=1M1D1M;NUMALT=1;MEANALT=5.0;LEN=1;MQM=60.339;MQMR=60.0;PAIRED=0.983051;PAIREDR=0.996599;technology.ILLUMINA=1.0;MQ0=0;END=64687879;HOMLEN=0;SVLEN=- [...]
+chr17 64688009 . A G 4009.28 PASS SOMATIC;NS=2;DP=521;DPB=521.0;AC=1;AN=3;AF=0.25;RO=371;AO=150;PRO=0.0;PAO=0.0;QR=14258;QA=5747;PQR=0.0;PQA=0.0;SRF=191;SRR=180;SAF=78;SAR=72;SRP=3.71852;SAP=3.53145;AB=0.36855;ABP=64.0943;RUN=1;RPP=3.24192;RPPR=6.10655;RPL=73.0;RPR=77.0;EPP=5.09491;EPPR=3.71852;DPRA=3.57018;ODDS=72.1237;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.457;Dels=0.0;FS=0.0;Haplo [...]
+chr17 64688343 . A G 17372.199999999997 REJECT NS=2;DP=465;DPB=524.0;AC=4;AN=4;AF=1.0;RO=0;AO=524;PRO=0.0;PAO=0.0;QR=0;QA=19762;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=229;SAR=295;SRP=0.0;SAP=21.0617;AB=0.0;ABP=0.0;RUN=1;RPP=5.81167;RPPR=0.0;RPL=249.0;RPR=275.0;EPP=4.07117;EPPR=0.0;DPRA=0.0;ODDS=77.795;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994275;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8574;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29 [...]
+chr17 64688759 . C T 8904.385 REJECT NS=2;DP=405;DPB=458.0;AC=3;AN=4;AF=0.75;RO=141;AO=317;PRO=0.0;PAO=0.0;QR=5318;QA=12046;PQR=0.0;PQA=0.0;SRF=66;SRR=75;SAF=174;SAR=143;SRP=4.25774;SAP=9.59322;AB=0.601695;ABP=34.8095;RUN=1;RPP=3.34595;RPPR=14.2373;RPL=155.0;RPR=162.0;EPP=3.07195;EPPR=3.0257;DPRA=0.0;ODDS=65.8877;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996845;PAIREDR=0.985816;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.509;Dels=0.0;FS=3.1755;Haplo [...]
+chr17 64689940 . T C 2795.74 PASS SOMATIC;NS=2;DP=427;DPB=427.0;AC=1;AN=3;AF=0.25;RO=320;AO=107;PRO=0.0;PAO=0.0;QR=12063;QA=4126;PQR=0.0;PQA=0.0;SRF=185;SRR=135;SAF=68;SAR=39;SRP=19.9749;SAP=20.0777;AB=0.342949;ABP=69.8527;RUN=1;RPP=3.51765;RPPR=13.8677;RPL=51.0;RPR=56.0;EPP=4.00471;EPPR=3.68889;DPRA=2.71304;ODDS=72.7178;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99375;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.582;Dels=0.0;FS=4.78 [...]
+chr17 64690885 . TA T 269.196 REJECT NS=2;DP=86;DPB=219.091;AC=2;AN=3;AF=0.5;RO=2;AO=15;PRO=60.7952;PAO=56.2952;QR=75;QA=285;PQR=2009.47;PQA=1866.97;SRF=0;SRR=2;SAF=1;SAR=14;SRP=7.35324;SAP=27.4756;AB=0.174419;ABP=82.1933;RUN=1;RPP=4.31318;RPPR=7.35324;RPL=6.0;RPR=9.0;EPP=3.15506;EPPR=7.35324;DPRA=0.0;ODDS=15.5437;GTI=0;TYPE=del;CIGAR=1M1D31M;NUMALT=7;MEANALT=13.0;LEN=1;MQM=58.1333;MQMR=57.0;PAIRED=0.733333;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr17 64690885 . TAA T 269.196 REJECT NS=2;DP=86;DPB=219.091;AC=2;AN=2;AF=0.25;RO=2;AO=18;PRO=60.7952;PAO=48.7952;QR=75;QA=378;PQR=2009.47;PQA=1564.47;SRF=0;SRR=2;SAF=0;SAR=18;SRP=7.35324;SAP=42.0968;AB=0.209302;ABP=66.1345;RUN=1;RPP=3.49285;RPPR=7.35324;RPL=8.0;RPR=10.0;EPP=3.49285;EPPR=7.35324;DPRA=0.0;ODDS=15.5437;GTI=0;TYPE=del;CIGAR=1M2D30M;NUMALT=7;MEANALT=13.0;LEN=2;MQM=60.2778;MQMR=57.0;PAIRED=0.944444;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-1.93 [...]
+chr17 64690885 . TAAA T 269.196 REJECT SOMATIC;NS=2;DP=86;DPB=219.091;AC=1;AN=3;AF=0.0;RO=2;AO=11;PRO=60.7952;PAO=39.7119;QR=75;QA=278;PQR=2009.47;PQA=1336.3;SRF=0;SRR=2;SAF=1;SAR=10;SRP=7.35324;SAP=19.0002;AB=0.127907;ABP=106.433;RUN=1;RPP=3.20771;RPPR=7.35324;RPL=6.0;RPR=5.0;EPP=3.20771;EPPR=7.35324;DPRA=0.0;ODDS=15.5437;GTI=0;TYPE=del;CIGAR=1M3D29M;NUMALT=7;MEANALT=13.0;LEN=3;MQM=59.8182;MQMR=57.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr17 64690885 . TAAAA T 269.196 REJECT SOMATIC;NS=2;DP=86;DPB=219.091;AC=1;AN=3;AF=0.0;RO=2;AO=11;PRO=60.7952;PAO=35.7619;QR=75;QA=213;PQR=2009.47;PQA=1161.25;SRF=0;SRR=2;SAF=1;SAR=10;SRP=7.35324;SAP=19.0002;AB=0.127907;ABP=106.433;RUN=1;RPP=7.94546;RPPR=7.35324;RPL=8.0;RPR=3.0;EPP=4.78696;EPPR=7.35324;DPRA=0.0;ODDS=15.5437;GTI=0;TYPE=del;CIGAR=1M4D28M;NUMALT=7;MEANALT=13.0;LEN=4;MQM=59.0909;MQMR=57.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr17 64690885 . TAAAAAA T 269.196 REJECT SOMATIC;NS=2;DP=86;DPB=219.091;AC=1;AN=3;AF=0.0;RO=2;AO=7;PRO=60.7952;PAO=28.9286;QR=75;QA=162;PQR=2009.47;PQA=970.75;SRF=0;SRR=2;SAF=3;SAR=4;SRP=7.35324;SAP=3.32051;AB=0.0813953;ABP=133.905;RUN=1;RPP=5.80219;RPPR=7.35324;RPL=2.0;RPR=5.0;EPP=3.32051;EPPR=7.35324;DPRA=0.0;ODDS=15.5437;GTI=0;TYPE=del;CIGAR=1M6D26M;NUMALT=7;MEANALT=13.0;LEN=6;MQM=60.0;MQMR=57.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr17 64690886 . A T 269.196 REJECT SOMATIC;NS=2;DP=86;DPB=219.091;AC=1;AN=3;AF=0.0;RO=2;AO=4;PRO=60.7952;PAO=24.7833;QR=75;QA=116;PQR=2009.47;PQA=845.74;SRF=0;SRR=2;SAF=3;SAR=1;SRP=7.35324;SAP=5.18177;AB=0.0677966;ABP=98.7391;RUN=1;RPP=11.6962;RPPR=7.35324;RPL=0.0;RPR=4.0;EPP=5.18177;EPPR=7.35324;DPRA=0.0;ODDS=15.5437;GTI=0;TYPE=snp;CIGAR=1M1X31M;NUMALT=7;MEANALT=18.0;LEN=1;MQM=59.25;MQMR=57.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr17 64690906 . AAAAGGTATC GGTATT 269.196 REJECT SOMATIC;NS=2;DP=86;DPB=219.091;AC=1;AN=3;AF=0.0;RO=2;AO=2;PRO=60.7952;PAO=13.9286;QR=75;QA=32;PQR=2009.47;PQA=429.06;SRF=0;SRR=2;SAF=2;SAR=0;SRP=7.35324;SAP=7.35324;AB=0.0740741;ABP=45.5551;RUN=1;RPP=7.35324;RPPR=7.35324;RPL=0.0;RPR=2.0;EPP=7.35324;EPPR=7.35324;DPRA=0.0;ODDS=15.5437;GTI=0;TYPE=complex;CIGAR=1M4D25M1X2M;NUMALT=7;MEANALT=8.0;LEN=29;MQM=49.0;MQMR=57.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP: [...]
+chr17 64691905 . G A 17985.8 REJECT NS=2;DP=467;DPB=540.0;AC=4;AN=4;AF=1.0;RO=1;AO=539;PRO=0.0;PAO=0.0;QR=30;QA=20931;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=260;SAR=279;SRP=5.18177;SAP=4.46466;AB=0.0;ABP=0.0;RUN=1;RPP=6.88189;RPPR=5.18177;RPL=285.0;RPR=254.0;EPP=3.11102;EPPR=5.18177;DPRA=0.0;ODDS=90.0567;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988868;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.437;Dels=0.0;FS=0.0;HaplotypeScore=6.8983;MLEAC=2; [...]
+chr17 64692964 . C T 3441.17 PASS SOMATIC;NS=2;DP=490;DPB=490.0;AC=1;AN=3;AF=0.25;RO=360;AO=130;PRO=0.0;PAO=0.0;QR=13930;QA=4955;PQR=0.0;PQA=0.0;SRF=174;SRR=186;SAF=59;SAR=71;SRP=3.87889;SAP=5.41562;AB=0.367232;ABP=57.2112;RUN=1;RPP=3.61163;RPPR=5.42305;RPL=62.0;RPR=68.0;EPP=3.27756;EPPR=4.55446;DPRA=2.60294;ODDS=85.8721;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.812;Dels=0.0;FS=1.3;Hapl [...]
+chr17 64694935 . T A 26.5478 REJECT NS=2;DP=71;DPB=98.2963;AC=2;AN=2;AF=0.0;RO=17;AO=3;PRO=19.3929;PAO=4.97619;QR=621;QA=48;PQR=683.381;PQA=130.381;SRF=2;SRR=15;SAF=0;SAR=3;SRP=24.5973;SAP=9.52472;AB=0.0666667;ABP=76.4061;RUN=1;RPP=9.52472;RPPR=9.26925;RPL=3.0;RPR=0.0;EPP=9.52472;EPPR=9.26925;DPRA=0.0;ODDS=0.216742;GTI=0;TYPE=snp;CIGAR=1X26M;NUMALT=6;MEANALT=16.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.941176;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr17 64694935 . TAC AAA 26.5478 REJECT NS=2;DP=71;DPB=98.2963;AC=2;AN=2;AF=0.0;RO=17;AO=6;PRO=19.3929;PAO=3.47619;QR=621;QA=120;PQR=683.381;PQA=93.381;SRF=2;SRR=15;SAF=0;SAR=6;SRP=24.5973;SAP=16.0391;AB=0.084507;ABP=109.474;RUN=1;RPP=4.45795;RPPR=9.26925;RPL=4.0;RPR=2.0;EPP=4.45795;EPPR=9.26925;DPRA=0.0;ODDS=0.216742;GTI=0;TYPE=complex;CIGAR=1X1M1X24M;NUMALT=6;MEANALT=13.5;LEN=27;MQM=58.8333;MQMR=60.0;PAIRED=1.0;PAIREDR=0.941176;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:A [...]
+chr17 64694935 . TACA AAC 26.5478 REJECT NS=2;DP=71;DPB=98.2963;AC=2;AN=2;AF=0.0;RO=17;AO=5;PRO=19.3929;PAO=2.47619;QR=621;QA=92;PQR=683.381;PQA=79.381;SRF=2;SRR=15;SAF=0;SAR=5;SRP=24.5973;SAP=13.8677;AB=0.0704225;ABP=116.814;RUN=1;RPP=3.44459;RPPR=9.26925;RPL=2.0;RPR=3.0;EPP=3.44459;EPPR=9.26925;DPRA=0.0;ODDS=0.216742;GTI=0;TYPE=complex;CIGAR=1X2M1D23M;NUMALT=6;MEANALT=13.5;LEN=26;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.941176;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO: [...]
+chr17 64694937 . C A 26.5478 REJECT NS=2;DP=71;DPB=98.2963;AC=2;AN=2;AF=0.0;RO=17;AO=6;PRO=19.3929;PAO=5.39286;QR=621;QA=97;PQR=683.381;PQA=146.214;SRF=2;SRR=15;SAF=0;SAR=6;SRP=24.5973;SAP=16.0391;AB=0.084507;ABP=109.474;RUN=1;RPP=4.45795;RPPR=9.26925;RPL=4.0;RPR=2.0;EPP=4.45795;EPPR=9.26925;DPRA=0.0;ODDS=0.216742;GTI=0;TYPE=snp;CIGAR=2M1X24M;NUMALT=6;MEANALT=13.5;LEN=1;MQM=56.6667;MQMR=60.0;PAIRED=0.833333;PAIREDR=0.941176;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;ALERT;BaseQRankS [...]
+chr17 64694937 . C CA 26.5478 REJECT NS=2;DP=71;DPB=98.2963;AC=2;AN=2;AF=0.0;RO=17;AO=5;PRO=19.3929;PAO=17.8929;QR=621;QA=86;PQR=683.381;PQA=630.381;SRF=2;SRR=15;SAF=0;SAR=5;SRP=24.5973;SAP=13.8677;AB=0.0704225;ABP=116.814;RUN=1;RPP=3.44459;RPPR=9.26925;RPL=3.0;RPR=2.0;EPP=3.44459;EPPR=9.26925;DPRA=0.0;ODDS=0.216742;GTI=0;TYPE=ins;CIGAR=3M1I24M;NUMALT=6;MEANALT=13.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.941176;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;ALERT;BaseQRankSum=1.8 [...]
+chr17 64694937 . CA C 26.5478 REJECT NS=2;DP=71;DPB=98.2963;AC=2;AN=4;AF=0.5;RO=17;AO=9;PRO=19.3929;PAO=13.3929;QR=621;QA=214;PQR=683.381;PQA=441.881;SRF=2;SRR=15;SAF=3;SAR=6;SRP=24.5973;SAP=5.18177;AB=0.126761;ABP=88.9211;RUN=1;RPP=3.25157;RPPR=9.26925;RPL=4.0;RPR=5.0;EPP=9.04217;EPPR=9.26925;DPRA=0.0;ODDS=0.216742;GTI=0;TYPE=del;CIGAR=3M1D23M;NUMALT=6;MEANALT=13.5;LEN=1;MQM=58.6667;MQMR=60.0;PAIRED=1.0;PAIREDR=0.941176;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.933;FS=0. [...]
+chr17 64695287 . C T 454.975 PASS SOMATIC;NS=2;DP=85;DPB=85.0;AC=1;AN=3;AF=0.25;RO=62;AO=21;PRO=0.0;PAO=0.0;QR=1954;QA=725;PQR=0.0;PQA=0.0;SRF=30;SRR=32;SAF=8;SAR=13;SRP=3.15039;SAP=5.59539;AB=0.375;ABP=10.6105;RUN=1;RPP=3.1137;RPPR=19.9618;RPL=11.0;RPR=10.0;EPP=11.386;EPPR=9.87495;DPRA=1.93103;ODDS=18.969;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=3.0;LEN=1;MQM=60.0;MQMR=59.871;PAIRED=0.904762;PAIREDR=0.967742;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.038;Dels=0.0;FS=0.0;Haploty [...]
+chr17 64695328 . CA C 140.506 REJECT NS=2;DP=49;DPB=100.189;AC=2;AN=3;AF=0.25;RO=3;AO=5;PRO=37.9833;PAO=23.9833;QR=112;QA=130;PQR=1351.93;PQA=832.933;SRF=0;SRR=3;SAF=2;SAR=3;SRP=9.52472;SAP=3.44459;AB=0.102041;ABP=70.4146;RUN=1;RPP=3.44459;RPPR=9.52472;RPL=2.0;RPR=3.0;EPP=6.91895;EPPR=9.52472;DPRA=0.0;ODDS=14.5941;GTI=0;TYPE=del;CIGAR=1M1D35M;NUMALT=4;MEANALT=17.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.8;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr17 64695328 . CAA C 140.506 REJECT NS=2;DP=49;DPB=100.189;AC=2;AN=3;AF=0.25;RO=3;AO=9;PRO=37.9833;PAO=21.4833;QR=112;QA=217;PQR=1351.93;PQA=743.433;SRF=0;SRR=3;SAF=4;SAR=5;SRP=9.52472;SAP=3.25157;AB=0.183673;ABP=45.5977;RUN=1;RPP=5.18177;RPPR=9.52472;RPL=3.0;RPR=6.0;EPP=9.04217;EPPR=9.52472;DPRA=0.0;ODDS=14.5941;GTI=0;TYPE=del;CIGAR=1M2D34M;NUMALT=4;MEANALT=17.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.917;FS=0.0;ML [...]
+chr17 64695328 . CAAA C 140.506 REJECT NS=2;DP=49;DPB=100.189;AC=2;AN=2;AF=0.0;RO=3;AO=3;PRO=37.9833;PAO=18.15;QR=112;QA=81;PQR=1351.93;PQA=646.1;SRF=0;SRR=3;SAF=2;SAR=1;SRP=9.52472;SAP=3.73412;AB=0.0612245;ABP=84.9501;RUN=1;RPP=9.52472;RPPR=9.52472;RPL=0.0;RPR=3.0;EPP=3.73412;EPPR=9.52472;DPRA=0.0;ODDS=14.5941;GTI=0;TYPE=del;CIGAR=1M3D33M;NUMALT=4;MEANALT=17.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr17 64695328 . CAAAAAA C 140.506 REJECT NS=2;DP=49;DPB=100.189;AC=2;AN=2;AF=0.0;RO=3;AO=2;PRO=37.9833;PAO=17.4;QR=112;QA=48;PQR=1351.93;PQA=620.6;SRF=0;SRR=3;SAF=1;SAR=1;SRP=9.52472;SAP=3.0103;AB=0.0555556;ABP=64.7766;RUN=1;RPP=7.35324;RPPR=9.52472;RPL=2.0;RPR=0.0;EPP=3.0103;EPPR=9.52472;DPRA=0.0;ODDS=14.5941;GTI=0;TYPE=del;CIGAR=1M6D30M;NUMALT=4;MEANALT=23.0;LEN=6;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr17 64695640 . G A 1384.89 REJECT NS=2;DP=333;DPB=380.0;AC=2;AN=4;AF=0.5;RO=308;AO=72;PRO=0.0;PAO=0.0;QR=11623;QA=2752;PQR=0.0;PQA=0.0;SRF=164;SRR=144;SAF=35;SAR=37;SRP=5.83039;SAP=3.13094;AB=0.189474;ABP=321.28;RUN=1;RPP=8.92153;RPPR=5.83039;RPL=29.0;RPR=43.0;EPP=7.35324;EPPR=4.02553;DPRA=0.0;ODDS=1.47438;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.972222;PAIREDR=0.987013;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.2235;Dels=0.0;FS=0.8905;Haplotype [...]
+chr17 64696212 . T A 10308.985 REJECT NS=2;DP=272;DPB=314.0;AC=4;AN=4;AF=1.0;RO=1;AO=313;PRO=0.0;PAO=0.0;QR=39;QA=12071;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=183;SAR=130;SRP=5.18177;SAP=22.4981;AB=0.0;ABP=0.0;RUN=1;RPP=3.18374;RPPR=5.18177;RPL=154.0;RPR=159.0;EPP=6.6803;EPPR=5.18177;DPRA=0.0;ODDS=55.5257;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99361;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.292;Dels=0.0;FS=0.0;HaplotypeScore=2.9328;MLEAC=2; [...]
+chr17 64696485 . A G 2049.19 PASS SOMATIC;NS=2;DP=293;DPB=293.0;AC=1;AN=3;AF=0.25;RO=214;AO=79;PRO=0.0;PAO=0.0;QR=8282;QA=3013;PQR=0.0;PQA=0.0;SRF=116;SRR=98;SAF=42;SAR=37;SRP=6.29795;SAP=3.69747;AB=0.359091;ABP=40.9518;RUN=1;RPP=7.6556;RPPR=9.86972;RPL=46.0;RPR=33.0;EPP=12.9331;EPPR=9.86972;DPRA=3.0137;ODDS=46.5561;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987342;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.671;Dels=0.0;FS=0.0;Hap [...]
+chr17 64698065 . C G 2346.73 PASS SOMATIC;NS=2;DP=305;DPB=305.0;AC=1;AN=3;AF=0.25;RO=216;AO=88;PRO=0.0;PAO=0.0;QR=8320;QA=3383;PQR=0.0;PQA=0.0;SRF=81;SRR=135;SAF=32;SAR=56;SRP=32.3252;SAP=17.2236;AB=0.37931;ABP=32.3626;RUN=1;RPP=7.84676;RPPR=26.1727;RPL=51.0;RPR=37.0;EPP=3.89863;EPPR=7.87601;DPRA=3.17808;ODDS=46.5346;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99537;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.108;Dels=0.0;FS=2.359;H [...]
+chr17 64698381 . G T 1315.76 PASS SOMATIC;NS=2;DP=160;DPB=160.0;AC=1;AN=3;AF=0.25;RO=109;AO=51;PRO=0.0;PAO=0.0;QR=4194;QA=1961;PQR=0.0;PQA=0.0;SRF=88;SRR=21;SAF=40;SAR=11;SRP=92.4391;SAP=38.8183;AB=0.41129;ABP=11.486;RUN=1;RPP=21.7871;RPPR=3.98647;RPL=15.0;RPR=36.0;EPP=12.5903;EPPR=11.7958;DPRA=3.44444;ODDS=23.5025;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.980392;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.35;Dels=0.0;FS=1.868;Hap [...]
+chr17 64699908 . A G 3608.2 REJECT NS=2;DP=111;DPB=131.0;AC=4;AN=4;AF=1.0;RO=0;AO=129;PRO=0.0;PAO=0.0;QR=0;QA=4459;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=113;SAR=16;SRP=0.0;SAP=161.393;AB=0.0;ABP=0.0;RUN=1;RPP=10.4337;RPPR=0.0;RPL=54.0;RPR=75.0;EPP=4.37378;EPPR=0.0;DPRA=0.0;ODDS=28.0384;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=59.4186;MQMR=0.0;PAIRED=0.984496;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=66.5153;MLEAC=2;MLEAF=1.0;MQ=59.515;QD=30.85;SOR=3 [...]
+chr17 64699915 . G GA 1739.625 REJECT NS=2;DP=103;DPB=182.407;AC=2;AN=3;AF=0.5;RO=14;AO=63;PRO=44.3333;PAO=56.3333;QR=520;QA=2122;PQR=1580.0;PQA=1985.5;SRF=11;SRR=3;SAF=55;SAR=8;SRP=12.937;SAP=79.1497;AB=0.605769;ABP=13.116;RUN=1;RPP=18.2106;RPPR=5.49198;RPL=21.0;RPR=42.0;EPP=12.9715;EPPR=3.63072;DPRA=0.0;ODDS=7.04526;GTI=0;TYPE=ins;CIGAR=1M1I26M;NUMALT=2;MEANALT=7.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984127;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.601;F [...]
+chr17 64699915 . G GAA 2065.52 REJECT NS=2;DP=104;DPB=182.407;AC=2;AN=2;AF=0.25;RO=14;AO=16;PRO=44.3333;PAO=42.3333;QR=520;QA=581;PQR=1580.0;PQA=1502.5;SRF=11;SRR=3;SAF=14;SAR=2;SRP=12.937;SAP=22.5536;AB=0.153846;ABP=111.25;RUN=1;RPP=16.582;RPPR=5.49198;RPL=3.0;RPR=13.0;EPP=7.89611;EPPR=3.63072;DPRA=0.0;ODDS=7.04526;GTI=0;TYPE=ins;CIGAR=1M2I26M;NUMALT=2;MEANALT=7.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr17 64700277 . T TA 2806.7 REJECT NS=2;DP=266;DPB=382.222;AC=2;AN=2;AF=0.0;RO=50;AO=15;PRO=69.0833;PAO=64.0833;QR=1800;QA=436;PQR=2395.77;PQA=2234.77;SRF=25;SRR=25;SAF=5;SAR=10;SRP=3.0103;SAP=6.62942;AB=0.056391;ABP=457.681;RUN=1;RPP=10.1038;RPPR=32.3686;RPL=4.0;RPR=11.0;EPP=3.15506;EPPR=14.1282;DPRA=0.0;ODDS=57.9809;GTI=0;TYPE=ins;CIGAR=1M1I26M;NUMALT=4;MEANALT=30.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr17 64700277 . TA T 2806.7 REJECT NS=2;DP=266;DPB=382.222;AC=2;AN=4;AF=0.5;RO=50;AO=97;PRO=69.0833;PAO=67.0833;QR=1800;QA=3348;PQR=2395.77;PQA=2272.77;SRF=25;SRR=25;SAF=49;SAR=48;SRP=3.0103;SAP=3.03269;AB=0.364662;ABP=45.3295;RUN=1;RPP=21.8372;RPPR=32.3686;RPL=34.0;RPR=63.0;EPP=6.79359;EPPR=14.1282;DPRA=0.0;ODDS=57.9809;GTI=0;TYPE=del;CIGAR=1M1D25M;NUMALT=4;MEANALT=30.0;LEN=1;MQM=60.1237;MQMR=60.0;PAIRED=0.989691;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.755; [...]
+chr17 64700277 . TAA T 2806.7 REJECT NS=2;DP=266;DPB=382.222;AC=2;AN=2;AF=0.0;RO=50;AO=33;PRO=69.0833;PAO=47.75;QR=1800;QA=1050;PQR=2395.77;PQA=1622.1;SRF=25;SRR=25;SAF=12;SAR=21;SRP=3.0103;SAP=8.34028;AB=0.12406;ABP=329.548;RUN=1;RPP=4.65535;RPPR=32.3686;RPL=14.0;RPR=19.0;EPP=4.65535;EPPR=14.1282;DPRA=0.0;ODDS=57.9809;GTI=0;TYPE=del;CIGAR=1M2D24M;NUMALT=4;MEANALT=30.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=0.939394;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.733 [...]
+chr17 64700277 . TAAA T 2806.7 REJECT NS=2;DP=266;DPB=382.222;AC=2;AN=2;AF=0.0;RO=50;AO=11;PRO=69.0833;PAO=44.0;QR=1800;QA=384;PQR=2395.77;PQA=1517.6;SRF=25;SRR=25;SAF=9;SAR=2;SRP=3.0103;SAP=12.6832;AB=0.0413534;ABP=489.028;RUN=1;RPP=7.94546;RPPR=32.3686;RPL=8.0;RPR=3.0;EPP=7.94546;EPPR=14.1282;DPRA=0.0;ODDS=57.9809;GTI=0;TYPE=del;CIGAR=1M3D23M;NUMALT=4;MEANALT=30.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr17 64701109 . G A 3947.81 PASS SOMATIC;NS=2;DP=518;DPB=518.0;AC=1;AN=3;AF=0.25;RO=374;AO=144;PRO=0.0;PAO=0.0;QR=14357;QA=5573;PQR=0.0;PQA=0.0;SRF=185;SRR=189;SAF=79;SAR=65;SRP=3.1032;SAP=5.96592;AB=0.38814;ABP=43.3318;RUN=1;RPP=3.55317;RPPR=3.84637;RPL=75.0;RPR=69.0;EPP=5.18177;EPPR=4.14829;DPRA=2.52381;ODDS=92.663;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997326;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.421;Dels=0.0;FS=4.068; [...]
+chr17 64701623 . G A 16619.5 REJECT NS=2;DP=433;DPB=503.0;AC=4;AN=4;AF=1.0;RO=0;AO=503;PRO=0.0;PAO=0.0;QR=0;QA=19417;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=270;SAR=233;SRP=0.0;SAP=8.92033;AB=0.0;ABP=0.0;RUN=1;RPP=3.98163;RPPR=0.0;RPL=244.0;RPR=259.0;EPP=4.25793;EPPR=0.0;DPRA=0.0;ODDS=89.7576;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994036;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.8294;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.895;SOR=0 [...]
+chr17 64702597 . C CA 699.74 PASS DP=76;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.8805;FS=9.25;MLEAC=1;MLEAF=0.5;MQ=54.35;MQRankSum=-0.6115;QD=9.915;RPA=14,15;RU=A;ReadPosRankSum=-0.5745;SOR=1.3335;STR;ClippingRankSum=-0.392 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:7,28:35:46.0:539,0,46:28:80:35:1:.:.:.:.:.:-0.00997748 0/1:32,59:110:99.0:935,0,351:59:65:91:.:1:.:.:.:.:-0.0533013
+chr17 64702755 . C A 1213.33 REJECT NS=2;DP=206;DPB=277.818;AC=2;AN=2;AF=0.0;RO=45;AO=12;PRO=33.6333;PAO=25.0833;QR=1607;QA=134;PQR=1156.0;PQA=818.0;SRF=28;SRR=17;SAF=0;SAR=12;SRP=8.84915;SAP=29.068;AB=0.0582524;ABP=352.175;RUN=1;RPP=21.1059;RPPR=38.1882;RPL=1.0;RPR=11.0;EPP=21.1059;EPPR=3.05855;DPRA=0.0;ODDS=67.9769;GTI=0;TYPE=snp;CIGAR=1X21M;NUMALT=5;MEANALT=20.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr17 64702755 . C CA 1103.53 REJECT NS=2;DP=192;DPB=277.818;AC=2;AN=4;AF=0.5;RO=45;AO=58;PRO=33.6333;PAO=35.1333;QR=1607;QA=1728;PQR=1156.0;PQA=1184.0;SRF=28;SRR=17;SAF=34;SAR=24;SRP=8.84915;SAP=6.75422;AB=0.281553;ABP=88.3934;RUN=1;RPP=75.4926;RPPR=38.1882;RPL=7.0;RPR=51.0;EPP=3.60933;EPPR=3.05855;DPRA=0.0;ODDS=67.9769;GTI=0;TYPE=ins;CIGAR=1M1I21M;NUMALT=5;MEANALT=20.5;LEN=1;MQM=60.1379;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.0375 [...]
+chr17 64702755 . CA C 1213.33 REJECT NS=2;DP=206;DPB=277.818;AC=2;AN=2;AF=0.0;RO=45;AO=15;PRO=33.6333;PAO=27.3833;QR=1607;QA=439;PQR=1156.0;PQA=922.667;SRF=28;SRR=17;SAF=9;SAR=6;SRP=8.84915;SAP=4.31318;AB=0.0728155;ABP=329.532;RUN=1;RPP=4.31318;RPPR=38.1882;RPL=6.0;RPR=9.0;EPP=6.62942;EPPR=3.05855;DPRA=0.0;ODDS=67.9769;GTI=0;TYPE=del;CIGAR=1M1D20M;NUMALT=5;MEANALT=20.5;LEN=1;MQM=59.9333;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr17 64702770 . GAGT AGAGG 1213.33 REJECT NS=2;DP=206;DPB=277.818;AC=2;AN=2;AF=0.0;RO=45;AO=18;PRO=33.6333;PAO=12.3833;QR=1607;QA=288;PQR=1156.0;PQA=403.667;SRF=28;SRR=17;SAF=18;SAR=0;SRP=8.84915;SAP=42.0968;AB=0.0873786;ABP=307.649;RUN=1;RPP=3.0103;RPPR=38.1882;RPL=9.0;RPR=9.0;EPP=3.0103;EPPR=3.05855;DPRA=0.0;ODDS=67.9769;GTI=0;TYPE=complex;CIGAR=1M1I17M1X3M;NUMALT=5;MEANALT=20.5;LEN=23;MQM=57.1111;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:Q [...]
+chr17 64702773 . T G 1213.33 REJECT NS=2;DP=206;DPB=277.818;AC=2;AN=2;AF=0.0;RO=45;AO=12;PRO=33.6333;PAO=12.3833;QR=1607;QA=189;PQR=1156.0;PQA=403.667;SRF=28;SRR=17;SAF=12;SAR=0;SRP=8.84915;SAP=29.068;AB=0.0582524;ABP=352.175;RUN=1;RPP=5.9056;RPPR=38.1882;RPL=8.0;RPR=4.0;EPP=5.9056;EPPR=3.05855;DPRA=0.0;ODDS=67.9769;GTI=0;TYPE=snp;CIGAR=18M1X3M;NUMALT=5;MEANALT=20.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr17 64703379 . T C 16483.85 REJECT NS=2;DP=430;DPB=489.0;AC=4;AN=4;AF=1.0;RO=0;AO=489;PRO=0.0;PAO=0.0;QR=0;QA=18910;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=245;SAR=244;SRP=0.0;SAP=3.01474;AB=0.0;ABP=0.0;RUN=1;RPP=8.45008;RPPR=0.0;RPL=262.0;RPR=227.0;EPP=3.76077;EPPR=0.0;DPRA=0.0;ODDS=77.3575;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99591;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9243;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=24.11;SOR=0. [...]
+chr17 64704385 . A G 2959.53 PASS SOMATIC;NS=2;DP=494;DPB=494.0;AC=1;AN=3;AF=0.25;RO=376;AO=117;PRO=0.0;PAO=0.0;QR=14250;QA=4446;PQR=0.0;PQA=0.0;SRF=181;SRR=195;SAF=55;SAR=62;SRP=4.14224;SAP=3.91972;AB=0.325;ABP=98.7722;RUN=1;RPP=12.8283;RPPR=3.1027;RPL=47.0;RPR=70.0;EPP=7.18621;EPPR=3.21821;DPRA=2.68657;ODDS=84.5167;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.982906;PAIREDR=0.99734;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.705;Dels=0.0;FS=1.3 [...]
+chr17 64705200 . T C 16526.8 REJECT NS=2;DP=434;DPB=501.0;AC=4;AN=4;AF=1.0;RO=0;AO=500;PRO=0.0;PAO=0.0;QR=0;QA=19226;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=267;SAR=233;SRP=0.0;SAP=8.03074;AB=0.0;ABP=0.0;RUN=1;RPP=4.41741;RPPR=0.0;RPL=259.0;RPR=241.0;EPP=5.51184;EPPR=0.0;DPRA=0.0;ODDS=85.4246;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.919;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.935;SOR=0.877 [...]
+chr17 64705419 . C T 9.61225 REJECT NS=2;DP=15;DPB=79.3333;AC=2;AN=2;AF=0.0;RO=0;AO=2;PRO=32.1829;PAO=18.711;QR=0;QA=38;PQR=1170.33;PQA=445.17;SRF=0;SRR=0;SAF=0;SAR=2;SRP=0.0;SAP=7.35324;AB=0.0;ABP=0.0;RUN=1;RPP=7.35324;RPPR=0.0;RPL=2.0;RPR=0.0;EPP=7.35324;EPPR=0.0;DPRA=0.0;ODDS=2.09051;GTI=0;TYPE=snp;CIGAR=1X38M;NUMALT=10;MEANALT=7.0;LEN=1;MQM=45.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB: [...]
+chr17 64705419 . CTTTTT C 9.61225 REJECT NS=2;DP=15;DPB=79.3333;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=32.1829;PAO=20.6829;QR=0;QA=40;PQR=1170.33;PQA=746.326;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.142857;ABP=10.7656;RUN=1;RPP=5.18177;RPPR=0.0;RPL=1.0;RPR=0.0;EPP=5.18177;EPPR=0.0;DPRA=0.875;ODDS=2.09051;GTI=0;TYPE=del;CIGAR=1M5D33M;NUMALT=10;MEANALT=5.0;LEN=5;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:C [...]
+chr17 64705419 . CTTTTTT C 9.61225 REJECT NS=2;DP=15;DPB=79.3333;AC=2;AN=3;AF=0.25;RO=0;AO=1;PRO=32.1829;PAO=20.3495;QR=0;QA=39;PQR=1170.33;PQA=705.993;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.0;ABP=0.0;RUN=1;RPP=5.18177;RPPR=0.0;RPL=0.0;RPR=1.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=2.09051;GTI=0;TYPE=del;CIGAR=1M6D32M;NUMALT=10;MEANALT=7.0;LEN=6;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:Cal [...]
+chr17 64705419 . CTTTTTTT C 9.61225 REJECT NS=2;DP=15;DPB=79.3333;AC=2;AN=2;AF=0.0;RO=0;AO=4;PRO=32.1829;PAO=15.0995;QR=0;QA=105;PQR=1170.33;PQA=536.493;SRF=0;SRR=0;SAF=2;SAR=2;SRP=0.0;SAP=3.0103;AB=0.428571;ABP=3.32051;RUN=1;RPP=3.0103;RPPR=0.0;RPL=2.0;RPR=2.0;EPP=3.0103;EPPR=0.0;DPRA=0.0;ODDS=2.09051;GTI=0;TYPE=del;CIGAR=1M7D31M;NUMALT=10;MEANALT=6.0;LEN=7;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-1.495;FS=0.0;MLEAC=1;MLEAF=0.5;MQ= [...]
+chr17 64705419 . CTTTTTTTT C 9.61225 REJECT NS=2;DP=15;DPB=79.3333;AC=2;AN=2;AF=0.0;RO=0;AO=2;PRO=32.1829;PAO=13.6995;QR=0;QA=31;PQR=1170.33;PQA=480.493;SRF=0;SRR=0;SAF=0;SAR=2;SRP=0.0;SAP=7.35324;AB=0.142857;ABP=10.7656;RUN=1;RPP=7.35324;RPPR=0.0;RPL=2.0;RPR=0.0;EPP=7.35324;EPPR=0.0;DPRA=0.0;ODDS=2.09051;GTI=0;TYPE=del;CIGAR=1M8D30M;NUMALT=10;MEANALT=6.0;LEN=8;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV: [...]
+chr17 64705419 . CTTTTTTTTT C 9.61225 REJECT NS=2;DP=15;DPB=79.3333;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=32.1829;PAO=12.1995;QR=0;QA=15;PQR=1170.33;PQA=426.993;SRF=0;SRR=0;SAF=0;SAR=1;SRP=0.0;SAP=5.18177;AB=0.0;ABP=0.0;RUN=1;RPP=5.18177;RPPR=0.0;RPL=1.0;RPR=0.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=2.09051;GTI=0;TYPE=del;CIGAR=1M9D29M;NUMALT=10;MEANALT=7.0;LEN=9;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:C [...]
+chr17 64705419 . CTTTTTTTTTTT C 9.61225 REJECT NS=2;DP=15;DPB=79.3333;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=32.1829;PAO=10.771;QR=0;QA=14;PQR=1170.33;PQA=373.136;SRF=0;SRR=0;SAF=0;SAR=1;SRP=0.0;SAP=5.18177;AB=0.0;ABP=0.0;RUN=1;RPP=5.18177;RPPR=0.0;RPL=1.0;RPR=0.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=2.09051;GTI=0;TYPE=del;CIGAR=1M11D27M;NUMALT=10;MEANALT=7.0;LEN=11;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallH [...]
+chr17 64705428 . TTTTTTT C 9.61225 REJECT NS=2;DP=15;DPB=79.3333;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=32.1829;PAO=7.61818;QR=0;QA=39;PQR=1170.33;PQA=262.427;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.0;ABP=0.0;RUN=1;RPP=5.18177;RPPR=0.0;RPL=0.0;RPR=1.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=2.09051;GTI=0;TYPE=complex;CIGAR=1M6D8M1X23M;NUMALT=10;MEANALT=7.0;LEN=33;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:Ca [...]
+chr17 64705431 . TTTTT C 9.61225 REJECT NS=2;DP=15;DPB=79.3333;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=32.1829;PAO=8.39596;QR=0;QA=15;PQR=1170.33;PQA=289.761;SRF=0;SRR=0;SAF=0;SAR=1;SRP=0.0;SAP=5.18177;AB=0.142857;ABP=10.7656;RUN=1;RPP=5.18177;RPPR=0.0;RPL=1.0;RPR=0.0;EPP=5.18177;EPPR=0.0;DPRA=0.875;ODDS=2.09051;GTI=0;TYPE=complex;CIGAR=1M4D11M1X22M;NUMALT=10;MEANALT=5.0;LEN=35;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr17 64705441 . TTTTTTGAG AA 9.61225 REJECT NS=2;DP=15;DPB=79.3333;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=32.1829;PAO=15.29;QR=0;QA=14;PQR=1170.33;PQA=547.883;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.142857;ABP=10.7656;RUN=1;RPP=5.18177;RPPR=0.0;RPL=0.0;RPR=1.0;EPP=5.18177;EPPR=0.0;DPRA=0.875;ODDS=2.09051;GTI=0;TYPE=complex;CIGAR=22M7D1M1X8M;NUMALT=10;MEANALT=5.0;LEN=32;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr17 64705556 . G C 497.144 PASS SOMATIC;NS=2;DP=90;DPB=90.0;AC=1;AN=3;AF=0.25;RO=66;AO=24;PRO=0.0;PAO=0.0;QR=2315;QA=797;PQR=0.0;PQA=0.0;SRF=33;SRR=33;SAF=14;SAR=10;SRP=3.0103;SAP=4.45795;AB=0.375;ABP=11.6962;RUN=1;RPP=3.37221;RPPR=3.53672;RPL=13.0;RPR=11.0;EPP=6.26751;EPPR=3.1419;DPRA=2.46154;ODDS=17.1952;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.875;MQMR=60.0;PAIRED=0.958333;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.006;Dels=0.0;FS=3.541;Haplotyp [...]
+chr17 64705799 . G GT 316.205 REJECT NS=2;DP=300;DPB=428.69;AC=2;AN=4;AF=0.5;RO=236;AO=28;PRO=118.333;PAO=72.3333;QR=8773;QA=1003;PQR=4250.0;PQA=2517.0;SRF=161;SRR=75;SAF=20;SAR=8;SRP=71.062;SAP=14.1779;AB=0.0933333;ABP=433.946;RUN=1;RPP=3.32051;RPPR=3.15752;RPL=15.0;RPR=13.0;EPP=5.80219;EPPR=3.0471;DPRA=0.0;ODDS=25.7367;GTI=0;TYPE=ins;CIGAR=1M1I28M;NUMALT=2;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.983051;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr17 64705799 . GT G 316.205 REJECT NS=2;DP=300;DPB=428.69;AC=2;AN=2;AF=0.0;RO=236;AO=18;PRO=118.333;PAO=63.3333;QR=8773;QA=651;PQR=4250.0;PQA=2240.0;SRF=161;SRR=75;SAF=11;SAR=7;SRP=71.062;SAP=4.9405;AB=0.06;ABP=507.487;RUN=1;RPP=3.49285;RPPR=3.15752;RPL=8.0;RPR=10.0;EPP=3.0103;EPPR=3.0471;DPRA=0.0;ODDS=25.7367;GTI=0;TYPE=del;CIGAR=1M1D27M;NUMALT=2;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.983051;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr17 64706781 . A G 3399.06 PASS SOMATIC;NS=2;DP=448;DPB=448.0;AC=1;AN=4;AF=0.25;RO=316;AO=131;PRO=0.0;PAO=0.0;QR=11884;QA=4905;PQR=0.0;PQA=0.0;SRF=127;SRR=189;SAF=60;SAR=71;SRP=29.4253;SAP=5.01601;AB=0.373219;ABP=52.0138;RUN=1;RPP=3.82253;RPPR=3.12025;RPL=62.0;RPR=69.0;EPP=8.99428;EPPR=17.5509;DPRA=3.61856;ODDS=60.8036;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987342;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.138;Dels=0.0;FS=4.304;Hapl [...]
+chr17 64706992 . C CA 43.3911 PASS SOMATIC;NS=2;DP=85;DPB=113.542;AC=2;AN=2;AF=0.0;RO=63;AO=7;PRO=28.0;PAO=19.0;QR=2343;QA=203;PQR=971.333;PQA=621.333;SRF=26;SRR=37;SAF=4;SAR=3;SRP=7.18091;SAP=3.32051;AB=0.107692;ABP=89.9026;RUN=1;RPP=10.7656;RPPR=8.83536;RPL=6.0;RPR=1.0;EPP=3.32051;EPPR=15.4532;DPRA=0.0;ODDS=1.86888;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=2;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984127;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr17 64706992 . CA C 43.3911 REJECT NS=2;DP=85;DPB=113.542;AC=2;AN=4;AF=0.5;RO=63;AO=10;PRO=28.0;PAO=20.0;QR=2343;QA=300;PQR=971.333;PQA=662.333;SRF=26;SRR=37;SAF=0;SAR=10;SRP=7.18091;SAP=24.725;AB=0.117647;ABP=110.945;RUN=1;RPP=6.48466;RPPR=8.83536;RPL=7.0;RPR=3.0;EPP=6.48466;EPPR=15.4532;DPRA=0.0;ODDS=1.86888;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=2;MEANALT=4.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984127;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr17 64707202 . T C 2271.63 PASS SOMATIC;NS=2;DP=314;DPB=314.0;AC=1;AN=3;AF=0.25;RO=224;AO=90;PRO=0.0;PAO=0.0;QR=8548;QA=3428;PQR=0.0;PQA=0.0;SRF=176;SRR=48;SAF=71;SAR=19;SRP=161.838;SAP=68.251;AB=0.376569;ABP=34.6375;RUN=1;RPP=37.8504;RPPR=96.1122;RPL=26.0;RPR=64.0;EPP=12.6613;EPPR=11.735;DPRA=3.18667;ODDS=47.7575;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.7778;MQMR=59.9688;PAIRED=1.0;PAIREDR=0.995536;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.775;Dels=0.0;FS=0. [...]
+chr17 64707461 . A G 4405.94 PASS SOMATIC;NS=2;DP=563;DPB=563.0;AC=1;AN=3;AF=0.25;RO=397;AO=165;PRO=0.0;PAO=0.0;QR=15360;QA=6263;PQR=0.0;PQA=0.0;SRF=197;SRR=200;SAF=78;SAR=87;SRP=3.05953;SAP=4.0763;AB=0.392857;ABP=44.8887;RUN=1;RPP=14.0782;RPPR=24.7196;RPL=68.0;RPR=97.0;EPP=25.133;EPPR=32.1584;DPRA=2.93706;ODDS=89.565;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993939;PAIREDR=0.992443;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.333;Dels=0.0;FS=0 [...]
+chr17 64707598 . A G 4022.49 PASS SOMATIC;NS=2;DP=554;DPB=554.0;AC=1;AN=3;AF=0.25;RO=400;AO=154;PRO=0.0;PAO=0.0;QR=14797;QA=5840;PQR=0.0;PQA=0.0;SRF=194;SRR=206;SAF=81;SAR=73;SRP=3.79203;SAP=3.91273;AB=0.357309;ABP=79.2335;RUN=1;RPP=8.65049;RPPR=4.40004;RPL=87.0;RPR=67.0;EPP=5.77399;EPPR=8.56927;DPRA=3.50407;ODDS=77.6305;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993506;PAIREDR=0.995;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.913;Dels=0.0;FS=0 [...]
+chr17 64708358 . C G 17061.55 REJECT NS=2;DP=452;DPB=510.0;AC=4;AN=4;AF=1.0;RO=0;AO=509;PRO=0.0;PAO=0.0;QR=0;QA=19373;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=287;SAR=222;SRP=0.0;SAP=21.0348;AB=0.0;ABP=0.0;RUN=1;RPP=3.11695;RPPR=0.0;RPL=252.0;RPR=257.0;EPP=14.9939;EPPR=0.0;DPRA=0.0;ODDS=76.0364;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=7.7927;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.91;SOR=0.9225 [...]
+chr17 64708396 . T C 18084.1 REJECT NS=2;DP=478;DPB=535.0;AC=4;AN=4;AF=1.0;RO=1;AO=534;PRO=0.0;PAO=0.0;QR=38;QA=20450;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=279;SAR=255;SRP=5.18177;SAP=5.35256;AB=0.0;ABP=0.0;RUN=1;RPP=9.51658;RPPR=5.18177;RPL=247.0;RPR=287.0;EPP=13.1764;EPPR=5.18177;DPRA=0.0;ODDS=74.2113;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994382;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.983;Dels=0.0;FS=0.0;HaplotypeScore=7.7393;MLEAC=2; [...]
+chr17 64708436 . T A 18457.8 REJECT NS=2;DP=506;DPB=573.0;AC=4;AN=4;AF=1.0;RO=0;AO=573;PRO=0.0;PAO=0.0;QR=0;QA=21151;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=268;SAR=305;SRP=0.0;SAP=8.19834;AB=0.0;ABP=0.0;RUN=1;RPP=3.19599;RPPR=0.0;RPL=283.0;RPR=290.0;EPP=37.2119;EPPR=0.0;DPRA=0.0;ODDS=86.0099;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99651;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8796;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.955;SOR=0. [...]
+chr17 64708866 . A G 16120.35 REJECT NS=2;DP=426;DPB=492.0;AC=4;AN=4;AF=1.0;RO=0;AO=491;PRO=0.0;PAO=0.0;QR=0;QA=18735;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=244;SAR=247;SRP=0.0;SAP=3.0501;AB=0.0;ABP=0.0;RUN=1;RPP=3.0501;RPPR=0.0;RPL=244.0;RPR=247.0;EPP=9.737;EPPR=0.0;DPRA=0.0;ODDS=84.7052;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995927;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8043;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.475;SOR=0.82 [...]
+chr17 64709029 . T C 8320.46 REJECT NS=2;DP=345;DPB=406.0;AC=3;AN=4;AF=0.75;RO=101;AO=305;PRO=0.0;PAO=0.0;QR=3924;QA=11647;PQR=0.0;PQA=0.0;SRF=46;SRR=55;SAF=146;SAR=159;SRP=4.75178;SAP=4.21351;AB=0.652921;ABP=62.1176;RUN=1;RPP=5.06786;RPPR=3.0318;RPL=161.0;RPR=144.0;EPP=6.77656;EPPR=3.0318;DPRA=0.0;ODDS=72.7085;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.963934;PAIREDR=0.970297;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.714;Dels=0.0;FS=1.7135;Haploty [...]
+chr17 64709167 . C CTTT 208.285 REJECT NS=2;DP=22;DPB=109.241;AC=2;AN=3;AF=0.25;RO=4;AO=5;PRO=62.0;PAO=63.5;QR=140;QA=87;PQR=2158.0;PQA=2160.0;SRF=1;SRR=3;SAF=1;SAR=4;SRP=5.18177;SAP=6.91895;AB=0.227273;ABP=17.2236;RUN=1;RPP=13.8677;RPPR=3.0103;RPL=5.0;RPR=0.0;EPP=6.91895;EPPR=5.18177;DPRA=0.0;ODDS=0.399576;GTI=0;TYPE=ins;CIGAR=1M3I28M;NUMALT=2;MEANALT=7.0;LEN=3;MQM=45.2;MQMR=44.5;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICO [...]
+chr17 64709167 . C CTTTT 208.285 REJECT NS=2;DP=22;DPB=109.241;AC=2;AN=3;AF=0.25;RO=4;AO=2;PRO=62.0;PAO=62.5;QR=140;QA=55;PQR=2158.0;PQA=2146.0;SRF=1;SRR=3;SAF=1;SAR=1;SRP=5.18177;SAP=3.0103;AB=0.117647;ABP=24.5973;RUN=1;RPP=7.35324;RPPR=3.0103;RPL=2.0;RPR=0.0;EPP=3.0103;EPPR=5.18177;DPRA=0.0;ODDS=0.399576;GTI=0;TYPE=ins;CIGAR=1M4I28M;NUMALT=2;MEANALT=10.0;LEN=4;MQM=50.0;MQMR=44.5;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICO [...]
+chr17 64709370 . A G 3643.395 REJECT NS=2;DP=161;DPB=184.0;AC=3;AN=4;AF=0.75;RO=47;AO=137;PRO=0.0;PAO=0.0;QR=1787;QA=5158;PQR=0.0;PQA=0.0;SRF=45;SRR=2;SAF=124;SAR=13;SRP=88.4369;SAP=198.3;AB=0.65942;ABP=33.4739;RUN=1;RPP=38.0233;RPPR=16.3625;RPL=45.0;RPR=92.0;EPP=54.5075;EPPR=16.3625;DPRA=0.0;ODDS=29.7364;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992701;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.458;Dels=0.0;FS=3.2805;HaplotypeScore=2.9 [...]
+chr17 64709437 . G T 1554.8 PASS SOMATIC;NS=2;DP=247;DPB=247.0;AC=1;AN=3;AF=0.25;RO=183;AO=64;PRO=0.0;PAO=0.0;QR=6869;QA=2416;PQR=0.0;PQA=0.0;SRF=148;SRR=35;SAF=50;SAR=14;SRP=154.527;SAP=46.9826;AB=0.336842;ABP=46.9426;RUN=1;RPP=3.55317;RPPR=3.30695;RPL=30.0;RPR=34.0;EPP=11.6962;EPPR=38.9049;DPRA=3.33333;ODDS=36.5965;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.6406;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.374;Dels=0.0;FS=0.694;Hap [...]
+chr17 64710287 . G A 3130.96 PASS SOMATIC;NS=2;DP=437;DPB=437.0;AC=1;AN=3;AF=0.25;RO=315;AO=122;PRO=0.0;PAO=0.0;QR=11813;QA=4577;PQR=0.0;PQA=0.0;SRF=157;SRR=158;SAF=54;SAR=68;SRP=3.01719;SAP=6.49889;AB=0.356725;ABP=63.9893;RUN=1;RPP=6.49889;RPPR=12.4476;RPL=54.0;RPR=68.0;EPP=3.0815;EPPR=7.31878;DPRA=3.6;ODDS=60.2108;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991803;PAIREDR=0.993651;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.912;Dels=0.0;FS=3.6 [...]
+chr17 64710423 . A T 14062.9 REJECT NS=2;DP=379;DPB=435.0;AC=4;AN=4;AF=1.0;RO=1;AO=433;PRO=0.0;PAO=0.0;QR=27;QA=16292;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=196;SAR=237;SRP=5.18177;SAP=11.4404;AB=0.0;ABP=0.0;RUN=1;RPP=13.1656;RPPR=5.18177;RPL=239.0;RPR=194.0;EPP=6.6662;EPPR=5.18177;DPRA=0.0;ODDS=69.7004;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997691;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8798;MLEAC=2;MLEAF=1.0;MQ=60.0;QD [...]
+chr17 64710488 . A C 2894.03 PASS SOMATIC;NS=2;DP=446;DPB=446.0;AC=1;AN=3;AF=0.25;RO=334;AO=112;PRO=0.0;PAO=0.0;QR=12755;QA=4269;PQR=0.0;PQA=0.0;SRF=177;SRR=157;SAF=58;SAR=54;SRP=5.61087;SAP=3.32051;AB=0.340426;ABP=75.7777;RUN=1;RPP=3.08785;RPPR=3.66044;RPL=55.0;RPR=57.0;EPP=4.94911;EPPR=17.9896;DPRA=2.81197;ODDS=73.9524;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991071;PAIREDR=0.994012;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.592;Dels=0.0;F [...]
+chr17 64711248 . G GT 531.594 REJECT NS=2;DP=258;DPB=352.818;AC=2;AN=3;AF=0.25;RO=149;AO=37;PRO=83.0;PAO=61.0;QR=5310;QA=1165;PQR=2846.0;PQA=2012.0;SRF=90;SRR=59;SAF=27;SAR=10;SRP=17.0156;SAP=19.9713;AB=0.143411;ABP=287.961;RUN=1;RPP=3.5385;RPPR=3.37464;RPL=17.0;RPR=20.0;EPP=3.5385;EPPR=3.72441;DPRA=0.0;ODDS=2.63821;GTI=1;TYPE=ins;CIGAR=1M1I21M;NUMALT=2;MEANALT=18.5;LEN=1;MQM=60.7027;MQMR=59.9664;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.169;FS [...]
+chr17 64711248 . GT G 531.594 REJECT NS=2;DP=258;DPB=352.818;AC=2;AN=3;AF=0.25;RO=149;AO=23;PRO=83.0;PAO=54.0;QR=5310;QA=731;PQR=2846.0;PQA=1825.0;SRF=90;SRR=59;SAF=12;SAR=11;SRP=17.0156;SAP=3.10471;AB=0.0891473;ABP=381.284;RUN=1;RPP=7.63648;RPPR=3.37464;RPL=8.0;RPR=15.0;EPP=5.3706;EPPR=3.72441;DPRA=0.0;ODDS=2.63821;GTI=1;TYPE=del;CIGAR=1M1D20M;NUMALT=2;MEANALT=18.5;LEN=1;MQM=60.0;MQMR=59.9664;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-1.413;FS=5.245;M [...]
+chr17 64711817 . G A 10046.435000000001 REJECT NS=2;DP=458;DPB=525.0;AC=3;AN=4;AF=0.75;RO=158;AO=367;PRO=0.0;PAO=0.0;QR=5959;QA=13828;PQR=0.0;PQA=0.0;SRF=74;SRR=84;SAF=166;SAR=201;SRP=4.38465;SAP=10.2584;AB=0.6;ABP=37.3196;RUN=1;RPP=13.9505;RPPR=3.2302;RPL=205.0;RPR=162.0;EPP=3.15822;EPPR=6.52863;DPRA=0.0;ODDS=81.9872;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9728;MQMR=60.0;PAIRED=0.989101;PAIREDR=0.993671;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.595;Dels=0.0;FS=0.0;H [...]
+chr17 64711852 . G GT 283.721 REJECT NS=2;DP=429;DPB=496.857;AC=2;AN=4;AF=0.5;RO=359;AO=43;PRO=73.5;PAO=64.5;QR=13547;QA=1589;PQR=2565.5;PQA=2243.5;SRF=181;SRR=178;SAF=20;SAR=23;SRP=3.06474;SAP=3.46479;AB=0.100233;ABP=598.515;RUN=1;RPP=5.48477;RPPR=4.75837;RPL=18.0;RPR=25.0;EPP=7.10075;EPPR=8.82307;DPRA=0.0;ODDS=30.4455;GTI=0;TYPE=ins;CIGAR=1M1I13M;NUMALT=1;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991643;technology.ILLUMINA=1.0;BaseQRankSum=-1.365;FS=5.41;MLEAC=1;MLEAF=0 [...]
+chr17 64712271 . G GT 300.85 REJECT NS=2;DP=411;DPB=467.667;AC=2;AN=2;AF=0.0;RO=300;AO=39;PRO=47.5;PAO=41.5;QR=11089;QA=1204;PQR=1665.33;PQA=1441.33;SRF=151;SRR=149;SAF=14;SAR=25;SRP=3.03925;SAP=9.74743;AB=0.0948905;ABP=588.88;RUN=1;RPP=4.40227;RPPR=7.90335;RPL=22.0;RPR=17.0;EPP=3.51141;EPPR=14.5915;DPRA=0.0;ODDS=7.64314;GTI=0;TYPE=ins;CIGAR=1M1I14M;NUMALT=2;MEANALT=11.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996667;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr17 64712271 . GT G 300.85 REJECT NS=2;DP=411;DPB=467.667;AC=2;AN=4;AF=0.5;RO=300;AO=46;PRO=47.5;PAO=37.0;QR=11089;QA=1510;PQR=1665.33;PQA=1275.33;SRF=151;SRR=149;SAF=21;SAR=25;SRP=3.03925;SAP=3.76559;AB=0.111922;ABP=540.653;RUN=1;RPP=6.03148;RPPR=7.90335;RPL=27.0;RPR=19.0;EPP=7.73089;EPPR=14.5915;DPRA=0.0;ODDS=7.64314;GTI=0;TYPE=del;CIGAR=1M1D13M;NUMALT=2;MEANALT=11.0;LEN=1;MQM=60.6522;MQMR=60.0;PAIRED=0.956522;PAIREDR=0.996667;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR: [...]
+chr17 64712333 . A C 9230.235 REJECT NS=2;DP=418;DPB=483.0;AC=3;AN=4;AF=0.75;RO=141;AO=341;PRO=0.0;PAO=0.0;QR=5161;QA=12863;PQR=0.0;PQA=0.0;SRF=76;SRR=65;SAF=188;SAR=153;SRP=4.87376;SAP=10.811;AB=0.600567;ABP=34.0199;RUN=1;RPP=3.32233;RPPR=4.25774;RPL=167.0;RPR=174.0;EPP=3.5261;EPPR=6.47542;DPRA=0.0;ODDS=81.4268;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.1173;MQMR=60.0;PAIRED=0.991202;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=5.601;Dels=0.0;FS=0.6495;Haplotype [...]
+chr17 64712547 . C T 3154.4 PASS SOMATIC;NS=2;DP=482;DPB=482.0;AC=1;AN=3;AF=0.25;RO=360;AO=122;PRO=0.0;PAO=0.0;QR=13899;QA=4683;PQR=0.0;PQA=0.0;SRF=186;SRR=174;SAF=54;SAR=68;SRP=3.87889;SAP=6.49889;AB=0.331522;ABP=93.7401;RUN=1;RPP=3.65106;RPPR=4.96463;RPL=64.0;RPR=58.0;EPP=6.49889;EPPR=23.3015;DPRA=3.22807;ODDS=72.0396;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997222;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.482;Dels=0.0;FS=11.1 [...]
+chr17 64712832 . A G 3884.17 PASS SOMATIC;NS=2;DP=498;DPB=498.0;AC=1;AN=3;AF=0.25;RO=353;AO=144;PRO=0.0;PAO=0.0;QR=13422;QA=5552;PQR=0.0;PQA=0.0;SRF=177;SRR=176;SAF=76;SAR=68;SRP=3.01645;SAP=3.9754;AB=0.373057;ABP=57.0383;RUN=1;RPP=13.2042;RPPR=13.3509;RPL=85.0;RPR=59.0;EPP=4.51827;EPPR=19.0103;DPRA=3.44643;ODDS=70.8714;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994334;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.564;Dels=0.0;FS=6.85 [...]
+chr17 64713025 . A G 15643.9 REJECT NS=2;DP=411;DPB=478.0;AC=4;AN=4;AF=1.0;RO=0;AO=478;PRO=0.0;PAO=0.0;QR=0;QA=18424;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=233;SAR=245;SRP=0.0;SAP=3.66447;AB=0.0;ABP=0.0;RUN=1;RPP=4.82743;RPPR=0.0;RPL=229.0;RPR=249.0;EPP=16.2572;EPPR=0.0;DPRA=0.0;ODDS=87.3153;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997908;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=25.245;SOR=0 [...]
+chr17 64713272 . T C 3888.05 PASS SOMATIC;NS=2;DP=480;DPB=480.0;AC=1;AN=3;AF=0.25;RO=334;AO=145;PRO=0.0;PAO=0.0;QR=12556;QA=5518;PQR=0.0;PQA=0.0;SRF=170;SRR=164;SAF=76;SAR=69;SRP=3.24435;SAP=3.74411;AB=0.384615;ABP=46.6068;RUN=1;RPP=3.14508;RPPR=3.03631;RPL=74.0;RPR=71.0;EPP=4.82236;EPPR=6.15698;DPRA=3.66019;ODDS=65.2841;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993103;PAIREDR=0.997006;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.476;Dels=0.0;F [...]
+chr17 64713437 . A G 14863.25 REJECT NS=2;DP=390;DPB=441.0;AC=4;AN=4;AF=1.0;RO=0;AO=440;PRO=0.0;PAO=0.0;QR=0;QA=16852;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=208;SAR=232;SRP=0.0;SAP=5.85295;AB=0.0;ABP=0.0;RUN=1;RPP=3.32615;RPPR=0.0;RPL=216.0;RPR=224.0;EPP=3.72096;EPPR=0.0;DPRA=0.0;ODDS=67.3709;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.7934;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.26;SOR=0.809 [...]
+chr17 64714367 . G A 2591.86 PASS SOMATIC;NS=2;DP=370;DPB=370.0;AC=1;AN=3;AF=0.25;RO=272;AO=98;PRO=0.0;PAO=0.0;QR=10401;QA=3777;PQR=0.0;PQA=0.0;SRF=98;SRR=174;SAF=43;SAR=55;SRP=49.1222;SAP=6.20103;AB=0.375969;ABP=37.4845;RUN=1;RPP=3.09893;RPPR=7.60871;RPL=48.0;RPR=50.0;EPP=20.3821;EPPR=59.3408;DPRA=0.0;ODDS=62.8725;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989796;PAIREDR=0.996324;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.597;Dels=0.0;FS=4.53 [...]
+chr17 64714579 . C T 691.674 PASS SOMATIC;NS=2;DP=97;DPB=97.0;AC=1;AN=3;AF=0.25;RO=69;AO=28;PRO=0.0;PAO=0.0;QR=2610;QA=1058;PQR=0.0;PQA=0.0;SRF=10;SRR=59;SAF=7;SAR=21;SRP=78.5712;SAP=18.2106;AB=0.4;ABP=9.09042;RUN=1;RPP=7.97367;RPPR=33.2536;RPL=18.0;RPR=10.0;EPP=10.7656;EPPR=61.1995;DPRA=2.59259;ODDS=17.8521;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.964286;PAIREDR=0.985507;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.055;Dels=0.0;FS=10.222;Hap [...]
+chr17 64715108 . A T 7952.5 REJECT NS=2;DP=361;DPB=408.0;AC=3;AN=4;AF=0.75;RO=123;AO=285;PRO=0.0;PAO=0.0;QR=4731;QA=10810;PQR=0.0;PQA=0.0;SRF=55;SRR=68;SAF=118;SAR=167;SRP=5.99387;SAP=21.304;AB=0.60828;ABP=34.9877;RUN=1;RPP=4.72462;RPPR=17.8575;RPL=150.0;RPR=135.0;EPP=4.29794;EPPR=3.87536;DPRA=0.0;ODDS=59.605;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992982;PAIREDR=0.99187;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.866;Dels=0.0;FS=0.213;HaplotypeSco [...]
+chr17 64715283 . C T 16120.9 REJECT NS=2;DP=423;DPB=482.0;AC=4;AN=4;AF=1.0;RO=0;AO=482;PRO=0.0;PAO=0.0;QR=0;QA=18514;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=272;SAR=210;SRP=0.0;SAP=20.328;AB=0.0;ABP=0.0;RUN=1;RPP=8.21823;RPPR=0.0;RPL=258.0;RPR=224.0;EPP=3.17248;EPPR=0.0;DPRA=0.0;ODDS=76.6694;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995851;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9661;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.18;SOR=1.0 [...]
+chr17 64715399 . A G 3734.41 PASS SOMATIC;NS=2;DP=496;DPB=496.0;AC=1;AN=3;AF=0.25;RO=357;AO=139;PRO=0.0;PAO=0.0;QR=13726;QA=5350;PQR=0.0;PQA=0.0;SRF=164;SRR=193;SAF=72;SAR=67;SRP=8.12573;SAP=3.40085;AB=0.371658;ABP=56.5191;RUN=1;RPP=3.77578;RPPR=3.16236;RPL=73.0;RPR=66.0;EPP=12.7741;EPPR=37.2247;DPRA=3.06557;ODDS=77.141;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.742;Dels=0.0;FS=4.101;Hap [...]
+chr17 64715615 . G A 4488.935 REJECT NS=2;DP=183;DPB=208.0;AC=3;AN=4;AF=0.75;RO=52;AO=156;PRO=0.0;PAO=0.0;QR=2017;QA=6070;PQR=0.0;PQA=0.0;SRF=12;SRR=40;SAF=31;SAR=125;SRP=35.7494;SAP=126.005;AB=0.672956;ABP=44.3229;RUN=1;RPP=11.028;RPPR=5.68288;RPL=90.0;RPR=66.0;EPP=3.51141;EPPR=13.7006;DPRA=0.0;ODDS=31.6119;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9359;MQMR=60.0;PAIRED=0.99359;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.163;Dels=0.0;FS=0.0;HaplotypeScore=2. [...]
+chr17 64716307 . C T 1549.56 REJECT NS=2;DP=414;DPB=462.0;AC=2;AN=4;AF=0.5;RO=374;AO=88;PRO=0.0;PAO=0.0;QR=14277;QA=3375;PQR=0.0;PQA=0.0;SRF=170;SRR=204;SAF=54;SAR=34;SRP=9.72212;SAP=12.8806;AB=0.190476;ABP=387.464;RUN=1;RPP=3.40511;RPPR=14.2509;RPL=46.0;RPR=42.0;EPP=3.40511;EPPR=4.49666;DPRA=0.0;ODDS=151.926;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.977273;PAIREDR=0.991979;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8965;Dels=0.0;FS=9.648;HaplotypeS [...]
+chr17 64716397 . G A 3061.88 PASS SOMATIC;NS=2;DP=439;DPB=439.0;AC=1;AN=3;AF=0.25;RO=323;AO=116;PRO=0.0;PAO=0.0;QR=12408;QA=4410;PQR=0.0;PQA=0.0;SRF=159;SRR=164;SAF=49;SAR=67;SRP=3.17837;SAP=9.07545;AB=0.37299;ABP=46.5864;RUN=1;RPP=3.0103;RPPR=4.14646;RPL=58.0;RPR=58.0;EPP=6.67934;EPPR=4.52294;DPRA=2.42969;ODDS=80.8317;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991379;PAIREDR=0.990712;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.825;Dels=0.0;FS= [...]
+chr17 64716626 . T C 8280.78 REJECT NS=2;DP=495;DPB=574.0;AC=2;AN=4;AF=0.5;RO=276;AO=297;PRO=0.0;PAO=0.0;QR=10606;QA=11439;PQR=0.0;PQA=0.0;SRF=155;SRR=121;SAF=160;SAR=137;SRP=12.1053;SAP=6.87801;AB=0.517422;ABP=4.52352;RUN=1;RPP=8.34028;RPPR=3.29354;RPL=162.0;RPR=135.0;EPP=3.89497;EPPR=7.54207;DPRA=0.0;ODDS=486.563;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993266;PAIREDR=0.985507;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.643;Dels=0.0;FS=0.896;Haplo [...]
+chr17 64717112 . A G 5092.335 REJECT NS=2;DP=210;DPB=243.0;AC=3;AN=4;AF=0.75;RO=61;AO=182;PRO=0.0;PAO=0.0;QR=2378;QA=7050;PQR=0.0;PQA=0.0;SRF=12;SRR=49;SAF=41;SAR=141;SRP=51.7438;SAP=122.322;AB=0.657303;ABP=41.2673;RUN=1;RPP=3.43982;RPPR=7.31765;RPL=94.0;RPR=88.0;EPP=18.4731;EPPR=3.90025;DPRA=0.0;ODDS=41.5681;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989011;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.435;Dels=0.0;FS=0.0;HaplotypeScore=2. [...]
+chr17 64717237 . G A 354.652 REJECT NS=2;DP=73;DPB=73.0;AC=1;AN=4;AF=0.25;RO=56;AO=17;PRO=0.0;PAO=0.0;QR=2124;QA=660;PQR=0.0;PQA=0.0;SRF=2;SRR=54;SAF=0;SAR=17;SRP=107.861;SAP=39.9253;AB=0.7;ABP=9.95901;RUN=1;RPP=9.26925;RPPR=3.63072;RPL=5.0;RPR=12.0;EPP=9.26925;EPPR=3.63072;DPRA=0.0;ODDS=13.3946;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.3529;MQMR=58.6964;PAIRED=1.0;PAIREDR=0.982143;technology.ILLUMINA=1.0;BaseQRankSum=-1.196;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.16;MQRankSum=-1. [...]
+chr17 64717513 . CA C 28.2751 REJECT NS=2;DP=35;DPB=53.9259;AC=2;AN=2;AF=0.0;RO=9;AO=4;PRO=13.1167;PAO=10.1167;QR=323;QA=90;PQR=427.733;PQA=341.067;SRF=8;SRR=1;SAF=2;SAR=2;SRP=14.8328;SAP=3.0103;AB=0.16;ABP=28.1125;RUN=1;RPP=5.18177;RPPR=22.5536;RPL=3.0;RPR=1.0;EPP=5.18177;EPPR=14.8328;DPRA=0.0;ODDS=4.1726;GTI=0;TYPE=del;CIGAR=1M1D25M;NUMALT=4;MEANALT=9.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV [...]
+chr17 64717513 . CAA C 34.04755 REJECT NS=2;DP=35;DPB=53.9259;AC=2;AN=4;AF=0.5;RO=9;AO=6;PRO=13.1167;PAO=9.86667;QR=323;QA=201;PQR=427.733;PQA=334.067;SRF=8;SRR=1;SAF=6;SAR=0;SRP=14.8328;SAP=16.0391;AB=0.171429;ABP=35.8306;RUN=1;RPP=3.0103;RPPR=22.5536;RPL=3.0;RPR=3.0;EPP=3.0103;EPPR=14.8328;DPRA=0.0;ODDS=4.1726;GTI=0;TYPE=del;CIGAR=1M2D24M;NUMALT=4;MEANALT=8.5;LEN=2;MQM=58.8333;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.847;FS=0.0;MLE [...]
+chr17 64717531 . AG A 28.2751 REJECT NS=2;DP=35;DPB=53.9259;AC=2;AN=2;AF=0.0;RO=9;AO=2;PRO=13.1167;PAO=6.45;QR=323;QA=4;PQR=427.733;PQA=203.067;SRF=8;SRR=1;SAF=2;SAR=0;SRP=14.8328;SAP=7.35324;AB=0.2;ABP=10.8276;RUN=1;RPP=7.35324;RPPR=22.5536;RPL=2.0;RPR=0.0;EPP=7.35324;EPPR=14.8328;DPRA=0.0;ODDS=4.1726;GTI=0;TYPE=del;CIGAR=19M1D7M;NUMALT=4;MEANALT=8.0;LEN=1;MQM=53.5;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:Cal [...]
+chr17 64717532 . G A 28.2751 REJECT NS=2;DP=35;DPB=53.9259;AC=2;AN=2;AF=0.0;RO=9;AO=2;PRO=13.1167;PAO=6.45;QR=323;QA=28;PQR=427.733;PQA=203.067;SRF=8;SRR=1;SAF=2;SAR=0;SRP=14.8328;SAP=7.35324;AB=0.08;ABP=41.3151;RUN=1;RPP=7.35324;RPPR=22.5536;RPL=0.0;RPR=2.0;EPP=7.35324;EPPR=14.8328;DPRA=0.0;ODDS=4.1726;GTI=0;TYPE=snp;CIGAR=19M1X7M;NUMALT=4;MEANALT=9.0;LEN=1;MQM=50.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:Ca [...]
+chr17 64717664 . A C 2595.33 REJECT NS=2;DP=172;DPB=195.0;AC=2;AN=4;AF=0.5;RO=101;AO=94;PRO=0.0;PAO=0.0;QR=3842;QA=3605;PQR=0.0;PQA=0.0;SRF=65;SRR=36;SAF=71;SAR=23;SRP=21.0916;SAP=56.2345;AB=0.482051;ABP=3.55595;RUN=1;RPP=8.9241;RPPR=6.64375;RPL=39.0;RPR=55.0;EPP=7.53805;EPPR=50.5032;DPRA=0.0;ODDS=110.972;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.980198;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.131;Dels=0.0;FS=8.0515;HaplotypeScore=1.93 [...]
+chr17 64717818 . C T 1997.445 REJECT NS=2;DP=266;DPB=312.0;AC=2;AN=4;AF=0.5;RO=221;AO=91;PRO=0.0;PAO=0.0;QR=8364;QA=3472;PQR=0.0;PQA=0.0;SRF=125;SRR=96;SAF=67;SAR=24;SRP=11.2737;SAP=47.1318;AB=0.291667;ABP=120.632;RUN=1;RPP=17.9243;RPPR=9.15134;RPL=33.0;RPR=58.0;EPP=3.60686;EPPR=4.67084;DPRA=0.0;ODDS=153.522;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989011;PAIREDR=0.99095;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.054;Dels=0.0;FS=13.482;HaplotypeSco [...]
+chr17 64717872 . C T 8155.89 REJECT NS=2;DP=317;DPB=365.0;AC=2;AN=4;AF=0.5;RO=98;AO=267;PRO=0.0;PAO=0.0;QR=3795;QA=10248;PQR=0.0;PQA=0.0;SRF=59;SRR=39;SAF=152;SAR=115;SRP=11.8735;SAP=14.1442;AB=0.731507;ABP=172.927;RUN=1;RPP=3.99438;RPPR=10.1895;RPL=128.0;RPR=139.0;EPP=3.0835;EPPR=8.68272;DPRA=0.0;ODDS=223.316;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988764;PAIREDR=0.989796;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5065;Dels=0.0;FS=2.3445;Haplotyp [...]
+chr17 64718146 . T A 15965.699999999999 REJECT NS=2;DP=425;DPB=484.0;AC=4;AN=4;AF=1.0;RO=1;AO=483;PRO=0.0;PAO=0.0;QR=27;QA=18395;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=258;SAR=225;SRP=5.18177;SAP=7.90623;AB=0.0;ABP=0.0;RUN=1;RPP=5.82018;RPPR=5.18177;RPL=229.0;RPR=254.0;EPP=7.90623;EPPR=5.18177;DPRA=0.0;ODDS=77.2895;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99793;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.59;Dels=0.0;FS=0.0;HaplotypeScore=3.9277 [...]
+chr17 64718170 . A G 7600.035 REJECT NS=2;DP=444;DPB=502.0;AC=2;AN=4;AF=0.5;RO=235;AO=267;PRO=0.0;PAO=0.0;QR=8932;QA=10163;PQR=0.0;PQA=0.0;SRF=119;SRR=116;SAF=137;SAR=130;SRP=3.09346;SAP=3.40881;AB=0.531873;ABP=7.43976;RUN=1;RPP=3.01843;RPPR=3.01954;RPL=134.0;RPR=133.0;EPP=6.59689;EPPR=21.7219;DPRA=0.0;ODDS=319.396;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996255;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.5855;Dels=0.0;FS=0.945;Haplotype [...]
+chr17 64718335 . A G 2871.66 PASS SOMATIC;NS=2;DP=467;DPB=467.0;AC=1;AN=3;AF=0.25;RO=350;AO=116;PRO=0.0;PAO=0.0;QR=13492;QA=4339;PQR=0.0;PQA=0.0;SRF=192;SRR=158;SAF=69;SAR=47;SRP=10.1824;SAP=12.0706;AB=0.326761;ABP=95.5517;RUN=1;RPP=9.07545;RPPR=8.59409;RPL=49.0;RPR=67.0;EPP=7.80251;EPPR=21.1018;DPRA=3.16964;ODDS=70.9027;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.974138;PAIREDR=0.994286;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.087;Dels=0.0;F [...]
+chr17 64718525 . A G 7654.200000000001 REJECT NS=2;DP=495;DPB=574.0;AC=2;AN=4;AF=0.5;RO=287;AO=286;PRO=0.0;PAO=0.0;QR=10855;QA=10876;PQR=0.0;PQA=0.0;SRF=141;SRR=146;SAF=156;SAR=130;SRP=3.19945;SAP=8.14287;AB=0.498258;ABP=3.02543;RUN=1;RPP=4.954;RPPR=4.28897;RPL=151.0;RPR=135.0;EPP=4.954;EPPR=3.19945;DPRA=0.0;ODDS=450.315;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996503;PAIREDR=0.996516;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.782;Dels=0.0;FS=3.279 [...]
+chr17 64719084 . A G 2262.16 REJECT NS=2;DP=452;DPB=516.0;AC=2;AN=4;AF=0.5;RO=407;AO=109;PRO=0.0;PAO=0.0;QR=15267;QA=4130;PQR=0.0;PQA=0.0;SRF=218;SRR=189;SAF=56;SAR=53;SRP=7.4973;SAP=3.1896;AB=0.21124;ABP=376.722;RUN=1;RPP=3.50834;RPPR=3.27173;RPL=57.0;RPR=52.0;EPP=3.03022;EPPR=8.82046;DPRA=0.0;ODDS=57.1958;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.981651;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.234;Dels=0.0;FS=1.801;HaplotypeScore=4. [...]
+chr17 64719284 . A AG 11666.8 REJECT NS=2;DP=325;DPB=460.8;AC=4;AN=4;AF=1.0;RO=0;AO=365;PRO=15.0;PAO=23.0;QR=0;QA=13573;PQR=488.5;PQA=777.5;SRF=0;SRR=0;SAF=176;SAR=189;SRP=0.0;SAP=4.01572;AB=0.0;ABP=0.0;RUN=1;RPP=15.0575;RPPR=0.0;RPL=205.0;RPR=160.0;EPP=3.15903;EPPR=0.0;DPRA=0.0;ODDS=69.0638;GTI=0;TYPE=ins;CIGAR=1M1I4M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99726;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=64719284;HOMLEN=2;HOMSEQ=GG;SVLEN=1;SVTYPE=INS;FS=0.0;MLEAC=2;MLE [...]
+chr17 64719727 . C G 3470.62 REJECT NS=2;DP=167;DPB=186.0;AC=3;AN=4;AF=0.75;RO=56;AO=129;PRO=0.0;PAO=0.0;QR=1931;QA=4646;PQR=0.0;PQA=0.0;SRF=43;SRR=13;SAF=97;SAR=32;SRP=37.909;SAP=74.1302;AB=0.61745;ABP=20.863;RUN=1;RPP=4.37378;RPPR=5.49198;RPL=60.0;RPR=69.0;EPP=3.83512;EPPR=4.40625;DPRA=0.0;ODDS=24.0316;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9767;MQMR=58.8393;PAIRED=0.992248;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.003;Dels=0.0;FS=0.3655;HaplotypeScore [...]
+chr17 64719741 . G A 1353.49 PASS SOMATIC;NS=2;DP=211;DPB=211.0;AC=1;AN=3;AF=0.25;RO=148;AO=63;PRO=0.0;PAO=0.0;QR=5331;QA=2115;PQR=0.0;PQA=0.0;SRF=100;SRR=48;SAF=47;SAR=16;SRP=42.6837;SAP=36.1339;AB=0.384146;ABP=22.1298;RUN=1;RPP=15.4532;RPPR=42.6837;RPL=22.0;RPR=41.0;EPP=4.69922;EPPR=3.94932;DPRA=3.48936;ODDS=29.3872;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.1746;MQMR=59.8446;PAIRED=1.0;PAIREDR=0.993243;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.154;Dels=0.0;FS [...]
+chr17 64719752 . C CA 1810.29 REJECT NS=2;DP=226;DPB=300.5;AC=2;AN=2;AF=0.0;RO=67;AO=32;PRO=40.3333;PAO=36.3333;QR=2329;QA=1071;PQR=1356.25;PQA=1231.25;SRF=38;SRR=29;SAF=25;SAR=7;SRP=5.63551;SAP=24.9965;AB=0.141593;ABP=255.17;RUN=1;RPP=12.7819;RPPR=57.4916;RPL=10.0;RPR=22.0;EPP=3.28173;EPPR=4.59839;DPRA=0.0;ODDS=18.297;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=3;MEANALT=21.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.41;FS=8.7 [...]
+chr17 64719752 . CA C 1810.29 PASS SOMATIC;NS=2;DP=226;DPB=300.5;AC=2;AN=2;AF=0.0;RO=67;AO=12;PRO=40.3333;PAO=27.8333;QR=2329;QA=417;PQR=1356.25;PQA=891.25;SRF=38;SRR=29;SAF=10;SAR=2;SRP=5.63551;SAP=14.5915;AB=0.0701754;ABP=277.416;RUN=1;RPP=14.5915;RPPR=57.4916;RPL=2.0;RPR=10.0;EPP=5.9056;EPPR=4.59839;DPRA=0.0;ODDS=18.297;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=3;MEANALT=31.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr17 64719760 . A G 1492.53 REJECT NS=2;DP=226;DPB=300.5;AC=2;AN=4;AF=0.5;RO=67;AO=54;PRO=40.3333;PAO=39.5;QR=2329;QA=2126;PQR=1356.25;PQA=1349.25;SRF=38;SRR=29;SAF=37;SAR=17;SRP=5.63551;SAP=19.0953;AB=0.238938;ABP=136.796;RUN=1;RPP=49.4959;RPPR=57.4916;RPL=10.0;RPR=44.0;EPP=3.6537;EPPR=4.59839;DPRA=0.0;ODDS=18.297;GTI=0;TYPE=snp;CIGAR=8M1X15M;NUMALT=3;MEANALT=21.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.5535;Dels=0. [...]
+chr17 64720413 . C CA 1502.18 REJECT NS=2;DP=198;DPB=287.8;AC=2;AN=4;AF=0.5;RO=60;AO=80;PRO=39.4833;PAO=35.8167;QR=2157;QA=2490;PQR=1372.73;PQA=1234.73;SRF=39;SRR=21;SAF=53;SAR=27;SRP=14.7363;SAP=21.3592;AB=0.380952;ABP=28.8612;RUN=1;RPP=13.8677;RPPR=3.58936;RPL=30.0;RPR=50.0;EPP=5.72464;EPPR=3.15506;DPRA=0.0;ODDS=39.8281;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=4;MEANALT=15.0;LEN=1;MQM=58.55;MQMR=60.0;PAIRED=0.9875;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.7 [...]
+chr17 64720413 . C CAA 1954.63 REJECT NS=2;DP=210;DPB=287.8;AC=2;AN=2;AF=0.0;RO=60;AO=12;PRO=39.4833;PAO=35.8167;QR=2157;QA=351;PQR=1372.73;PQA=1240.73;SRF=39;SRR=21;SAF=4;SAR=8;SRP=14.7363;SAP=5.9056;AB=0.0571429;ABP=360.745;RUN=1;RPP=3.73412;RPPR=3.58936;RPL=7.0;RPR=5.0;EPP=9.52472;EPPR=3.15506;DPRA=0.0;ODDS=39.8281;GTI=0;TYPE=ins;CIGAR=1M2I19M;NUMALT=4;MEANALT=15.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr17 64720413 . CA C 1954.63 REJECT NS=2;DP=210;DPB=287.8;AC=2;AN=2;AF=0.0;RO=60;AO=24;PRO=39.4833;PAO=31.9;QR=2157;QA=785;PQR=1372.73;PQA=1096.65;SRF=39;SRR=21;SAF=14;SAR=10;SRP=14.7363;SAP=4.45795;AB=0.114286;ABP=274.382;RUN=1;RPP=12.0581;RPPR=3.58936;RPL=7.0;RPR=17.0;EPP=6.26751;EPPR=3.15506;DPRA=0.0;ODDS=39.8281;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=4;MEANALT=15.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr17 64720427 . GAACT AGAACG 1954.63 REJECT NS=2;DP=210;DPB=287.8;AC=2;AN=2;AF=0.0;RO=60;AO=7;PRO=39.4833;PAO=11.9833;QR=2157;QA=104;PQR=1372.73;PQA=377.15;SRF=39;SRR=21;SAF=7;SAR=0;SRP=14.7363;SAP=18.2106;AB=0.0333333;ABP=400.245;RUN=1;RPP=18.2106;RPPR=3.58936;RPL=7.0;RPR=0.0;EPP=18.2106;EPPR=3.15506;DPRA=0.0;ODDS=39.8281;GTI=0;TYPE=complex;CIGAR=1M1I17M1X1M;NUMALT=4;MEANALT=15.0;LEN=21;MQM=57.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:A [...]
+chr17 64721750 . A G 4392.6 REJECT NS=2;DP=137;DPB=161.0;AC=4;AN=4;AF=1.0;RO=2;AO=158;PRO=0.0;PAO=0.0;QR=18;QA=5387;PQR=0.0;PQA=0.0;SRF=0;SRR=2;SAF=35;SAR=123;SRP=7.35324;SAP=109.44;AB=0.0;ABP=0.0;RUN=1;RPP=37.369;RPPR=7.35324;RPL=104.0;RPR=54.0;EPP=66.5602;EPPR=7.35324;DPRA=0.0;ODDS=32.892;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.5886;MQMR=60.0;PAIRED=0.993671;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=12.6781;MLEAC=2;MLEAF=1.0;MQ=59.865;QD [...]
+chr17 64721765 . CA C 97.73 PASS SOMATIC;DP=90;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-0.097;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.66;MQRankSum=-1.04;QD=1.09;RPA=13,12;RU=A;ReadPosRankSum=0.546;SOR=0.685;STR GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.00997748 0/1:60,16:90:99.0:135,0,1160:16:21:76:.:1:.:.:.:.:-0.0533013
+chr17 64721778 . ATTAGC TTAGT 2817.5 REJECT SOMATIC;NS=2;DP=94;DPB=123.263;AC=1;AN=3;AF=0.0;RO=14;AO=10;PRO=15.8333;PAO=12.5;QR=512;QA=295;PQR=530.583;PQA=404.75;SRF=6;SRR=8;SAF=4;SAR=6;SRP=3.63072;SAP=3.87889;AB=0.119403;ABP=87.3088;RUN=1;RPP=6.48466;RPPR=3.0103;RPL=7.0;RPR=3.0;EPP=16.9077;EPPR=5.49198;DPRA=0.0;ODDS=6.03284;GTI=0;TYPE=complex;CIGAR=1M1D16M1X;NUMALT=3;MEANALT=6.5;LEN=18;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.928571;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:Q [...]
+chr17 64721779 . TTAGC ATTAGT 2817.5 REJECT SOMATIC;NS=2;DP=94;DPB=123.263;AC=1;AN=3;AF=0.0;RO=14;AO=8;PRO=15.8333;PAO=12.3333;QR=512;QA=155;PQR=530.583;PQA=423.583;SRF=6;SRR=8;SAF=1;SAR=7;SRP=3.63072;SAP=12.7819;AB=0.0746269;ABP=108.311;RUN=1;RPP=7.35324;RPPR=3.0103;RPL=6.0;RPR=2.0;EPP=12.7819;EPPR=5.49198;DPRA=0.0;ODDS=6.03284;GTI=0;TYPE=complex;CIGAR=1M1I17M1X;NUMALT=3;MEANALT=6.5;LEN=20;MQM=57.5;MQMR=60.0;PAIRED=1.0;PAIREDR=0.928571;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP: [...]
+chr17 64721783 . C T 2493.135 REJECT NS=2;DP=91;DPB=123.263;AC=3;AN=4;AF=0.75;RO=14;AO=50;PRO=15.8333;PAO=16.3333;QR=512;QA=1728;PQR=530.583;PQA=577.083;SRF=6;SRR=8;SAF=25;SAR=25;SRP=3.63072;SAP=3.0103;AB=0.41791;ABP=6.93191;RUN=1;RPP=14.1282;RPPR=3.0103;RPL=17.0;RPR=33.0;EPP=11.5225;EPPR=5.49198;DPRA=0.0;ODDS=6.03284;GTI=0;TYPE=snp;CIGAR=18M1X;NUMALT=3;MEANALT=6.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.928571;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.787;Dels [...]
+chr17 64721928 . G A 1325.99 REJECT NS=2;DP=204;DPB=266.13;AC=2;AN=2;AF=0.0;RO=43;AO=7;PRO=27.85;PAO=18.9167;QR=1553;QA=119;PQR=948.217;PQA=617.083;SRF=32;SRR=11;SAF=1;SAR=6;SRP=25.2805;SAP=10.7656;AB=0.0343137;ABP=387.276;RUN=1;RPP=3.32051;RPPR=14.3727;RPL=3.0;RPR=4.0;EPP=3.32051;EPPR=3.46479;DPRA=0.0;ODDS=13.6092;GTI=0;TYPE=snp;CIGAR=1X22M;NUMALT=5;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr17 64721928 . G GA 931.86 REJECT NS=2;DP=194;DPB=266.13;AC=2;AN=2;AF=0.375;RO=43;AO=48;PRO=27.85;PAO=27.85;QR=1553;QA=1511;PQR=948.217;PQA=949.217;SRF=32;SRR=11;SAF=36;SAR=12;SRP=25.2805;SAP=29.068;AB=0.235294;ABP=127.167;RUN=1;RPP=17.6677;RPPR=14.3727;RPL=15.0;RPR=33.0;EPP=4.6389;EPPR=3.46479;DPRA=0.0;ODDS=13.6092;GTI=0;TYPE=ins;CIGAR=1M1I22M;NUMALT=5;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.9075;FS=3. [...]
+chr17 64721928 . G GAA 1325.99 REJECT NS=2;DP=204;DPB=266.13;AC=2;AN=2;AF=0.0;RO=43;AO=14;PRO=27.85;PAO=24.85;QR=1553;QA=431;PQR=948.217;PQA=837.217;SRF=32;SRR=11;SAF=9;SAR=5;SRP=25.2805;SAP=5.49198;AB=0.0686275;ABP=332.733;RUN=1;RPP=3.63072;RPPR=14.3727;RPL=6.0;RPR=8.0;EPP=3.0103;EPPR=3.46479;DPRA=0.0;ODDS=13.6092;GTI=0;TYPE=ins;CIGAR=1M2I22M;NUMALT=5;MEANALT=11.5;LEN=2;MQM=59.8571;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr17 64721928 . GA G 1325.99 REJECT NS=2;DP=204;DPB=266.13;AC=2;AN=3;AF=0.25;RO=43;AO=59;PRO=27.85;PAO=22.7667;QR=1553;QA=1898;PQR=948.217;PQA=755.133;SRF=32;SRR=11;SAF=45;SAR=14;SRP=25.2805;SAP=38.3795;AB=0.289216;ABP=81.7368;RUN=1;RPP=13.6468;RPPR=14.3727;RPL=21.0;RPR=38.0;EPP=9.23028;EPPR=3.46479;DPRA=0.0;ODDS=13.6092;GTI=0;TYPE=del;CIGAR=1M1D21M;NUMALT=5;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983051;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=2.54;FS=3 [...]
+chr17 64721928 . GAA G 1325.99 REJECT NS=2;DP=204;DPB=266.13;AC=2;AN=2;AF=0.0;RO=43;AO=13;PRO=27.85;PAO=22.7667;QR=1553;QA=470;PQR=948.217;PQA=755.133;SRF=32;SRR=11;SAF=11;SAR=2;SRP=25.2805;SAP=16.5402;AB=0.0637255;ABP=340.27;RUN=1;RPP=3.17734;RPPR=14.3727;RPL=6.0;RPR=7.0;EPP=3.17734;EPPR=3.46479;DPRA=0.0;ODDS=13.6092;GTI=0;TYPE=del;CIGAR=1M2D20M;NUMALT=5;MEANALT=11.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr17 64722145 . A G 16487.199999999997 REJECT NS=2;DP=435;DPB=500.0;AC=4;AN=4;AF=1.0;RO=0;AO=499;PRO=0.0;PAO=0.0;QR=0;QA=19132;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=250;SAR=249;SRP=0.0;SAP=3.01465;AB=0.0;ABP=0.0;RUN=1;RPP=4.92938;RPPR=0.0;RPL=260.0;RPR=239.0;EPP=3.22353;EPPR=0.0;DPRA=0.0;ODDS=84.7961;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.98998;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9304;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=34 [...]
+chr17 64722212 . T C 11008.085 REJECT NS=2;DP=436;DPB=504.0;AC=3;AN=4;AF=0.75;RO=111;AO=392;PRO=0.0;PAO=0.0;QR=4239;QA=14959;PQR=0.0;PQA=0.0;SRF=59;SRR=52;SAF=214;SAR=178;SRP=3.96888;SAP=10.1895;AB=0.699187;ABP=130.174;RUN=1;RPP=5.6914;RPPR=3.18637;RPL=185.0;RPR=207.0;EPP=4.80509;EPPR=5.3774;DPRA=0.0;ODDS=84.511;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.0306;MQMR=59.9369;PAIRED=0.997449;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.327;Dels=0.0;FS=0.9365;Haplot [...]
+chr17 64722235 . CGCAGGTGTGCAGGACAGAAAGCTCAGGTGTTT C 3730.73 PASS DP=107;AC=2;AN=4;AF=1.0;BaseQRankSum=-0.086;FS=2.332;MLEAC=2;MLEAF=1.0;MQ=58.14;MQRankSum=1.549;QD=34.87;ReadPosRankSum=1.205;SOR=0.719;ClippingRankSum=1.14 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:3,91:94:99.0:3768,137,0:91:97:94:1:.:.:.:.:.:-0.00997748 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0533013
+chr17 64722267 . T C 9583.04 REJECT NS=2;DP=362;DPB=362.0;AC=4;AN=4;AF=1.0;RO=1;AO=361;PRO=0.0;PAO=0.0;QR=30;QA=12837;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=190;SAR=171;SRP=5.18177;SAP=5.18177;AB=0.0;ABP=0.0;RUN=1;RPP=183.038;RPPR=5.18177;RPL=267.0;RPR=94.0;EPP=4.36371;EPPR=5.18177;DPRA=0.0;ODDS=56.43;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=47.4183;MQMR=18.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=49;BaseQRankSum=1.323;Dels=0.0;FS=0.0;HaplotypeScore=13.9045;MLEAC=2;MLE [...]
+chr17 64722845 . C CT 28.2376 REJECT NS=2;DP=125;DPB=152.579;AC=2;AN=2;AF=0.0;RO=75;AO=16;PRO=19.4167;PAO=18.4167;QR=2723;QA=269;PQR=660.417;PQA=623.417;SRF=18;SRR=57;SAF=3;SAR=13;SRP=47.0478;SAP=16.582;AB=0.128;ABP=153.259;RUN=1;RPP=3.55317;RPPR=18.3264;RPL=9.0;RPR=7.0;EPP=5.18177;EPPR=3.27088;DPRA=0.0;ODDS=4.75924;GTI=0;TYPE=ins;CIGAR=1M1I18M;NUMALT=3;MEANALT=9.5;LEN=1;MQM=57.9375;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986667;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr17 64722845 . CT C 28.2376 REJECT NS=2;DP=125;DPB=152.579;AC=2;AN=4;AF=0.5;RO=75;AO=13;PRO=19.4167;PAO=16.9167;QR=2723;QA=361;PQR=660.417;PQA=546.417;SRF=18;SRR=57;SAF=5;SAR=8;SRP=47.0478;SAP=4.51363;AB=0.104;ABP=173.271;RUN=1;RPP=7.18621;RPPR=18.3264;RPL=9.0;RPR=4.0;EPP=3.17734;EPPR=3.27088;DPRA=0.0;ODDS=4.75924;GTI=0;TYPE=del;CIGAR=1M1D17M;NUMALT=3;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986667;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr17 64722845 . CTT C 28.2376 REJECT NS=2;DP=125;DPB=152.579;AC=2;AN=2;AF=0.0;RO=75;AO=6;PRO=19.4167;PAO=15.25;QR=2723;QA=170;PQR=660.417;PQA=504.75;SRF=18;SRR=57;SAF=1;SAR=5;SRP=47.0478;SAP=8.80089;AB=0.048;ABP=224.831;RUN=1;RPP=4.45795;RPPR=18.3264;RPL=4.0;RPR=2.0;EPP=8.80089;EPPR=3.27088;DPRA=0.0;ODDS=4.75924;GTI=0;TYPE=del;CIGAR=1M2D16M;NUMALT=3;MEANALT=9.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986667;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr17 64722900 . T G 1483.11 REJECT NS=2;DP=108;DPB=121.0;AC=2;AN=4;AF=0.5;RO=61;AO=60;PRO=0.0;PAO=0.0;QR=2274;QA=2131;PQR=0.0;PQA=0.0;SRF=18;SRR=43;SAF=11;SAR=49;SRP=25.259;SAP=55.2704;AB=0.495868;ABP=3.02825;RUN=1;RPP=3.15506;RPPR=3.0459;RPL=29.0;RPR=31.0;EPP=3.0103;EPPR=18.709;DPRA=0.0;ODDS=64.129;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.7833;MQMR=59.9836;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.905;Dels=0.0;FS=5.5885;HaplotypeScore=5.9285; [...]
+chr17 64723014 . G A 1416.87 REJECT NS=2;DP=91;DPB=102.0;AC=2;AN=4;AF=0.5;RO=49;AO=53;PRO=0.0;PAO=0.0;QR=1815;QA=2006;PQR=0.0;PQA=0.0;SRF=33;SRR=16;SAF=38;SAR=15;SRP=15.8176;SAP=24.6841;AB=0.519608;ABP=3.35092;RUN=1;RPP=21.0786;RPPR=6.59988;RPL=16.0;RPR=37.0;EPP=24.6841;EPPR=5.18177;DPRA=0.0;ODDS=52.4381;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6335;Dels=0.0;FS=2.0965;HaplotypeScore=0.0;MLEAC [...]
+chr17 64723320 . GA G 11195.25 REJECT NS=2;DP=327;DPB=348.9;AC=4;AN=4;AF=1.0;RO=0;AO=362;PRO=25.5;PAO=30.5;QR=0;QA=13191;PQR=793.5;PQA=983.5;SRF=0;SRR=0;SAF=199;SAR=163;SRP=0.0;SAP=10.7844;AB=0.0;ABP=0.0;RUN=1;RPP=4.54593;RPPR=0.0;RPL=173.0;RPR=189.0;EPP=13.5917;EPPR=0.0;DPRA=0.0;ODDS=63.5549;GTI=0;TYPE=del;CIGAR=1M1D8M;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.221;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.375;QD=33.865;RPA=5,4;RU=A;SOR=0.9215;S [...]
+chr17 64723342 . A G 1459.1799999999998 REJECT NS=2;DP=362;DPB=406.0;AC=2;AN=4;AF=0.5;RO=323;AO=82;PRO=0.0;PAO=0.0;QR=12290;QA=3151;PQR=0.0;PQA=0.0;SRF=180;SRR=143;SAF=55;SAR=27;SRP=12.2138;SAP=23.7717;AB=0.20197;ABP=316.237;RUN=1;RPP=9.78953;RPPR=8.6642;RPL=33.0;RPR=49.0;EPP=5.65844;EPPR=7.91124;DPRA=0.0;ODDS=185.651;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.3659;MQMR=60.1548;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.4925;Dels=0.0;FS=6.7325;Hapl [...]
+chr17 64723450 . G A 2829.81 PASS SOMATIC;NS=2;DP=463;DPB=463.0;AC=1;AN=3;AF=0.25;RO=350;AO=113;PRO=0.0;PAO=0.0;QR=13242;QA=4286;PQR=0.0;PQA=0.0;SRF=155;SRR=195;SAF=60;SAR=53;SRP=12.937;SAP=3.95191;AB=0.316527;ABP=107.393;RUN=1;RPP=3.95191;RPPR=6.58392;RPL=53.0;RPR=60.0;EPP=7.33403;EPPR=3.63072;DPRA=3.36792;ODDS=67.0522;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991429;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.157;Dels=0.0;FS=8.71 [...]
+chr17 64723758 . A AT 1665.64 REJECT NS=2;DP=408;DPB=442.625;AC=2;AN=4;AF=0.5;RO=319;AO=87;PRO=26.0;PAO=20.0;QR=12069;QA=3128;PQR=907.0;PQA=701.0;SRF=176;SRR=143;SAF=49;SAR=38;SRP=10.4233;SAP=6.03039;AB=0.213235;ABP=294.435;RUN=1;RPP=3.03526;RPPR=3.07156;RPL=43.0;RPR=44.0;EPP=3.03526;EPPR=7.97269;DPRA=0.0;ODDS=102.533;GTI=0;TYPE=ins;CIGAR=1M1I7M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.977011;PAIREDR=0.996865;technology.ILLUMINA=1.0;BaseQRankSum=-1.239;FS=6.613;MLEAC=1;MLEA [...]
+chr17 64723927 . G A 2989.2700000000004 PASS DP=190;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-0.68;Dels=0.0;FS=3.9025;HaplotypeScore=6.8978;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.3895;QD=16.115;ReadPosRankSum=-1.3405;SOR=0.74;ClippingRankSum=-0.73 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:49,40:89:99.0:1526,0,2950:40:45:89:1:.:.:.:.:.:-0.00997748 0/1:166,125:291:99.0:4509,0,6239:125:43:291:.:1:.:.:.:.:-0.0533013
+chr17 64723927 . GCCAA ACCAG 5023.69 REJECT NS=2;DP=362;DPB=382.0;AC=2;AN=4;AF=0.5;RO=207;AO=152;PRO=22.0;PAO=18.0;QR=7826;QA=5737;PQR=556.0;PQA=642.0;SRF=103;SRR=104;SAF=71;SAR=81;SRP=3.02079;SAP=4.4389;AB=0.41989;ABP=23.1894;RUN=1;RPP=8.7247;RPPR=3.86001;RPL=66.0;RPR=86.0;EPP=4.4389;EPPR=3.27256;DPRA=0.0;ODDS=277.296;GTI=0;TYPE=complex;CIGAR=1X3M1X;NUMALT=1;MEANALT=2.5;LEN=5;MQM=60.0;MQMR=60.0;PAIRED=0.993421;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr17 64723931 . A G 2986.2700000000004 PASS DP=193;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-0.26;Dels=0.0;FS=5.1865;HaplotypeScore=8.8638;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.381;QD=15.745;ReadPosRankSum=-0.735;SOR=0.8325;ClippingRankSum=-0.407 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:53,40:93:99.0:1541,0,3010:40:43:93:1:.:.:.:.:.:-0.00997748 0/1:169,124:293:99.0:4488,0,6299:124:42:293:.:1:.:.:.:.:-0.0533013
+chr17 64724614 . G C 13707.65 REJECT NS=2;DP=366;DPB=419.0;AC=4;AN=4;AF=1.0;RO=0;AO=419;PRO=0.0;PAO=0.0;QR=0;QA=15856;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=220;SAR=199;SRP=0.0;SAP=5.29579;AB=0.0;ABP=0.0;RUN=1;RPP=17.568;RPPR=0.0;RPL=183.0;RPR=236.0;EPP=3.05694;EPPR=0.0;DPRA=0.0;ODDS=69.79;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99284;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9966;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.685;SOR=0.79 [...]
+chr17 64724724 . A G 2907.675 REJECT NS=2;DP=455;DPB=525.0;AC=2;AN=4;AF=0.5;RO=391;AO=134;PRO=0.0;PAO=0.0;QR=14855;QA=5133;PQR=0.0;PQA=0.0;SRF=218;SRR=173;SAF=65;SAR=69;SRP=14.2564;SAP=3.26958;AB=0.255238;ABP=276.198;RUN=1;RPP=13.9649;RPPR=16.3446;RPL=54.0;RPR=80.0;EPP=15.715;EPPR=4.6153;DPRA=0.0;ODDS=206.774;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985075;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.1435;Dels=0.0;FS=5.519;HaplotypeScore= [...]
+chr17 64724943 . T C 3711.88 PASS SOMATIC;NS=2;DP=503;DPB=503.0;AC=1;AN=3;AF=0.25;RO=363;AO=140;PRO=0.0;PAO=0.0;QR=13772;QA=5343;PQR=0.0;PQA=0.0;SRF=180;SRR=183;SAF=73;SAR=67;SRP=3.06414;SAP=3.56868;AB=0.367454;ABP=61.1499;RUN=1;RPP=9.21451;RPPR=3.73412;RPL=60.0;RPR=80.0;EPP=4.56135;EPPR=3.73412;DPRA=3.12295;ODDS=77.0824;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986226;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.714;Dels=0.0;FS=2.8 [...]
+chr17 64725031 . A G 10978.985 REJECT NS=2;DP=476;DPB=553.0;AC=3;AN=4;AF=0.75;RO=154;AO=399;PRO=0.0;PAO=0.0;QR=5909;QA=15285;PQR=0.0;PQA=0.0;SRF=79;SRR=75;SAF=195;SAR=204;SRP=3.23591;SAP=3.45113;AB=0.614035;ABP=48.0779;RUN=1;RPP=10.4608;RPPR=3.91273;RPL=181.0;RPR=218.0;EPP=3.14636;EPPR=4.42035;DPRA=0.0;ODDS=97.0156;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997494;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.037;Dels=0.0;FS=0.1865;Haplotyp [...]
+chr17 64725479 . A G 2918.865 REJECT NS=2;DP=138;DPB=160.0;AC=3;AN=4;AF=0.75;RO=44;AO=116;PRO=0.0;PAO=0.0;QR=1706;QA=4260;PQR=0.0;PQA=0.0;SRF=35;SRR=9;SAF=95;SAR=21;SRP=36.372;SAP=105.519;AB=0.623932;ABP=18.6189;RUN=1;RPP=5.70592;RPPR=3.0103;RPL=52.0;RPR=64.0;EPP=9.07545;EPPR=3.20771;DPRA=0.0;ODDS=27.8296;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.431;MQMR=59.6818;PAIRED=0.991379;PAIREDR=0.977273;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.543;Dels=0.0;FS=0.0;HaplotypeSc [...]
+chr17 64725765 . T C 11838.15 REJECT NS=2;DP=309;DPB=346.0;AC=4;AN=4;AF=1.0;RO=0;AO=346;PRO=0.0;PAO=0.0;QR=0;QA=13347;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=140;SAR=206;SRP=0.0;SAP=30.3483;AB=0.0;ABP=0.0;RUN=1;RPP=24.1225;RPPR=0.0;RPL=202.0;RPR=144.0;EPP=4.24038;EPPR=0.0;DPRA=0.0;ODDS=49.2934;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.985549;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.804;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.035;SOR=1 [...]
+chr17 64725898 . C CT 33.77 PASS DP=22;AC=1;AN=4;AF=0.5;BaseQRankSum=0.55;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.24;MQRankSum=-1.3;QD=1.53;ReadPosRankSum=0.55;SOR=0.368;ClippingRankSum=-0.55 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:3,4:7:21.0:71,0,21:4:57:7:1:.:.:.:.:.:-0.00997748 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0533013
+chr17 64725975 . C T 61.0479 REJECT NS=2;DP=82;DPB=83.0;AC=2;AN=2;AF=0.0;RO=76;AO=3;PRO=1.0;PAO=0.5;QR=2556;QA=48;PQR=16.5;PQA=0.0;SRF=29;SRR=47;SAF=0;SAR=3;SRP=12.2676;SAP=9.52472;AB=0.0833333;ABP=39.2015;RUN=1;RPP=9.52472;RPPR=3.46745;RPL=3.0;RPR=0.0;EPP=9.52472;EPPR=3.12459;DPRA=0.0;ODDS=14.0568;GTI=0;TYPE=snp;CIGAR=1X1M;NUMALT=2;MEANALT=1.5;LEN=1;MQM=55.3333;MQMR=58.7237;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:Call [...]
+chr17 64725976 . C T 61.0479 REJECT NS=2;DP=82;DPB=83.0;AC=2;AN=3;AF=0.25;RO=76;AO=3;PRO=1.0;PAO=0.5;QR=2556;QA=48;PQR=16.5;PQA=16.5;SRF=29;SRR=47;SAF=0;SAR=3;SRP=12.2676;SAP=9.52472;AB=0.0;ABP=0.0;RUN=1;RPP=9.52472;RPPR=3.46745;RPL=3.0;RPR=0.0;EPP=9.52472;EPPR=3.12459;DPRA=0.0;ODDS=14.0568;GTI=0;TYPE=snp;CIGAR=1M1X;NUMALT=2;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=58.7237;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:C [...]
+chr17 64726023 . T C 2346.4449999999997 REJECT NS=2;DP=71;DPB=84.0;AC=4;AN=4;AF=1.0;RO=0;AO=84;PRO=0.0;PAO=0.0;QR=0;QA=2970;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=41;SAR=43;SRP=0.0;SAP=3.1137;AB=0.0;ABP=0.0;RUN=1;RPP=4.66476;RPPR=0.0;RPL=38.0;RPR=46.0;EPP=3.94093;EPPR=0.0;DPRA=0.0;ODDS=20.5285;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=51.7143;MQMR=0.0;PAIRED=0.988095;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=51.925;QD=30.6;S [...]
+chr17 64726049 . T C 2489.84 REJECT NS=2;DP=75;DPB=90.0;AC=4;AN=4;AF=1.0;RO=1;AO=89;PRO=0.0;PAO=0.0;QR=16;QA=3151;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=54;SAR=35;SRP=5.18177;SAP=11.8182;AB=0.0;ABP=0.0;RUN=1;RPP=11.8182;RPPR=5.18177;RPL=35.0;RPR=54.0;EPP=36.4119;EPPR=5.18177;DPRA=0.0;ODDS=21.7467;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=52.4944;MQMR=40.0;PAIRED=0.977528;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.505;Dels=0.0;FS=0.0;HaplotypeScore=3.866;MLEAC=2;MLEAF= [...]
+chr17 64726462 . T C 3820.0299999999997 REJECT NS=2;DP=262;DPB=308.0;AC=2;AN=4;AF=0.5;RO=162;AO=146;PRO=0.0;PAO=0.0;QR=6107;QA=5556;PQR=0.0;PQA=0.0;SRF=47;SRR=115;SAF=47;SAR=99;SRP=64.9911;SAP=43.2272;AB=0.474026;ABP=4.81516;RUN=1;RPP=13.0645;RPPR=16.7362;RPL=86.0;RPR=60.0;EPP=5.15203;EPPR=9.49791;DPRA=0.0;ODDS=289.133;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993151;PAIREDR=0.993827;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.2835;Dels=0.0;FS=4.1095 [...]
+chr17 64726790 . A G 3554.66 PASS SOMATIC;NS=2;DP=481;DPB=481.0;AC=1;AN=3;AF=0.25;RO=347;AO=133;PRO=0.0;PAO=0.0;QR=13360;QA=5118;PQR=0.0;PQA=0.0;SRF=204;SRR=143;SAF=78;SAR=55;SRP=26.2957;SAP=11.6472;AB=0.365385;ABP=60.3038;RUN=1;RPP=3.41847;RPPR=9.82509;RPL=64.0;RPR=69.0;EPP=3.02663;EPPR=9.82509;DPRA=3.11111;ODDS=73.3458;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992481;PAIREDR=0.997118;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.22;Dels=0.0;FS [...]
+chr17 64726827 . G A 15375.8 REJECT NS=2;DP=408;DPB=451.0;AC=4;AN=4;AF=1.0;RO=1;AO=449;PRO=0.0;PAO=0.0;QR=16;QA=17177;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=246;SAR=203;SRP=5.18177;SAP=11.9525;AB=0.0;ABP=0.0;RUN=1;RPP=14.6221;RPPR=5.18177;RPL=249.0;RPR=200.0;EPP=10.3662;EPPR=5.18177;DPRA=0.0;ODDS=56.0445;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995546;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.561;Dels=0.0;FS=1.587;HaplotypeScore=3.9326;MLEAC= [...]
+chr17 64727100 . G C 5699.125 REJECT NS=2;DP=349;DPB=401.0;AC=2;AN=4;AF=0.5;RO=199;AO=201;PRO=0.0;PAO=0.0;QR=7713;QA=7734;PQR=0.0;PQA=0.0;SRF=69;SRR=130;SAF=83;SAR=118;SRP=43.6136;SAP=16.2444;AB=0.501247;ABP=3.01572;RUN=1;RPP=5.44105;RPPR=6.16385;RPL=108.0;RPR=93.0;EPP=3.10753;EPPR=3.2831;DPRA=0.0;ODDS=323.036;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99005;PAIREDR=0.984925;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7825;Dels=0.0;FS=3.917;HaplotypeS [...]
+chr17 64727195 . G A 393.847 REJECT NS=2;DP=198;DPB=198.0;AC=1;AN=4;AF=0.25;RO=169;AO=29;PRO=0.0;PAO=0.0;QR=6423;QA=1049;PQR=0.0;PQA=0.0;SRF=38;SRR=131;SAF=10;SAR=19;SRP=114.141;SAP=9.07545;AB=0.4;ABP=6.91895;RUN=1;RPP=9.07545;RPPR=39.103;RPL=19.0;RPR=10.0;EPP=3.68421;EPPR=3.02315;DPRA=0.0;ODDS=9.68432;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9655;MQMR=60.0;PAIRED=0.965517;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-2.375;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum= [...]
+chr17 64727205 . A G 3230.87 REJECT NS=2;DP=159;DPB=179.0;AC=3;AN=4;AF=0.75;RO=59;AO=120;PRO=0.0;PAO=0.0;QR=2296;QA=4522;PQR=0.0;PQA=0.0;SRF=9;SRR=50;SAF=26;SAR=94;SRP=64.8789;SAP=86.6844;AB=0.578571;ABP=10.5174;RUN=1;RPP=4.16842;RPPR=22.4799;RPL=64.0;RPR=56.0;EPP=13.4334;EPPR=3.93042;DPRA=0.0;ODDS=25.3509;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.725;MQMR=60.0;PAIRED=0.983333;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.435;Dels=0.0;FS=0.4355;HaplotypeScore=1 [...]
+chr17 64727468 . A G 353.313 REJECT NS=2;DP=79;DPB=82.75;AC=2;AN=4;AF=0.5;RO=47;AO=19;PRO=2.0;PAO=0.5;QR=1647;QA=652;PQR=64.0;PQA=17.0;SRF=41;SRR=6;SAF=18;SAR=1;SRP=59.6072;SAP=36.0395;AB=0.240506;ABP=49.2159;RUN=1;RPP=12.2676;RPPR=23.3852;RPL=14.0;RPR=5.0;EPP=8.61041;EPPR=16.3625;DPRA=0.0;ODDS=13.1777;GTI=0;TYPE=snp;CIGAR=1M1X2M;NUMALT=2;MEANALT=6.5;LEN=1;MQM=53.2105;MQMR=54.0213;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.588;Dels=0.04;FS=0.0; [...]
+chr17 64727468 . AGA GG 353.313 REJECT NS=2;DP=79;DPB=82.75;AC=2;AN=2;AF=0.0;RO=47;AO=4;PRO=2.0;PAO=1.5;QR=1647;QA=144;PQR=64.0;PQA=49.0;SRF=41;SRR=6;SAF=4;SAR=0;SRP=59.6072;SAP=11.6962;AB=0.0506329;ABP=141.572;RUN=1;RPP=11.6962;RPPR=23.3852;RPL=0.0;RPR=4.0;EPP=11.6962;EPPR=16.3625;DPRA=0.0;ODDS=13.1777;GTI=0;TYPE=complex;CIGAR=1M1D1M1X;NUMALT=2;MEANALT=6.5;LEN=2;MQM=52.0;MQMR=54.0213;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr17 64727488 . AGAAT GGAAG 71.4143 REJECT NS=2;DP=146;DPB=165.4;AC=2;AN=2;AF=0.0;RO=117;AO=4;PRO=44.0;PAO=0.0;QR=4003;QA=49;PQR=1189.5;PQA=0.0;SRF=76;SRR=41;SAF=4;SAR=0;SRP=25.7458;SAP=11.6962;AB=0.0;ABP=0.0;RUN=1;RPP=11.6962;RPPR=143.488;RPL=4.0;RPR=0.0;EPP=11.6962;EPPR=14.61;DPRA=0.0;ODDS=11.4515;GTI=0;TYPE=complex;CIGAR=1X3M1X;NUMALT=2;MEANALT=5.0;LEN=5;MQM=55.0;MQMR=59.4957;PAIRED=1.0;PAIREDR=0.991453;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr17 64727492 . T G 71.4143 REJECT NS=2;DP=146;DPB=165.4;AC=2;AN=3;AF=0.25;RO=117;AO=11;PRO=44.0;PAO=10.0;QR=4003;QA=185;PQR=1189.5;PQA=229.5;SRF=76;SRR=41;SAF=11;SAR=0;SRP=25.7458;SAP=26.8965;AB=0.0744681;ABP=150.855;RUN=1;RPP=26.8965;RPPR=143.488;RPL=11.0;RPR=0.0;EPP=26.8965;EPPR=14.61;DPRA=0.0;ODDS=11.4515;GTI=0;TYPE=snp;CIGAR=4M1X;NUMALT=2;MEANALT=5.0;LEN=1;MQM=57.0909;MQMR=59.4957;PAIRED=1.0;PAIREDR=0.991453;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr17 64727631 . C T 12179.65 REJECT NS=2;DP=319;DPB=365.0;AC=4;AN=4;AF=1.0;RO=0;AO=365;PRO=0.0;PAO=0.0;QR=0;QA=14088;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=193;SAR=172;SRP=0.0;SAP=5.63391;AB=0.0;ABP=0.0;RUN=1;RPP=73.6932;RPPR=0.0;RPL=128.0;RPR=237.0;EPP=5.15798;EPPR=0.0;DPRA=0.0;ODDS=60.4674;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991781;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.91;SOR=0.79 [...]
+chr17 64727722 . C G 2688.12 PASS SOMATIC;NS=2;DP=390;DPB=390.0;AC=1;AN=3;AF=0.25;RO=288;AO=101;PRO=0.0;PAO=0.0;QR=11128;QA=3948;PQR=0.0;PQA=0.0;SRF=121;SRR=167;SAF=48;SAR=53;SRP=18.9646;SAP=3.54779;AB=0.336667;ABP=72.5264;RUN=1;RPP=3.54779;RPPR=11.7263;RPL=48.0;RPR=53.0;EPP=3.0318;EPPR=8.92153;DPRA=3.33333;ODDS=57.1256;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.980198;PAIREDR=0.989583;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.074;Dels=0.0;F [...]
+chr17 64727942 . G A 242.724 REJECT NS=2;DP=42;DPB=42.0;AC=2;AN=4;AF=0.5;RO=29;AO=13;PRO=0.0;PAO=0.0;QR=924;QA=459;PQR=0.0;PQA=0.0;SRF=5;SRR=24;SAF=5;SAR=8;SRP=30.0414;SAP=4.51363;AB=0.309524;ABP=16.2459;RUN=1;RPP=4.51363;RPPR=3.68421;RPL=5.0;RPR=8.0;EPP=11.1951;EPPR=6.67934;DPRA=0.0;ODDS=0.003371;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=48.5385;MQMR=51.8276;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.348;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.34;MQRankSum=-0.348 [...]
+chr17 64728235 . G GA 2332.53 REJECT NS=2;DP=163;DPB=252.385;AC=2;AN=2;AF=0.5;RO=5;AO=27;PRO=41.4667;PAO=64.9667;QR=167;QA=853;PQR=1454.38;PQA=2247.88;SRF=4;SRR=1;SAF=22;SAR=5;SRP=6.91895;SAP=26.2531;AB=0.165644;ABP=161.288;RUN=1;RPP=3.09072;RPPR=3.44459;RPL=14.0;RPR=13.0;EPP=6.95112;EPPR=3.44459;DPRA=0.0;ODDS=34.8143;GTI=0;TYPE=ins;CIGAR=1M1I38M;NUMALT=5;MEANALT=29.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.962963;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.7415; [...]
+chr17 64728235 . GA G 2332.53 PASS SOMATIC;NS=2;DP=163;DPB=252.385;AC=1;AN=3;AF=0.25;RO=5;AO=20;PRO=41.4667;PAO=41.9667;QR=167;QA=574;PQR=1454.38;PQA=1460.13;SRF=4;SRR=1;SAF=10;SAR=10;SRP=6.91895;SAP=3.0103;AB=0.173913;ABP=109.224;RUN=1;RPP=6.91895;RPPR=3.44459;RPL=7.0;RPR=13.0;EPP=3.44459;EPPR=3.44459;DPRA=0.0;ODDS=34.8143;GTI=0;TYPE=del;CIGAR=1M1D37M;NUMALT=5;MEANALT=39.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr17 64728235 . GAAAAAAAAAATCAA G 2332.53 REJECT NS=2;DP=163;DPB=252.385;AC=2;AN=2;AF=0.375;RO=5;AO=31;PRO=41.4667;PAO=29.4667;QR=167;QA=838;PQR=1454.38;PQA=1011.88;SRF=4;SRR=1;SAF=23;SAR=8;SRP=6.91895;SAP=18.771;AB=0.190184;ABP=138.907;RUN=1;RPP=8.68415;RPPR=3.44459;RPL=20.0;RPR=11.0;EPP=14.8483;EPPR=3.44459;DPRA=0.0;ODDS=34.8143;GTI=0;TYPE=del;CIGAR=1M14D24M;NUMALT=5;MEANALT=29.5;LEN=14;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;END=64728 [...]
+chr17 64728235 . GAAAAAAAAAATCAAA G 2332.53 REJECT NS=2;DP=163;DPB=252.385;AC=0;AN=4;AF=0.0;RO=5;AO=4;PRO=41.4667;PAO=28.1667;QR=167;QA=120;PQR=1454.38;PQA=975.583;SRF=4;SRR=1;SAF=1;SAR=3;SRP=6.91895;SAP=5.18177;AB=0.0245399;ABP=323.069;RUN=1;RPP=3.0103;RPPR=3.44459;RPL=2.0;RPR=2.0;EPP=5.18177;EPPR=3.44459;DPRA=0.0;ODDS=34.8143;GTI=0;TYPE=del;CIGAR=1M15D23M;NUMALT=5;MEANALT=29.5;LEN=15;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:Q [...]
+chr17 64728245 . ATC TCA 2332.53 PASS SOMATIC;NS=2;DP=163;DPB=252.385;AC=0;AN=4;AF=0.0;RO=5;AO=6;PRO=41.4667;PAO=32.9667;QR=167;QA=196;PQR=1454.38;PQA=1104.13;SRF=4;SRR=1;SAF=6;SAR=0;SRP=6.91895;SAP=16.0391;AB=0.0521739;ABP=203.333;RUN=1;RPP=3.0103;RPPR=3.44459;RPL=3.0;RPR=3.0;EPP=3.0103;EPPR=3.44459;DPRA=0.0;ODDS=34.8143;GTI=0;TYPE=mnp;CIGAR=10M3X26M;NUMALT=5;MEANALT=39.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr17 64728525 . C T 17593.05 REJECT NS=2;DP=461;DPB=527.0;AC=4;AN=4;AF=1.0;RO=0;AO=527;PRO=0.0;PAO=0.0;QR=0;QA=20248;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=280;SAR=247;SRP=0.0;SAP=7.49746;AB=0.0;ABP=0.0;RUN=1;RPP=6.97004;RPPR=0.0;RPL=279.0;RPR=248.0;EPP=7.49746;EPPR=0.0;DPRA=0.0;ODDS=85.3913;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9886;MQMR=0.0;PAIRED=0.996205;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.035;SO [...]
+chr17 64728707 . C T 4296.61 PASS SOMATIC;NS=2;DP=537;DPB=537.0;AC=1;AN=3;AF=0.25;RO=376;AO=161;PRO=0.0;PAO=0.0;QR=14233;QA=6038;PQR=0.0;PQA=0.0;SRF=189;SRR=187;SAF=88;SAR=73;SRP=3.0334;SAP=6.04497;AB=0.405542;ABP=33.7774;RUN=1;RPP=3.13169;RPPR=5.32038;RPL=82.0;RPR=79.0;EPP=4.10278;EPPR=4.14224;DPRA=2.83571;ODDS=88.2502;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993789;PAIREDR=0.986702;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.106;Dels=0.0;FS [...]
+chr17 64783081 . G A 13328.9 REJECT NS=2;DP=345;DPB=389.0;AC=4;AN=4;AF=1.0;RO=0;AO=389;PRO=0.0;PAO=0.0;QR=0;QA=15105;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=168;SAR=221;SRP=0.0;SAP=18.6907;AB=0.0;ABP=0.0;RUN=1;RPP=3.01588;RPPR=0.0;RPL=194.0;RPR=195.0;EPP=29.5871;EPPR=0.0;DPRA=0.0;ODDS=59.2476;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994859;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.705;SOR=0.98 [...]
+chr17 66416357 . C T 1544.1 REJECT NS=2;DP=309;DPB=352.0;AC=2;AN=4;AF=0.5;RO=274;AO=78;PRO=0.0;PAO=0.0;QR=10419;QA=2991;PQR=0.0;PQA=0.0;SRF=158;SRR=116;SAF=43;SAR=35;SRP=16.9901;SAP=4.79202;AB=0.221591;ABP=239.997;RUN=1;RPP=3.45573;RPPR=11.1256;RPL=37.0;RPR=41.0;EPP=12.0303;EPPR=15.6904;DPRA=0.0;ODDS=140.89;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99635;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.2925;Dels=0.0;FS=2.0775;HaplotypeScore=4. [...]
+chr17 66524987 . G A 5485.955 REJECT NS=2;DP=245;DPB=283.0;AC=3;AN=4;AF=0.75;RO=82;AO=201;PRO=0.0;PAO=0.0;QR=3144;QA=7724;PQR=0.0;PQA=0.0;SRF=57;SRR=25;SAF=135;SAR=66;SRP=30.1272;SAP=54.445;AB=0.607656;ABP=24.0497;RUN=1;RPP=88.5836;RPPR=30.1272;RPL=56.0;RPR=145.0;EPP=21.1707;EPPR=3.96363;DPRA=0.0;ODDS=47.1793;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995025;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.116;Dels=0.0;FS=0.928;HaplotypeScore=4 [...]
+chr17 66539847 . C T 4981.165000000001 REJECT NS=2;DP=313;DPB=360.0;AC=2;AN=4;AF=0.5;RO=180;AO=180;PRO=0.0;PAO=0.0;QR=6890;QA=6897;PQR=0.0;PQA=0.0;SRF=104;SRR=76;SAF=104;SAR=76;SRP=12.4683;SAP=12.4683;AB=0.5;ABP=3.0103;RUN=1;RPP=3.20332;RPPR=4.74748;RPL=88.0;RPR=92.0;EPP=7.83579;EPPR=4.74748;DPRA=0.0;ODDS=300.467;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994444;PAIREDR=0.994444;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.5095;Dels=0.0;FS=2.138;Haplot [...]
+chr17 72013922 . G C 11028.05 REJECT NS=2;DP=310;DPB=357.0;AC=4;AN=4;AF=1.0;RO=0;AO=357;PRO=0.0;PAO=0.0;QR=0;QA=13124;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=94;SAR=263;SRP=0.0;SAP=176.734;AB=0.0;ABP=0.0;RUN=1;RPP=27.152;RPPR=0.0;RPL=210.0;RPR=147.0;EPP=20.0962;EPPR=0.0;DPRA=0.0;ODDS=62.8854;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994398;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=10.8276;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.015;SOR=2 [...]
+chr17 74732507 . A G 9606.18 REJECT NS=2;DP=262;DPB=301.0;AC=4;AN=4;AF=1.0;RO=0;AO=300;PRO=0.0;PAO=0.0;QR=0;QA=11347;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=61;SAR=239;SRP=0.0;SAP=232.347;AB=0.0;ABP=0.0;RUN=1;RPP=11.3777;RPPR=0.0;RPL=167.0;RPR=133.0;EPP=14.5915;EPPR=0.0;DPRA=0.0;ODDS=52.9985;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996667;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8399;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.1;SOR=2.60 [...]
+chr17 74733099 . G A 8728.560000000001 REJECT NS=2;DP=385;DPB=444.0;AC=3;AN=4;AF=0.75;RO=122;AO=322;PRO=0.0;PAO=0.0;QR=4710;QA=12006;PQR=0.0;PQA=0.0;SRF=62;SRR=60;SAF=178;SAR=144;SRP=3.0815;SAP=10.806;AB=0.624615;ABP=46.8473;RUN=1;RPP=3.1182;RPPR=4.7902;RPL=163.0;RPR=159.0;EPP=3.1182;EPPR=3.65106;DPRA=0.0;ODDS=74.1508;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.981366;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.638;Dels=0.0;FS=1.228;Haplot [...]
+chr17 78681626 . C T 824.027 REJECT NS=2;DP=203;DPB=236.0;AC=2;AN=4;AF=0.5;RO=189;AO=47;PRO=0.0;PAO=0.0;QR=7270;QA=1771;PQR=0.0;PQA=0.0;SRF=153;SRR=36;SAF=40;SAR=7;SRP=160.287;SAP=53.3238;AB=0.199153;ABP=188.542;RUN=1;RPP=23.3852;RPPR=60.9277;RPL=13.0;RPR=34.0;EPP=8.60069;EPPR=5.59539;DPRA=0.0;ODDS=2.72416;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994709;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.3035;Dels=0.0;FS=1.3425;HaplotypeScore=1. [...]
+chr17 78765219 . A G 9470.485 REJECT NS=2;DP=258;DPB=295.0;AC=4;AN=4;AF=1.0;RO=0;AO=295;PRO=0.0;PAO=0.0;QR=0;QA=11051;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=188;SAR=107;SRP=0.0;SAP=51.3053;AB=0.0;ABP=0.0;RUN=1;RPP=53.7197;RPPR=0.0;RPL=106.0;RPR=189.0;EPP=8.37641;EPPR=0.0;DPRA=0.0;ODDS=49.8492;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.989831;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=25.395;SOR=1 [...]
+chr17 78820329 . C T 1238.65 REJECT NS=1;DP=109;DPB=109.0;AC=1;AN=4;AF=0.5;RO=61;AO=48;PRO=0.0;PAO=0.0;QR=2346;QA=1767;PQR=0.0;PQA=0.0;SRF=24;SRR=37;SAF=18;SAR=30;SRP=9.02635;SAP=9.52472;AB=0.440367;ABP=6.37708;RUN=1;RPP=3.19126;RPPR=4.7546;RPL=23.0;RPR=25.0;EPP=4.6389;EPPR=3.90025;DPRA=0.0;ODDS=285.209;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.979167;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.826;FS=0.754;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum= [...]
+chr17 78820374 . G A 1029.01 REJECT NS=1;DP=78;DPB=78.0;AC=1;AN=4;AF=0.5;RO=40;AO=38;PRO=0.0;PAO=0.0;QR=1529;QA=1465;PQR=0.0;PQA=0.0;SRF=15;SRR=25;SAF=12;SAR=26;SRP=8.43898;SAP=14.2105;AB=0.487179;ABP=3.12166;RUN=1;RPP=21.525;RPPR=8.43898;RPL=28.0;RPR=10.0;EPP=5.06748;EPPR=3.0103;DPRA=0.0;ODDS=236.937;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.444;FS=2.006;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.056;Q [...]
+chr17 78865546 . T C 1541.325 REJECT NS=2;DP=324;DPB=377.0;AC=2;AN=4;AF=0.5;RO=298;AO=79;PRO=0.0;PAO=0.0;QR=11352;QA=3047;PQR=0.0;PQA=0.0;SRF=158;SRR=140;SAF=42;SAR=37;SRP=5.37123;SAP=3.69747;AB=0.209549;ABP=279.26;RUN=1;RPP=3.69747;RPPR=11.4339;RPL=37.0;RPR=42.0;EPP=20.1897;EPPR=7.93619;DPRA=0.0;ODDS=108.162;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993289;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.525;Dels=0.0;FS=0.7115;HaplotypeScore= [...]
+chr17 78865630 . A G 1396.58 REJECT NS=2;DP=303;DPB=352.0;AC=2;AN=4;AF=0.5;RO=281;AO=71;PRO=0.0;PAO=0.0;QR=10815;QA=2689;PQR=0.0;PQA=0.0;SRF=126;SRR=155;SAF=28;SAR=43;SRP=9.50926;SAP=9.89173;AB=0.201705;ABP=275.061;RUN=1;RPP=3.7749;RPPR=33.6814;RPL=38.0;RPR=33.0;EPP=3.7749;EPPR=16.0005;DPRA=0.0;ODDS=77.9115;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985915;PAIREDR=0.992883;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.904;Dels=0.0;FS=3.474;HaplotypeScor [...]
+chr17 78896488 . C T 1052.94 REJECT NS=1;DP=87;DPB=87.0;AC=1;AN=4;AF=0.5;RO=46;AO=41;PRO=0.0;PAO=0.0;QR=1791;QA=1540;PQR=0.0;PQA=0.0;SRF=25;SRR=21;SAF=23;SAR=18;SRP=3.76559;SAP=4.33437;AB=0.471264;ABP=3.63429;RUN=1;RPP=47.552;RPPR=25.858;RPL=6.0;RPR=35.0;EPP=4.33437;EPPR=6.03148;DPRA=0.0;ODDS=242.449;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.97561;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.657;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=1.733; [...]
+chr17 78897561 . C T 11198.5 REJECT NS=2;DP=296;DPB=345.0;AC=4;AN=4;AF=1.0;RO=0;AO=345;PRO=0.0;PAO=0.0;QR=0;QA=13162;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=172;SAR=173;SRP=0.0;SAP=3.01659;AB=0.0;ABP=0.0;RUN=1;RPP=3.31871;RPPR=0.0;RPL=169.0;RPR=176.0;EPP=3.52012;EPPR=0.0;DPRA=0.0;ODDS=64.8153;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994203;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.962;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.37;SOR=0.8 [...]
+chr17 78897587 . A G 11627.75 REJECT NS=2;DP=313;DPB=362.0;AC=4;AN=4;AF=1.0;RO=1;AO=360;PRO=0.0;PAO=0.0;QR=40;QA=13573;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=180;SAR=180;SRP=5.18177;SAP=3.0103;AB=0.0;ABP=0.0;RUN=1;RPP=20.5992;RPPR=5.18177;RPL=153.0;RPR=207.0;EPP=4.19255;EPPR=5.18177;DPRA=0.0;ODDS=58.5744;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991667;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.661;Dels=0.0;FS=1.5275;HaplotypeScore=4.8377;MLEA [...]
+chr17 78897674 . C T 15568.5 REJECT NS=2;DP=412;DPB=475.0;AC=4;AN=4;AF=1.0;RO=0;AO=475;PRO=0.0;PAO=0.0;QR=0;QA=18074;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=246;SAR=229;SRP=0.0;SAP=4.33147;AB=0.0;ABP=0.0;RUN=1;RPP=8.61041;RPPR=0.0;RPL=220.0;RPR=255.0;EPP=3.78289;EPPR=0.0;DPRA=0.0;ODDS=82.2051;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993684;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.8988;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.835;SOR=0 [...]
+chr17 78897732 . CT TA 1729.92 REJECT NS=2;DP=402;DPB=456.5;AC=2;AN=4;AF=0.5;RO=370;AO=82;PRO=6.0;PAO=1.0;QR=14265;QA=3038;PQR=72.0;PQA=31.0;SRF=197;SRR=173;SAF=44;SAR=38;SRP=6.39075;SAP=3.96363;AB=0.181015;ABP=403.371;RUN=1;RPP=20.9117;RPPR=5.85082;RPL=54.0;RPR=28.0;EPP=5.65844;EPPR=3.38591;DPRA=0.0;ODDS=113.995;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=1;MEANALT=1.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=0.987805;PAIREDR=0.997297;technology.ILLUMINA=1.0;MQ0=0;JOINED;BaseQRankSum=-0.35;Dels=0.0;FS=0.364; [...]
+chr17 78919558 . C T 1142.05 REJECT NS=2;DP=314;DPB=357.0;AC=2;AN=4;AF=0.5;RO=287;AO=70;PRO=0.0;PAO=0.0;QR=11069;QA=2671;PQR=0.0;PQA=0.0;SRF=105;SRR=182;SAF=23;SAR=47;SRP=47.8697;SAP=20.8784;AB=0.196078;ABP=289.432;RUN=1;RPP=6.1124;RPPR=15.7289;RPL=40.0;RPR=30.0;EPP=3.50664;EPPR=15.7289;DPRA=0.0;ODDS=147.742;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986063;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1365;Dels=0.0;FS=0.321;HaplotypeScore=4 [...]
+chr17 78935197 . C T 2629.75 PASS SOMATIC;NS=2;DP=333;DPB=333.0;AC=1;AN=3;AF=0.25;RO=234;AO=99;PRO=0.0;PAO=0.0;QR=9020;QA=3816;PQR=0.0;PQA=0.0;SRF=153;SRR=81;SAF=74;SAR=25;SRP=51.1168;SAP=55.674;AB=0.392857;ABP=28.1373;RUN=1;RPP=3.55865;RPPR=16.4103;RPL=47.0;RPR=52.0;EPP=16.7191;EPPR=32.1117;DPRA=3.11111;ODDS=51.5388;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991453;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.692;Dels=0.0;FS=6.866; [...]
+chr17 78938134 . C T 1629.0349999999999 REJECT NS=2;DP=321;DPB=365.0;AC=2;AN=4;AF=0.5;RO=284;AO=81;PRO=0.0;PAO=0.0;QR=10989;QA=3125;PQR=0.0;PQA=0.0;SRF=109;SRR=175;SAF=20;SAR=61;SRP=36.3164;SAP=48.0751;AB=0.221918;ABP=248.173;RUN=1;RPP=3.25157;RPPR=15.2439;RPL=39.0;RPR=42.0;EPP=12.6881;EPPR=54.4222;DPRA=0.0;ODDS=118.429;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.8475;Dels=0.0;FS=14.8925;Haplot [...]
+chr18 4517485 . G A 1936.09 REJECT NS=2;DP=370;DPB=427.0;AC=2;AN=4;AF=0.5;RO=328;AO=99;PRO=0.0;PAO=0.0;QR=12517;QA=3798;PQR=0.0;PQA=0.0;SRF=162;SRR=166;SAF=48;SAR=51;SRP=3.11623;SAP=3.20771;AB=0.23185;ABP=269.695;RUN=1;RPP=6.71716;RPPR=3.67233;RPL=43.0;RPR=56.0;EPP=9.34924;EPPR=14.6886;DPRA=0.0;ODDS=206.206;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989899;PAIREDR=0.993902;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.509;Dels=0.0;FS=3.2835;HaplotypeSco [...]
+chr18 23602146 . G A 5412.8150000000005 REJECT NS=2;DP=401;DPB=467.0;AC=2;AN=4;AF=0.5;RO=260;AO=206;PRO=0.0;PAO=0.0;QR=10037;QA=7793;PQR=0.0;PQA=0.0;SRF=127;SRR=133;SAF=110;SAR=96;SRP=3.31097;SAP=5.07636;AB=0.441113;ABP=17.076;RUN=1;RPP=6.42563;RPPR=11.5626;RPL=112.0;RPR=94.0;EPP=4.06441;EPPR=3.31097;DPRA=0.0;ODDS=372.328;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990291;PAIREDR=0.988462;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.1565;Dels=0.0;FS=2. [...]
+chr18 23602401 . T A 380.437 REJECT NS=2;DP=223;DPB=313.28;AC=2;AN=2;AF=0.0;RO=105;AO=11;PRO=55.8667;PAO=26.7833;QR=3821;QA=263;PQR=2004.5;PQA=896.75;SRF=56;SRR=49;SAF=1;SAR=10;SRP=4.02365;SAP=19.0002;AB=0.0465116;ABP=310.248;RUN=1;RPP=3.20771;RPPR=3.03098;RPL=5.0;RPR=6.0;EPP=3.20771;EPPR=6.50534;DPRA=0.0;ODDS=3.32601;GTI=0;TYPE=snp;CIGAR=1X24M;NUMALT=4;MEANALT=17.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990476;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr18 23602401 . T TA 380.437 REJECT NS=2;DP=223;DPB=313.28;AC=2;AN=3;AF=0.25;RO=105;AO=30;PRO=55.8667;PAO=45.8667;QR=3821;QA=863;PQR=2004.5;PQA=1541.5;SRF=56;SRR=49;SAF=17;SAR=13;SRP=4.02365;SAP=4.16842;AB=0.145349;ABP=190.918;RUN=1;RPP=26.4622;RPPR=3.03098;RPL=6.0;RPR=24.0;EPP=7.64277;EPPR=6.50534;DPRA=0.0;ODDS=3.32601;GTI=0;TYPE=ins;CIGAR=1M1I24M;NUMALT=4;MEANALT=17.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990476;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.6 [...]
+chr18 23602401 . TA T 380.437 REJECT NS=2;DP=223;DPB=313.28;AC=2;AN=2;AF=0.0;RO=105;AO=30;PRO=55.8667;PAO=35.2;QR=3821;QA=855;PQR=2004.5;PQA=1214.5;SRF=56;SRR=49;SAF=8;SAR=22;SRP=4.02365;SAP=17.1973;AB=0.139535;ABP=197.13;RUN=1;RPP=4.16842;RPPR=3.03098;RPL=17.0;RPR=13.0;EPP=13.4334;EPPR=6.50534;DPRA=0.0;ODDS=3.32601;GTI=0;TYPE=del;CIGAR=1M1D23M;NUMALT=4;MEANALT=17.5;LEN=1;MQM=59.5333;MQMR=60.0;PAIRED=0.933333;PAIREDR=0.990476;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr18 23602416 . C A 380.437 REJECT NS=2;DP=223;DPB=313.28;AC=2;AN=2;AF=0.0;RO=105;AO=5;PRO=55.8667;PAO=26.2833;QR=3821;QA=70;PQR=2004.5;PQA=931.75;SRF=56;SRR=49;SAF=5;SAR=0;SRP=4.02365;SAP=13.8677;AB=0.0116279;ABP=359.334;RUN=1;RPP=6.91895;RPPR=3.03098;RPL=4.0;RPR=1.0;EPP=6.91895;EPPR=6.50534;DPRA=0.0;ODDS=3.32601;GTI=0;TYPE=snp;CIGAR=15M1X9M;NUMALT=4;MEANALT=17.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990476;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr18 23604916 . T TA 9984.415 REJECT NS=2;DP=287;DPB=384.5;AC=4;AN=4;AF=1.0;RO=0;AO=310;PRO=20.0;PAO=26.0;QR=0;QA=11396;PQR=558.5;PQA=781.5;SRF=0;SRR=0;SAF=158;SAR=152;SRP=0.0;SAP=3.26247;AB=0.0;ABP=0.0;RUN=1;RPP=10.1832;RPPR=0.0;RPL=171.0;RPR=139.0;EPP=7.04504;EPPR=0.0;DPRA=0.0;ODDS=54.8065;GTI=0;TYPE=ins;CIGAR=1M1I7M;NUMALT=1;MEANALT=3.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.983871;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=23604916;HOMLEN=3;HOMSEQ=AAA;SVLEN=1;SVTYPE=INS;BaseQRankSum=-0 [...]
+chr18 23604930 . T TA 11748.3 REJECT NS=2;DP=308;DPB=469.333;AC=4;AN=4;AF=1.0;RO=0;AO=341;PRO=10.0;PAO=15.0;QR=0;QA=12943;PQR=345.5;PQA=519.5;SRF=0;SRR=0;SAF=184;SAR=157;SRP=0.0;SAP=7.65254;AB=0.0;ABP=0.0;RUN=1;RPP=9.1299;RPPR=0.0;RPL=155.0;RPR=186.0;EPP=4.08648;EPPR=0.0;DPRA=0.0;ODDS=56.1207;GTI=0;TYPE=ins;CIGAR=1M1I2M;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.982405;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=23604930;HOMLEN=0;SVLEN=1;SVTYPE=INS;BaseQRankSum=0.617;FS=0.0; [...]
+chr18 23605826 . G GA 649.438 REJECT NS=2;DP=317;DPB=397.316;AC=2;AN=4;AF=0.5;RO=212;AO=50;PRO=70.0;PAO=53.0;QR=7777;QA=1601;PQR=2434.83;PQA=1836.83;SRF=114;SRR=98;SAF=28;SAR=22;SRP=5.63246;SAP=4.57376;AB=0.157729;ABP=325.573;RUN=1;RPP=3.0103;RPPR=3.05127;RPL=25.0;RPR=25.0;EPP=14.1282;EPPR=4.03458;DPRA=0.0;ODDS=34.6768;GTI=0;TYPE=ins;CIGAR=1M1I18M;NUMALT=2;MEANALT=10.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995283;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.123;FS=0. [...]
+chr18 23605826 . GA G 649.438 REJECT NS=2;DP=317;DPB=397.316;AC=2;AN=2;AF=0.0;RO=212;AO=23;PRO=70.0;PAO=50.0;QR=7777;QA=814;PQR=2434.83;PQA=1689.33;SRF=114;SRR=98;SAF=14;SAR=9;SRP=5.63246;SAP=5.3706;AB=0.0725552;ABP=506.086;RUN=1;RPP=3.86001;RPPR=3.05127;RPL=13.0;RPR=10.0;EPP=5.3706;EPPR=4.03458;DPRA=0.0;ODDS=34.6768;GTI=0;TYPE=del;CIGAR=1M1D17M;NUMALT=2;MEANALT=10.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995283;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr18 23608187 . G T 5977.115 REJECT NS=2;DP=376;DPB=430.0;AC=2;AN=4;AF=0.5;RO=221;AO=209;PRO=0.0;PAO=0.0;QR=8308;QA=8029;PQR=0.0;PQA=0.0;SRF=109;SRR=112;SAF=104;SAR=105;SRP=3.09873;SAP=3.02069;AB=0.486047;ABP=3.73749;RUN=1;RPP=3.10381;RPPR=3.25594;RPL=106.0;RPR=103.0;EPP=3.27005;EPPR=5.84992;DPRA=0.0;ODDS=310.736;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995215;PAIREDR=0.99095;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.8605;Dels=0.0;FS=0.0;Haplotyp [...]
+chr18 23610558 . A C 5591.42 REJECT NS=2;DP=388;DPB=447.0;AC=2;AN=4;AF=0.5;RO=238;AO=209;PRO=0.0;PAO=0.0;QR=9071;QA=7916;PQR=0.0;PQA=0.0;SRF=133;SRR=105;SAF=101;SAR=108;SRP=10.1634;SAP=3.5194;AB=0.467562;ABP=7.09578;RUN=1;RPP=8.50651;RPPR=4.79857;RPL=116.0;RPR=93.0;EPP=11.7481;EPPR=8.26563;DPRA=0.0;ODDS=386.096;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995215;PAIREDR=0.995798;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.541;Dels=0.0;FS=4.977;Haplotype [...]
+chr18 36002816 . T C 9339.98 REJECT NS=2;DP=360;DPB=407.0;AC=2;AN=4;AF=0.5;RO=96;AO=311;PRO=0.0;PAO=0.0;QR=3651;QA=11731;PQR=0.0;PQA=0.0;SRF=50;SRR=46;SAF=164;SAR=147;SRP=3.37221;SAP=5.02816;AB=0.764128;ABP=249.635;RUN=1;RPP=24.1315;RPPR=4.45795;RPL=128.0;RPR=183.0;EPP=27.3154;EPPR=16.0391;DPRA=0.0;ODDS=243.542;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9807;MQMR=60.0;PAIRED=0.990354;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5755;Dels=0.0;FS=1.453;HaplotypeS [...]
+chr18 42456653 . G A 6051.68 REJECT NS=2;DP=390;DPB=439.0;AC=2;AN=4;AF=0.5;RO=223;AO=215;PRO=0.0;PAO=0.0;QR=8472;QA=8125;PQR=0.0;PQA=0.0;SRF=96;SRR=127;SAF=96;SAR=119;SRP=12.3681;SAP=8.35313;AB=0.489749;ABP=3.41096;RUN=1;RPP=3.2628;RPPR=3.48744;RPL=110.0;RPR=105.0;EPP=8.35313;EPPR=10.109;DPRA=0.0;ODDS=290.556;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.6512;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.6925;Dels=0.0;FS=0.3985;HaplotypeScore= [...]
+chr18 42456670 . C CTCTT 5030.03 REJECT NS=2;DP=397;DPB=708.333;AC=2;AN=4;AF=0.5;RO=238;AO=193;PRO=12.5;PAO=18.5;QR=8862;QA=6762;PQR=385.5;PQA=599.5;SRF=95;SRR=143;SAF=77;SAR=116;SRP=24.0316;SAP=20.1233;AB=0.446759;ABP=13.6465;RUN=1;RPP=8.96216;RPPR=10.1634;RPL=108.0;RPR=85.0;EPP=8.96216;EPPR=4.79857;DPRA=0.0;ODDS=215.984;GTI=0;TYPE=ins;CIGAR=1M4I2M;NUMALT=1;MEANALT=1.5;LEN=4;MQM=60.5699;MQMR=60.0;PAIRED=0.994819;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=42456670;HOMLEN=0;SVLEN=4;SVT [...]
+chr18 42529996 . G C 4546.365 REJECT NS=2;DP=270;DPB=308.0;AC=2;AN=4;AF=0.5;RO=147;AO=160;PRO=0.0;PAO=0.0;QR=5636;QA=6084;PQR=0.0;PQA=0.0;SRF=68;SRR=79;SAF=82;SAR=78;SRP=4.7977;SAP=3.22745;AB=0.519481;ABP=4.02553;RUN=1;RPP=7.40753;RPPR=12.2428;RPL=71.0;RPR=89.0;EPP=5.67035;EPPR=3.73412;DPRA=0.0;ODDS=232.934;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993197;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.8225;Dels=0.0;FS=5.217;HaplotypeScore=4. [...]
+chr18 42532693 . C A 3362.74 PASS SOMATIC;NS=2;DP=428;DPB=428.0;AC=1;AN=3;AF=0.25;RO=303;AO=125;PRO=0.0;PAO=0.0;QR=11505;QA=4783;PQR=0.0;PQA=0.0;SRF=146;SRR=157;SAF=62;SAR=63;SRP=3.87746;SAP=3.02767;AB=0.383436;ABP=41.484;RUN=1;RPP=5.11229;RPPR=3.87746;RPL=68.0;RPR=57.0;EPP=4.41741;EPPR=5.59743;DPRA=3.19608;ODDS=64.6194;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.9967;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.989;Dels=0.0;FS=0.0;Ha [...]
+chr18 42532923 . T C 1964.485 REJECT NS=2;DP=328;DPB=379.0;AC=2;AN=4;AF=0.5;RO=279;AO=97;PRO=0.0;PAO=0.0;QR=10667;QA=3657;PQR=0.0;PQA=0.0;SRF=133;SRR=146;SAF=45;SAR=52;SRP=4.32564;SAP=4.10723;AB=0.255937;ABP=199.102;RUN=1;RPP=9.47994;RPPR=5.2596;RPL=40.0;RPR=57.0;EPP=8.04722;EPPR=5.81998;DPRA=0.0;ODDS=182.204;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996416;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.845;Dels=0.0;FS=4.4735;HaplotypeScore= [...]
+chr18 42533130 . A G 9547.32 REJECT NS=2;DP=376;DPB=431.0;AC=2;AN=4;AF=0.5;RO=110;AO=320;PRO=0.0;PAO=0.0;QR=4058;QA=11983;PQR=0.0;PQA=0.0;SRF=66;SRR=44;SAF=167;SAR=153;SRP=12.5648;SAP=4.34033;AB=0.742459;ABP=223.085;RUN=1;RPP=6.29465;RPPR=3.32615;RPL=149.0;RPR=171.0;EPP=3.11887;EPPR=5.85295;DPRA=0.0;ODDS=221.886;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.9875;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.446;Dels=0.0;FS=3.1455;HaplotypeScore [...]
+chr18 42533315 . T A 1676.32 PASS SOMATIC;NS=2;DP=289;DPB=289.0;AC=1;AN=3;AF=0.25;RO=219;AO=70;PRO=0.0;PAO=0.0;QR=8307;QA=2639;PQR=0.0;PQA=0.0;SRF=66;SRR=153;SAF=25;SAR=45;SRP=78.06;SAP=15.4187;AB=0.316742;ABP=67.4765;RUN=1;RPP=38.8706;RPPR=64.8923;RPL=52.0;RPR=18.0;EPP=3.50664;EPPR=3.09954;DPRA=3.25;ODDS=43.4356;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995434;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.994;Dels=0.0;FS=3.59;Haplot [...]
+chr18 48577782 . G C 8319.77 REJECT NS=2;DP=360;DPB=415.0;AC=3;AN=4;AF=0.75;RO=113;AO=302;PRO=0.0;PAO=0.0;QR=4378;QA=11502;PQR=0.0;PQA=0.0;SRF=44;SRR=69;SAF=104;SAR=198;SRP=15.0207;SAP=66.5438;AB=0.630719;ABP=48.4267;RUN=1;RPP=15.694;RPPR=13.1759;RPL=172.0;RPR=130.0;EPP=30.6498;EPPR=3.49071;DPRA=0.0;ODDS=69.0074;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996689;PAIREDR=0.99115;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.648;Dels=0.0;FS=0.733;Haplotyp [...]
+chr18 48584855 . A AT 557.924 REJECT NS=2;DP=101;DPB=152.0;AC=2;AN=2;AF=0.0;RO=20;AO=12;PRO=27.5;PAO=26.5;QR=719;QA=252;PQR=977.083;PQA=906.083;SRF=8;SRR=12;SAF=2;SAR=10;SRP=4.74748;SAP=14.5915;AB=0.118812;ABP=130.482;RUN=1;RPP=29.068;RPPR=30.8051;RPL=12.0;RPR=0.0;EPP=14.5915;EPPR=3.0103;DPRA=0.0;ODDS=11.3265;GTI=0;TYPE=ins;CIGAR=1M1I24M;NUMALT=4;MEANALT=14.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr18 48584855 . A ATT 557.924 REJECT NS=2;DP=101;DPB=152.0;AC=2;AN=4;AF=0.5;RO=20;AO=30;PRO=27.5;PAO=23.5;QR=719;QA=702;PQR=977.083;PQA=823.083;SRF=8;SRR=12;SAF=8;SAR=22;SRP=4.74748;SAP=17.1973;AB=0.29703;ABP=39.1513;RUN=1;RPP=31.9633;RPPR=30.8051;RPL=25.0;RPR=5.0;EPP=4.16842;EPPR=3.0103;DPRA=0.0;ODDS=11.3265;GTI=0;TYPE=ins;CIGAR=1M2I24M;NUMALT=4;MEANALT=14.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.3645;FS=1.6175;MLE [...]
+chr18 48584855 . A TTT 557.924 REJECT NS=2;DP=101;DPB=152.0;AC=2;AN=2;AF=0.0;RO=20;AO=6;PRO=27.5;PAO=3.0;QR=719;QA=84;PQR=977.083;PQA=67.0;SRF=8;SRR=12;SAF=0;SAR=6;SRP=4.74748;SAP=16.0391;AB=0.0594059;ABP=173.31;RUN=1;RPP=3.0103;RPPR=30.8051;RPL=3.0;RPR=3.0;EPP=3.0103;EPPR=3.0103;DPRA=0.0;ODDS=11.3265;GTI=0;TYPE=complex;CIGAR=1X2I24M;NUMALT=4;MEANALT=14.0;LEN=27;MQM=68.8333;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr18 48584855 . AT A 557.924 REJECT NS=2;DP=101;DPB=152.0;AC=2;AN=2;AF=0.0;RO=20;AO=6;PRO=27.5;PAO=14.5;QR=719;QA=193;PQR=977.083;PQA=507.75;SRF=8;SRR=12;SAF=1;SAR=5;SRP=4.74748;SAP=8.80089;AB=0.0789474;ABP=120.041;RUN=1;RPP=8.80089;RPPR=30.8051;RPL=5.0;RPR=1.0;EPP=16.0391;EPPR=3.0103;DPRA=0.0;ODDS=11.3265;GTI=0;TYPE=del;CIGAR=1M1D23M;NUMALT=4;MEANALT=17.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMIC [...]
+chr18 49867224 . T C 12421.5 REJECT NS=2;DP=332;DPB=378.0;AC=4;AN=4;AF=1.0;RO=0;AO=378;PRO=0.0;PAO=0.0;QR=0;QA=14335;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=167;SAR=211;SRP=0.0;SAP=14.1319;AB=0.0;ABP=0.0;RUN=1;RPP=31.159;RPPR=0.0;RPL=224.0;RPR=154.0;EPP=29.5735;EPPR=0.0;DPRA=0.0;ODDS=60.8611;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8915;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.0;MQ=59.99;QD=33.135;SOR=1.0 [...]
+chr18 50450240 . T G 4245.78 REJECT NS=2;DP=283;DPB=320.0;AC=2;AN=4;AF=0.5;RO=166;AO=154;PRO=0.0;PAO=0.0;QR=6394;QA=5888;PQR=0.0;PQA=0.0;SRF=52;SRR=114;SAF=44;SAR=110;SRP=53.2943;SAP=64.4319;AB=0.48125;ABP=3.98746;RUN=1;RPP=64.4319;RPPR=44.0328;RPL=110.0;RPR=44.0;EPP=3.0667;EPPR=3.84749;DPRA=0.0;ODDS=228.721;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7995;Dels=0.0;FS=1.1555;HaplotypeScore=2.924 [...]
+chr18 50683691 . G A 1164.42 PASS SOMATIC;NS=2;DP=201;DPB=201.0;AC=1;AN=3;AF=0.25;RO=151;AO=50;PRO=0.0;PAO=0.0;QR=5727;QA=1896;PQR=0.0;PQA=0.0;SRF=98;SRR=53;SAF=40;SAR=10;SRP=32.131;SAP=42.0968;AB=0.342466;ABP=34.4818;RUN=1;RPP=47.4821;RPPR=155.574;RPL=9.0;RPR=41.0;EPP=14.1282;EPPR=4.17513;DPRA=2.65455;ODDS=35.3264;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.066;Dels=0.0;FS=8.994;Haplotyp [...]
+chr18 50831933 . C T 1899.16 PASS SOMATIC;NS=2;DP=253;DPB=253.0;AC=1;AN=3;AF=0.25;RO=177;AO=76;PRO=0.0;PAO=0.0;QR=6764;QA=2913;PQR=0.0;PQA=0.0;SRF=125;SRR=52;SAF=62;SAR=14;SRP=68.3876;SAP=68.8402;AB=0.383838;ABP=26.2165;RUN=1;RPP=58.3257;RPPR=51.7028;RPL=16.0;RPR=60.0;EPP=10.3247;EPPR=3.31701;DPRA=3.6;ODDS=35.3538;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.983051;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.195;Dels=0.0;FS=11.83;Hapl [...]
+chr18 50832102 . A G 5391.605 REJECT NS=2;DP=322;DPB=368.0;AC=2;AN=4;AF=0.5;RO=175;AO=193;PRO=0.0;PAO=0.0;QR=6736;QA=7416;PQR=0.0;PQA=0.0;SRF=65;SRR=110;SAF=86;SAR=107;SRP=28.1373;SAP=7.97206;AB=0.524457;ABP=4.92214;RUN=1;RPP=47.6661;RPPR=25.9535;RPL=128.0;RPR=65.0;EPP=6.26188;EPPR=5.80219;DPRA=0.0;ODDS=260.084;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.984456;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.109;Dels=0.0;FS=5.065;HaplotypeScor [...]
+chr18 50929276 . A G 1259.2 REJECT NS=2;DP=287;DPB=325.0;AC=2;AN=4;AF=0.5;RO=255;AO=69;PRO=0.0;PAO=0.0;QR=9799;QA=2617;PQR=0.0;PQA=0.0;SRF=102;SRR=153;SAF=21;SAR=48;SRP=25.1593;SAP=25.9524;AB=0.212308;ABP=236.654;RUN=1;RPP=14.3712;RPPR=45.9373;RPL=44.0;RPR=25.0;EPP=3.79707;EPPR=14.6681;DPRA=0.0;ODDS=124.35;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.984314;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.15;Dels=0.0;FS=2.9185;HaplotypeScore=1.9 [...]
+chr18 50936994 . T C 7842.280000000001 REJECT NS=2;DP=334;DPB=378.0;AC=3;AN=4;AF=0.75;RO=103;AO=275;PRO=0.0;PAO=0.0;QR=4022;QA=10511;PQR=0.0;PQA=0.0;SRF=41;SRR=62;SAF=94;SAR=181;SRP=12.3076;SAP=62.7771;AB=0.646048;ABP=56.924;RUN=1;RPP=19.0002;RPPR=6.5732;RPL=160.0;RPR=115.0;EPP=3.08137;EPPR=10.621;DPRA=0.0;ODDS=55.2631;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989091;PAIREDR=0.990291;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.074;Dels=0.0;FS=1.3845 [...]
+chr18 50937026 . A G 5560.96 REJECT NS=2;DP=250;DPB=281.0;AC=3;AN=4;AF=0.75;RO=84;AO=197;PRO=0.0;PAO=0.0;QR=3241;QA=7524;PQR=0.0;PQA=0.0;SRF=32;SRR=52;SAF=57;SAR=140;SRP=13.3506;SAP=78.9457;AB=0.61991;ABP=30.6106;RUN=1;RPP=49.5812;RPPR=36.513;RPL=131.0;RPR=66.0;EPP=3.90314;EPPR=4.66476;DPRA=0.0;ODDS=38.4249;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.979695;PAIREDR=0.988095;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.712;Dels=0.0;FS=3.6375;HaplotypeSco [...]
+chr18 50942653 . C T 7728.27 REJECT NS=2;DP=336;DPB=391.0;AC=3;AN=4;AF=0.75;RO=108;AO=283;PRO=0.0;PAO=0.0;QR=4061;QA=10797;PQR=0.0;PQA=0.0;SRF=39;SRR=69;SAF=111;SAR=172;SRP=21.1059;SAP=31.5617;AB=0.617021;ABP=36.5526;RUN=1;RPP=3.20213;RPPR=3.73412;RPL=144.0;RPR=139.0;EPP=13.5147;EPPR=5.9056;DPRA=0.0;ODDS=68.974;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.196;Dels=0.0;FS=0.2335;HaplotypeScore=9.7 [...]
+chr18 60985879 . T C 1259.85 REJECT NS=2;DP=317;DPB=356.0;AC=2;AN=4;AF=0.5;RO=290;AO=66;PRO=0.0;PAO=0.0;QR=11139;QA=2556;PQR=0.0;PQA=0.0;SRF=132;SRR=158;SAF=35;SAR=31;SRP=8.07208;SAP=3.53672;AB=0.185393;ABP=309.066;RUN=1;RPP=5.11597;RPPR=9.74935;RPL=37.0;RPR=29.0;EPP=4.19474;EPPR=16.2188;DPRA=0.0;ODDS=61.6195;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996552;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.7325;Dels=0.0;FS=2.426;HaplotypeScore= [...]
+chr18 61084121 . G A 6547.56 REJECT NS=2;DP=366;DPB=418.0;AC=2;AN=4;AF=0.5;RO=189;AO=228;PRO=0.0;PAO=0.0;QR=7304;QA=8826;PQR=0.0;PQA=0.0;SRF=96;SRR=93;SAF=103;SAR=125;SRP=3.1137;SAP=7.61992;AB=0.545455;ABP=10.5118;RUN=1;RPP=5.44844;RPPR=3.02179;RPL=122.0;RPR=106.0;EPP=3.35316;EPPR=9.08812;DPRA=0.0;ODDS=276.1;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.982456;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6335;Dels=0.0;FS=4.161;HaplotypeScore=6 [...]
+chr18 61085648 . A AT 922.277 REJECT NS=2;DP=218;DPB=264.0;AC=2;AN=2;AF=0.0;RO=128;AO=20;PRO=36.8333;PAO=30.8333;QR=4694;QA=612;PQR=1322.83;PQA=1103.83;SRF=46;SRR=82;SAF=6;SAR=14;SRP=24.9965;SAP=9.95901;AB=0.0917431;ABP=318.611;RUN=1;RPP=18.6449;RPPR=8.50684;RPL=16.0;RPR=4.0;EPP=3.0103;EPPR=22.6214;DPRA=0.0;ODDS=41.2509;GTI=0;TYPE=ins;CIGAR=1M1I17M;NUMALT=2;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=59.9219;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr18 61085648 . AT A 746.0035 REJECT NS=2;DP=218;DPB=264.0;AC=2;AN=4;AF=0.5;RO=128;AO=49;PRO=36.8333;PAO=29.3333;QR=4694;QA=1614;PQR=1322.83;PQA=1033.33;SRF=46;SRR=82;SAF=15;SAR=34;SRP=24.9965;SAP=19.0083;AB=0.224771;ABP=146.447;RUN=1;RPP=10.4997;RPPR=8.50684;RPL=31.0;RPR=18.0;EPP=6.59988;EPPR=22.6214;DPRA=0.0;ODDS=41.2509;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=2;MEANALT=7.5;LEN=1;MQM=60.0;MQMR=59.9219;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.67 [...]
+chr18 63003979 . A C 13233.7 REJECT NS=2;DP=349;DPB=398.0;AC=4;AN=4;AF=1.0;RO=0;AO=398;PRO=0.0;PAO=0.0;QR=0;QA=15260;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=165;SAR=233;SRP=0.0;SAP=28.2387;AB=0.0;ABP=0.0;RUN=1;RPP=17.7632;RPPR=0.0;RPL=225.0;RPR=173.0;EPP=4.07967;EPPR=0.0;DPRA=0.0;ODDS=64.8174;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992462;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.933;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.175;SOR=1. [...]
+chr18 67511067 . A G 2272.4 PASS SOMATIC;NS=2;DP=300;DPB=300.0;AC=1;AN=3;AF=0.25;RO=214;AO=86;PRO=0.0;PAO=0.0;QR=8260;QA=3300;PQR=0.0;PQA=0.0;SRF=148;SRR=66;SAF=57;SAR=29;SRP=71.2392;SAP=22.806;AB=0.383929;ABP=29.2231;RUN=1;RPP=15.2311;RPPR=81.5892;RPL=32.0;RPR=54.0;EPP=9.47422;EPPR=3.65971;DPRA=2.94737;ODDS=48.4512;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.985981;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.85;Dels=0.0;FS=0.537;Hap [...]
+chr18 72033902 . C A 1457.045 REJECT NS=2;DP=347;DPB=399.0;AC=2;AN=4;AF=0.5;RO=315;AO=84;PRO=0.0;PAO=0.0;QR=12120;QA=3192;PQR=0.0;PQA=0.0;SRF=165;SRR=150;SAF=42;SAR=42;SRP=4.56135;SAP=3.0103;AB=0.210526;ABP=293.416;RUN=1;RPP=6.73282;RPPR=3.01719;RPL=36.0;RPR=48.0;EPP=3.42391;EPPR=12.4476;DPRA=0.0;ODDS=181.266;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993651;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.153;Dels=0.0;FS=1.377;HaplotypeScore=2 [...]
+chr18 73511459 . C A 10072.585 REJECT NS=2;DP=268;DPB=308.0;AC=4;AN=4;AF=1.0;RO=0;AO=307;PRO=0.0;PAO=0.0;QR=0;QA=11742;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=207;SAR=100;SRP=0.0;SAP=83.9914;AB=0.0;ABP=0.0;RUN=1;RPP=72.3347;RPPR=0.0;RPL=104.0;RPR=203.0;EPP=32.8946;EPPR=0.0;DPRA=0.0;ODDS=54.2089;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996743;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9993;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.205;SOR [...]
+chr18 75012021 . C T 5531.780000000001 REJECT NS=2;DP=375;DPB=429.0;AC=2;AN=4;AF=0.5;RO=226;AO=203;PRO=0.0;PAO=0.0;QR=8747;QA=7783;PQR=0.0;PQA=0.0;SRF=93;SRR=133;SAF=86;SAR=117;SRP=18.3836;SAP=13.29;AB=0.473193;ABP=5.68794;RUN=1;RPP=14.6592;RPPR=4.39389;RPL=85.0;RPR=118.0;EPP=12.0064;EPPR=7.66071;DPRA=0.0;ODDS=346.112;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986726;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.538;Dels=0.0;FS=0.5685;Haplot [...]
+chr19 2190947 . TTGG T . PASS SOMATIC;AC=1;AN=4 GT:AD:DP:MM:MQS:NQSBQ:NQSMM:REnd:RStart:SC:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:25,0:25:0.24,0.0:60.0,0.0:37.0439,0.0:0.0,0.0:0,0:0,0:23,2,0,0:0:0:25:.:.:.:.:0:.:0.00145514 0/1:30,13:43:0.2,0.153846:60.0,60.0:38.1809,37.0231:0.0,0.00769231:75,6:25,6:26,4,13,0:13:30:43:.:.:.:.:1:.:-0.483792
+chr19 2215467 . C T 1478.775 REJECT NS=2;DP=290;DPB=334.0;AC=2;AN=4;AF=0.5;RO=259;AO=75;PRO=0.0;PAO=0.0;QR=9850;QA=2802;PQR=0.0;PQA=0.0;SRF=148;SRR=111;SAF=46;SAR=29;SRP=14.4881;SAP=11.3777;AB=0.224551;ABP=223.122;RUN=1;RPP=18.3264;RPPR=12.1405;RPL=26.0;RPR=49.0;EPP=3.73412;EPPR=4.42721;DPRA=0.0;ODDS=94.0406;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.973333;PAIREDR=0.992278;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.818;Dels=0.0;FS=2.376;HaplotypeSco [...]
+chr19 2226676 . G A 6177.765 REJECT NS=2;DP=362;DPB=412.0;AC=2;AN=4;AF=0.5;RO=196;AO=216;PRO=0.0;PAO=0.0;QR=7532;QA=8225;PQR=0.0;PQA=0.0;SRF=78;SRR=118;SAF=105;SAR=111;SRP=20.7366;SAP=3.37221;AB=0.524272;ABP=5.11853;RUN=1;RPP=4.01561;RPPR=6.59988;RPL=113.0;RPR=103.0;EPP=3.17115;EPPR=3.40914;DPRA=0.0;ODDS=324.679;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990741;PAIREDR=0.979592;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.735;Dels=0.0;FS=5.315;Haplotyp [...]
+chr19 2226772 . G C 6257.64 REJECT NS=2;DP=397;DPB=457.0;AC=2;AN=4;AF=0.5;RO=231;AO=226;PRO=0.0;PAO=0.0;QR=8770;QA=8474;PQR=0.0;PQA=0.0;SRF=116;SRR=115;SAF=109;SAR=117;SRP=3.0197;SAP=3.62523;AB=0.49453;ABP=3.12909;RUN=1;RPP=12.8492;RPPR=13.2472;RPL=129.0;RPR=97.0;EPP=3.3562;EPPR=9.86313;DPRA=0.0;ODDS=336.974;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9248;MQMR=60.0;PAIRED=0.99115;PAIREDR=0.991342;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3625;Dels=0.0;FS=0.5425;Haplotyp [...]
+chr19 2227926 . T C 187.77 PASS DP=63;AC=1;AN=4;AF=0.5;BaseQRankSum=-3.733;FS=56.185;MLEAC=1;MLEAF=0.5;MQ=59.88;MQRankSum=0.989;QD=2.98;ReadPosRankSum=-2.539;SOR=5.131;ClippingRankSum=0.543 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:50,12:62:99.0:216,0,2695:12:19:62:1:.:.:.:.:.:0.00145514 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.216332
+chr19 2227932 . G C 150.77 PASS DP=62;AC=1;AN=4;AF=0.5;BaseQRankSum=-4.017;FS=50.57;MLEAC=1;MLEAF=0.5;MQ=59.88;MQRankSum=-0.608;QD=2.43;ReadPosRankSum=-3.243;SOR=4.971;ClippingRankSum=0.921 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:51,11:62:99.0:179,0,3249:11:18:62:1:.:.:.:.:.:0.00145514 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.216332
+chr19 2227934 . T C 148.77 PASS DP=64;AC=1;AN=4;AF=0.5;BaseQRankSum=-4.324;FS=49.834;MLEAC=1;MLEAF=0.5;MQ=59.88;MQRankSum=-0.053;QD=2.32;ReadPosRankSum=-3.113;SOR=4.971;ClippingRankSum=0.712 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:53,11:64:99.0:177,0,3245:11:17:64:1:.:.:.:.:.:0.00145514 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.216332
+chr19 2227935 . G T 148.77 PASS DP=64;AC=1;AN=4;AF=0.5;BaseQRankSum=-4.733;FS=47.561;MLEAC=1;MLEAF=0.5;MQ=59.88;MQRankSum=0.089;QD=2.32;ReadPosRankSum=-3.451;SOR=4.971;ClippingRankSum=0.249 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:53,11:64:99.0:177,0,3245:11:17:64:1:.:.:.:.:.:0.00145514 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.216332
+chr19 2227941 . G C 139.77 PASS DP=65;AC=1;AN=4;AF=0.5;BaseQRankSum=-2.213;FS=38.338;MLEAC=1;MLEAF=0.5;MQ=59.88;MQRankSum=-0.218;QD=2.15;ReadPosRankSum=-4.09;SOR=4.608;ClippingRankSum=-0.959 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:56,9:65:99.0:168,0,3301:9:14:65:1:.:.:.:.:.:0.00145514 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.216332
+chr19 3110349 . T G 1074.28 PASS SOMATIC;NS=2;DP=246;DPB=246.0;AC=1;AN=3;AF=0.25;RO=196;AO=50;PRO=0.0;PAO=0.0;QR=7536;QA=1877;PQR=0.0;PQA=0.0;SRF=55;SRR=141;SAF=9;SAR=41;SRP=84.9501;SAP=47.4821;AB=0.277778;ABP=80.2182;RUN=1;RPP=32.3686;RPPR=20.7366;RPL=38.0;RPR=12.0;EPP=9.26414;EPPR=4.11819;DPRA=2.72727;ODDS=42.2131;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.98;PAIREDR=0.989796;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.736;Dels=0.0;FS=4.836;H [...]
+chr19 3113305 . G C 8137.185 REJECT NS=2;DP=218;DPB=253.0;AC=4;AN=4;AF=1.0;RO=0;AO=253;PRO=0.0;PAO=0.0;QR=0;QA=9649;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=180;SAR=73;SRP=0.0;SAP=101.276;AB=0.0;ABP=0.0;RUN=1;RPP=80.4709;RPPR=0.0;RPL=79.0;RPR=174.0;EPP=11.2585;EPPR=0.0;DPRA=0.0;ODDS=46.7601;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996047;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9157;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.355;SOR=1.94 [...]
+chr19 3119184 . T G 8604.135 REJECT NS=2;DP=231;DPB=262.0;AC=4;AN=4;AF=1.0;RO=0;AO=260;PRO=0.0;PAO=0.0;QR=0;QA=9848;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=121;SAR=139;SRP=0.0;SAP=5.71629;AB=0.0;ABP=0.0;RUN=1;RPP=46.3061;RPPR=0.0;RPL=94.0;RPR=166.0;EPP=10.5269;EPPR=0.0;DPRA=0.0;ODDS=42.34;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996154;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.9574;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.655;SOR=0.863 [...]
+chr19 3119239 . C T 2753.76 PASS SOMATIC;NS=2;DP=384;DPB=384.0;AC=1;AN=3;AF=0.25;RO=278;AO=106;PRO=0.0;PAO=0.0;QR=10673;QA=4007;PQR=0.0;PQA=0.0;SRF=134;SRR=144;SAF=52;SAR=54;SRP=3.79141;SAP=3.09224;AB=0.363014;ABP=50.6042;RUN=1;RPP=9.64763;RPPR=11.0088;RPL=44.0;RPR=62.0;EPP=3.74778;EPPR=9.13416;DPRA=3.17391;ODDS=58.3758;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8058;PAIRED=1.0;PAIREDR=0.996403;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.794;Dels=0.0;FS= [...]
+chr19 3121908 . C G 1457.58 PASS SOMATIC;NS=2;DP=238;DPB=238.0;AC=1;AN=3;AF=0.25;RO=178;AO=60;PRO=0.0;PAO=0.0;QR=6773;QA=2283;PQR=0.0;PQA=0.0;SRF=148;SRR=30;SAF=51;SAR=9;SRP=172.873;SAP=66.8516;AB=0.340909;ABP=41.702;RUN=1;RPP=3.15506;RPPR=10.0371;RPL=29.0;RPR=31.0;EPP=5.32654;EPPR=3.20549;DPRA=2.83871;ODDS=39.6517;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983333;PAIREDR=0.994382;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.039;Dels=0.0;FS=0.0; [...]
+chr19 4099187 . T C 1495.92 PASS SOMATIC;NS=2;DP=214;DPB=214.0;AC=1;AN=3;AF=0.25;RO=155;AO=59;PRO=0.0;PAO=0.0;QR=5894;QA=2269;PQR=0.0;PQA=0.0;SRF=127;SRR=28;SAF=47;SAR=12;SRP=140.317;SAP=48.096;AB=0.364198;ABP=28.9607;RUN=1;RPP=11.2913;RPPR=65.8989;RPL=22.0;RPR=37.0;EPP=5.99147;EPPR=10.4213;DPRA=3.11538;ODDS=33.4356;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987097;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.167;Dels=0.0;FS=0.0;Hapl [...]
+chr19 4101062 . G T 3396.17 PASS SOMATIC;NS=2;DP=527;DPB=527.0;AC=1;AN=3;AF=0.25;RO=390;AO=137;PRO=0.0;PAO=0.0;QR=15044;QA=5260;PQR=0.0;PQA=0.0;SRF=228;SRR=162;SAF=77;SAR=60;SRP=27.264;SAP=7.591;AB=0.336634;ABP=96.6631;RUN=1;RPP=3.40655;RPPR=8.02139;RPL=66.0;RPR=71.0;EPP=3.15295;EPPR=6.77419;DPRA=0.0;ODDS=74.5746;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=50.9197;MQMR=52.6051;PAIRED=1.0;PAIREDR=0.994872;technology.ILLUMINA=1.0;MQ0=2;VT=SNP;BaseQRankSum=-0.179;Dels=0.0;FS=0.56 [...]
+chr19 4102449 . G A 979.343 REJECT NS=1;DP=93;DPB=93.0;AC=1;AN=4;AF=0.5;RO=55;AO=38;PRO=0.0;PAO=0.0;QR=2098;QA=1423;PQR=0.0;PQA=0.0;SRF=19;SRR=36;SAF=16;SAR=22;SRP=14.4204;SAP=5.06748;AB=0.408602;ABP=9.75821;RUN=1;RPP=3.9246;RPPR=6.20829;RPL=21.0;RPR=17.0;EPP=3.0103;EPPR=6.20829;DPRA=0.0;ODDS=225.502;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=2.516;FS=4.109;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.21;QD= [...]
+chr19 7501602 . G A 5937.675 REJECT NS=2;DP=371;DPB=423.0;AC=2;AN=4;AF=0.5;RO=214;AO=209;PRO=0.0;PAO=0.0;QR=8258;QA=8068;PQR=0.0;PQA=0.0;SRF=117;SRR=97;SAF=113;SAR=96;SRP=7.06913;SAP=6.01296;AB=0.49409;ABP=3.13864;RUN=1;RPP=3.10381;RPPR=10.9656;RPL=106.0;RPR=103.0;EPP=8.50651;EPPR=4.99913;DPRA=0.0;ODDS=337.827;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.985646;PAIREDR=0.995327;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.099;Dels=0.0;FS=2.245;Haplotype [...]
+chr19 7501616 . A G 3233.84 PASS SOMATIC;NS=2;DP=433;DPB=433.0;AC=1;AN=3;AF=0.25;RO=313;AO=120;PRO=0.0;PAO=0.0;QR=11947;QA=4650;PQR=0.0;PQA=0.0;SRF=164;SRR=149;SAF=59;SAR=61;SRP=4.57126;SAP=3.08268;AB=0.366972;ABP=53.2729;RUN=1;RPP=4.16842;RPPR=5.01527;RPL=56.0;RPR=64.0;EPP=11.7686;EPPR=6.06979;DPRA=3.08491;ODDS=67.1567;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991667;PAIREDR=0.996805;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.45;Dels=0.0;FS= [...]
+chr19 7501651 . T C 3369.77 PASS SOMATIC;DP=304;AC=1;AN=3;AF=0.5;MQ0=0;VT=SNP;BaseQRankSum=2.535;Dels=0.0;FS=0.448;HaplotypeScore=2.9637;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.061;QD=11.08;ReadPosRankSum=0.482;SOR=0.65 GT:AD:BQ:DP:FA:SS:GMIMUT:GMIMAF:GMICOV:GQ:PL:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0:93,0:.:93:0.0:0:0:0:93:.:.:.:.:.:.:.:0:0.00145514 0/1:194,65:34.0:259:0.126:2:65:23:259:99.0:3398,0,7455:.:1:.:.:.:1:-0.216332
+chr19 7501651 . TTGA CTGG 2592.12 PASS SOMATIC;NS=2;DP=398;DPB=404.5;AC=1;AN=4;AF=0.25;RO=295;AO=103;PRO=11.0;PAO=1.0;QR=11117;QA=3855;PQR=388.0;PQA=39.0;SRF=129;SRR=166;SAF=42;SAR=61;SRP=13.0874;SAP=10.621;AB=0.342193;ABP=68.1184;RUN=1;RPP=12.3076;RPPR=6.90423;RPL=62.0;RPR=41.0;EPP=10.621;EPPR=14.2063;DPRA=3.10309;ODDS=64.6554;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=1;MEANALT=1.0;LEN=4;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99661;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr19 7501654 . A G 3565.77 PASS SOMATIC;DP=304;AC=1;AN=3;AF=0.5;MQ0=0;VT=SNP;BaseQRankSum=3.122;Dels=0.0;FS=0.0;HaplotypeScore=1.9972;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.34;QD=11.73;ReadPosRankSum=-0.313;SOR=0.677 GT:AD:BQ:DP:FA:SS:GMIMUT:GMIMAF:GMICOV:GQ:PL:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0:92,0:.:92:0.0:0:0:0:92:.:.:.:.:.:.:.:0:0.00145514 0/1:192,67:36.0:260:0.139:2:67:24:260:99.0:3594,0,7446:.:1:.:.:.:1:-0.216332
+chr19 9001373 . C T 89.4467 REJECT NS=2;DP=385;DPB=385.0;AC=1;AN=4;AF=0.25;RO=369;AO=16;PRO=0.0;PAO=0.0;QR=14040;QA=621;PQR=0.0;PQA=0.0;SRF=194;SRR=175;SAF=9;SAR=7;SRP=5.13469;SAP=3.55317;AB=0.122222;ABP=114.576;RUN=1;RPP=7.89611;RPPR=7.95937;RPL=5.0;RPR=11.0;EPP=3.0103;EPPR=7.95937;DPRA=0.0;ODDS=20.5959;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.1084;PAIRED=1.0;PAIREDR=0.98645;technology.ILLUMINA=1.0;BaseQRankSum=1.319;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.25;MQRankSum [...]
+chr19 10471789 . A T 5410.275 REJECT NS=2;DP=368;DPB=421.0;AC=2;AN=4;AF=0.5;RO=226;AO=195;PRO=0.0;PAO=0.0;QR=8783;QA=7477;PQR=0.0;PQA=0.0;SRF=92;SRR=134;SAF=80;SAR=115;SRP=19.9593;SAP=16.6516;AB=0.463183;ABP=7.96703;RUN=1;RPP=13.7118;RPPR=14.1175;RPL=113.0;RPR=82.0;EPP=12.3755;EPPR=9.5055;DPRA=0.0;ODDS=309.121;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.979487;PAIREDR=0.995575;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.9385;Dels=0.0;FS=5.939;Haplotyp [...]
+chr19 10600442 . G C 5115.29 REJECT NS=2;DP=328;DPB=369.0;AC=2;AN=4;AF=0.5;RO=190;AO=179;PRO=0.0;PAO=0.0;QR=7233;QA=6880;PQR=0.0;PQA=0.0;SRF=91;SRR=99;SAF=88;SAR=91;SRP=3.74174;SAP=3.11948;AB=0.485095;ABP=3.72235;RUN=1;RPP=17.8709;RPPR=5.93607;RPL=107.0;RPR=72.0;EPP=3.11948;EPPR=3.05602;DPRA=0.0;ODDS=242.332;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994413;PAIREDR=0.994737;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.361;Dels=0.0;FS=1.404;HaplotypeSco [...]
+chr19 11105608 . T C 5461.34 REJECT NS=2;DP=376;DPB=429.0;AC=2;AN=4;AF=0.5;RO=234;AO=195;PRO=0.0;PAO=0.0;QR=8906;QA=7464;PQR=0.0;PQA=0.0;SRF=96;SRR=138;SAF=73;SAR=122;SRP=19.3799;SAP=29.7472;AB=0.454545;ABP=10.7092;RUN=1;RPP=3.11052;RPPR=12.5128;RPL=99.0;RPR=96.0;EPP=7.03031;EPPR=15.0369;DPRA=0.0;ODDS=265.696;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994872;PAIREDR=0.995726;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.8675;Dels=0.0;FS=2.1035;Haplotype [...]
+chr19 11107133 . T C 5426.73 REJECT NS=2;DP=328;DPB=372.0;AC=2;AN=4;AF=0.5;RO=182;AO=190;PRO=0.0;PAO=0.0;QR=6984;QA=7227;PQR=0.0;PQA=0.0;SRF=113;SRR=69;SAF=110;SAR=80;SRP=26.109;SAP=13.2962;AB=0.510753;ABP=3.38389;RUN=1;RPP=3.42174;RPPR=11.0758;RPL=98.0;RPR=92.0;EPP=3.42174;EPPR=18.4731;DPRA=0.0;ODDS=247.187;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9451;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.633;Dels=0.0;FS=3.1995;HaplotypeScore=5.8 [...]
+chr19 11136215 . C G 749.124 REJECT NS=1;DP=57;DPB=57.0;AC=1;AN=4;AF=0.5;RO=27;AO=30;PRO=0.0;PAO=0.0;QR=998;QA=1088;PQR=0.0;PQA=0.0;SRF=8;SRR=19;SAF=6;SAR=24;SRP=12.7417;SAP=26.4622;AB=0.526316;ABP=3.35316;RUN=1;RPP=10.2485;RPPR=6.95112;RPL=20.0;RPR=10.0;EPP=3.29983;EPPR=9.52472;DPRA=0.0;ODDS=156.656;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.966667;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.598;FS=1.236;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0. [...]
+chr19 11170839 . T C 907.582 REJECT NS=1;DP=93;DPB=93.0;AC=1;AN=4;AF=0.5;RO=56;AO=36;PRO=0.0;PAO=0.0;QR=2068;QA=1338;PQR=0.0;PQA=0.0;SRF=17;SRR=39;SAF=17;SAR=19;SRP=21.778;SAP=3.25157;AB=0.387097;ABP=13.3073;RUN=1;RPP=3.9754;RPPR=3.16541;RPL=20.0;RPR=16.0;EPP=3.25157;EPPR=3.0103;DPRA=0.0;ODDS=208.979;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.982143;technology.ILLUMINA=1.0;BaseQRankSum=1.074;FS=9.164;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=1.08 [...]
+chr19 13054781 . G T 5388.72 REJECT NS=2;DP=320;DPB=366.0;AC=2;AN=4;AF=0.5;RO=177;AO=188;PRO=0.0;PAO=0.0;QR=6739;QA=7198;PQR=0.0;PQA=0.0;SRF=61;SRR=116;SAF=69;SAR=119;SRP=40.1216;SAP=31.8863;AB=0.513661;ABP=3.6036;RUN=1;RPP=4.67356;RPPR=25.6942;RPL=88.0;RPR=100.0;EPP=10.8184;EPPR=3.02257;DPRA=0.0;ODDS=242.779;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9574;MQMR=60.0;PAIRED=0.968085;PAIREDR=0.988701;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6215;Dels=0.0;FS=0.6805;Haplot [...]
+chr19 14218639 . G A 5309.725 REJECT NS=2;DP=344;DPB=400.0;AC=2;AN=4;AF=0.5;RO=211;AO=189;PRO=0.0;PAO=0.0;QR=7958;QA=7236;PQR=0.0;PQA=0.0;SRF=116;SRR=95;SAF=104;SAR=85;SRP=7.54878;SAP=7.15793;AB=0.4725;ABP=5.63778;RUN=1;RPP=5.59539;RPPR=3.02059;RPL=102.0;RPR=87.0;EPP=4.95199;EPPR=7.54878;DPRA=0.0;ODDS=287.159;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995261;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3735;Dels=0.0;FS=0.3635;HaplotypeScore [...]
+chr19 14219413 . G A 131.171 REJECT NS=2;DP=26;DPB=28.0;AC=2;AN=4;AF=0.5;RO=20;AO=8;PRO=0.0;PAO=0.0;QR=705;QA=299;PQR=0.0;PQA=0.0;SRF=0;SRR=20;SAF=0;SAR=8;SRP=46.4397;SAP=20.3821;AB=0.285714;ABP=14.1779;RUN=1;RPP=3.0103;RPPR=3.44459;RPL=4.0;RPR=4.0;EPP=3.0103;EPPR=3.44459;DPRA=0.0;ODDS=11.3787;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=50.25;MQMR=57.15;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.5295;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=1;MLEAF=0. [...]
+chr19 14219546 . AT A 12.048 REJECT SOMATIC;NS=2;DP=9;DPB=10.9375;AC=1;AN=4;AF=0.25;RO=5;AO=2;PRO=3.5;PAO=2.5;QR=182;QA=67;PQR=96.5;PQA=77.5;SRF=1;SRR=4;SAF=1;SAR=1;SRP=6.91895;SAP=3.0103;AB=0.285714;ABP=5.80219;RUN=1;RPP=7.35324;RPPR=3.44459;RPL=0.0;RPR=2.0;EPP=3.0103;EPPR=6.91895;DPRA=3.5;ODDS=1.6392;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.8;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB: [...]
+chr19 14222209 . C A 1455.37 REJECT NS=2;DP=234;DPB=341.042;AC=2;AN=2;AF=0.0;RO=84;AO=5;PRO=51.2167;PAO=35.4333;QR=3024;QA=60;PQR=1732.15;PQA=1173.13;SRF=42;SRR=42;SAF=0;SAR=5;SRP=3.0103;SAP=13.8677;AB=0.0213675;ABP=468.633;RUN=1;RPP=3.44459;RPPR=122.545;RPL=2.0;RPR=3.0;EPP=3.44459;EPPR=6.73282;DPRA=0.0;ODDS=131.95;GTI=0;TYPE=snp;CIGAR=1X23M;NUMALT=5;MEANALT=27.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr19 14222209 . C CA 1455.37 REJECT NS=2;DP=234;DPB=341.042;AC=2;AN=2;AF=0.0;RO=84;AO=20;PRO=51.2167;PAO=49.8833;QR=3024;QA=574;PQR=1732.15;PQA=1687.48;SRF=42;SRR=42;SAF=8;SAR=12;SRP=3.0103;SAP=4.74748;AB=0.0854701;ABP=352.265;RUN=1;RPP=38.1882;RPPR=122.545;RPL=1.0;RPR=19.0;EPP=3.44459;EPPR=6.73282;DPRA=0.0;ODDS=131.95;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=5;MEANALT=27.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-1.61 [...]
+chr19 14222209 . CA C 1455.37 REJECT NS=2;DP=234;DPB=341.042;AC=2;AN=2;AF=0.0;RO=84;AO=21;PRO=51.2167;PAO=42.3;QR=3024;QA=714;PQR=1732.15;PQA=1438.4;SRF=42;SRR=42;SAF=16;SAR=5;SRP=3.0103;SAP=15.5221;AB=0.0897436;ABP=345.101;RUN=1;RPP=40.3389;RPPR=122.545;RPL=1.0;RPR=20.0;EPP=20.4855;EPPR=6.73282;DPRA=0.0;ODDS=131.95;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=5;MEANALT=27.0;LEN=1;MQM=60.9524;MQMR=60.0;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr19 14222229 . T G 1455.37 REJECT NS=2;DP=234;DPB=341.042;AC=2;AN=2;AF=0.0;RO=84;AO=19;PRO=51.2167;PAO=23.8833;QR=3024;QA=301;PQR=1732.15;PQA=708.817;SRF=42;SRR=42;SAF=19;SAR=0;SRP=3.0103;SAP=44.2683;AB=0.0811966;ABP=359.503;RUN=1;RPP=5.8675;RPPR=122.545;RPL=7.0;RPR=12.0;EPP=5.8675;EPPR=6.73282;DPRA=0.0;ODDS=131.95;GTI=0;TYPE=snp;CIGAR=20M1X3M;NUMALT=5;MEANALT=27.0;LEN=1;MQM=57.8947;MQMR=60.0;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr19 14222229 . TGGT GGGG 1455.37 REJECT NS=2;DP=234;DPB=341.042;AC=2;AN=4;AF=0.5;RO=84;AO=9;PRO=51.2167;PAO=19.2833;QR=3024;QA=42;PQR=1732.15;PQA=608.017;SRF=42;SRR=42;SAF=9;SAR=0;SRP=3.0103;SAP=22.5536;AB=0.0384615;ABP=435.968;RUN=1;RPP=5.18177;RPPR=122.545;RPL=6.0;RPR=3.0;EPP=5.18177;EPPR=6.73282;DPRA=0.0;ODDS=131.95;GTI=0;TYPE=complex;CIGAR=20M1X2M1X;NUMALT=5;MEANALT=27.0;LEN=24;MQM=59.8889;MQMR=60.0;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:Q [...]
+chr19 14222509 . C T 2736.07 PASS SOMATIC;NS=2;DP=427;DPB=427.0;AC=1;AN=3;AF=0.25;RO=319;AO=108;PRO=0.0;PAO=0.0;QR=12168;QA=4053;PQR=0.0;PQA=0.0;SRF=181;SRR=138;SAF=56;SAR=52;SRP=15.5967;SAP=3.332;AB=0.345161;ABP=67.5661;RUN=1;RPP=3.0103;RPPR=4.97756;RPL=54.0;RPR=54.0;EPP=5.9056;EPPR=6.61127;DPRA=0.0;ODDS=70.5486;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996865;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.968;Dels=0.0;FS=7.32;Haplo [...]
+chr19 14227724 . T C 15729.349999999999 REJECT NS=2;DP=420;DPB=482.0;AC=4;AN=4;AF=1.0;RO=0;AO=482;PRO=0.0;PAO=0.0;QR=0;QA=18126;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=218;SAR=264;SRP=0.0;SAP=12.5432;AB=0.0;ABP=0.0;RUN=1;RPP=16.1473;RPPR=0.0;RPL=214.0;RPR=268.0;EPP=3.89331;EPPR=0.0;DPRA=0.0;ODDS=78.4185;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.989627;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.762;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30 [...]
+chr19 14227830 . T G 257.972 REJECT NS=2;DP=380;DPB=396.25;AC=2;AN=2;AF=0.0;RO=298;AO=29;PRO=14.0;PAO=6.0;QR=9644;QA=443;PQR=383.5;PQA=119.0;SRF=228;SRR=70;SAF=1;SAR=28;SRP=184.918;SAP=57.5966;AB=0.0791367;ABP=430.712;RUN=1;RPP=3.08518;RPPR=11.4339;RPL=14.0;RPR=15.0;EPP=3.68421;EPPR=7.93619;DPRA=0.0;ODDS=18.4414;GTI=0;TYPE=snp;CIGAR=1X3M;NUMALT=3;MEANALT=5.5;LEN=1;MQM=59.2069;MQMR=59.906;PAIRED=0.965517;PAIREDR=0.996644;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr19 14227830 . TGGA GGGG 257.972 REJECT NS=2;DP=380;DPB=396.25;AC=2;AN=2;AF=0.0;RO=298;AO=21;PRO=14.0;PAO=2.0;QR=9644;QA=293;PQR=383.5;PQA=42.5;SRF=228;SRR=70;SAF=0;SAR=21;SRP=184.918;SAP=48.6112;AB=0.0539568;ABP=483.421;RUN=1;RPP=5.59539;RPPR=11.4339;RPL=8.0;RPR=13.0;EPP=5.59539;EPPR=7.93619;DPRA=0.0;ODDS=18.4414;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=3;MEANALT=5.5;LEN=4;MQM=59.0476;MQMR=59.906;PAIRED=1.0;PAIREDR=0.996644;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA: [...]
+chr19 14227833 . A G 257.972 REJECT NS=2;DP=380;DPB=396.25;AC=2;AN=3;AF=0.25;RO=298;AO=27;PRO=14.0;PAO=10.0;QR=9644;QA=381;PQR=383.5;PQA=307.0;SRF=228;SRR=70;SAF=0;SAR=27;SRP=184.918;SAP=61.6401;AB=0.0611511;ABP=468.049;RUN=1;RPP=6.95112;RPPR=11.4339;RPL=10.0;RPR=17.0;EPP=6.95112;EPPR=7.93619;DPRA=0.0;ODDS=18.4414;GTI=0;TYPE=snp;CIGAR=3M1X;NUMALT=3;MEANALT=5.5;LEN=1;MQM=59.3333;MQMR=59.906;PAIRED=1.0;PAIREDR=0.996644;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr19 14627050 . G A 14412.15 REJECT NS=2;DP=386;DPB=441.0;AC=4;AN=4;AF=1.0;RO=0;AO=439;PRO=0.0;PAO=0.0;QR=0;QA=16606;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=221;SAR=218;SRP=0.0;SAP=3.05482;AB=0.0;ABP=0.0;RUN=1;RPP=3.01525;RPPR=0.0;RPL=220.0;RPR=219.0;EPP=4.79595;EPPR=0.0;DPRA=0.0;ODDS=72.3212;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997722;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.7673;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.725;SOR= [...]
+chr19 14627093 . T C 3699.77 PASS SOMATIC;NS=2;DP=452;DPB=452.0;AC=1;AN=3;AF=0.25;RO=315;AO=137;PRO=0.0;PAO=0.0;QR=11847;QA=5229;PQR=0.0;PQA=0.0;SRF=177;SRR=138;SAF=77;SAR=60;SRP=13.4954;SAP=7.591;AB=0.395954;ABP=35.5447;RUN=1;RPP=10.0002;RPPR=6.65699;RPL=79.0;RPR=58.0;EPP=4.92817;EPPR=3.34808;DPRA=3.26415;ODDS=67.0824;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993651;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.804;Dels=0.0;FS=0.849 [...]
+chr19 14628242 . G A 3260.19 PASS SOMATIC;NS=2;DP=493;DPB=493.0;AC=1;AN=3;AF=0.25;RO=363;AO=129;PRO=0.0;PAO=0.0;QR=12085;QA=4807;PQR=0.0;PQA=0.0;SRF=153;SRR=210;SAF=52;SAR=77;SRP=22.4459;SAP=13.531;AB=0.354396;ABP=70.0396;RUN=1;RPP=19.1869;RPPR=44.2204;RPL=80.0;RPR=49.0;EPP=11.915;EPPR=17.3731;DPRA=2.82171;ODDS=80.3905;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9767;MQMR=60.0826;PAIRED=0.992248;PAIREDR=0.991736;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=4.365;Dels=0 [...]
+chr19 14628247 . G GA 447.579 REJECT NS=2;DP=347;DPB=500.077;AC=2;AN=4;AF=0.5;RO=258;AO=42;PRO=139.667;PAO=85.6667;QR=9557;QA=1306;PQR=4970.17;PQA=2982.17;SRF=123;SRR=135;SAF=17;SAR=25;SRP=4.22228;SAP=6.31921;AB=0.121037;ABP=435.859;RUN=1;RPP=3.21711;RPPR=10.5852;RPL=22.0;RPR=20.0;EPP=16.2459;EPPR=25.7687;DPRA=0.0;ODDS=28.3184;GTI=0;TYPE=ins;CIGAR=1M1I25M;NUMALT=2;MEANALT=12.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992248;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.1 [...]
+chr19 14628247 . GA G 447.579 REJECT NS=2;DP=347;DPB=500.077;AC=2;AN=2;AF=0.0;RO=258;AO=16;PRO=139.667;PAO=72.6667;QR=9557;QA=527;PQR=4970.17;PQA=2549.67;SRF=123;SRR=135;SAF=10;SAR=6;SRP=4.22228;SAP=5.18177;AB=0.0461095;ABP=623.945;RUN=1;RPP=11.6962;RPPR=10.5852;RPL=12.0;RPR=4.0;EPP=5.18177;EPPR=25.7687;DPRA=0.0;ODDS=28.3184;GTI=0;TYPE=del;CIGAR=1M1D24M;NUMALT=2;MEANALT=12.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.992248;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:Q [...]
+chr19 14628524 . C T 4845.835 REJECT NS=2;DP=218;DPB=246.0;AC=3;AN=4;AF=0.75;RO=73;AO=173;PRO=0.0;PAO=0.0;QR=2786;QA=6548;PQR=0.0;PQA=0.0;SRF=19;SRR=54;SAF=56;SAR=117;SRP=39.4494;SAP=49.7158;AB=0.617801;ABP=26.0325;RUN=1;RPP=8.54567;RPPR=24.6953;RPL=97.0;RPR=76.0;EPP=5.13156;EPPR=21.6017;DPRA=0.0;ODDS=35.284;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99422;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.241;Dels=0.0;FS=1.447;HaplotypeScore=2.9 [...]
+chr19 14629138 . C T 868.037 PASS SOMATIC;NS=2;DP=193;DPB=193.0;AC=1;AN=3;AF=0.25;RO=155;AO=38;PRO=0.0;PAO=0.0;QR=6048;QA=1458;PQR=0.0;PQA=0.0;SRF=31;SRR=124;SAF=8;SAR=30;SRP=124.178;SAP=30.668;AB=0.281481;ABP=59.0021;RUN=1;RPP=5.06748;RPPR=8.06773;RPL=22.0;RPR=16.0;EPP=5.06748;EPPR=4.70545;DPRA=2.32759;ODDS=37.2247;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9613;PAIRED=0.973684;PAIREDR=0.993548;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.487;Dels=0.0;FS [...]
+chr19 14629150 . G A 3826.0550000000003 REJECT NS=2;DP=150;DPB=177.0;AC=3;AN=4;AF=0.75;RO=33;AO=143;PRO=0.0;PAO=0.0;QR=1246;QA=5401;PQR=0.0;PQA=0.0;SRF=5;SRR=28;SAF=22;SAR=121;SRP=37.8197;SAP=151.84;AB=0.725806;ABP=57.9275;RUN=1;RPP=8.49213;RPPR=6.23461;RPL=81.0;RPR=62.0;EPP=4.24029;EPPR=3.0761;DPRA=0.0;ODDS=34.0806;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.958;MQMR=60.0;PAIRED=0.993007;PAIREDR=0.969697;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.008;Dels=0.0;FS=0.0;Hap [...]
+chr19 15354015 . T G 24.4314 REJECT NS=1;DP=68;DPB=68.0;AC=1;AN=4;AF=0.5;RO=43;AO=22;PRO=0.0;PAO=0.0;QR=1171;QA=466;PQR=0.0;PQA=0.0;SRF=38;SRR=5;SAF=0;SAR=22;SRP=58.0041;SAP=50.7827;AB=0.323529;ABP=21.4039;RUN=1;RPP=50.7827;RPPR=11.5447;RPL=0.0;RPR=22.0;EPP=50.7827;EPPR=3.46479;DPRA=0.0;ODDS=5.62193;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=3.0;LEN=1;MQM=58.6364;MQMR=59.8605;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:Ca [...]
+chr19 15411453 . C CA 112.897 REJECT NS=1;DP=42;DPB=63.0833;AC=1;AN=3;AF=0.0;RO=26;AO=5;PRO=21.1667;PAO=8.16667;QR=914;QA=166;PQR=728.833;PQA=299.833;SRF=8;SRR=18;SAF=0;SAR=5;SRP=11.3621;SAP=13.8677;AB=0.119048;ABP=55.9529;RUN=1;RPP=6.91895;RPPR=43.4331;RPL=4.0;RPR=1.0;EPP=6.91895;EPPR=6.01695;DPRA=0.0;ODDS=4.0606;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=2;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.961538;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr19 15411453 . CA C 112.897 REJECT NS=1;DP=42;DPB=63.0833;AC=1;AN=4;AF=0.5;RO=26;AO=6;PRO=21.1667;PAO=7.66667;QR=914;QA=194;PQR=728.833;PQA=270.333;SRF=8;SRR=18;SAF=2;SAR=4;SRP=11.3621;SAP=4.45795;AB=0.142857;ABP=49.5419;RUN=1;RPP=4.45795;RPPR=43.4331;RPL=4.0;RPR=2.0;EPP=4.45795;EPPR=6.01695;DPRA=0.0;ODDS=4.0606;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=2;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.961538;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr19 17941294 . T C 2698.51 REJECT NS=2;DP=223;DPB=250.0;AC=2;AN=4;AF=0.5;RO=146;AO=104;PRO=0.0;PAO=0.0;QR=5324;QA=3877;PQR=0.0;PQA=0.0;SRF=108;SRR=38;SAF=72;SAR=32;SRP=75.8885;SAP=36.4176;AB=0.416;ABP=18.3322;RUN=1;RPP=30.0702;RPPR=24.4871;RPL=34.0;RPR=70.0;EPP=3.34437;EPPR=3.54573;DPRA=0.0;ODDS=120.464;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986301;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.232;Dels=0.0;FS=2.9145;HaplotypeScore=4.92 [...]
+chr19 17951178 . G A 1141.31 REJECT NS=2;DP=241;DPB=274.0;AC=2;AN=4;AF=0.5;RO=215;AO=59;PRO=0.0;PAO=0.0;QR=8249;QA=2238;PQR=0.0;PQA=0.0;SRF=83;SRR=132;SAF=23;SAR=36;SRP=27.2601;SAP=9.23028;AB=0.215328;ABP=195.875;RUN=1;RPP=43.0905;RPPR=181.667;RPL=46.0;RPR=13.0;EPP=3.0471;EPPR=4.23238;DPRA=0.0;ODDS=63.9927;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995349;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.421;Dels=0.0;FS=0.868;HaplotypeScore=9.7 [...]
+chr19 17952185 . G T 520.4435 REJECT NS=2;DP=140;DPB=160.0;AC=2;AN=4;AF=0.5;RO=126;AO=34;PRO=0.0;PAO=0.0;QR=4776;QA=1231;PQR=0.0;PQA=0.0;SRF=80;SRR=46;SAF=27;SAR=7;SRP=22.9327;SAP=28.557;AB=0.2125;ABP=117.881;RUN=1;RPP=19.3602;RPPR=25.3454;RPL=9.0;RPR=25.0;EPP=15.5282;EPPR=5.49198;DPRA=0.0;ODDS=48.5348;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.970588;PAIREDR=0.992063;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.019;Dels=0.0;FS=4.5495;HaplotypeScore=1. [...]
+chr19 17955021 . G A 900.41 REJECT NS=1;DP=78;DPB=78.0;AC=1;AN=4;AF=0.5;RO=43;AO=35;PRO=0.0;PAO=0.0;QR=1619;QA=1316;PQR=0.0;PQA=0.0;SRF=26;SRR=17;SAF=23;SAR=12;SRP=7.10075;SAP=10.5174;AB=0.448718;ABP=4.79202;RUN=1;RPP=20.9405;RPPR=17.6046;RPL=9.0;RPR=26.0;EPP=4.56135;EPPR=4.27278;DPRA=0.0;ODDS=207.327;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.976744;technology.ILLUMINA=1.0;BaseQRankSum=-1.238;FS=1.969;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=1. [...]
+chr19 18273013 . G A 2789.67 PASS SOMATIC;NS=2;DP=390;DPB=390.0;AC=1;AN=3;AF=0.25;RO=284;AO=106;PRO=0.0;PAO=0.0;QR=10624;QA=4023;PQR=0.0;PQA=0.0;SRF=170;SRR=114;SAF=61;SAR=45;SRP=26.9882;SAP=8.25461;AB=0.377224;ABP=39.8017;RUN=1;RPP=4.32138;RPPR=12.9196;RPL=49.0;RPR=57.0;EPP=16.8586;EPPR=7.41441;DPRA=2.57798;ODDS=68.9228;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.981132;PAIREDR=0.996479;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.411;Dels=0.0;F [...]
+chr19 18273047 . T C 12912.0 REJECT NS=2;DP=351;DPB=401.0;AC=4;AN=4;AF=1.0;RO=0;AO=401;PRO=0.0;PAO=0.0;QR=0;QA=14972;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=228;SAR=173;SRP=0.0;SAP=19.3911;AB=0.0;ABP=0.0;RUN=1;RPP=3.01572;RPPR=0.0;RPL=200.0;RPR=201.0;EPP=3.01572;EPPR=0.0;DPRA=0.0;ODDS=65.3946;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8803;MQMR=0.0;PAIRED=0.987531;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=9.6877;MLEAC=2;MLEAF=1.0;MQ=59.95;QD=29.59;SO [...]
+chr19 18276856 . T C 8431.52 REJECT NS=2;DP=226;DPB=259.0;AC=4;AN=4;AF=1.0;RO=0;AO=259;PRO=0.0;PAO=0.0;QR=0;QA=9898;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=164;SAR=95;SRP=0.0;SAP=42.9268;AB=0.0;ABP=0.0;RUN=1;RPP=199.273;RPPR=0.0;RPL=53.0;RPR=206.0;EPP=3.08576;EPPR=0.0;DPRA=0.0;ODDS=44.9245;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.9132;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.095;SOR=1.3125 GT [...]
+chr19 18279638 . T C 13440.5 REJECT NS=2;DP=359;DPB=415.0;AC=4;AN=4;AF=1.0;RO=0;AO=415;PRO=0.0;PAO=0.0;QR=0;QA=15744;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=153;SAR=262;SRP=0.0;SAP=65.1772;AB=0.0;ABP=0.0;RUN=1;RPP=23.7779;RPPR=0.0;RPL=239.0;RPR=176.0;EPP=4.1876;EPPR=0.0;DPRA=0.0;ODDS=72.6896;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992771;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.8126;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.69;SOR=1.3 [...]
+chr19 21008943 . G T 1054.48 REJECT NS=1;DP=88;DPB=88.0;AC=1;AN=4;AF=0.5;RO=49;AO=39;PRO=0.0;PAO=0.0;QR=1855;QA=1520;PQR=0.0;PQA=0.0;SRF=34;SRR=15;SAF=27;SAR=12;SRP=19.0083;SAP=15.538;AB=0.443182;ABP=5.47788;RUN=1;RPP=9.74743;RPPR=22.5536;RPL=14.0;RPR=25.0;EPP=12.42;EPPR=3.40914;DPRA=0.0;ODDS=242.803;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.115;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=2.394;QD=1 [...]
+chr19 21008970 . C G 1594.93 REJECT NS=1;DP=121;DPB=121.0;AC=1;AN=4;AF=0.5;RO=63;AO=58;PRO=0.0;PAO=0.0;QR=2456;QA=2219;PQR=0.0;PQA=0.0;SRF=38;SRR=25;SAF=36;SAR=22;SRP=8.83536;SAP=10.3484;AB=0.479339;ABP=3.45895;RUN=1;RPP=17.986;RPPR=3.872;RPL=19.0;RPR=39.0;EPP=5.40641;EPPR=12.9715;DPRA=0.0;ODDS=367.246;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.691;FS=0.693;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.008; [...]
+chr19 21009030 . C T 1597.12 REJECT NS=1;DP=118;DPB=118.0;AC=1;AN=4;AF=0.5;RO=61;AO=57;PRO=0.0;PAO=0.0;QR=2322;QA=2195;PQR=0.0;PQA=0.0;SRF=27;SRR=34;SAF=21;SAR=36;SRP=4.7546;SAP=11.5819;AB=0.483051;ABP=3.30474;RUN=1;RPP=3.35316;RPPR=13.2981;RPL=30.0;RPR=27.0;EPP=3.35316;EPPR=5.89373;DPRA=0.0;ODDS=367.749;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=1.858;FS=3.405;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.485 [...]
+chr19 24007173 . AGTT A 8563.82 REJECT NS=2;DP=255;DPB=215.091;AC=4;AN=4;AF=1.0;RO=0;AO=264;PRO=25.0;PAO=26.0;QR=0;QA=9698;PQR=899.0;PQA=934.0;SRF=0;SRR=0;SAF=72;SAR=192;SRP=0.0;SAP=121.454;AB=0.0;ABP=0.0;RUN=1;RPP=16.1707;RPPR=0.0;RPL=152.0;RPR=112.0;EPP=21.9613;EPPR=0.0;DPRA=0.0;ODDS=37.3693;GTI=0;TYPE=del;CIGAR=1M3D7M;NUMALT=1;MEANALT=2.5;LEN=3;MQM=60.0758;MQMR=0.0;PAIRED=0.973485;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=24007176;HOMLEN=5;HOMSEQ=GTTGT;SVLEN=-3;SVTYPE=DEL;FS=0.0;M [...]
+chr19 30303508 . C CGGACG 413.855 REJECT NS=2;DP=70;DPB=129.407;AC=1;AN=4;AF=0.25;RO=46;AO=21;PRO=50.5;PAO=51.5;QR=1728;QA=672;PQR=1823.0;PQA=1858.0;SRF=34;SRR=12;SAF=19;SAR=2;SRP=25.858;SAP=32.8939;AB=0.434783;ABP=4.70971;RUN=1;RPP=3.1137;RPPR=51.3492;RPL=11.0;RPR=10.0;EPP=3.1137;EPPR=15.095;DPRA=0.0;ODDS=9.19736;GTI=0;TYPE=ins;CIGAR=1M5I26M;NUMALT=1;MEANALT=2.5;LEN=5;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.956522;technology.ILLUMINA=1.0;END=30303508;HOMLEN=27;HOMSEQ=GGACGGGACGGGACGGGAC [...]
+chr19 31503180 . C T 2079.15 REJECT NS=2;DP=318;DPB=363.0;AC=2;AN=4;AF=0.5;RO=262;AO=101;PRO=0.0;PAO=0.0;QR=10088;QA=3852;PQR=0.0;PQA=0.0;SRF=96;SRR=166;SAF=39;SAR=62;SRP=43.6218;SAP=14.3837;AB=0.278237;ABP=158.07;RUN=1;RPP=18.6836;RPPR=39.1131;RPL=64.0;RPR=37.0;EPP=4.06379;EPPR=27.1783;DPRA=0.0;ODDS=231.236;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.676;Dels=0.0;FS=1.595;HaplotypeScore=3.866;M [...]
+chr19 31770009 . C T 5840.49 REJECT NS=2;DP=327;DPB=376.0;AC=2;AN=4;AF=0.5;RO=170;AO=206;PRO=0.0;PAO=0.0;QR=6484;QA=7871;PQR=0.0;PQA=0.0;SRF=74;SRR=96;SAF=95;SAR=111;SRP=9.19261;SAP=5.70883;AB=0.547872;ABP=10.4949;RUN=1;RPP=3.38978;RPPR=4.28764;RPL=106.0;RPR=100.0;EPP=3.17896;EPPR=3.47014;DPRA=0.0;ODDS=297.827;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990291;PAIREDR=0.994118;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3445;Dels=0.0;FS=0.8515;Haplotyp [...]
+chr19 33792631 . C A 1110.55 REJECT NS=1;DP=84;DPB=84.0;AC=1;AN=4;AF=0.5;RO=41;AO=43;PRO=0.0;PAO=0.0;QR=1544;QA=1558;PQR=0.0;PQA=0.0;SRF=15;SRR=26;SAF=13;SAR=30;SRP=9.41879;SAP=17.6046;AB=0.511905;ABP=3.1137;RUN=1;RPP=3.0608;RPPR=3.48696;RPL=22.0;RPR=21.0;EPP=5.48477;EPPR=3.06326;DPRA=0.0;ODDS=255.315;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=1.238;FS=1.961;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=2.148;QD [...]
+chr19 36211499 . T C 149.071 REJECT NS=2;DP=323;DPB=338.8;AC=2;AN=2;AF=0.0;RO=264;AO=16;PRO=11.0;PAO=11.5;QR=9379;QA=245;PQR=277.0;PQA=210.0;SRF=19;SRR=245;SAF=15;SAR=1;SRP=423.124;SAP=29.6108;AB=0.0495356;ABP=572.306;RUN=1;RPP=22.5536;RPPR=4.19474;RPL=14.0;RPR=2.0;EPP=29.6108;EPPR=3.0432;DPRA=0.0;ODDS=1.66453;GTI=1;TYPE=snp;CIGAR=1X4M;NUMALT=3;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=59.9886;PAIRED=1.0;PAIREDR=0.977273;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr19 36211499 . TCCCA CCCCC 149.071 REJECT NS=2;DP=323;DPB=338.8;AC=2;AN=4;AF=0.5;RO=264;AO=19;PRO=11.0;PAO=4.5;QR=9379;QA=378;PQR=277.0;PQA=52.0;SRF=19;SRR=245;SAF=19;SAR=0;SRP=423.124;SAP=44.2683;AB=0.0588235;ABP=549.072;RUN=1;RPP=28.7251;RPPR=4.19474;RPL=17.0;RPR=2.0;EPP=28.7251;EPPR=3.0432;DPRA=0.0;ODDS=1.66453;GTI=1;TYPE=complex;CIGAR=1X3M1X;NUMALT=3;MEANALT=5.0;LEN=5;MQM=58.7368;MQMR=59.9886;PAIRED=1.0;PAIREDR=0.977273;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr19 36211503 . A C 149.071 REJECT NS=2;DP=323;DPB=338.8;AC=2;AN=2;AF=0.0;RO=264;AO=18;PRO=11.0;PAO=4.0;QR=9379;QA=375;PQR=277.0;PQA=119.0;SRF=19;SRR=245;SAF=18;SAR=0;SRP=423.124;SAP=42.0968;AB=0.0557276;ABP=556.763;RUN=1;RPP=33.8935;RPPR=4.19474;RPL=17.0;RPR=1.0;EPP=33.8935;EPPR=3.0432;DPRA=0.0;ODDS=1.66453;GTI=1;TYPE=snp;CIGAR=4M1X;NUMALT=3;MEANALT=5.0;LEN=1;MQM=58.8889;MQMR=59.9886;PAIRED=1.0;PAIREDR=0.977273;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr19 36212124 . T C 353.818 REJECT NS=2;DP=259;DPB=273.75;AC=2;AN=2;AF=0.0;RO=207;AO=20;PRO=19.0;PAO=11.0;QR=6861;QA=321;PQR=517.5;PQA=224.0;SRF=24;SRR=183;SAF=19;SAR=1;SRP=268.213;SAP=38.1882;AB=0.0772201;ABP=405.118;RUN=1;RPP=30.8051;RPPR=4.27961;RPL=18.0;RPR=2.0;EPP=38.1882;EPPR=10.6577;DPRA=0.0;ODDS=33.3946;GTI=0;TYPE=snp;CIGAR=1X3M;NUMALT=2;MEANALT=6.0;LEN=1;MQM=55.6;MQMR=59.6184;PAIRED=1.0;PAIREDR=0.990338;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr19 36212124 . TCCA CCCC 353.818 REJECT NS=2;DP=259;DPB=273.75;AC=2;AN=4;AF=0.5;RO=207;AO=17;PRO=19.0;PAO=2.0;QR=6861;QA=250;PQR=517.5;PQA=38.5;SRF=24;SRR=183;SAF=17;SAR=0;SRP=268.213;SAP=39.9253;AB=0.0656371;ABP=427.454;RUN=1;RPP=24.5973;RPPR=4.27961;RPL=15.0;RPR=2.0;EPP=24.5973;EPPR=10.6577;DPRA=0.0;ODDS=33.3946;GTI=0;TYPE=complex;CIGAR=1X2M1X;NUMALT=2;MEANALT=6.0;LEN=4;MQM=56.8235;MQMR=59.6184;PAIRED=1.0;PAIREDR=0.990338;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr19 36212143 . T C 33.77 PASS SOMATIC;DP=219;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-5.024;Dels=0.0;FS=114.524;HaplotypeScore=24.9733;MLEAC=1;MLEAF=0.5;MQ=58.93;MQRankSum=-2.708;QD=0.15;ReadPosRankSum=-0.837;SOR=6.802 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:0.000209978 0/1:186,32:219:62.0:62,0,6156:32:15:218:.:1:.:.:.:.:-0.143127
+chr19 36214632 . A AG 12611.1 REJECT NS=2;DP=347;DPB=528.333;AC=4;AN=4;AF=1.0;RO=0;AO=384;PRO=10.5;PAO=12.5;QR=0;QA=14070;PQR=321.5;PQA=358.5;SRF=0;SRR=0;SAF=171;SAR=213;SRP=0.0;SAP=12.9855;AB=0.0;ABP=0.0;RUN=1;RPP=14.976;RPPR=0.0;RPL=215.0;RPR=169.0;EPP=13.9581;EPPR=0.0;DPRA=0.0;ODDS=61.1563;GTI=0;TYPE=ins;CIGAR=1M1I2M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0521;MQMR=0.0;PAIRED=0.992188;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=36214632;HOMLEN=1;HOMSEQ=G;SVLEN=1;SVTYPE=INS;FS=0.0;MLEAC=2 [...]
+chr19 36221051 . G A 1976.17 REJECT NS=2;DP=383;DPB=436.0;AC=2;AN=4;AF=0.5;RO=343;AO=93;PRO=0.0;PAO=0.0;QR=13075;QA=3599;PQR=0.0;PQA=0.0;SRF=180;SRR=163;SAF=46;SAR=47;SRP=4.83991;SAP=3.03365;AB=0.213303;ABP=314.288;RUN=1;RPP=28.4375;RPPR=125.328;RPL=63.0;RPR=30.0;EPP=3.59403;EPPR=3.06728;DPRA=0.0;ODDS=67.5028;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.978495;PAIREDR=0.997085;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.455;Dels=0.0;FS=2.4415;HaplotypeS [...]
+chr19 36224705 . A G 14515.9 REJECT NS=2;DP=390;DPB=442.0;AC=4;AN=4;AF=1.0;RO=1;AO=441;PRO=0.0;PAO=0.0;QR=16;QA=16638;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=228;SAR=213;SRP=5.18177;SAP=4.11819;AB=0.0;ABP=0.0;RUN=1;RPP=3.05462;RPPR=5.18177;RPL=222.0;RPR=219.0;EPP=5.61508;EPPR=5.18177;DPRA=0.0;ODDS=67.9149;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988662;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.609;Dels=0.0;FS=0.0;HaplotypeScore=6.7768;MLEAC=2; [...]
+chr19 37513703 . A T 3534.75 REJECT NS=1;DP=107;DPB=107.0;AC=2;AN=4;AF=1.0;RO=0;AO=107;PRO=0.0;PAO=0.0;QR=0;QA=3985;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=62;SAR=45;SRP=0.0;SAP=8.8753;AB=0.0;ABP=0.0;RUN=1;RPP=3.03059;RPPR=0.0;RPL=53.0;RPR=54.0;EPP=15.6941;EPPR=0.0;DPRA=0.0;ODDS=71.3106;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.990654;PAIREDR=0.0;technology.ILLUMINA=1.0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.95;SOR=1.051 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr19 40636400 . T G 5244.61 REJECT NS=2;DP=390;DPB=438.0;AC=2;AN=4;AF=0.5;RO=249;AO=189;PRO=0.0;PAO=0.0;QR=9644;QA=7245;PQR=0.0;PQA=0.0;SRF=121;SRR=128;SAF=83;SAR=106;SRP=3.43762;SAP=9.08812;AB=0.431507;ABP=20.858;RUN=1;RPP=3.57327;RPPR=6.85616;RPL=91.0;RPR=98.0;EPP=22.3238;EPPR=11.391;DPRA=0.0;ODDS=210.805;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994709;PAIREDR=0.983936;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3745;Dels=0.0;FS=2.8865;HaplotypeS [...]
+chr19 40637615 . T C 2608.27 PASS SOMATIC;NS=2;DP=432;DPB=432.0;AC=1;AN=3;AF=0.25;RO=327;AO=105;PRO=0.0;PAO=0.0;QR=12552;QA=3941;PQR=0.0;PQA=0.0;SRF=137;SRR=190;SAF=36;SAR=69;SRP=21.6637;SAP=25.5316;AB=0.33123;ABP=81.4368;RUN=1;RPP=3.03098;RPPR=12.1013;RPL=52.0;RPR=53.0;EPP=6.50534;EPPR=18.9544;DPRA=2.75652;ODDS=72.7478;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990476;PAIREDR=0.990826;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-2.426;Dels=0.0;F [...]
+chr19 40638641 . A G 2649.4 PASS SOMATIC;NS=2;DP=467;DPB=467.0;AC=1;AN=3;AF=0.25;RO=356;AO=110;PRO=0.0;PAO=0.0;QR=13244;QA=4004;PQR=0.0;PQA=0.0;SRF=168;SRR=188;SAF=46;SAR=64;SRP=5.45016;SAP=9.40627;AB=0.335366;ABP=80.23;RUN=1;RPP=4.98437;RPPR=3.22989;RPL=60.0;RPR=50.0;EPP=6.87947;EPPR=18.2594;DPRA=2.35971;ODDS=86.8844;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9831;PAIRED=0.990909;PAIREDR=0.980337;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.666;Dels=0.0; [...]
+chr19 40742320 . T C 2988.475 REJECT NS=2;DP=192;DPB=222.0;AC=2;AN=4;AF=0.5;RO=111;AO=111;PRO=0.0;PAO=0.0;QR=4282;QA=4230;PQR=0.0;PQA=0.0;SRF=32;SRR=79;SAF=24;SAR=87;SRP=46.2246;SAP=80.6551;AB=0.5;ABP=3.0103;RUN=1;RPP=35.8954;RPPR=62.1878;RPL=76.0;RPR=35.0;EPP=11.6375;EPPR=3.96888;DPRA=0.0;ODDS=187.517;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.005;Dels=0.0;FS=3.7095;HaplotypeScore=3.9562;MLEA [...]
+chr19 40750323 . T TA 76.2235 REJECT NS=1;DP=70;DPB=100.826;AC=1;AN=4;AF=0.5;RO=53;AO=8;PRO=31.5;PAO=29.5;QR=1992;QA=260;PQR=1048.5;PQA=970.5;SRF=31;SRR=22;SAF=6;SAR=2;SRP=6.32897;SAP=7.35324;AB=0.114286;ABP=93.4676;RUN=1;RPP=4.09604;RPPR=59.0998;RPL=3.0;RPR=5.0;EPP=4.09604;EPPR=3.05127;DPRA=0.0;ODDS=17.5511;GTI=0;TYPE=ins;CIGAR=1M1I22M;NUMALT=1;MEANALT=8.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.875;PAIREDR=0.981132;technology.ILLUMINA=1.0;BaseQRankSum=0.522;FS=7.046;MLEAC=1;MLEAF=0.5;MQ=60.1 [...]
+chr19 40761212 . G A 2041.03 PASS SOMATIC;NS=2;DP=284;DPB=284.0;AC=1;AN=3;AF=0.25;RO=207;AO=77;PRO=0.0;PAO=0.0;QR=7888;QA=2974;PQR=0.0;PQA=0.0;SRF=67;SRR=140;SAF=24;SAR=53;SRP=58.9126;SAP=26.7273;AB=0.392857;ABP=22.5536;RUN=1;RPP=30.1114;RPPR=68.4797;RPL=54.0;RPR=23.0;EPP=5.29458;EPPR=3.10471;DPRA=2.22727;ODDS=55.9112;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995169;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.333;Dels=0.0;FS=0.0;Ha [...]
+chr19 40886223 . G A 1867.44 REJECT NS=2;DP=375;DPB=428.0;AC=2;AN=4;AF=0.5;RO=334;AO=94;PRO=0.0;PAO=0.0;QR=12665;QA=3550;PQR=0.0;PQA=0.0;SRF=162;SRR=172;SAF=36;SAR=58;SRP=3.66044;SAP=14.1911;AB=0.219626;ABP=295.246;RUN=1;RPP=3.84193;RPPR=11.4361;RPL=50.0;RPR=44.0;EPP=10.4949;EPPR=13.4126;DPRA=0.0;ODDS=120.09;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997006;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0835;Dels=0.0;FS=1.3515;HaplotypeScore= [...]
+chr19 40886993 . C T 2995.46 PASS SOMATIC;NS=2;DP=415;DPB=415.0;AC=1;AN=3;AF=0.25;RO=301;AO=114;PRO=0.0;PAO=0.0;QR=11534;QA=4319;PQR=0.0;PQA=0.0;SRF=143;SRR=158;SAF=50;SAR=64;SRP=4.63349;SAP=6.74371;AB=0.372549;ABP=46.1843;RUN=1;RPP=6.74371;RPPR=17.619;RPL=50.0;RPR=64.0;EPP=3.69603;EPPR=28.1229;DPRA=2.80734;ODDS=68.9774;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991228;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.38;Dels=0.0;FS=3.999 [...]
+chr19 40890938 . T C 6212.185 REJECT NS=2;DP=337;DPB=382.0;AC=2;AN=4;AF=0.5;RO=169;AO=213;PRO=0.0;PAO=0.0;QR=6497;QA=8238;PQR=0.0;PQA=0.0;SRF=87;SRR=82;SAF=137;SAR=76;SRP=3.33152;SAP=40.9448;AB=0.557592;ABP=14.0155;RUN=1;RPP=6.69059;RPPR=5.90131;RPL=97.0;RPR=116.0;EPP=5.95657;EPPR=13.8163;DPRA=0.0;ODDS=258.339;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994083;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.2415;Dels=0.0;FS=9.594;HaplotypeScore [...]
+chr19 40890981 . C A 3735.09 PASS SOMATIC;NS=2;DP=401;DPB=401.0;AC=1;AN=3;AF=0.25;RO=266;AO=135;PRO=0.0;PAO=0.0;QR=10188;QA=5197;PQR=0.0;PQA=0.0;SRF=114;SRR=152;SAF=71;SAR=64;SRP=14.7983;SAP=3.79846;AB=0.425868;ABP=18.1421;RUN=1;RPP=4.95658;RPPR=7.71244;RPL=73.0;RPR=62.0;EPP=27.4756;EPPR=5.10014;DPRA=3.77381;ODDS=53.4394;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992593;PAIREDR=0.992481;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.22;Dels=0.0;FS [...]
+chr19 41725271 . A G 743.21 REJECT NS=1;DP=52;DPB=52.0;AC=1;AN=4;AF=0.5;RO=25;AO=27;PRO=0.0;PAO=0.0;QR=974;QA=1043;PQR=0.0;PQA=0.0;SRF=16;SRR=9;SAF=15;SAR=12;SRP=7.26639;SAP=3.73412;AB=0.519231;ABP=3.17734;RUN=1;RPP=9.52472;RPPR=13.5202;RPL=9.0;RPR=18.0;EPP=6.95112;EPPR=3.09716;DPRA=0.0;ODDS=156.07;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=0.037;FS=2.35;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=1.612;QD=18. [...]
+chr19 41743861 . A G 9928.785 REJECT NS=2;DP=268;DPB=315.0;AC=4;AN=4;AF=1.0;RO=1;AO=314;PRO=0.0;PAO=0.0;QR=16;QA=11857;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=220;SAR=94;SRP=5.18177;SAP=112.801;AB=0.0;ABP=0.0;RUN=1;RPP=18.9437;RPPR=5.18177;RPL=133.0;RPR=181.0;EPP=3.12095;EPPR=5.18177;DPRA=0.0;ODDS=61.0095;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996815;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.656;Dels=0.0;FS=0.0;HaplotypeScore=2.8799;MLEAC=2; [...]
+chr19 41759631 . AC A 4007.64 REJECT NS=2;DP=265;DPB=275.556;AC=2;AN=2;AF=0.0;RO=52;AO=45;PRO=27.6667;PAO=20.6667;QR=1804;QA=1271;PQR=950.5;PQA=718.5;SRF=24;SRR=28;SAF=15;SAR=30;SRP=3.67845;SAP=13.8677;AB=0.169811;ABP=253.959;RUN=1;RPP=28.5372;RPPR=13.7006;RPL=34.0;RPR=11.0;EPP=3.05855;EPPR=5.68288;DPRA=0.0;ODDS=30.1987;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=2;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.977778;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr19 41759631 . ACCC A 3092.7299999999996 PASS DP=171;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=4.5645;FS=1.034;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.376;QD=18.37;RPA=12,9;RU=C;ReadPosRankSum=0.071;SOR=0.9065;STR;ClippingRankSum=-2.086 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:38,38:76:99.0:1476,0,1167:38:50:76:1:.:.:.:.:.:0.000209978 0/1:110,108:259:99.0:4691,0,2915:108:50:218:.:1:.:.:.:.:-0.143127
+chr19 41759634 . CCCC T 4007.64 REJECT NS=2;DP=265;DPB=275.556;AC=2;AN=4;AF=0.5;RO=52;AO=128;PRO=27.6667;PAO=30.6667;QR=1804;QA=4449;PQR=950.5;PQA=1147.0;SRF=24;SRR=28;SAF=50;SAR=78;SRP=3.67845;SAP=16.3106;AB=0.483019;ABP=3.67403;RUN=1;RPP=60.0793;RPPR=13.7006;RPL=93.0;RPR=35.0;EPP=3.62103;EPPR=5.68288;DPRA=0.0;ODDS=30.1987;GTI=0;TYPE=complex;CIGAR=1M3D2M1X11M;NUMALT=2;MEANALT=13.0;LEN=15;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:A [...]
+chr19 41759637 . C T 2307.77 PASS DP=159;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=0.5545;Dels=0.0;FS=2.7215;HaplotypeScore=101.468;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.4055;QD=16.06;ReadPosRankSum=1.154;SOR=0.888;ClippingRankSum=0.355 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:37,38:75:99.0:1474,0,1590:38:51:75:1:.:.:.:.:.:0.000209978 0/1:149,93:242:99.0:3198,0,5477:93:38:242:.:1:.:.:.:.:-0.143127
+chr19 42791994 . T C 6200.825000000001 REJECT NS=2;DP=444;DPB=504.0;AC=2;AN=4;AF=0.5;RO=266;AO=237;PRO=0.0;PAO=0.0;QR=9998;QA=8950;PQR=0.0;PQA=0.0;SRF=98;SRR=168;SAF=88;SAR=149;SRP=43.0111;SAP=37.1033;AB=0.470238;ABP=6.88793;RUN=1;RPP=5.65821;RPPR=3.82664;RPL=127.0;RPR=110.0;EPP=11.8153;EPPR=3.30418;DPRA=0.0;ODDS=308.144;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991561;PAIREDR=0.992481;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.4375;Dels=0.0;FS=3.58 [...]
+chr19 42793590 . G A 5221.84 REJECT NS=2;DP=331;DPB=376.0;AC=2;AN=4;AF=0.5;RO=189;AO=186;PRO=0.0;PAO=0.0;QR=7300;QA=7119;PQR=0.0;PQA=0.0;SRF=75;SRR=114;SAF=80;SAR=106;SRP=20.4855;SAP=10.9023;AB=0.494681;ABP=3.1027;RUN=1;RPP=97.5744;RPPR=98.153;RPL=138.0;RPR=48.0;EPP=4.17776;EPPR=17.0847;DPRA=0.0;ODDS=244.777;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983871;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0465;Dels=0.0;FS=1.4625;HaplotypeScore [...]
+chr19 45814860 . G T 11711.6 REJECT NS=2;DP=433;DPB=501.0;AC=2;AN=4;AF=0.5;RO=121;AO=380;PRO=0.0;PAO=0.0;QR=4597;QA=14615;PQR=0.0;PQA=0.0;SRF=59;SRR=62;SAF=190;SAR=190;SRP=3.17181;SAP=3.0103;AB=0.758483;ABP=293.758;RUN=1;RPP=5.77607;RPPR=3.45895;RPL=179.0;RPR=201.0;EPP=13.0905;EPPR=9.48883;DPRA=0.0;ODDS=191.687;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992105;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.271;Dels=0.0;FS=3.2105;HaplotypeScor [...]
+chr19 45814908 . C T 17100.199999999997 REJECT NS=2;DP=454;DPB=520.0;AC=4;AN=4;AF=1.0;RO=0;AO=520;PRO=0.0;PAO=0.0;QR=0;QA=19769;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=259;SAR=261;SRP=0.0;SAP=3.027;AB=0.0;ABP=0.0;RUN=1;RPP=3.07711;RPPR=0.0;RPL=258.0;RPR=262.0;EPP=17.0581;EPPR=0.0;DPRA=0.0;ODDS=86.6399;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.998077;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9304;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27. [...]
+chr19 45815248 . T C 13327.349999999999 REJECT NS=2;DP=357;DPB=406.0;AC=4;AN=4;AF=1.0;RO=1;AO=405;PRO=0.0;PAO=0.0;QR=39;QA=15297;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=193;SAR=212;SRP=5.18177;SAP=4.94586;AB=0.0;ABP=0.0;RUN=1;RPP=4.21667;RPPR=5.18177;RPL=210.0;RPR=195.0;EPP=39.9468;EPPR=5.18177;DPRA=0.0;ODDS=64.7692;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997531;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.185;Dels=0.0;FS=1.5195;HaplotypeScore= [...]
+chr19 45818527 . G A 2102.865 REJECT NS=2;DP=373;DPB=428.0;AC=2;AN=4;AF=0.5;RO=318;AO=109;PRO=0.0;PAO=0.0;QR=11911;QA=4161;PQR=0.0;PQA=0.0;SRF=126;SRR=192;SAF=50;SAR=59;SRP=32.7554;SAP=4.62396;AB=0.254673;ABP=226.753;RUN=1;RPP=3.03022;RPPR=3.69315;RPL=55.0;RPR=54.0;EPP=3.98647;EPPR=12.8707;DPRA=0.0;ODDS=270.312;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.651;Dels=0.0;FS=3.4655;HaplotypeScore=5.9 [...]
+chr19 45818581 . G A 1723.445 REJECT NS=2;DP=256;DPB=292.0;AC=2;AN=4;AF=0.5;RO=207;AO=84;PRO=0.0;PAO=0.0;QR=8001;QA=3171;PQR=0.0;PQA=0.0;SRF=54;SRR=153;SAF=23;SAR=61;SRP=105.825;SAP=40.3389;AB=0.287671;ABP=117.355;RUN=1;RPP=17.9004;RPPR=52.9542;RPL=54.0;RPR=30.0;EPP=15.5221;EPPR=3.10471;DPRA=0.0;ODDS=180.554;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6455;Dels=0.0;FS=2.9025;HaplotypeScore=1.913 [...]
+chr19 45854919 . T G 1826.16 REJECT NS=1;DP=124;DPB=124.0;AC=1;AN=4;AF=0.5;RO=59;AO=65;PRO=0.0;PAO=0.0;QR=2133;QA=2464;PQR=0.0;PQA=0.0;SRF=23;SRR=36;SAF=32;SAR=33;SRP=9.23028;SAP=3.04371;AB=0.524194;ABP=3.64073;RUN=1;RPP=8.65613;RPPR=11.2913;RPL=39.0;RPR=26.0;EPP=3.04371;EPPR=9.23028;DPRA=0.0;ODDS=348.562;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=3.801;FS=5.599;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0.42 [...]
+chr19 45855524 . G A 3232.8 PASS SOMATIC;NS=2;DP=410;DPB=410.0;AC=1;AN=3;AF=0.25;RO=289;AO=120;PRO=0.0;PAO=0.0;QR=10925;QA=4639;PQR=0.0;PQA=0.0;SRF=169;SRR=120;SAF=73;SAR=47;SRP=21.0508;SAP=15.2429;AB=0.380952;ABP=41.7866;RUN=1;RPP=3.66174;RPPR=13.2966;RPL=63.0;RPR=57.0;EPP=26.4622;EPPR=3.19814;DPRA=3.31579;ODDS=60.1812;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99308;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.137;Dels=0.0;FS=2.545 [...]
+chr19 45865002 . C A 5507.12 REJECT NS=2;DP=347;DPB=392.0;AC=2;AN=4;AF=0.5;RO=199;AO=192;PRO=0.0;PAO=0.0;QR=7615;QA=7372;PQR=0.0;PQA=0.0;SRF=86;SRR=113;SAF=93;SAR=99;SRP=10.9651;SAP=3.41745;AB=0.489796;ABP=3.36483;RUN=1;RPP=5.22701;RPPR=3.2831;RPL=89.0;RPR=103.0;EPP=5.9056;EPPR=3.02121;DPRA=0.0;ODDS=242.283;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989583;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.464;Dels=0.0;FS=2.4405;HaplotypeScore=2. [...]
+chr19 45868309 . T G 5323.780000000001 REJECT NS=2;DP=347;DPB=401.0;AC=2;AN=4;AF=0.5;RO=199;AO=202;PRO=0.0;PAO=0.0;QR=7579;QA=7698;PQR=0.0;PQA=0.0;SRF=92;SRR=107;SAF=105;SAR=97;SRP=5.46548;SAP=3.69829;AB=0.503741;ABP=3.05904;RUN=1;RPP=27.778;RPPR=12.1872;RPL=77.0;RPR=125.0;EPP=10.2772;EPPR=7.82246;DPRA=0.0;ODDS=248.231;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.697;Dels=0.0;FS=5.053;HaplotypeSc [...]
+chr19 45922323 . G T 932.941 REJECT NS=2;DP=216;DPB=247.0;AC=2;AN=4;AF=0.5;RO=196;AO=51;PRO=0.0;PAO=0.0;QR=7445;QA=1912;PQR=0.0;PQA=0.0;SRF=123;SRR=73;SAF=34;SAR=17;SRP=30.7077;SAP=15.3153;AB=0.206478;ABP=187.849;RUN=1;RPP=55.1682;RPPR=152.089;RPL=8.0;RPR=43.0;EPP=3.05288;EPPR=3.40914;DPRA=0.0;ODDS=26.3882;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6085;Dels=0.0;FS=0.0;HaplotypeScore=6.8234;MLE [...]
+chr19 45923653 . A G 5727.64 REJECT NS=2;DP=403;DPB=462.0;AC=2;AN=4;AF=0.5;RO=246;AO=215;PRO=0.0;PAO=0.0;QR=9278;QA=8184;PQR=0.0;PQA=0.0;SRF=103;SRR=143;SAF=99;SAR=116;SRP=17.1337;SAP=5.92916;AB=0.465368;ABP=7.82326;RUN=1;RPP=4.23238;RPPR=5.27004;RPL=113.0;RPR=102.0;EPP=10.3731;EPPR=4.74042;DPRA=0.0;ODDS=370.626;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990698;PAIREDR=0.995935;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.034;Dels=0.0;FS=4.7855;Haploty [...]
+chr19 46021514 . C T 15312.9 REJECT NS=2;DP=396;DPB=452.0;AC=4;AN=4;AF=1.0;RO=0;AO=452;PRO=0.0;PAO=0.0;QR=0;QA=17596;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=206;SAR=246;SRP=0.0;SAP=10.6969;AB=0.0;ABP=0.0;RUN=1;RPP=35.3134;RPPR=0.0;RPL=267.0;RPR=185.0;EPP=21.4774;EPPR=0.0;DPRA=0.0;ODDS=72.9482;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997788;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9243;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.12;SOR=0. [...]
+chr19 49588420 . T G 2905.24 PASS SOMATIC;NS=2;DP=363;DPB=363.0;AC=1;AN=3;AF=0.25;RO=254;AO=109;PRO=0.0;PAO=0.0;QR=9499;QA=4177;PQR=0.0;PQA=0.0;SRF=109;SRR=145;SAF=38;SAR=71;SRP=14.0899;SAP=24.7051;AB=0.392086;ABP=31.1301;RUN=1;RPP=8.76769;RPPR=47.3289;RPL=63.0;RPR=46.0;EPP=22.1551;EPPR=21.1002;DPRA=3.27059;ODDS=53.9091;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.265;Dels=0.0;FS=9.777;Hap [...]
+chr19 50140068 . C T 12787.2 REJECT NS=2;DP=345;DPB=391.0;AC=4;AN=4;AF=1.0;RO=0;AO=391;PRO=0.0;PAO=0.0;QR=0;QA=14667;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=144;SAR=247;SRP=0.0;SAP=61.9288;AB=0.0;ABP=0.0;RUN=1;RPP=3.06028;RPPR=0.0;RPL=194.0;RPR=197.0;EPP=3.94886;EPPR=0.0;DPRA=0.0;ODDS=61.7081;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997442;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=7.8367;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.075;SOR=1 [...]
+chr19 50140092 . G A 12785.599999999999 REJECT NS=2;DP=342;DPB=389.0;AC=4;AN=4;AF=1.0;RO=0;AO=389;PRO=0.0;PAO=0.0;QR=0;QA=14601;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=144;SAR=245;SRP=0.0;SAP=59.9542;AB=0.0;ABP=0.0;RUN=1;RPP=3.01588;RPPR=0.0;RPL=194.0;RPR=195.0;EPP=5.02547;EPPR=0.0;DPRA=0.0;ODDS=62.3014;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997429;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.8989;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=2 [...]
+chr19 50919797 . C T 1287.94 REJECT NS=1;DP=94;DPB=94.0;AC=1;AN=4;AF=0.5;RO=47;AO=47;PRO=0.0;PAO=0.0;QR=1740;QA=1772;PQR=0.0;PQA=0.0;SRF=22;SRR=25;SAF=28;SAR=19;SRP=3.42611;SAP=6.75262;AB=0.5;ABP=3.0103;RUN=1;RPP=3.42611;RPPR=6.75262;RPL=22.0;RPR=25.0;EPP=3.42611;EPPR=3.42611;DPRA=0.0;ODDS=289.933;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.978723;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=0.699;FS=6.784;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=1.003;Q [...]
+chr19 52500769 . ACT A 6262.75 REJECT NS=2;DP=362;DPB=313.75;AC=2;AN=4;AF=0.5;RO=193;AO=223;PRO=17.0;PAO=11.0;QR=7337;QA=8308;PQR=542.5;PQA=313.5;SRF=88;SRR=105;SAF=112;SAR=111;SRP=6.26188;SAP=3.02004;AB=0.536058;ABP=7.7082;RUN=1;RPP=3.25374;RPPR=7.97206;RPL=114.0;RPR=109.0;EPP=10.109;EPPR=3.02155;DPRA=0.0;ODDS=375.342;GTI=0;TYPE=del;CIGAR=1M2D1M;NUMALT=1;MEANALT=1.0;LEN=2;MQM=60.1794;MQMR=60.0;PAIRED=0.995516;PAIREDR=0.994819;technology.ILLUMINA=1.0;MQ0=0;END=52500771;HOMLEN=0;SVLEN=-2; [...]
+chr19 52693297 . C CT . PASS SOMATIC;AC=1;AN=4 GT:AD:DP:MM:MQS:NQSBQ:NQSMM:REnd:RStart:SC:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:36,0:36:0.166667,0.0:60.0,0.0:37.9371,0.0:0.00285714,0.0:0,0:0,0:29,7,0,0:0:0:36:.:.:.:.:0:.:0.000209978 0/1:62,29:91:0.0967742,0.172414:60.0,61.3793:38.5118,37.0394:0.0,0.0:73,11:26,11:55,7,22,7:29:32:91:.:.:.:.:1:.:-0.147664
+chr19 52694426 . C T 4092.5 PASS SOMATIC;NS=2;DP=521;DPB=521.0;AC=1;AN=3;AF=0.25;RO=367;AO=153;PRO=0.0;PAO=0.0;QR=14057;QA=5821;PQR=0.0;PQA=0.0;SRF=225;SRR=142;SAF=93;SAR=60;SRP=43.7713;SAP=18.4661;AB=0.393316;ABP=41.466;RUN=1;RPP=14.9463;RPPR=34.541;RPL=62.0;RPR=91.0;EPP=10.5182;EPPR=16.0806;DPRA=2.94697;ODDS=82.7024;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.973856;PAIREDR=0.983651;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.175;Dels=0.0;FS= [...]
+chr19 52694464 . G A 4724.86 PASS SOMATIC;NS=2;DP=632;DPB=632.0;AC=1;AN=3;AF=0.25;RO=456;AO=175;PRO=0.0;PAO=0.0;QR=17546;QA=6743;PQR=0.0;PQA=0.0;SRF=234;SRR=222;SAF=82;SAR=93;SRP=3.69603;SAP=4.51172;AB=0.370763;ABP=71.4853;RUN=1;RPP=7.48974;RPPR=9.18185;RPL=78.0;RPR=97.0;EPP=5.80219;EPPR=10.6295;DPRA=2.95;ODDS=100.818;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.982857;PAIREDR=0.991228;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.621;Dels=0.0;FS= [...]
+chr19 54170028 . G A 132.887 REJECT SOMATIC;NS=2;DP=272;DPB=272.0;AC=1;AN=4;AF=0.25;RO=238;AO=33;PRO=0.0;PAO=0.0;QR=8768;QA=1215;PQR=0.0;PQA=0.0;SRF=194;SRR=44;SAF=24;SAR=9;SRP=208.297;SAP=17.8158;AB=0.13198;ABP=234.763;RUN=1;RPP=10.9724;RPPR=11.2218;RPL=22.0;RPR=11.0;EPP=6.23461;EPPR=33.7029;DPRA=0.0;ODDS=6.41468;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=32.8182;MQMR=28.8824;PAIRED=1.0;PAIREDR=0.995798;technology.ILLUMINA=1.0;MQ0=4;BaseQRankSum=0.819;Dels=0.0;FS=0.0;Haploty [...]
+chr19 54170045 . A G 305.06 REJECT NS=2;DP=344;DPB=344.0;AC=2;AN=4;AF=0.5;RO=234;AO=108;PRO=0.0;PAO=0.0;QR=7538;QA=2679;PQR=0.0;PQA=0.0;SRF=214;SRR=20;SAF=2;SAR=106;SRP=352.265;SAP=220.479;AB=0.313953;ABP=106.433;RUN=1;RPP=220.479;RPPR=3.93828;RPL=2.0;RPR=106.0;EPP=237.529;EPPR=6.01695;DPRA=0.0;ODDS=34.9478;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=32.3241;MQMR=29.2821;PAIRED=1.0;PAIREDR=0.995726;technology.ILLUMINA=1.0;MQ0=97;BaseQRankSum=-4.657;Dels=0.0;FS=266.108;Haplotyp [...]
+chr19 54170104 . C A 2127.64 REJECT NS=2;DP=294;DPB=294.0;AC=2;AN=4;AF=0.5;RO=180;AO=113;PRO=0.0;PAO=0.0;QR=6716;QA=4238;PQR=0.0;PQA=0.0;SRF=125;SRR=55;SAF=82;SAR=31;SRP=62.1226;SAP=52.9926;AB=0.384354;ABP=37.163;RUN=1;RPP=9.94748;RPPR=7.83579;RPL=66.0;RPR=47.0;EPP=17.0192;EPPR=33.1696;DPRA=0.0;ODDS=109.394;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=33.3363;MQMR=33.8389;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=97;BaseQRankSum=1.0555;Dels=0.0;FS=0.287;HaplotypeScore= [...]
+chr19 54170149 . C G 7829.67 REJECT NS=2;DP=269;DPB=285.0;AC=4;AN=4;AF=1.0;RO=0;AO=285;PRO=0.0;PAO=0.0;QR=0;QA=10668;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=244;SAR=41;SRP=0.0;SAP=316.99;AB=0.0;ABP=0.0;RUN=1;RPP=4.72462;RPPR=0.0;RPL=135.0;RPR=150.0;EPP=5.21225;EPPR=0.0;DPRA=0.0;ODDS=45.9558;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=35.7825;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=38;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=35.74;QD=31.545;SOR=4.0075 [...]
+chr19 54182249 . T C 3175.45 PASS SOMATIC;NS=2;DP=496;DPB=496.0;AC=1;AN=3;AF=0.25;RO=368;AO=128;PRO=0.0;PAO=0.0;QR=14097;QA=4841;PQR=0.0;PQA=0.0;SRF=229;SRR=139;SAF=76;SAR=52;SRP=50.8063;SAP=12.7819;AB=0.335958;ABP=92.0635;RUN=1;RPP=3.28173;RPPR=5.3706;RPL=66.0;RPR=62.0;EPP=5.45321;EPPR=17.7622;DPRA=3.31304;ODDS=72.6865;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=54.9453;MQMR=58.4728;PAIRED=0.992188;PAIREDR=0.991848;technology.ILLUMINA=1.0;MQ0=1;VT=SNP;BaseQRankSum=1.088;Dels= [...]
+chr19 54189967 . G A 1406.44 PASS SOMATIC;NS=2;DP=267;DPB=267.0;AC=1;AN=3;AF=0.25;RO=205;AO=62;PRO=0.0;PAO=0.0;QR=7839;QA=2364;PQR=0.0;PQA=0.0;SRF=45;SRR=160;SAF=8;SAR=54;SRP=143.097;SAP=77.1206;AB=0.319588;ABP=57.8568;RUN=1;RPP=38.8746;RPPR=4.80044;RPL=47.0;RPR=15.0;EPP=30.4689;EPPR=3.27511;DPRA=2.65753;ODDS=46.5547;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995122;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.813;Dels=0.0;FS=2.747; [...]
+chr19 54201756 . C G 5298.8 REJECT NS=2;DP=358;DPB=411.0;AC=2;AN=4;AF=0.5;RO=210;AO=197;PRO=0.0;PAO=0.0;QR=7768;QA=7193;PQR=0.0;PQA=0.0;SRF=107;SRR=103;SAF=88;SAR=109;SRP=3.17575;SAP=7.87131;AB=0.479319;ABP=4.5372;RUN=1;RPP=7.87131;RPPR=5.65743;RPL=109.0;RPR=88.0;EPP=3.1095;EPPR=5.03701;DPRA=0.0;ODDS=242.471;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=59.7462;MQMR=60.0952;PAIRED=0.994924;PAIREDR=0.995238;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6885;Dels=0.0;FS=4.203;Haplo [...]
+chr19 54201810 . G GT 1530.89 REJECT NS=2;DP=256;DPB=331.6;AC=2;AN=3;AF=0.25;RO=91;AO=50;PRO=34.15;PAO=36.15;QR=3283;QA=1381;PQR=1174.52;PQA=1216.02;SRF=32;SRR=59;SAF=21;SAR=29;SRP=20.4059;SAP=5.78978;AB=0.195312;ABP=209.436;RUN=1;RPP=5.78978;RPPR=3.22506;RPL=21.0;RPR=29.0;EPP=11.5225;EPPR=4.94315;DPRA=0.0;ODDS=123.035;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=4;MEANALT=15.0;LEN=1;MQM=59.9;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.692;FS=4. [...]
+chr19 54201810 . G GTT 1530.89 REJECT NS=2;DP=256;DPB=331.6;AC=2;AN=2;AF=0.0;RO=91;AO=15;PRO=34.15;PAO=38.15;QR=3283;QA=436;PQR=1174.52;PQA=1211.02;SRF=32;SRR=59;SAF=6;SAR=9;SRP=20.4059;SAP=4.31318;AB=0.0585938;ABP=436.253;RUN=1;RPP=4.31318;RPPR=3.22506;RPL=9.0;RPR=6.0;EPP=10.1038;EPPR=4.94315;DPRA=0.0;ODDS=123.035;GTI=0;TYPE=ins;CIGAR=1M2I19M;NUMALT=4;MEANALT=15.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr19 54201810 . GT G 1530.89 REJECT NS=2;DP=256;DPB=331.6;AC=2;AN=3;AF=0.25;RO=91;AO=52;PRO=34.15;PAO=30.15;QR=3283;QA=1636;PQR=1174.52;PQA=1036.85;SRF=32;SRR=59;SAF=25;SAR=27;SRP=20.4059;SAP=3.17734;AB=0.203125;ABP=198.986;RUN=1;RPP=4.51363;RPPR=3.22506;RPL=29.0;RPR=23.0;EPP=9.02361;EPPR=4.94315;DPRA=0.0;ODDS=123.035;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=4;MEANALT=15.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=1.246;FS=5.783;ML [...]
+chr19 54201810 . GTT G 1530.89 REJECT NS=2;DP=256;DPB=331.6;AC=2;AN=2;AF=0.0;RO=91;AO=9;PRO=34.15;PAO=27.4;QR=3283;QA=273;PQR=1174.52;PQA=917.6;SRF=32;SRR=59;SAF=3;SAR=6;SRP=20.4059;SAP=5.18177;AB=0.0351562;ABP=483.482;RUN=1;RPP=5.18177;RPPR=3.22506;RPL=3.0;RPR=6.0;EPP=9.04217;EPPR=4.94315;DPRA=0.0;ODDS=123.035;GTI=0;TYPE=del;CIGAR=1M2D17M;NUMALT=4;MEANALT=15.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr19 54201875 . C G 5286.86 REJECT NS=2;DP=315;DPB=361.0;AC=2;AN=4;AF=0.5;RO=171;AO=190;PRO=0.0;PAO=0.0;QR=6109;QA=7039;PQR=0.0;PQA=0.0;SRF=82;SRR=89;SAF=90;SAR=100;SRP=3.63253;SAP=4.15318;AB=0.526316;ABP=5.18177;RUN=1;RPP=4.65605;RPPR=3.63253;RPL=101.0;RPR=89.0;EPP=9.59329;EPPR=4.03889;DPRA=0.0;ODDS=240.297;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9842;MQMR=59.5556;PAIRED=0.984211;PAIREDR=0.988304;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.2785;Dels=0.0;FS=0.644;Hapl [...]
+chr19 54649671 . T C 11686.3 REJECT NS=2;DP=321;DPB=369.0;AC=4;AN=4;AF=1.0;RO=0;AO=368;PRO=0.0;PAO=0.0;QR=0;QA=13831;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=175;SAR=193;SRP=0.0;SAP=4.92214;AB=0.0;ABP=0.0;RUN=1;RPP=3.10471;RPPR=0.0;RPL=182.0;RPR=186.0;EPP=4.16685;EPPR=0.0;DPRA=0.0;ODDS=70.3829;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9592;MQMR=0.0;PAIRED=0.994565;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.673;Dels=0.04;FS=2.7295;HaplotypeScore=22.1981;MLEAC=2;MLEAF= [...]
+chr19 54652203 . T C 4846.78 REJECT NS=2;DP=298;DPB=339.0;AC=2;AN=4;AF=0.5;RO=165;AO=173;PRO=0.0;PAO=0.0;QR=5827;QA=6475;PQR=0.0;PQA=0.0;SRF=85;SRR=80;SAF=83;SAR=90;SRP=3.33931;SAP=3.62534;AB=0.510324;ABP=3.32417;RUN=1;RPP=10.8552;RPPR=4.0763;RPL=74.0;RPR=99.0;EPP=3.12327;EPPR=3.33931;DPRA=0.0;ODDS=214.935;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993939;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.526;Dels=0.0;FS=1.826;HaplotypeScore=5.86 [...]
+chr19 54657069 . C T 2375.01 PASS SOMATIC;NS=2;DP=338;DPB=338.0;AC=1;AN=3;AF=0.25;RO=246;AO=92;PRO=0.0;PAO=0.0;QR=9407;QA=3484;PQR=0.0;PQA=0.0;SRF=156;SRR=90;SAF=60;SAR=32;SRP=41.4613;SAP=21.515;AB=0.369478;ABP=39.8556;RUN=1;RPP=12.4515;RPPR=4.74042;RPL=36.0;RPR=56.0;EPP=12.4515;EPPR=7.28263;DPRA=2.79775;ODDS=56.5545;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9472;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-1.751;Dels=0.0;FS=0.501;Ha [...]
+chr19 54657815 . A G 4183.535 REJECT NS=2;DP=263;DPB=304.0;AC=2;AN=4;AF=0.5;RO=151;AO=153;PRO=0.0;PAO=0.0;QR=5587;QA=5857;PQR=0.0;PQA=0.0;SRF=58;SRR=93;SAF=65;SAR=88;SRP=20.6265;SAP=10.5182;AB=0.503289;ABP=3.03887;RUN=1;RPP=74.5553;RPPR=40.4143;RPL=112.0;RPR=41.0;EPP=16.6494;EPPR=9.35215;DPRA=0.0;ODDS=254.115;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993377;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.608;Dels=0.0;FS=1.9845;HaplotypeScore= [...]
+chr20 9288522 . G A 9883.73 REJECT NS=2;DP=373;DPB=426.0;AC=2;AN=4;AF=0.5;RO=102;AO=323;PRO=0.0;PAO=0.0;QR=3920;QA=12369;PQR=0.0;PQA=0.0;SRF=47;SRR=55;SAF=138;SAR=185;SRP=4.37279;SAP=17.861;AB=0.758216;ABP=249.722;RUN=1;RPP=14.3114;RPPR=3.7767;RPL=182.0;RPR=141.0;EPP=4.52294;EPPR=15.2727;DPRA=0.0;ODDS=113.875;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1855;Dels=0.0;FS=7.8555;HaplotypeScore=7.79 [...]
+chr20 9368102 . A G 1582.54 REJECT NS=2;DP=337;DPB=383.0;AC=2;AN=4;AF=0.5;RO=304;AO=79;PRO=0.0;PAO=0.0;QR=11757;QA=3014;PQR=0.0;PQA=0.0;SRF=192;SRR=112;SAF=53;SAR=26;SRP=48.7255;SAP=23.0483;AB=0.206266;ABP=290.036;RUN=1;RPP=12.9331;RPPR=42.1254;RPL=30.0;RPR=49.0;EPP=10.954;EPPR=34.1252;DPRA=0.0;ODDS=45.7756;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996711;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.7275;Dels=0.0;FS=0.0;HaplotypeScore=7.7 [...]
+chr20 9370506 . G GT 817.215 REJECT NS=2;DP=271;DPB=331.95;AC=2;AN=4;AF=0.5;RO=207;AO=50;PRO=64.5;PAO=51.5;QR=7766;QA=1754;PQR=2321.5;PQA=1838.5;SRF=140;SRR=67;SAF=35;SAR=15;SRP=58.9126;SAP=20.3821;AB=0.184502;ABP=237.313;RUN=1;RPP=17.0814;RPPR=28.1973;RPL=16.0;RPR=34.0;EPP=5.78978;EPPR=7.63648;DPRA=0.0;ODDS=10.4844;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=1;MEANALT=5.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.985507;technology.ILLUMINA=1.0;BaseQRankSum=-0.32;FS=0.0;MLEAC=1;MLEAF=0.5;MQ= [...]
+chr20 9374341 . A T 1700.24 REJECT NS=2;DP=271;DPB=306.0;AC=2;AN=4;AF=0.5;RO=227;AO=79;PRO=0.0;PAO=0.0;QR=8737;QA=2953;PQR=0.0;PQA=0.0;SRF=75;SRR=152;SAF=27;SAR=52;SRP=59.7269;SAP=20.1897;AB=0.25817;ABP=158.448;RUN=1;RPP=15.1321;RPPR=56.8188;RPL=50.0;RPR=29.0;EPP=10.954;EPPR=6.46361;DPRA=0.0;ODDS=95.6269;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995595;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4565;Dels=0.0;FS=2.468;HaplotypeScore=3.932 [...]
+chr20 10511586 . A T 6393.21 REJECT NS=2;DP=254;DPB=291.0;AC=2;AN=4;AF=0.5;RO=69;AO=222;PRO=0.0;PAO=0.0;QR=2557;QA=8305;PQR=0.0;PQA=0.0;SRF=38;SRR=31;SAF=121;SAR=101;SRP=4.55236;SAP=6.92286;AB=0.762887;ABP=177.691;RUN=1;RPP=211.511;RPPR=84.8654;RPL=38.0;RPR=184.0;EPP=3.63631;EPPR=5.55942;DPRA=0.0;ODDS=113.725;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9855;PAIRED=0.995495;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1505;Dels=0.0;FS=2.731;HaplotypeSc [...]
+chr20 25504932 . G C 1460.31 REJECT NS=2;DP=351;DPB=401.0;AC=2;AN=4;AF=0.5;RO=320;AO=81;PRO=0.0;PAO=0.0;QR=12334;QA=3085;PQR=0.0;PQA=0.0;SRF=166;SRR=154;SAF=35;SAR=46;SRP=3.98746;SAP=6.2541;AB=0.201995;ABP=312.329;RUN=1;RPP=3.25157;RPPR=16.1477;RPL=42.0;RPR=39.0;EPP=22.5536;EPPR=18.6449;DPRA=0.0;ODDS=123.967;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987654;PAIREDR=0.99375;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.05;Dels=0.0;FS=3.6435;HaplotypeScor [...]
+chr20 30959704 . A G 2190.94 REJECT NS=1;DP=158;DPB=158.0;AC=1;AN=4;AF=0.5;RO=81;AO=77;PRO=0.0;PAO=0.0;QR=2970;QA=2984;PQR=0.0;PQA=0.0;SRF=48;SRR=33;SAF=48;SAR=29;SRP=9.04217;SAP=13.1908;AB=0.487342;ABP=3.2302;RUN=1;RPP=4.39215;RPPR=19.7655;RPL=35.0;RPR=42.0;EPP=6.42261;EPPR=3.68051;DPRA=0.0;ODDS=499.497;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.974026;PAIREDR=0.987654;technology.ILLUMINA=1.0;BaseQRankSum=1.984;FS=1.31;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRank [...]
+chr20 31019024 . C T 5616.3150000000005 REJECT NS=2;DP=346;DPB=392.0;AC=2;AN=4;AF=0.5;RO=196;AO=196;PRO=0.0;PAO=0.0;QR=7464;QA=7572;PQR=0.0;PQA=0.0;SRF=96;SRR=100;SAF=91;SAR=105;SRP=3.18756;SAP=5.18177;AB=0.5;ABP=3.0103;RUN=1;RPP=10.4997;RPPR=9.39177;RPL=111.0;RPR=85.0;EPP=4.60567;EPPR=4.60567;DPRA=0.0;ODDS=306.008;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994898;PAIREDR=0.994898;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6085;Dels=0.0;FS=1.9505;Hap [...]
+chr20 31019360 . AT A 1284.66 REJECT NS=2;DP=266;DPB=313.812;AC=2;AN=4;AF=0.5;RO=207;AO=59;PRO=61.0;PAO=42.0;QR=7789;QA=2188;PQR=2137.5;PQA=1459.5;SRF=85;SRR=122;SAF=26;SAR=33;SRP=17.3714;SAP=4.81373;AB=0.221805;ABP=181.822;RUN=1;RPP=11.2913;RPPR=18.9659;RPL=22.0;RPR=37.0;EPP=3.93042;EPPR=4.78314;DPRA=0.0;ODDS=82.7176;GTI=0;TYPE=del;CIGAR=1M1D14M;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995169;technology.ILLUMINA=1.0;BaseQRankSum=1.127;FS=1.056;MLEAC=1;MLEAF=0.5 [...]
+chr20 31022959 . T C 14757.75 REJECT NS=2;DP=387;DPB=441.0;AC=4;AN=4;AF=1.0;RO=0;AO=441;PRO=0.0;PAO=0.0;QR=0;QA=16961;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=215;SAR=226;SRP=0.0;SAP=3.6061;AB=0.0;ABP=0.0;RUN=1;RPP=6.08778;RPPR=0.0;RPL=233.0;RPR=208.0;EPP=6.59988;EPPR=0.0;DPRA=0.0;ODDS=71.7132;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997732;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.9325;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.42;SOR=0. [...]
+chr20 36030939 . G C 15306.7 REJECT NS=2;DP=403;DPB=468.0;AC=4;AN=4;AF=1.0;RO=0;AO=468;PRO=0.0;PAO=0.0;QR=0;QA=17966;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=244;SAR=224;SRP=0.0;SAP=4.86626;AB=0.0;ABP=0.0;RUN=1;RPP=19.7139;RPPR=0.0;RPL=264.0;RPR=204.0;EPP=4.19811;EPPR=0.0;DPRA=0.0;ODDS=85.4043;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99359;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.966;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.025;SOR=1.0 [...]
+chr20 40714479 . G A 1113.895 REJECT NS=2;DP=314;DPB=363.0;AC=2;AN=4;AF=0.5;RO=298;AO=65;PRO=0.0;PAO=0.0;QR=11498;QA=2527;PQR=0.0;PQA=0.0;SRF=123;SRR=175;SAF=23;SAR=42;SRP=22.7139;SAP=15.0703;AB=0.179063;ABP=327.768;RUN=1;RPP=3.31097;RPPR=4.0596;RPL=34.0;RPR=31.0;EPP=7.05258;EPPR=42.9129;DPRA=0.0;ODDS=95.2507;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993289;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.151;Dels=0.0;FS=1.28;HaplotypeScore=4. [...]
+chr20 40714524 . C G 943.6485 REJECT NS=2;DP=218;DPB=253.0;AC=2;AN=4;AF=0.5;RO=201;AO=51;PRO=0.0;PAO=0.0;QR=7613;QA=1936;PQR=0.0;PQA=0.0;SRF=47;SRR=154;SAF=10;SAR=41;SRP=126.698;SAP=43.9277;AB=0.201581;ABP=198.709;RUN=1;RPP=10.206;RPPR=60.5813;RPL=32.0;RPR=19.0;EPP=3.05288;EPPR=3.28038;DPRA=0.0;ODDS=68.3159;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995025;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.2605;Dels=0.0;FS=1.095;HaplotypeScore=4. [...]
+chr20 40743829 . A G 925.394 REJECT NS=2;DP=237;DPB=270.0;AC=2;AN=4;AF=0.5;RO=220;AO=50;PRO=0.0;PAO=0.0;QR=8448;QA=1939;PQR=0.0;PQA=0.0;SRF=147;SRR=73;SAF=33;SAR=17;SRP=57.0602;SAP=14.1282;AB=0.185185;ABP=235.438;RUN=1;RPP=17.0814;RPPR=72.6553;RPL=16.0;RPR=34.0;EPP=9.26414;EPPR=7.78754;DPRA=0.0;ODDS=52.9977;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990909;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.969;Dels=0.0;FS=2.094;HaplotypeScore=0.0 [...]
+chr20 46267950 . C T 10956.349999999999 REJECT NS=2;DP=286;DPB=327.0;AC=4;AN=4;AF=1.0;RO=0;AO=327;PRO=0.0;PAO=0.0;QR=0;QA=12679;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=99;SAR=228;SRP=0.0;SAP=113.516;AB=0.0;ABP=0.0;RUN=1;RPP=50.9886;RPPR=0.0;RPL=206.0;RPR=121.0;EPP=4.92943;EPPR=0.0;DPRA=0.0;ODDS=54.9046;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993884;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.82 [...]
+chr20 46268493 . A G 1590.08 REJECT NS=2;DP=350;DPB=405.0;AC=2;AN=4;AF=0.5;RO=320;AO=85;PRO=0.0;PAO=0.0;QR=12268;QA=3264;PQR=0.0;PQA=0.0;SRF=148;SRR=172;SAF=40;SAR=45;SRP=6.91895;SAP=3.64897;AB=0.209877;ABP=299.108;RUN=1;RPP=3.64897;RPPR=14.9805;RPL=40.0;RPR=45.0;EPP=3.03585;EPPR=22.7978;DPRA=0.0;ODDS=144.754;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99375;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.674;Dels=0.0;FS=1.942;HaplotypeScore=4. [...]
+chr20 46279836 . ACAG A 1468.62 REJECT NS=2;DP=227;DPB=313.552;AC=2;AN=4;AF=0.5;RO=148;AO=63;PRO=112.0;PAO=101.0;QR=5676;QA=2364;PQR=4018.5;PQA=3603.5;SRF=97;SRR=51;SAF=43;SAR=20;SRP=34.0565;SAP=21.2438;AB=0.277533;ABP=100.593;RUN=1;RPP=8.83536;RPPR=3.5385;RPL=25.0;RPR=38.0;EPP=12.9715;EPPR=3.24505;DPRA=0.0;ODDS=6.58809;GTI=0;TYPE=del;CIGAR=1M3D25M;NUMALT=1;MEANALT=7.0;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.581;FS=1.303;MLEAC=1;MLEAF= [...]
+chr20 49191228 . A C 5475.66 REJECT NS=2;DP=218;DPB=258.0;AC=2;AN=4;AF=0.5;RO=60;AO=198;PRO=0.0;PAO=0.0;QR=2336;QA=7372;PQR=0.0;PQA=0.0;SRF=20;SRR=40;SAF=56;SAR=142;SRP=17.4868;SAP=84.1225;AB=0.767442;ABP=163.295;RUN=1;RPP=256.393;RPPR=60.9162;RPL=175.0;RPR=23.0;EPP=32.6652;EPPR=5.32654;DPRA=0.0;ODDS=70.0238;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.979798;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.6885;Dels=0.0;FS=6.774;HaplotypeScore= [...]
+chr20 49196284 . C T 2153.825 REJECT NS=2;DP=329;DPB=382.0;AC=2;AN=4;AF=0.5;RO=284;AO=98;PRO=0.0;PAO=0.0;QR=10678;QA=3643;PQR=0.0;PQA=0.0;SRF=162;SRR=122;SAF=62;SAR=36;SRP=15.2439;SAP=17.989;AB=0.256545;ABP=199.671;RUN=1;RPP=4.4284;RPPR=3.04088;RPL=45.0;RPR=53.0;EPP=3.0103;EPPR=11.8491;DPRA=0.0;ODDS=94.716;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.996;Dels=0.0;FS=4.653;HaplotypeScore=9.7568;M [...]
+chr20 51870849 . T C 15641.75 REJECT NS=2;DP=415;DPB=476.0;AC=4;AN=4;AF=1.0;RO=0;AO=476;PRO=0.0;PAO=0.0;QR=0;QA=18108;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=243;SAR=233;SRP=0.0;SAP=3.46649;AB=0.0;ABP=0.0;RUN=1;RPP=3.08329;RPPR=0.0;RPL=240.0;RPR=236.0;EPP=3.46649;EPPR=0.0;DPRA=0.0;ODDS=79.1217;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9391;MQMR=0.0;PAIRED=0.989496;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.7456;MLEAC=2;MLEAF=1.0;MQ=59.97;QD=30.795; [...]
+chr20 52185814 . C A 4232.34 REJECT NS=2;DP=282;DPB=325.0;AC=2;AN=4;AF=0.5;RO=174;AO=151;PRO=0.0;PAO=0.0;QR=6624;QA=5875;PQR=0.0;PQA=0.0;SRF=48;SRR=126;SAF=41;SAR=110;SRP=78.937;SAP=71.4764;AB=0.464615;ABP=6.54479;RUN=1;RPP=32.131;RPPR=21.031;RPL=98.0;RPR=53.0;EPP=5.44062;EPPR=7.05373;DPRA=0.0;ODDS=238.128;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994253;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.7635;Dels=0.0;FS=5.5635;HaplotypeScore=1. [...]
+chr20 52188399 . G GA 10.3882 REJECT NS=2;DP=270;DPB=304.235;AC=1;AN=4;AF=0.25;RO=236;AO=22;PRO=43.5;PAO=27.5;QR=8810;QA=759;PQR=1577.5;PQA=978.5;SRF=96;SRR=140;SAF=4;SAR=18;SRP=20.8237;SAP=22.3561;AB=0.115942;ABP=91.4113;RUN=1;RPP=3.40511;RPPR=64.8789;RPL=12.0;RPR=10.0;EPP=3.40511;EPPR=4.81373;DPRA=0.0;ODDS=2.29606;GTI=0;TYPE=ins;CIGAR=1M1I16M;NUMALT=1;MEANALT=5.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.991525;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:Ca [...]
+chr20 52297394 . C T 3011.27 PASS SOMATIC;NS=2;DP=432;DPB=432.0;AC=1;AN=3;AF=0.25;RO=318;AO=114;PRO=0.0;PAO=0.0;QR=12263;QA=4445;PQR=0.0;PQA=0.0;SRF=214;SRR=104;SAF=81;SAR=33;SRP=85.6355;SAP=46.8969;AB=0.35625;ABP=60.4457;RUN=1;RPP=25.0298;RPPR=15.0558;RPL=40.0;RPR=74.0;EPP=3.31507;EPPR=12.8707;DPRA=2.85714;ODDS=70.7946;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990566;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=3.382;Dels=0.0;FS=2.76 [...]
+chr20 54945211 . T G 1947.63 PASS SOMATIC;NS=2;DP=360;DPB=360.0;AC=1;AN=3;AF=0.25;RO=281;AO=79;PRO=0.0;PAO=0.0;QR=10755;QA=2994;PQR=0.0;PQA=0.0;SRF=172;SRR=109;SAF=41;SAR=38;SRP=33.6814;SAP=3.25768;AB=0.313492;ABP=79.1497;RUN=1;RPP=3.25768;RPPR=13.5895;RPL=38.0;RPR=41.0;EPP=15.1321;EPPR=16.0005;DPRA=2.33333;ODDS=68.3877;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.8101;MQMR=60.0;PAIRED=0.987342;PAIREDR=0.996441;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.194;Dels=0.0 [...]
+chr20 54945309 . T C 3398.95 PASS SOMATIC;NS=2;DP=418;DPB=418.0;AC=1;AN=3;AF=0.25;RO=294;AO=124;PRO=0.0;PAO=0.0;QR=11261;QA=4792;PQR=0.0;PQA=0.0;SRF=152;SRR=142;SAF=62;SAR=62;SRP=3.7489;SAP=3.0103;AB=0.393651;ABP=33.9555;RUN=1;RPP=5.53201;RPPR=5.40335;RPL=68.0;RPR=56.0;EPP=3.0103;EPPR=8.00321;DPRA=3.05825;ODDS=65.2389;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.3065;MQMR=59.3299;PAIRED=1.0;PAIREDR=0.996599;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.41;Dels=0.0;FS=0 [...]
+chr20 54959296 . G C 3190.85 PASS SOMATIC;NS=2;DP=370;DPB=370.0;AC=1;AN=3;AF=0.25;RO=254;AO=116;PRO=0.0;PAO=0.0;QR=9808;QA=4500;PQR=0.0;PQA=0.0;SRF=150;SRR=104;SAF=77;SAR=39;SRP=21.1002;SAP=30.0414;AB=0.42029;ABP=18.2421;RUN=1;RPP=24.6501;RPPR=9.7128;RPL=41.0;RPR=75.0;EPP=10.4981;EPPR=14.0899;DPRA=2.93617;ODDS=59.6292;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996063;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.461;Dels=0.0;FS=5.045; [...]
+chr20 54961463 . T C 13208.0 REJECT NS=2;DP=356;DPB=410.0;AC=4;AN=4;AF=1.0;RO=0;AO=410;PRO=0.0;PAO=0.0;QR=0;QA=15433;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=207;SAR=203;SRP=0.0;SAP=3.09504;AB=0.0;ABP=0.0;RUN=1;RPP=10.6581;RPPR=0.0;RPL=224.0;RPR=186.0;EPP=3.77296;EPPR=0.0;DPRA=0.0;ODDS=71.6461;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.361;MQMR=0.0;PAIRED=0.997561;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.924;MLEAC=2;MLEAF=1.0;MQ=59.36;QD=30.465;SOR [...]
+chr20 54961541 . A T 2515.59 PASS SOMATIC;NS=2;DP=376;DPB=376.0;AC=1;AN=3;AF=0.25;RO=277;AO=98;PRO=0.0;PAO=0.0;QR=10628;QA=3748;PQR=0.0;PQA=0.0;SRF=119;SRR=158;SAF=46;SAR=52;SRP=14.9338;SAP=3.80798;AB=0.33677;ABP=70.3558;RUN=1;RPP=7.35324;RPPR=3.39442;RPL=56.0;RPR=42.0;EPP=13.7347;EPPR=21.8323;DPRA=3.42353;ODDS=53.4073;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.6787;PAIRED=1.0;PAIREDR=0.98917;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=1.785;Dels=0.0;FS=0.4 [...]
+chr20 55067135 . G A 5641.31 REJECT NS=2;DP=379;DPB=429.0;AC=2;AN=4;AF=0.5;RO=222;AO=204;PRO=0.0;PAO=0.0;QR=8580;QA=7771;PQR=0.0;PQA=0.0;SRF=105;SRR=117;SAF=99;SAR=105;SRP=4.41882;SAP=3.3935;AB=0.475524;ABP=5.24251;RUN=1;RPP=9.14152;RPPR=3.04943;RPL=90.0;RPR=114.0;EPP=10.206;EPPR=15.687;DPRA=0.0;ODDS=320.057;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995098;PAIREDR=0.990991;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4595;Dels=0.0;FS=5.813;HaplotypeSc [...]
+chr20 61502364 . T C 9465.61 REJECT NS=2;DP=371;DPB=423.0;AC=2;AN=4;AF=0.5;RO=108;AO=315;PRO=0.0;PAO=0.0;QR=3999;QA=11892;PQR=0.0;PQA=0.0;SRF=44;SRR=64;SAF=144;SAR=171;SRP=11.0528;SAP=8.03571;AB=0.744681;ABP=222.976;RUN=1;RPP=20.9405;RPPR=23.5991;RPL=183.0;RPR=132.0;EPP=3.34808;EPPR=4.2971;DPRA=0.0;ODDS=202.772;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9683;MQMR=60.0;PAIRED=1.0;PAIREDR=0.981481;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0145;Dels=0.0;FS=2.1785;Haplotype [...]
+chr20 61502378 . C T 8836.42 REJECT NS=2;DP=351;DPB=397.0;AC=2;AN=4;AF=0.5;RO=101;AO=296;PRO=0.0;PAO=0.0;QR=3864;QA=11110;PQR=0.0;PQA=0.0;SRF=44;SRR=57;SAF=133;SAR=163;SRP=6.64375;SAP=9.61275;AB=0.745592;ABP=210.996;RUN=1;RPP=14.748;RPPR=4.06379;RPL=168.0;RPR=128.0;EPP=4.44817;EPPR=6.64375;DPRA=0.0;ODDS=187.88;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9628;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990099;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.399;Dels=0.0;FS=0.9815;HaplotypeS [...]
+chr20 61502405 . A G 7088.96 REJECT NS=2;DP=280;DPB=320.0;AC=2;AN=4;AF=0.5;RO=83;AO=237;PRO=0.0;PAO=0.0;QR=3234;QA=8953;PQR=0.0;PQA=0.0;SRF=33;SRR=50;SAF=97;SAR=140;SRP=10.5712;SAP=19.9514;AB=0.740625;ABP=163.944;RUN=1;RPP=19.9514;RPPR=3.24576;RPL=140.0;RPR=97.0;EPP=6.3179;EPPR=3.66436;DPRA=0.0;ODDS=139.545;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987952;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.0955;Dels=0.0;FS=2.25;HaplotypeScore=6.7 [...]
+chr20 62331989 . T G 1838.06 REJECT NS=1;DP=125;DPB=125.0;AC=1;AN=4;AF=0.5;RO=59;AO=66;PRO=0.0;PAO=0.0;QR=2138;QA=2487;PQR=0.0;PQA=0.0;SRF=26;SRR=33;SAF=25;SAR=41;SRP=4.81373;SAP=11.433;AB=0.528;ABP=3.86152;RUN=1;RPP=3.0103;RPPR=5.99147;RPL=33.0;RPR=33.0;EPP=6.30041;EPPR=9.23028;DPRA=0.0;ODDS=351.175;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.393;FS=2.353;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-1.58;QD [...]
+chr20 62332638 . A AC 10914.415 REJECT NS=2;DP=344;DPB=464.2;AC=2;AN=3;AF=0.5;RO=0;AO=280;PRO=14.5;PAO=18.5;QR=0;QA=10213;PQR=462.0;PQA=612.0;SRF=0;SRR=0;SAF=122;SAR=158;SRP=0.0;SAP=13.0611;AB=0.73107;ABP=180.634;RUN=1;RPP=9.99003;RPPR=0.0;RPL=125.0;RPR=155.0;EPP=11.9754;EPPR=0.0;DPRA=0.0;ODDS=178.425;GTI=0;TYPE=ins;CIGAR=1M1I4M;NUMALT=2;MEANALT=2.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996429;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;END=62332638;HOMLEN=2;HOMSEQ=CC;SVLEN=1; [...]
+chr20 62332641 . T C 6840.435 REJECT NS=2;DP=346;DPB=464.2;AC=2;AN=2;AF=0.5;RO=0;AO=98;PRO=14.5;PAO=13.0;QR=0;QA=3749;PQR=462.0;PQA=409.0;SRF=0;SRR=0;SAF=56;SAR=42;SRP=0.0;SAP=7.35324;AB=0.255875;ABP=201.272;RUN=1;RPP=4.4284;RPPR=0.0;RPL=53.0;RPR=45.0;EPP=3.36483;EPPR=0.0;DPRA=0.0;ODDS=178.425;GTI=0;TYPE=snp;CIGAR=3M1X1M;NUMALT=2;MEANALT=2.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.989796;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.0705;Dels=0.0;FS=7.7145;Haplotype [...]
+chr21 15536025 . CA C 3240.99 REJECT NS=2;DP=237;DPB=251.6;AC=2;AN=4;AF=0.5;RO=145;AO=127;PRO=6.5;PAO=6.5;QR=5401;QA=4612;PQR=166.0;PQA=166.0;SRF=94;SRR=51;SAF=81;SAR=46;SRP=30.7003;SAP=23.9556;AB=0.466912;ABP=5.59691;RUN=1;RPP=58.5624;RPPR=33.336;RPL=35.0;RPR=92.0;EPP=6.8574;EPPR=5.54119;DPRA=0.0;ODDS=213.753;GTI=0;TYPE=del;CIGAR=1M1D3M;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.2362;MQMR=60.0;PAIRED=0.984252;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=15536026;HOMLEN=1;HOMSEQ=A;SVLEN=-1;SVTYP [...]
+chr21 15589167 . T C 4961.355 REJECT NS=2;DP=323;DPB=363.0;AC=2;AN=4;AF=0.5;RO=183;AO=180;PRO=0.0;PAO=0.0;QR=6953;QA=6954;PQR=0.0;PQA=0.0;SRF=101;SRR=82;SAF=104;SAR=76;SRP=7.29391;SAP=12.4683;AB=0.495868;ABP=3.06414;RUN=1;RPP=28.5372;RPPR=10.4265;RPL=67.0;RPR=113.0;EPP=5.37479;EPPR=3.59173;DPRA=0.0;ODDS=168.821;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.983607;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.6715;Dels=0.0;FS=1.0025;HaplotypeSco [...]
+chr21 15589279 . C G 3689.085 REJECT NS=2;DP=252;DPB=290.0;AC=2;AN=4;AF=0.5;RO=151;AO=139;PRO=0.0;PAO=0.0;QR=5692;QA=5316;PQR=0.0;PQA=0.0;SRF=43;SRR=108;SAF=52;SAR=87;SRP=63.7684;SAP=22.1474;AB=0.47931;ABP=4.08855;RUN=1;RPP=53.7665;RPPR=15.1044;RPL=98.0;RPR=41.0;EPP=11.2744;EPPR=9.35215;DPRA=0.0;ODDS=215.381;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.980132;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.261;Dels=0.0;FS=8.056;HaplotypeScore=3. [...]
+chr21 25503065 . T A 4006.025 REJECT NS=2;DP=265;DPB=299.0;AC=2;AN=4;AF=0.5;RO=151;AO=148;PRO=0.0;PAO=0.0;QR=5658;QA=5536;PQR=0.0;PQA=0.0;SRF=113;SRR=38;SAF=103;SAR=45;SRP=83.9012;SAP=52.3673;AB=0.494983;ABP=3.07566;RUN=1;RPP=42.6837;RPPR=75.503;RPL=48.0;RPR=100.0;EPP=3.5385;EPPR=4.75035;DPRA=0.0;ODDS=209.896;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993243;PAIREDR=0.993377;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.888;Dels=0.0;FS=2.573;HaplotypeS [...]
+chr21 36174277 . A AG 13262.85 REJECT NS=2;DP=369;DPB=492.571;AC=4;AN=4;AF=1.0;RO=1;AO=400;PRO=26.0;PAO=38.0;QR=22;QA=14924;PQR=834.5;PQA=1267.5;SRF=0;SRR=1;SAF=183;SAR=217;SRP=5.18177;SAP=9.28586;AB=0.0;ABP=0.0;RUN=1;RPP=5.63778;RPPR=5.18177;RPL=189.0;RPR=211.0;EPP=4.40004;EPPR=5.18177;DPRA=0.0;ODDS=64.8176;GTI=0;TYPE=ins;CIGAR=1M1I6M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.125;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=36174277;HOMLEN=2;HOMSEQ=GG;SVLEN=1;SVTYPE=INS;FS [...]
+chr21 36174790 . G A 15385.55 REJECT NS=2;DP=405;DPB=465.0;AC=4;AN=4;AF=1.0;RO=0;AO=465;PRO=0.0;PAO=0.0;QR=0;QA=17869;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=217;SAR=248;SRP=0.0;SAP=7.49801;AB=0.0;ABP=0.0;RUN=1;RPP=7.49801;RPPR=0.0;RPL=248.0;RPR=217.0;EPP=43.3997;EPPR=0.0;DPRA=0.0;ODDS=79.1771;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993548;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.7817;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.13;SOR=0 [...]
+chr21 36175845 . GA G 33.6605 REJECT NS=2;DP=174;DPB=286.441;AC=2;AN=4;AF=0.5;RO=141;AO=19;PRO=125.5;PAO=103.5;QR=5292;QA=593;PQR=4467.0;PQA=3658.0;SRF=113;SRR=28;SAF=14;SAR=5;SRP=114.279;SAP=12.2676;AB=0.109195;ABP=233.835;RUN=1;RPP=22.325;RPPR=14.2373;RPL=3.0;RPR=16.0;EPP=4.03889;EPPR=3.39531;DPRA=0.0;ODDS=3.61276;GTI=0;TYPE=del;CIGAR=1M1D32M;NUMALT=1;MEANALT=4.5;LEN=1;MQM=60.5263;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:Call [...]
+chr21 36177039 . C A 439.534 REJECT NS=2;DP=88;DPB=151.333;AC=2;AN=2;AF=0.0;RO=18;AO=3;PRO=22.3964;PAO=5.46786;QR=614;QA=48;PQR=798.638;PQA=167.666;SRF=6;SRR=12;SAF=0;SAR=3;SRP=7.35324;SAP=9.52472;AB=0.0340909;ABP=168.931;RUN=1;RPP=9.52472;RPPR=4.9405;RPL=0.0;RPR=3.0;EPP=9.52472;EPPR=4.9405;DPRA=0.0;ODDS=28.5662;GTI=0;TYPE=snp;CIGAR=1X23M;NUMALT=8;MEANALT=15.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr21 36177039 . C T 439.534 REJECT NS=2;DP=88;DPB=151.333;AC=2;AN=2;AF=0.0;RO=18;AO=4;PRO=22.3964;PAO=4.46786;QR=614;QA=46;PQR=798.638;PQA=151.666;SRF=6;SRR=12;SAF=0;SAR=4;SRP=7.35324;SAP=11.6962;AB=0.0454545;ABP=160.936;RUN=1;RPP=5.18177;RPPR=4.9405;RPL=1.0;RPR=3.0;EPP=5.18177;EPPR=4.9405;DPRA=0.0;ODDS=28.5662;GTI=0;TYPE=snp;CIGAR=1X23M;NUMALT=8;MEANALT=15.0;LEN=1;MQM=52.5;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr21 36177039 . C CT 439.534 REJECT NS=2;DP=88;DPB=151.333;AC=2;AN=4;AF=0.5;RO=18;AO=21;PRO=22.3964;PAO=19.8964;QR=614;QA=660;PQR=798.638;PQA=683.638;SRF=6;SRR=12;SAF=9;SAR=12;SRP=7.35324;SAP=3.94093;AB=0.238636;ABP=55.2243;RUN=1;RPP=11.386;RPPR=4.9405;RPL=15.0;RPR=6.0;EPP=3.94093;EPPR=4.9405;DPRA=0.0;ODDS=28.5662;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=8;MEANALT=15.0;LEN=1;MQM=59.0476;MQMR=60.0;PAIRED=0.952381;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.942;F [...]
+chr21 36177039 . C CTT 439.534 REJECT NS=2;DP=88;DPB=151.333;AC=2;AN=2;AF=0.0;RO=18;AO=6;PRO=22.3964;PAO=18.8964;QR=614;QA=159;PQR=798.638;PQA=670.638;SRF=6;SRR=12;SAF=2;SAR=4;SRP=7.35324;SAP=4.45795;AB=0.0681818;ABP=145.538;RUN=1;RPP=8.80089;RPPR=4.9405;RPL=5.0;RPR=1.0;EPP=3.0103;EPPR=4.9405;DPRA=0.0;ODDS=28.5662;GTI=0;TYPE=ins;CIGAR=1M2I23M;NUMALT=8;MEANALT=15.0;LEN=2;MQM=53.6667;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr21 36177039 . CT C 439.534 REJECT NS=2;DP=88;DPB=151.333;AC=2;AN=2;AF=0.0;RO=18;AO=10;PRO=22.3964;PAO=11.6964;QR=614;QA=264;PQR=798.638;PQA=409.038;SRF=6;SRR=12;SAF=1;SAR=9;SRP=7.35324;SAP=16.9077;AB=0.113636;ABP=117.111;RUN=1;RPP=3.0103;RPPR=4.9405;RPL=5.0;RPR=5.0;EPP=3.87889;EPPR=4.9405;DPRA=0.0;ODDS=28.5662;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=8;MEANALT=15.0;LEN=1;MQM=56.3;MQMR=60.0;PAIRED=0.8;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr21 36177039 . CTT C 439.534 REJECT NS=2;DP=88;DPB=151.333;AC=2;AN=2;AF=0.0;RO=18;AO=3;PRO=22.3964;PAO=11.6964;QR=614;QA=85;PQR=798.638;PQA=409.038;SRF=6;SRR=12;SAF=2;SAR=1;SRP=7.35324;SAP=3.73412;AB=0.0545455;ABP=97.8049;RUN=1;RPP=3.73412;RPPR=4.9405;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=4.9405;DPRA=0.0;ODDS=28.5662;GTI=0;TYPE=del;CIGAR=1M2D21M;NUMALT=8;MEANALT=18.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr21 36177058 . G T 439.534 REJECT NS=2;DP=88;DPB=151.333;AC=2;AN=2;AF=0.0;RO=18;AO=3;PRO=22.3964;PAO=14.5536;QR=614;QA=42;PQR=798.638;PQA=521.152;SRF=6;SRR=12;SAF=3;SAR=0;SRP=7.35324;SAP=9.52472;AB=0.0340909;ABP=168.931;RUN=1;RPP=3.73412;RPPR=4.9405;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=4.9405;DPRA=0.0;ODDS=28.5662;GTI=0;TYPE=snp;CIGAR=19M1X4M;NUMALT=8;MEANALT=15.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr21 36177059 . A G 439.534 REJECT NS=2;DP=88;DPB=151.333;AC=2;AN=2;AF=0.0;RO=18;AO=3;PRO=22.3964;PAO=15.9286;QR=614;QA=18;PQR=798.638;PQA=573.527;SRF=6;SRR=12;SAF=3;SAR=0;SRP=7.35324;SAP=9.52472;AB=0.0340909;ABP=168.931;RUN=1;RPP=9.52472;RPPR=4.9405;RPL=3.0;RPR=0.0;EPP=9.52472;EPPR=4.9405;DPRA=0.0;ODDS=28.5662;GTI=0;TYPE=snp;CIGAR=20M1X3M;NUMALT=8;MEANALT=15.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chr21 36180986 . A G 13378.55 REJECT NS=2;DP=351;DPB=396.0;AC=4;AN=4;AF=1.0;RO=0;AO=395;PRO=0.0;PAO=0.0;QR=0;QA=15173;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=211;SAR=184;SRP=0.0;SAP=7.0179;AB=0.0;ABP=0.0;RUN=1;RPP=3.14773;RPPR=0.0;RPL=200.0;RPR=195.0;EPP=3.67549;EPPR=0.0;DPRA=0.0;ODDS=59.2465;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992405;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8698;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.16;SOR=0. [...]
+chr21 36181014 . G A 13000.15 REJECT NS=2;DP=349;DPB=398.0;AC=4;AN=4;AF=1.0;RO=0;AO=398;PRO=0.0;PAO=0.0;QR=0;QA=15022;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=215;SAR=183;SRP=0.0;SAP=8.5972;AB=0.0;ABP=0.0;RUN=1;RPP=7.28777;RPPR=0.0;RPL=185.0;RPR=213.0;EPP=21.3642;EPPR=0.0;DPRA=0.0;ODDS=64.8379;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997487;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.8208;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.675;SOR=0 [...]
+chr21 36182049 . G C 10219.2 REJECT NS=2;DP=388;DPB=445.0;AC=2;AN=4;AF=0.5;RO=104;AO=340;PRO=0.0;PAO=0.0;QR=3935;QA=12777;PQR=0.0;PQA=0.0;SRF=49;SRR=55;SAF=162;SAR=178;SRP=3.76196;SAP=4.64529;AB=0.764045;ABP=272.492;RUN=1;RPP=8.01746;RPPR=4.34659;RPL=156.0;RPR=184.0;EPP=4.64529;EPPR=9.77527;DPRA=0.0;ODDS=147.359;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=59.7692;PAIRED=0.994118;PAIREDR=0.990385;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.0565;Dels=0.0;FS=4.257;Hap [...]
+chr21 36182159 . G A 8704.06 REJECT NS=2;DP=338;DPB=391.0;AC=2;AN=4;AF=0.5;RO=104;AO=287;PRO=0.0;PAO=0.0;QR=3953;QA=10947;PQR=0.0;PQA=0.0;SRF=50;SRR=54;SAF=158;SAR=129;SRP=3.34437;SAP=9.3734;AB=0.734015;ABP=188.996;RUN=1;RPP=17.0;RPPR=5.09825;RPL=122.0;RPR=165.0;EPP=4.28897;EPPR=3.09382;DPRA=0.0;ODDS=182.353;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0348;MQMR=60.0;PAIRED=0.993031;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.6415;Dels=0.0;FS=3.3225;HaplotypeSc [...]
+chr21 36184939 . C A 9684.73 REJECT NS=2;DP=370;DPB=419.0;AC=2;AN=4;AF=0.5;RO=102;AO=317;PRO=0.0;PAO=0.0;QR=3849;QA=12116;PQR=0.0;PQA=0.0;SRF=48;SRR=54;SAF=156;SAR=161;SRP=3.7767;SAP=3.18155;AB=0.756563;ABP=242.572;RUN=1;RPP=14.5253;RPPR=11.5259;RPL=179.0;RPR=138.0;EPP=7.29159;EPPR=4.37279;DPRA=0.0;ODDS=215.167;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990536;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9315;Dels=0.0;FS=4.078;HaplotypeScor [...]
+chr21 36186319 . G A 9796.87 REJECT NS=2;DP=362;DPB=419.0;AC=2;AN=4;AF=0.5;RO=99;AO=320;PRO=0.0;PAO=0.0;QR=3781;QA=12236;PQR=0.0;PQA=0.0;SRF=55;SRR=44;SAF=159;SAR=161;SRP=5.66432;SAP=3.03744;AB=0.763723;ABP=256.129;RUN=1;RPP=9.95901;RPPR=4.78696;RPL=176.0;RPR=144.0;EPP=7.59754;EPPR=4.78696;DPRA=0.0;ODDS=165.797;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99375;PAIREDR=0.989899;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0405;Dels=0.0;FS=2.635;Haplotyp [...]
+chr21 36186396 . A G 8935.35 REJECT NS=2;DP=346;DPB=396.0;AC=2;AN=4;AF=0.5;RO=101;AO=295;PRO=0.0;PAO=0.0;QR=3895;QA=11202;PQR=0.0;PQA=0.0;SRF=61;SRR=40;SAF=160;SAR=135;SRP=12.4917;SAP=7.61088;AB=0.744949;ABP=209.388;RUN=1;RPP=3.19432;RPPR=3.54779;RPL=145.0;RPR=150.0;EPP=4.2543;EPPR=4.75178;DPRA=0.0;ODDS=200.613;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989831;PAIREDR=0.990099;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3385;Dels=0.0;FS=10.1585;Haplo [...]
+chr21 36186747 . T C 9697.61 REJECT NS=2;DP=355;DPB=405.0;AC=2;AN=4;AF=0.5;RO=90;AO=315;PRO=0.0;PAO=0.0;QR=3343;QA=12086;PQR=0.0;PQA=0.0;SRF=40;SRR=50;SAF=140;SAR=175;SRP=5.42305;SAP=11.4549;AB=0.777778;ABP=274.444;RUN=1;RPP=8.80779;RPPR=4.55446;RPL=172.0;RPR=143.0;EPP=3.07234;EPPR=3.0103;DPRA=0.0;ODDS=118.078;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993651;PAIREDR=0.977778;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.833;Dels=0.0;FS=1.5325;Haplotype [...]
+chr21 36187446 . C G 1393.0900000000001 REJECT NS=2;DP=392;DPB=442.0;AC=2;AN=4;AF=0.5;RO=360;AO=82;PRO=0.0;PAO=0.0;QR=13589;QA=2992;PQR=0.0;PQA=0.0;SRF=210;SRR=150;SAF=48;SAR=34;SRP=24.725;SAP=8.20065;AB=0.18552;ABP=382.694;RUN=1;RPP=3.0103;RPPR=8.43898;RPL=41.0;RPR=41.0;EPP=9.78953;EPPR=11.7203;DPRA=0.0;ODDS=76.5506;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994444;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.072;Dels=0.0;FS=2.3955;Haplot [...]
+chr21 36187686 . T C 8866.43 REJECT NS=2;DP=331;DPB=388.0;AC=2;AN=4;AF=0.5;RO=98;AO=290;PRO=0.0;PAO=0.0;QR=3772;QA=11097;PQR=0.0;PQA=0.0;SRF=58;SRR=40;SAF=154;SAR=136;SRP=10.1895;SAP=5.43636;AB=0.747423;ABP=209.323;RUN=1;RPP=3.04025;RPPR=4.4284;RPL=144.0;RPR=146.0;EPP=3.04025;EPPR=4.4284;DPRA=0.0;ODDS=163.063;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996552;PAIREDR=0.989796;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.63;Dels=0.0;FS=4.572;HaplotypeSc [...]
+chr21 36187900 . T G 10693.9 REJECT NS=2;DP=393;DPB=449.0;AC=2;AN=4;AF=0.5;RO=101;AO=348;PRO=0.0;PAO=0.0;QR=3841;QA=13345;PQR=0.0;PQA=0.0;SRF=56;SRR=45;SAF=208;SAR=140;SRP=5.61177;SAP=31.8634;AB=0.775056;ABP=298.065;RUN=1;RPP=3.63429;RPPR=4.06379;RPL=179.0;RPR=169.0;EPP=3.03526;EPPR=4.75178;DPRA=0.0;ODDS=158.568;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991379;PAIREDR=0.990099;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.625;Dels=0.0;FS=10.341;Haploty [...]
+chr21 36188046 . C T 9270.96 REJECT NS=2;DP=352;DPB=409.0;AC=2;AN=4;AF=0.5;RO=98;AO=311;PRO=0.0;PAO=0.0;QR=3673;QA=11617;PQR=0.0;PQA=0.0;SRF=38;SRR=60;SAF=151;SAR=160;SRP=13.7347;SAP=3.57586;AB=0.760391;ABP=243.884;RUN=1;RPP=3.85515;RPPR=31.7269;RPL=150.0;RPR=161.0;EPP=10.6139;EPPR=3.0103;DPRA=0.0;ODDS=151.003;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.666;Dels=0.0;FS=7.877;HaplotypeScore=4.809 [...]
+chr21 36190040 . A C 13743.15 REJECT NS=2;DP=362;DPB=421.0;AC=4;AN=4;AF=1.0;RO=0;AO=421;PRO=0.0;PAO=0.0;QR=0;QA=16152;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=190;SAR=231;SRP=0.0;SAP=11.6807;AB=0.0;ABP=0.0;RUN=1;RPP=3.26304;RPPR=0.0;RPL=207.0;RPR=214.0;EPP=3.6344;EPPR=0.0;DPRA=0.0;ODDS=77.9132;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9947;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.6;SOR=0.8895 G [...]
+chr21 36190600 . T C 13078.2 REJECT NS=2;DP=348;DPB=400.0;AC=4;AN=4;AF=1.0;RO=0;AO=400;PRO=0.0;PAO=0.0;QR=0;QA=15218;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=157;SAR=243;SRP=0.0;SAP=43.1608;AB=0.0;ABP=0.0;RUN=1;RPP=22.5536;RPPR=0.0;RPL=230.0;RPR=170.0;EPP=21.2724;EPPR=0.0;DPRA=0.0;ODDS=67.9719;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.9925;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.7877;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.655;SOR=1.4 [...]
+chr21 36191308 . T C 14382.25 REJECT NS=2;DP=382;DPB=432.0;AC=4;AN=4;AF=1.0;RO=1;AO=431;PRO=0.0;PAO=0.0;QR=40;QA=16393;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=220;SAR=211;SRP=5.18177;SAP=3.4184;AB=0.0;ABP=0.0;RUN=1;RPP=3.01534;RPPR=5.18177;RPL=215.0;RPR=216.0;EPP=7.24744;EPPR=5.18177;DPRA=0.0;ODDS=65.4086;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993039;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.699;Dels=0.0;FS=0.0;HaplotypeScore=3.9302;MLEAC=2 [...]
+chr21 36191365 . A G 14481.25 REJECT NS=2;DP=382;DPB=428.0;AC=4;AN=4;AF=1.0;RO=0;AO=428;PRO=0.0;PAO=0.0;QR=0;QA=16287;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=220;SAR=208;SRP=0.0;SAP=3.74089;AB=0.0;ABP=0.0;RUN=1;RPP=5.03971;RPPR=0.0;RPL=224.0;RPR=204.0;EPP=3.74089;EPPR=0.0;DPRA=0.0;ODDS=61.6922;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992991;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.9153;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.565;SOR= [...]
+chr21 36191646 . G C 11334.55 REJECT NS=2;DP=301;DPB=348.0;AC=4;AN=4;AF=1.0;RO=0;AO=348;PRO=0.0;PAO=0.0;QR=0;QA=13221;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=149;SAR=199;SRP=0.0;SAP=18.61;AB=0.0;ABP=0.0;RUN=1;RPP=3.23494;RPPR=0.0;RPL=171.0;RPR=177.0;EPP=3.11014;EPPR=0.0;DPRA=0.0;ODDS=62.2847;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991379;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.9238;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.985;SOR=0. [...]
+chr21 36192484 . C G 13725.8 REJECT NS=2;DP=369;DPB=416.0;AC=4;AN=4;AF=1.0;RO=0;AO=416;PRO=0.0;PAO=0.0;QR=0;QA=15612;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=179;SAR=237;SRP=0.0;SAP=20.57;AB=0.0;ABP=0.0;RUN=1;RPP=3.19822;RPPR=0.0;RPL=211.0;RPR=205.0;EPP=15.0369;EPPR=0.0;DPRA=0.0;ODDS=62.2958;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995192;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=9.7727;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=29.81;SOR=0.93 [...]
+chr21 36192941 . C CA 489.2665 REJECT NS=2;DP=130;DPB=186.611;AC=2;AN=4;AF=0.5;RO=78;AO=28;PRO=24.25;PAO=21.75;QR=2797;QA=974;PQR=817.417;PQA=700.917;SRF=62;SRR=16;SAF=20;SAR=8;SRP=61.9184;SAP=14.1779;AB=0.2;ABP=112.453;RUN=1;RPP=14.1779;RPPR=4.01252;RPL=8.0;RPR=20.0;EPP=7.97367;EPPR=3.12166;DPRA=0.0;ODDS=48.145;GTI=0;TYPE=ins;CIGAR=1M1I17M;NUMALT=3;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987179;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.1125;FS=1.4 [...]
+chr21 36192941 . C CAA 588.803 REJECT NS=2;DP=140;DPB=186.611;AC=2;AN=2;AF=0.0;RO=78;AO=4;PRO=24.25;PAO=20.75;QR=2797;QA=130;PQR=817.417;PQA=660.917;SRF=62;SRR=16;SAF=1;SAR=3;SRP=61.9184;SAP=5.18177;AB=0.0285714;ABP=273.266;RUN=1;RPP=5.18177;RPPR=4.01252;RPL=3.0;RPR=1.0;EPP=3.0103;EPPR=3.12166;DPRA=0.0;ODDS=48.145;GTI=0;TYPE=ins;CIGAR=1M2I17M;NUMALT=3;MEANALT=9.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987179;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr21 36192941 . CA C 588.803 REJECT NS=2;DP=140;DPB=186.611;AC=2;AN=2;AF=0.0;RO=78;AO=10;PRO=24.25;PAO=17.25;QR=2797;QA=338;PQR=817.417;PQA=571.75;SRF=62;SRR=16;SAF=7;SAR=3;SRP=61.9184;SAP=6.48466;AB=0.0714286;ABP=226.362;RUN=1;RPP=6.48466;RPPR=4.01252;RPL=3.0;RPR=7.0;EPP=3.87889;EPPR=3.12166;DPRA=0.0;ODDS=48.145;GTI=0;TYPE=del;CIGAR=1M1D16M;NUMALT=3;MEANALT=9.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.987179;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr21 36193871 . T C 14729.2 REJECT NS=2;DP=392;DPB=445.0;AC=4;AN=4;AF=1.0;RO=0;AO=444;PRO=0.0;PAO=0.0;QR=0;QA=16958;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=219;SAR=225;SRP=0.0;SAP=3.18637;AB=0.0;ABP=0.0;RUN=1;RPP=3.71456;RPPR=0.0;RPL=216.0;RPR=228.0;EPP=7.41193;EPPR=0.0;DPRA=0.0;ODDS=69.8508;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995495;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=7.7901;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.32;SOR=0. [...]
+chr21 36194538 . C G 14944.9 REJECT NS=2;DP=395;DPB=451.0;AC=4;AN=4;AF=1.0;RO=0;AO=451;PRO=0.0;PAO=0.0;QR=0;QA=17233;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=232;SAR=219;SRP=0.0;SAP=3.824;AB=0.0;ABP=0.0;RUN=1;RPP=3.13067;RPPR=0.0;RPL=228.0;RPR=223.0;EPP=3.59289;EPPR=0.0;DPRA=0.0;ODDS=72.3462;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.988914;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9243;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32.195;SOR=0.8 [...]
+chr21 36195727 . GTTTTTTTTTTT G 51.9076 REJECT NS=2;DP=39;DPB=90.575;AC=2;AN=2;AF=0.0;RO=0;AO=3;PRO=32.4639;PAO=30.4639;QR=0;QA=43;PQR=1174.48;PQA=1043.48;SRF=0;SRR=0;SAF=0;SAR=3;SRP=0.0;SAP=9.52472;AB=0.0769231;ABP=63.6445;RUN=1;RPP=9.52472;RPPR=0.0;RPL=3.0;RPR=0.0;EPP=9.52472;EPPR=0.0;DPRA=0.0;ODDS=4.59914;GTI=0;TYPE=del;CIGAR=1M11D28M;NUMALT=8;MEANALT=10.0;LEN=11;MQM=54.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr21 36195727 . GTTTTTTTTTTTT G 51.9076 REJECT NS=2;DP=39;DPB=90.575;AC=3;AN=4;AF=0.5;RO=0;AO=15;PRO=32.4639;PAO=24.6306;QR=0;QA=275;PQR=1174.48;PQA=883.817;SRF=0;SRR=0;SAF=5;SAR=10;SRP=0.0;SAP=6.62942;AB=0.384615;ABP=7.52028;RUN=1;RPP=6.62942;RPPR=0.0;RPL=10.0;RPR=5.0;EPP=10.1038;EPPR=0.0;DPRA=0.0;ODDS=4.59914;GTI=0;TYPE=del;CIGAR=1M12D27M;NUMALT=8;MEANALT=10.0;LEN=12;MQM=55.3333;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=1.123;FS=0.0;MLEAC=1 [...]
+chr21 36195727 . GTTTTTTTTTTTTT G 51.9076 REJECT NS=2;DP=39;DPB=90.575;AC=2;AN=2;AF=0.0;RO=0;AO=4;PRO=32.4639;PAO=20.4639;QR=0;QA=46;PQR=1174.48;PQA=723.65;SRF=0;SRR=0;SAF=1;SAR=3;SRP=0.0;SAP=5.18177;AB=0.148148;ABP=32.0437;RUN=1;RPP=5.18177;RPPR=0.0;RPL=3.0;RPR=1.0;EPP=3.0103;EPPR=0.0;DPRA=0.0;ODDS=4.59914;GTI=0;TYPE=del;CIGAR=1M13D26M;NUMALT=8;MEANALT=14.0;LEN=13;MQM=55.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr21 36195727 . GTTTTTTTTTTTTTT G 51.9076 REJECT NS=2;DP=39;DPB=90.575;AC=2;AN=2;AF=0.0;RO=0;AO=2;PRO=32.4639;PAO=16.4639;QR=0;QA=49;PQR=1174.48;PQA=583.936;SRF=0;SRR=0;SAF=1;SAR=1;SRP=0.0;SAP=3.0103;AB=0.166667;ABP=14.5915;RUN=1;RPP=3.0103;RPPR=0.0;RPL=1.0;RPR=1.0;EPP=7.35324;EPPR=0.0;DPRA=0.0;ODDS=4.59914;GTI=0;TYPE=del;CIGAR=1M14D25M;NUMALT=8;MEANALT=6.0;LEN=14;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr21 36195731 . TTTTTTTTTTTTT A 51.9076 REJECT NS=2;DP=39;DPB=90.575;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=32.4639;PAO=7.88889;QR=0;QA=15;PQR=1174.48;PQA=276.111;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.0833333;ABP=21.1059;RUN=1;RPP=5.18177;RPPR=0.0;RPL=1.0;RPR=0.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=4.59914;GTI=0;TYPE=complex;CIGAR=1M12D3M1X23M;NUMALT=8;MEANALT=6.0;LEN=28;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr21 36195746 . TTTTTTTTTTTTCAGATGGA CAGAGGGG 51.9076 REJECT NS=2;DP=39;DPB=90.575;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=32.4639;PAO=18.7639;QR=0;QA=14;PQR=1174.48;PQA=675.95;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.0833333;ABP=21.1059;RUN=1;RPP=5.18177;RPPR=0.0;RPL=0.0;RPR=1.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=4.59914;GTI=0;TYPE=complex;CIGAR=1M12D22M1X2M1X1M;NUMALT=8;MEANALT=6.0;LEN=28;MQM=58.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR: [...]
+chr21 36195746 . TTTTTTTTTTTTCAGATGGA CAGATGGG 51.9076 REJECT NS=2;DP=39;DPB=90.575;AC=2;AN=2;AF=0.0;RO=0;AO=2;PRO=32.4639;PAO=18.7639;QR=0;QA=32;PQR=1174.48;PQA=675.95;SRF=0;SRR=0;SAF=2;SAR=0;SRP=0.0;SAP=7.35324;AB=0.0740741;ABP=45.5551;RUN=1;RPP=3.0103;RPPR=0.0;RPL=1.0;RPR=1.0;EPP=3.0103;EPPR=0.0;DPRA=0.0;ODDS=4.59914;GTI=0;TYPE=complex;CIGAR=1M12D25M1X1M;NUMALT=8;MEANALT=14.0;LEN=28;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr21 36195747 . TTTTTTTTTTTCAGATGGAG AGATGGAA 51.9076 REJECT NS=2;DP=39;DPB=90.575;AC=2;AN=2;AF=0.0;RO=0;AO=1;PRO=32.4639;PAO=22.0972;QR=0;QA=14;PQR=1174.48;PQA=800.617;SRF=0;SRR=0;SAF=1;SAR=0;SRP=0.0;SAP=5.18177;AB=0.0833333;ABP=21.1059;RUN=1;RPP=5.18177;RPPR=0.0;RPL=1.0;RPR=0.0;EPP=5.18177;EPPR=0.0;DPRA=0.0;ODDS=4.59914;GTI=0;TYPE=complex;CIGAR=20M12D7M1X;NUMALT=8;MEANALT=6.0;LEN=28;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr21 36198190 . A G 1584.4299999999998 REJECT NS=2;DP=374;DPB=420.0;AC=2;AN=4;AF=0.5;RO=331;AO=89;PRO=0.0;PAO=0.0;QR=12686;QA=3431;PQR=0.0;PQA=0.0;SRF=169;SRR=162;SAF=40;SAR=49;SRP=3.33176;SAP=4.98658;AB=0.211905;ABP=305.796;RUN=1;RPP=7.13366;RPPR=3.8041;RPL=51.0;RPR=38.0;EPP=4.20583;EPPR=3.8041;DPRA=0.0;ODDS=193.811;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993958;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.463;Dels=0.0;FS=3.9065;Haplot [...]
+chr21 36198900 . AT A 107.518 REJECT SOMATIC;NS=2;DP=34;DPB=42.9615;AC=1;AN=4;AF=0.25;RO=18;AO=9;PRO=14.5;PAO=13.5;QR=641;QA=270;PQR=505.0;PQA=467.0;SRF=16;SRR=2;SAF=9;SAR=0;SRP=26.6552;SAP=22.5536;AB=0.296296;ABP=12.7417;RUN=1;RPP=9.04217;RPPR=3.49285;RPL=2.0;RPR=7.0;EPP=9.04217;EPPR=3.49285;DPRA=0.0;ODDS=2.98656;GTI=0;TYPE=del;CIGAR=1M1D24M;NUMALT=1;MEANALT=4.5;LEN=1;MQM=62.0;MQMR=58.8889;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.133;FS=2.738;MLEAC=1;MLEAF=0. [...]
+chr21 36200031 . C G 8982.5 REJECT NS=2;DP=235;DPB=268.0;AC=4;AN=4;AF=1.0;RO=0;AO=268;PRO=0.0;PAO=0.0;QR=0;QA=10326;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=122;SAR=146;SRP=0.0;SAP=7.67735;AB=0.0;ABP=0.0;RUN=1;RPP=12.3768;RPPR=0.0;RPL=117.0;RPR=151.0;EPP=8.4876;EPPR=0.0;DPRA=0.0;ODDS=44.904;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9997;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.35;SOR=0.899 GT:G [...]
+chr21 36202440 . T C 6703.205 REJECT NS=2;DP=435;DPB=500.0;AC=2;AN=4;AF=0.5;RO=254;AO=245;PRO=0.0;PAO=0.0;QR=9767;QA=9282;PQR=0.0;PQA=0.0;SRF=135;SRR=119;SAF=119;SAR=126;SRP=5.19887;SAP=3.44459;AB=0.49;ABP=3.44459;RUN=1;RPP=3.09007;RPPR=3.0445;RPL=121.0;RPR=124.0;EPP=4.08274;EPPR=3.0103;DPRA=0.0;ODDS=420.175;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996063;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.759;Dels=0.0;FS=3.8215;HaplotypeScore=4 [...]
+chr21 36202775 . C T 11514.5 REJECT NS=2;DP=431;DPB=497.0;AC=2;AN=4;AF=0.5;RO=123;AO=374;PRO=0.0;PAO=0.0;QR=4806;QA=14380;PQR=0.0;PQA=0.0;SRF=68;SRR=55;SAF=190;SAR=184;SRP=5.99387;SAP=3.21932;AB=0.752515;ABP=278.272;RUN=1;RPP=3.59091;RPPR=3.45166;RPL=182.0;RPR=192.0;EPP=11.3943;EPPR=3.45166;DPRA=0.0;ODDS=190.788;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994652;PAIREDR=0.97561;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.2495;Dels=0.0;FS=2.165;Haploty [...]
+chr21 36203846 . G A 5190.09 REJECT NS=2;DP=369;DPB=424.0;AC=2;AN=4;AF=0.5;RO=231;AO=191;PRO=0.0;PAO=0.0;QR=8808;QA=7136;PQR=0.0;PQA=0.0;SRF=109;SRR=122;SAF=99;SAR=92;SRP=4.59895;SAP=3.56738;AB=0.450472;ABP=12.0444;RUN=1;RPP=3.93119;RPPR=5.12537;RPL=91.0;RPR=100.0;EPP=9.02448;EPPR=7.15584;DPRA=0.0;ODDS=271.929;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989529;PAIREDR=0.995671;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.2535;Dels=0.0;FS=3.8925;Haploty [...]
+chr21 36204381 . A AG 12854.900000000001 REJECT NS=2;DP=367;DPB=521.0;AC=4;AN=4;AF=1.0;RO=0;AO=407;PRO=16.0;PAO=25.0;QR=0;QA=14552;PQR=532.0;PQA=849.0;SRF=0;SRR=0;SAF=193;SAR=214;SRP=0.0;SAP=5.36317;AB=0.0;ABP=0.0;RUN=1;RPP=4.21075;RPPR=0.0;RPL=196.0;RPR=211.0;EPP=3.44246;EPPR=0.0;DPRA=0.0;ODDS=76.4937;GTI=0;TYPE=ins;CIGAR=1M1I4M;NUMALT=1;MEANALT=3.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=36204381;HOMLEN=2;HOMSEQ=GG;SVLEN=1;SVTYPE=INS;BaseQRankSu [...]
+chr21 36205590 . T A 455.542 REJECT NS=2;DP=138;DPB=161.0;AC=2;AN=4;AF=0.5;RO=129;AO=32;PRO=0.0;PAO=0.0;QR=4717;QA=1184;PQR=0.0;PQA=0.0;SRF=102;SRR=27;SAF=28;SAR=4;SRP=97.6966;SAP=42.0968;AB=0.198758;ABP=129.913;RUN=1;RPP=20.3821;RPPR=11.915;RPL=8.0;RPR=24.0;EPP=30.1537;EPPR=26.0548;DPRA=0.0;ODDS=31.6764;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=45.6562;MQMR=59.2016;PAIRED=1.0;PAIREDR=0.984496;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.199;Dels=0.0;FS=8.8425;HaplotypeScore [...]
+chr21 36206142 . C G 8461.28 REJECT NS=2;DP=388;DPB=439.0;AC=3;AN=4;AF=0.75;RO=138;AO=301;PRO=0.0;PAO=0.0;QR=5261;QA=11512;PQR=0.0;PQA=0.0;SRF=75;SRR=63;SAF=157;SAR=144;SRP=5.27618;SAP=4.2295;AB=0.591716;ABP=27.706;RUN=1;RPP=3.19065;RPPR=8.10854;RPL=148.0;RPR=153.0;EPP=5.61462;EPPR=3.26206;DPRA=0.0;ODDS=63.9904;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996678;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.113;Dels=0.0;FS=0.655;HaplotypeScor [...]
+chr21 36206315 . CGT C 168.072 REJECT SOMATIC;NS=2;DP=365;DPB=439.8;AC=1;AN=4;AF=0.25;RO=308;AO=36;PRO=87.0;PAO=72.0;QR=11580;QA=1209;PQR=3161.5;PQA=2598.5;SRF=147;SRR=161;SAF=18;SAR=18;SRP=4.39215;SAP=3.0103;AB=0.112676;ABP=373.078;RUN=1;RPP=3.25157;RPPR=7.07124;RPL=19.0;RPR=17.0;EPP=5.18177;EPPR=3.0385;DPRA=0.0;ODDS=18.1064;GTI=0;TYPE=del;CIGAR=1M2D17M;NUMALT=1;MEANALT=5.5;LEN=2;MQM=60.8333;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996753;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr21 36206932 . G A 13371.7 REJECT NS=2;DP=360;DPB=411.0;AC=4;AN=4;AF=1.0;RO=0;AO=411;PRO=0.0;PAO=0.0;QR=0;QA=15363;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=194;SAR=217;SRP=0.0;SAP=5.80521;AB=0.0;ABP=0.0;RUN=1;RPP=5.80521;RPPR=0.0;RPL=217.0;RPR=194.0;EPP=6.31242;EPPR=0.0;DPRA=0.0;ODDS=65.806;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9927;MQMR=0.0;PAIRED=0.997567;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8679;MLEAC=2;MLEAF=1.0;MQ=59.985;QD=28.305;S [...]
+chr21 36208062 . C T 14296.7 REJECT NS=2;DP=374;DPB=427.0;AC=4;AN=4;AF=1.0;RO=0;AO=427;PRO=0.0;PAO=0.0;QR=0;QA=16483;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=212;SAR=215;SRP=0.0;SAP=3.05607;AB=0.0;ABP=0.0;RUN=1;RPP=3.13744;RPPR=0.0;RPL=216.0;RPR=211.0;EPP=3.86974;EPPR=0.0;DPRA=0.0;ODDS=70.4957;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.992974;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=33.21;SOR=0.732 [...]
+chr21 36208167 . G A 2307.95 REJECT NS=2;DP=381;DPB=451.0;AC=2;AN=4;AF=0.5;RO=337;AO=114;PRO=0.0;PAO=0.0;QR=12922;QA=4241;PQR=0.0;PQA=0.0;SRF=163;SRR=174;SAF=57;SAR=57;SRP=3.78997;SAP=3.0103;AB=0.252772;ABP=242.445;RUN=1;RPP=5.75321;RPPR=4.87248;RPL=63.0;RPR=51.0;EPP=15.8868;EPPR=3.53223;DPRA=0.0;ODDS=162.787;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991228;PAIREDR=0.997033;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.123;Dels=0.0;FS=2.072;HaplotypeS [...]
+chr21 36209023 . T A 1614.65 REJECT NS=2;DP=349;DPB=397.0;AC=2;AN=4;AF=0.5;RO=308;AO=89;PRO=0.0;PAO=0.0;QR=11719;QA=3345;PQR=0.0;PQA=0.0;SRF=152;SRR=156;SAF=37;SAR=52;SRP=3.1231;SAP=8.49998;AB=0.224181;ABP=265.343;RUN=1;RPP=3.22989;RPPR=15.4469;RPL=43.0;RPR=46.0;EPP=8.49998;EPPR=13.1908;DPRA=0.0;ODDS=210.617;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988764;PAIREDR=0.993506;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.6015;Dels=0.0;FS=5.624;HaplotypeS [...]
+chr21 36211188 . C G 6730.39 REJECT NS=2;DP=388;DPB=448.0;AC=2;AN=4;AF=0.5;RO=208;AO=239;PRO=0.0;PAO=0.0;QR=7929;QA=9073;PQR=0.0;PQA=0.0;SRF=89;SRR=119;SAF=108;SAR=131;SRP=12.4061;SAP=7.81661;AB=0.533482;ABP=7.37263;RUN=1;RPP=3.01939;RPPR=3.0103;RPL=120.0;RPR=119.0;EPP=3.74624;EPPR=4.05428;DPRA=0.0;ODDS=382.737;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995816;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.5755;Dels=0.0;FS=1.668;HaplotypeScor [...]
+chr21 36212037 . T C 14021.5 REJECT NS=2;DP=374;DPB=433.0;AC=4;AN=4;AF=1.0;RO=1;AO=432;PRO=0.0;PAO=0.0;QR=31;QA=16450;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=215;SAR=217;SRP=5.18177;SAP=3.03041;AB=0.0;ABP=0.0;RUN=1;RPP=4.2971;RPPR=5.18177;RPL=208.0;RPR=224.0;EPP=3.99551;EPPR=5.18177;DPRA=0.0;ODDS=76.6748;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993056;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.535;Dels=0.0;FS=0.0;HaplotypeScore=4.8787;MLEAC=2;M [...]
+chr21 36212920 . G GC 11956.5 REJECT NS=2;DP=328;DPB=513.667;AC=4;AN=4;AF=1.0;RO=0;AO=371;PRO=11.5;PAO=12.5;QR=0;QA=13592;PQR=336.0;PQA=370.0;SRF=0;SRR=0;SAF=213;SAR=158;SRP=0.0;SAP=20.7157;AB=0.0;ABP=0.0;RUN=1;RPP=5.12324;RPPR=0.0;RPL=176.0;RPR=195.0;EPP=3.15663;EPPR=0.0;DPRA=0.0;ODDS=70.858;GTI=0;TYPE=ins;CIGAR=1M1I2M;NUMALT=1;MEANALT=3.0;LEN=1;MQM=60.0809;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=36212920;HOMLEN=1;HOMSEQ=C;SVLEN=1;SVTYPE=INS;FS=0.0;MLEAC=2;MLEA [...]
+chr21 36212920 . G GCTGCGGGAGCCACTGCCAAGTCTAGCTGTCAGGTTGGTCTCAGAGCTCTGTCTTGATCCCCACCAGGTCGCCCAGCCTGCGATCCCACCTGGC . PASS SOMATIC;AC=1;AN=4;END=36212920;HOMLEN=0;SVLEN=93;SVTYPE=DUP:TANDEM;NTLEN=0 GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:-0.00365044 0/1:270,26:26:9:296:.:.:.:1:.:.:-0.00665809
+chr21 36213879 . T C 4789.53 REJECT NS=2;DP=324;DPB=362.0;AC=2;AN=4;AF=0.5;RO=190;AO=172;PRO=0.0;PAO=0.0;QR=7350;QA=6485;PQR=0.0;PQA=0.0;SRF=97;SRR=93;SAF=90;SAR=82;SRP=3.19316;SAP=3.81829;AB=0.475138;ABP=4.95383;RUN=1;RPP=7.10075;RPPR=6.71323;RPL=77.0;RPR=95.0;EPP=3.0608;EPPR=11.9705;DPRA=0.0;ODDS=233.19;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.989474;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.3325;Dels=0.0;FS=1.9415;HaplotypeScore=9. [...]
+chr21 36213897 . A G 10087.7 REJECT NS=2;DP=367;DPB=413.0;AC=2;AN=4;AF=0.5;RO=82;AO=331;PRO=0.0;PAO=0.0;QR=3132;QA=12543;PQR=0.0;PQA=0.0;SRF=44;SRR=38;SAF=178;SAR=153;SRP=3.96363;SAP=7.11051;AB=0.801453;ABP=328.999;RUN=1;RPP=8.52755;RPPR=15.8273;RPL=151.0;RPR=180.0;EPP=6.48072;EPPR=8.20065;DPRA=0.0;ODDS=88.6954;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996979;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4645;Dels=0.0;FS=1.0765;HaplotypeSco [...]
+chr21 36214789 . C CA 74.7447 REJECT;LowQual NS=2;DP=32;DPB=104.789;AC=3;AN=4;AF=0.75;RO=5;AO=6;PRO=81.8333;PAO=80.8333;QR=174;QA=139;PQR=2936.67;PQA=2896.67;SRF=3;SRR=2;SAF=3;SAR=3;SRP=3.44459;SAP=3.0103;AB=0.166667;ABP=31.9633;RUN=1;RPP=4.45795;RPPR=6.91895;RPL=2.0;RPR=4.0;EPP=8.80089;EPPR=3.44459;DPRA=0.0;ODDS=1.5694;GTI=0;TYPE=ins;CIGAR=1M1I37M;NUMALT=2;MEANALT=11.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.508;FS=1 [...]
+chr21 36214809 . AAAATTAAATCAATC TTAAATAAATA 74.7447 REJECT SOMATIC;NS=2;DP=32;DPB=104.789;AC=1;AN=3;AF=0.0;RO=5;AO=2;PRO=81.8333;PAO=11.3333;QR=174;QA=32;PQR=2936.67;PQA=383.667;SRF=3;SRR=2;SAF=2;SAR=0;SRP=3.44459;SAP=7.35324;AB=0.0666667;ABP=51.9408;RUN=1;RPP=3.0103;RPPR=6.91895;RPL=1.0;RPR=1.0;EPP=3.0103;EPPR=3.44459;DPRA=15.0;ODDS=1.5694;GTI=0;TYPE=complex;CIGAR=1M4D25M1X3M1X3M;NUMALT=2;MEANALT=20.0;LEN=34;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIAL [...]
+chr21 36215354 . G A 54.4061 REJECT SOMATIC;NS=2;DP=24;DPB=24.0;AC=1;AN=4;AF=0.25;RO=20;AO=4;PRO=0.0;PAO=0.0;QR=733;QA=150;PQR=0.0;PQA=0.0;SRF=13;SRR=7;SAF=1;SAR=3;SRP=6.91895;SAP=5.18177;AB=0.235294;ABP=13.3567;RUN=1;RPP=3.0103;RPPR=3.0103;RPL=2.0;RPR=2.0;EPP=5.18177;EPPR=13.8677;DPRA=2.42857;ODDS=5.41505;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.85;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.061;Dels=0.0;FS=11.994;HaplotypeScore=0.0;MLE [...]
+chr21 36215976 . G C 3672.63 REJECT NS=2;DP=321;DPB=369.0;AC=2;AN=4;AF=0.5;RO=195;AO=172;PRO=0.0;PAO=0.0;QR=7408;QA=5539;PQR=0.0;PQA=0.0;SRF=90;SRR=105;SAF=92;SAR=80;SRP=5.51585;SAP=4.82828;AB=0.466125;ABP=6.68827;RUN=1;RPP=3.2123;RPPR=3.28869;RPL=88.0;RPR=84.0;EPP=10.2822;EPPR=5.51585;DPRA=0.0;ODDS=255.403;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994186;PAIREDR=0.989744;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-3.372;Dels=0.01;FS=1.0815;HaplotypeS [...]
+chr21 36216281 . A G 5496.955 REJECT NS=2;DP=372;DPB=418.0;AC=2;AN=4;AF=0.5;RO=223;AO=195;PRO=0.0;PAO=0.0;QR=8562;QA=7469;PQR=0.0;PQA=0.0;SRF=106;SRR=117;SAF=95;SAR=100;SRP=4.18854;SAP=3.28869;AB=0.466507;ABP=7.08311;RUN=1;RPP=3.11052;RPPR=3.48744;RPL=96.0;RPR=99.0;EPP=7.92117;EPPR=3.25374;DPRA=0.0;ODDS=281.663;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9179;MQMR=60.0;PAIRED=0.994872;PAIREDR=0.991031;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.017;Dels=0.0;FS=0.6155;Haplo [...]
+chr21 36216883 . ATGAG A 4197.59 REJECT NS=2;DP=288;DPB=297.0;AC=2;AN=4;AF=0.5;RO=145;AO=160;PRO=42.5;PAO=31.5;QR=5442;QA=5691;PQR=1392.0;PQA=1023.0;SRF=73;SRR=72;SAF=86;SAR=74;SRP=3.02528;SAP=4.96463;AB=0.512821;ABP=3.45573;RUN=1;RPP=9.579;RPPR=8.41652;RPL=69.0;RPR=91.0;EPP=3.06459;EPPR=4.82236;DPRA=0.0;ODDS=191.007;GTI=0;TYPE=del;CIGAR=1M4D9M;NUMALT=1;MEANALT=4.5;LEN=4;MQM=61.6875;MQMR=60.0;PAIRED=0.9875;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=36216887;HOMLEN=11;HOMSEQ=TGAGTGAGTG [...]
+chr21 36217802 . C T 6408.77 REJECT NS=2;DP=403;DPB=456.0;AC=2;AN=4;AF=0.5;RO=232;AO=223;PRO=0.0;PAO=0.0;QR=8927;QA=8582;PQR=0.0;PQA=0.0;SRF=110;SRR=122;SAF=95;SAR=128;SRP=4.35811;SAP=13.6145;AB=0.489035;ABP=3.4865;RUN=1;RPP=9.09627;RPPR=5.40641;RPL=124.0;RPR=99.0;EPP=3.48744;EPPR=12.5947;DPRA=0.0;ODDS=295.584;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99569;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.7735;Dels=0.0;FS=4.7525;HaplotypeScore [...]
+chr21 36218264 . A G 6223.51 REJECT NS=2;DP=376;DPB=440.0;AC=2;AN=4;AF=0.5;RO=216;AO=224;PRO=0.0;PAO=0.0;QR=8292;QA=8496;PQR=0.0;PQA=0.0;SRF=101;SRR=115;SAF=122;SAR=102;SRP=4.98071;SAP=6.88793;AB=0.509091;ABP=3.32615;RUN=1;RPP=3.04908;RPPR=9.8062;RPL=111.0;RPR=113.0;EPP=3.04908;EPPR=7.03155;DPRA=0.0;ODDS=383.344;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.99537;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.505;Dels=0.0;FS=5.3895;HaplotypeSco [...]
+chr21 36218373 . T C 12527.7 REJECT NS=2;DP=335;DPB=386.0;AC=4;AN=4;AF=1.0;RO=0;AO=386;PRO=0.0;PAO=0.0;QR=0;QA=14603;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=192;SAR=194;SRP=0.0;SAP=3.0328;AB=0.0;ABP=0.0;RUN=1;RPP=26.0527;RPPR=0.0;RPL=225.0;RPR=161.0;EPP=7.42075;EPPR=0.0;DPRA=0.0;ODDS=67.3464;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994819;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.8239;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.44;SOR=0.7 [...]
+chr21 36218449 . A C 10913.05 REJECT NS=2;DP=326;DPB=373.0;AC=4;AN=4;AF=1.0;RO=2;AO=364;PRO=0.0;PAO=0.0;QR=43;QA=13083;PQR=0.0;PQA=0.0;SRF=0;SRR=2;SAF=123;SAR=241;SRP=7.35324;SAP=86.0751;AB=0.0;ABP=0.0;RUN=1;RPP=80.539;RPPR=7.35324;RPL=239.0;RPR=125.0;EPP=77.8426;EPPR=7.35324;DPRA=0.0;ODDS=60.67;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986264;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.872;Dels=0.0;FS=0.0;HaplotypeScore=58.1273;MLEAC=2;M [...]
+chr21 36218491 . C T 495.887 REJECT NS=2;DP=137;DPB=244.258;AC=2;AN=2;AF=0.0;RO=18;AO=11;PRO=41.1516;PAO=26.8;QR=636;QA=188;PQR=1453.55;PQA=811.3;SRF=6;SRR=12;SAF=0;SAR=11;SRP=7.35324;SAP=26.8965;AB=0.080292;ABP=212.629;RUN=1;RPP=7.94546;RPPR=4.9405;RPL=8.0;RPR=3.0;EPP=7.94546;EPPR=4.9405;DPRA=0.0;ODDS=10.976;GTI=0;TYPE=snp;CIGAR=1X30M;NUMALT=9;MEANALT=26.0;LEN=1;MQM=60.0;MQMR=58.9444;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr21 36218491 . C CT 495.887 REJECT NS=2;DP=137;DPB=244.258;AC=2;AN=2;AF=0.0;RO=18;AO=11;PRO=41.1516;PAO=38.6516;QR=636;QA=300;PQR=1453.55;PQA=1303.05;SRF=6;SRR=12;SAF=6;SAR=5;SRP=7.35324;SAP=3.20771;AB=0.080292;ABP=212.629;RUN=1;RPP=3.20771;RPPR=4.9405;RPL=5.0;RPR=6.0;EPP=3.20771;EPPR=4.9405;DPRA=0.0;ODDS=10.976;GTI=0;TYPE=ins;CIGAR=1M1I30M;NUMALT=9;MEANALT=26.0;LEN=1;MQM=60.0;MQMR=58.9444;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr21 36218491 . CT C 474.8085 REJECT NS=2;DP=137;DPB=244.258;AC=2;AN=4;AF=0.5;RO=18;AO=19;PRO=41.1516;PAO=36.5183;QR=636;QA=517;PQR=1453.55;PQA=1289.31;SRF=6;SRR=12;SAF=9;SAR=10;SRP=7.35324;SAP=3.12459;AB=0.138686;ABP=158.358;RUN=1;RPP=8.61041;RPPR=4.9405;RPL=6.0;RPR=13.0;EPP=4.03889;EPPR=4.9405;DPRA=0.0;ODDS=10.976;GTI=0;TYPE=del;CIGAR=1M1D29M;NUMALT=9;MEANALT=26.0;LEN=1;MQM=58.8421;MQMR=58.9444;PAIRED=0.947368;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0. [...]
+chr21 36218491 . CTT C 495.887 REJECT NS=2;DP=137;DPB=244.258;AC=2;AN=2;AF=0.0;RO=18;AO=12;PRO=41.1516;PAO=36.6611;QR=636;QA=278;PQR=1453.55;PQA=1260.88;SRF=6;SRR=12;SAF=3;SAR=9;SRP=7.35324;SAP=9.52472;AB=0.0875912;ABP=205.401;RUN=1;RPP=5.9056;RPPR=4.9405;RPL=8.0;RPR=4.0;EPP=3.73412;EPPR=4.9405;DPRA=0.0;ODDS=10.976;GTI=0;TYPE=del;CIGAR=1M2D28M;NUMALT=9;MEANALT=26.0;LEN=2;MQM=60.0;MQMR=58.9444;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr21 36218491 . CTTT C 495.887 REJECT NS=2;DP=137;DPB=244.258;AC=2;AN=2;AF=0.0;RO=18;AO=3;PRO=41.1516;PAO=32.5111;QR=636;QA=44;PQR=1453.55;PQA=1147.83;SRF=6;SRR=12;SAF=0;SAR=3;SRP=7.35324;SAP=9.52472;AB=0.0218978;ABP=275.015;RUN=1;RPP=3.73412;RPPR=4.9405;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=4.9405;DPRA=0.0;ODDS=10.976;GTI=0;TYPE=del;CIGAR=1M3D27M;NUMALT=9;MEANALT=26.0;LEN=3;MQM=60.0;MQMR=58.9444;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr21 36218512 . TCAAATG CAAATT 495.887 REJECT NS=2;DP=137;DPB=244.258;AC=2;AN=2;AF=0.0;RO=18;AO=6;PRO=41.1516;PAO=17.4516;QR=636;QA=114;PQR=1453.55;PQA=616.845;SRF=6;SRR=12;SAF=6;SAR=0;SRP=7.35324;SAP=16.0391;AB=0.0606061;ABP=169.029;RUN=1;RPP=4.45795;RPPR=4.9405;RPL=2.0;RPR=4.0;EPP=4.45795;EPPR=4.9405;DPRA=0.0;ODDS=10.976;GTI=0;TYPE=complex;CIGAR=1M1D25M1X3M;NUMALT=9;MEANALT=36.0;LEN=30;MQM=60.0;MQMR=58.9444;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:Q [...]
+chr21 36218513 . CAAATG TCAAATT 495.887 REJECT NS=2;DP=137;DPB=244.258;AC=2;AN=2;AF=0.0;RO=18;AO=3;PRO=41.1516;PAO=16.2516;QR=636;QA=59;PQR=1453.55;PQA=575.245;SRF=6;SRR=12;SAF=3;SAR=0;SRP=7.35324;SAP=9.52472;AB=0.0218978;ABP=275.015;RUN=1;RPP=3.73412;RPPR=4.9405;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=4.9405;DPRA=0.0;ODDS=10.976;GTI=0;TYPE=complex;CIGAR=1M1I26M1X3M;NUMALT=9;MEANALT=26.0;LEN=32;MQM=60.0;MQMR=58.9444;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR [...]
+chr21 36218513 . CAAATG TTCAAATT 495.887 REJECT NS=2;DP=137;DPB=244.258;AC=2;AN=2;AF=0.0;RO=18;AO=2;PRO=41.1516;PAO=16.2516;QR=636;QA=43;PQR=1453.55;PQA=575.245;SRF=6;SRR=12;SAF=2;SAR=0;SRP=7.35324;SAP=7.35324;AB=0.0526316;ABP=69.0688;RUN=1;RPP=3.0103;RPPR=4.9405;RPL=1.0;RPR=1.0;EPP=3.0103;EPPR=4.9405;DPRA=0.0;ODDS=10.976;GTI=0;TYPE=complex;CIGAR=1M2I26M1X3M;NUMALT=9;MEANALT=16.0;LEN=33;MQM=60.0;MQMR=58.9444;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR: [...]
+chr21 36218518 . G T 495.887 REJECT NS=2;DP=137;DPB=244.258;AC=2;AN=2;AF=0.0;RO=18;AO=7;PRO=41.1516;PAO=19.7516;QR=636;QA=123;PQR=1453.55;PQA=696.745;SRF=6;SRR=12;SAF=7;SAR=0;SRP=7.35324;SAP=18.2106;AB=0.0510949;ABP=242.807;RUN=1;RPP=18.2106;RPPR=4.9405;RPL=0.0;RPR=7.0;EPP=18.2106;EPPR=4.9405;DPRA=0.0;ODDS=10.976;GTI=0;TYPE=snp;CIGAR=27M1X3M;NUMALT=9;MEANALT=26.0;LEN=1;MQM=60.0;MQMR=58.9444;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr21 36218774 . C A 6037.72 REJECT NS=2;DP=351;DPB=400.0;AC=2;AN=4;AF=0.5;RO=181;AO=217;PRO=0.0;PAO=0.0;QR=6690;QA=8052;PQR=0.0;PQA=0.0;SRF=80;SRR=101;SAF=111;SAR=106;SRP=8.30101;SAP=3.26047;AB=0.5425;ABP=9.28586;RUN=1;RPP=13.9077;RPPR=3.59816;RPL=92.0;RPR=125.0;EPP=13.9077;EPPR=10.5085;DPRA=0.0;ODDS=289.557;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995392;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.511;Dels=0.0;FS=4.516;HaplotypeScore=5 [...]
+chr21 36218903 . A AG 10911.45 REJECT NS=2;DP=301;DPB=477.667;AC=4;AN=4;AF=1.0;RO=0;AO=346;PRO=9.0;PAO=13.0;QR=0;QA=12597;PQR=215.0;PQA=369.0;SRF=0;SRR=0;SAF=188;SAR=158;SRP=0.0;SAP=8.65864;AB=0.0;ABP=0.0;RUN=1;RPP=17.47;RPPR=0.0;RPL=197.0;RPR=149.0;EPP=7.93063;EPPR=0.0;DPRA=0.0;ODDS=71.5762;GTI=0;TYPE=ins;CIGAR=1M1I2M;NUMALT=1;MEANALT=2.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=36218903;HOMLEN=1;HOMSEQ=G;SVLEN=1;SVTYPE=INS;FS=0.0;MLEAC=2;MLEAF=1. [...]
+chr21 36219317 . A G 5012.65 REJECT NS=2;DP=332;DPB=382.0;AC=2;AN=4;AF=0.5;RO=197;AO=185;PRO=0.0;PAO=0.0;QR=7546;QA=7070;PQR=0.0;PQA=0.0;SRF=105;SRR=92;SAF=100;SAR=85;SRP=4.87314;SAP=5.65128;AB=0.484293;ABP=3.82887;RUN=1;RPP=3.30374;RPPR=3.28587;RPL=90.0;RPR=95.0;EPP=5.65128;EPPR=3.55041;DPRA=0.0;ODDS=313.509;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994924;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.8285;Dels=0.0;FS=0.218;HaplotypeScore [...]
+chr21 36219566 . A G 6389.58 REJECT NS=2;DP=422;DPB=481.0;AC=2;AN=4;AF=0.5;RO=245;AO=235;PRO=0.0;PAO=0.0;QR=9531;QA=8968;PQR=0.0;PQA=0.0;SRF=127;SRR=118;SAF=118;SAR=117;SRP=3.72822;SAP=3.01954;AB=0.488565;ABP=3.55655;RUN=1;RPP=3.24131;RPPR=4.50817;RPL=115.0;RPR=120.0;EPP=3.01954;EPPR=3.23188;DPRA=0.0;ODDS=317.63;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991489;PAIREDR=0.995918;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.191;Dels=0.0;FS=0.3965;Haplot [...]
+chr21 36219716 . T G 4587.125 REJECT NS=2;DP=321;DPB=363.0;AC=2;AN=4;AF=0.5;RO=194;AO=169;PRO=0.0;PAO=0.0;QR=7402;QA=6372;PQR=0.0;PQA=0.0;SRF=72;SRR=122;SAF=66;SAR=103;SRP=30.9932;SAP=20.6005;AB=0.465565;ABP=6.74906;RUN=1;RPP=3.33152;RPPR=3.05507;RPL=87.0;RPR=82.0;EPP=3.6399;EPPR=3.05507;DPRA=0.0;ODDS=267.917;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.1395;Dels=0.0;FS=0.2275;HaplotypeScore=3.88 [...]
+chr21 36219771 . CAAT C 3491.83 REJECT NS=2;DP=286;DPB=289.556;AC=2;AN=4;AF=0.5;RO=167;AO=139;PRO=38.0;PAO=24.0;QR=6214;QA=4924;PQR=1285.5;PQA=816.5;SRF=75;SRR=92;SAF=56;SAR=83;SRP=6.76812;SAP=14.3988;AB=0.451299;ABP=9.35551;RUN=1;RPP=3.1509;RPPR=5.20778;RPL=68.0;RPR=71.0;EPP=5.65044;EPPR=3.64744;DPRA=0.0;ODDS=214.15;GTI=0;TYPE=del;CIGAR=1M3D5M;NUMALT=1;MEANALT=2.0;LEN=3;MQM=60.2878;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=36219774;HOMLEN=4;HOMSEQ=AATA;SVLEN=-3; [...]
+chr21 36220206 . C T 5732.700000000001 REJECT NS=2;DP=421;DPB=480.0;AC=2;AN=4;AF=0.5;RO=261;AO=219;PRO=0.0;PAO=0.0;QR=9695;QA=8107;PQR=0.0;PQA=0.0;SRF=131;SRR=130;SAF=96;SAR=123;SRP=3.01862;SAP=10.2386;AB=0.45625;ABP=10.9905;RUN=1;RPP=18.0916;RPPR=8.21019;RPL=129.0;RPR=90.0;EPP=4.21006;EPPR=3.68421;DPRA=0.0;ODDS=365.015;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.2374;MQMR=60.1149;PAIRED=0.990868;PAIREDR=0.996169;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4575;Dels=0.0;F [...]
+chr21 36220214 . C CT 2650.5 REJECT NS=2;DP=310;DPB=438.138;AC=2;AN=4;AF=0.5;RO=167;AO=94;PRO=135.5;PAO=122.5;QR=6245;QA=3113;PQR=4852.5;PQA=4305.5;SRF=81;SRR=86;SAF=37;SAR=57;SRP=3.33537;SAP=12.2506;AB=0.303226;ABP=107.269;RUN=1;RPP=14.1911;RPPR=12.4894;RPL=58.0;RPR=36.0;EPP=6.33681;EPPR=17.1704;DPRA=0.0;ODDS=170.693;GTI=0;TYPE=ins;CIGAR=1M1I28M;NUMALT=1;MEANALT=17.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989362;PAIREDR=0.994012;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.7435;FS=5.999;MLE [...]
+chr21 36220493 . G A 5727.4 REJECT NS=2;DP=359;DPB=414.0;AC=2;AN=4;AF=0.5;RO=208;AO=205;PRO=0.0;PAO=0.0;QR=8000;QA=7843;PQR=0.0;PQA=0.0;SRF=111;SRR=97;SAF=114;SAR=91;SRP=5.0565;SAP=8.61376;AB=0.495169;ABP=3.09422;RUN=1;RPP=3.52933;RPPR=3.05206;RPL=106.0;RPR=99.0;EPP=6.07155;EPPR=3.67845;DPRA=0.0;ODDS=350.921;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995122;PAIREDR=0.995192;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0095;Dels=0.0;FS=6.43;HaplotypeSc [...]
+chr21 36220679 . T C 6171.895 REJECT NS=2;DP=357;DPB=404.0;AC=2;AN=4;AF=0.5;RO=188;AO=216;PRO=0.0;PAO=0.0;QR=7239;QA=8289;PQR=0.0;PQA=0.0;SRF=78;SRR=110;SAF=86;SAR=130;SRP=14.8379;SAP=22.4731;AB=0.534653;ABP=7.22425;RUN=1;RPP=5.5839;RPPR=6.75262;RPL=116.0;RPR=100.0;EPP=4.45795;EPPR=3.0565;DPRA=0.0;ODDS=264.357;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.986111;PAIREDR=0.994681;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.967;Dels=0.0;FS=1.651;HaplotypeS [...]
+chr21 36220720 . A C 4741.65 REJECT NS=2;DP=283;DPB=327.0;AC=2;AN=4;AF=0.5;RO=157;AO=170;PRO=0.0;PAO=0.0;QR=6030;QA=6450;PQR=0.0;PQA=0.0;SRF=63;SRR=94;SAF=59;SAR=111;SRP=16.3019;SAP=37.5495;AB=0.519878;ABP=4.13256;RUN=1;RPP=21.455;RPPR=10.3269;RPL=104.0;RPR=66.0;EPP=6.28028;EPPR=3.68802;DPRA=0.0;ODDS=264.192;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.982353;PAIREDR=0.993631;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.456;Dels=0.0;FS=11.2195;Haplotype [...]
+chr21 36220771 . A G 2918.9849999999997 REJECT NS=2;DP=182;DPB=216.0;AC=2;AN=4;AF=0.5;RO=109;AO=107;PRO=0.0;PAO=0.0;QR=4191;QA=4115;PQR=0.0;PQA=0.0;SRF=32;SRR=77;SAF=28;SAR=79;SRP=43.3519;SAP=55.7953;AB=0.49537;ABP=3.05051;RUN=1;RPP=10.3365;RPPR=15.4614;RPL=63.0;RPR=44.0;EPP=8.8753;EPPR=3.98647;DPRA=0.0;ODDS=189.697;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3315;Dels=0.0;FS=2.717;HaplotypeSco [...]
+chr21 36221072 . T C 6901.225 REJECT NS=2;DP=295;DPB=333.0;AC=3;AN=4;AF=0.75;RO=92;AO=241;PRO=0.0;PAO=0.0;QR=3427;QA=9198;PQR=0.0;PQA=0.0;SRF=50;SRR=42;SAF=151;SAR=90;SRP=4.52089;SAP=36.5375;AB=0.646154;ABP=51.2504;RUN=1;RPP=22.914;RPPR=3.86001;RPL=97.0;RPR=144.0;EPP=10.5879;EPPR=3.86001;DPRA=0.0;ODDS=46.5403;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991701;PAIREDR=0.978261;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.825;Dels=0.0;FS=4.231;HaplotypeSc [...]
+chr21 36221088 . C T 5088.01 REJECT NS=2;DP=311;DPB=350.0;AC=2;AN=4;AF=0.5;RO=170;AO=179;PRO=0.0;PAO=0.0;QR=6412;QA=6804;PQR=0.0;PQA=0.0;SRF=85;SRR=85;SAF=104;SAR=75;SRP=3.0103;SAP=13.2126;AB=0.511429;ABP=3.40737;RUN=1;RPP=16.2211;RPPR=3.21467;RPL=73.0;RPR=106.0;EPP=8.36013;EPPR=4.28764;DPRA=0.0;ODDS=210.428;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988827;PAIREDR=0.994118;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.285;Dels=0.0;FS=6.283;HaplotypeSco [...]
+chr21 36221564 . T TAA 814.73 PASS DP=48;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-0.524;FS=15.3165;MLEAC=1;MLEAF=0.5;MQ=58.39;MQRankSum=0.1505;QD=12.255;RPA=2,4;RU=A;ReadPosRankSum=0.799;SOR=2.405;STR;ClippingRankSum=-0.849 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:11,4:15:99.0:122,0,444:4:27:15:1:.:.:.:.:.:-0.0106314 0/1:31,39:75:99.0:1582,0,1191:39:56:70:.:1:.:.:.:.:-0.197241
+chr21 36221567 . T A 156.77 PASS SOMATIC;DP=76;AC=1;AN=4;AF=0.5;MQ0=1;BaseQRankSum=-3.234;Dels=0.0;FS=1.452;HaplotypeScore=32.8742;MLEAC=1;MLEAF=0.5;MQ=57.57;MQRankSum=1.177;QD=2.06;ReadPosRankSum=-3.873;SOR=0.967 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0106314 0/1:66,10:76:99.0:185,0,2399:10:13:76:.:1:.:.:.:.:-0.197241
+chr21 36221609 . TTA T 530.73 PASS SOMATIC;DP=46;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=1.604;FS=9.039;MLEAC=1;MLEAF=0.5;MQ=47.48;MQRankSum=-3.273;QD=11.54;RPA=5,4;RU=TA;ReadPosRankSum=3.016;SOR=3.033;STR GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0106314 0/1:21,15:41:99.0:568,0,662:15:42:36:.:1:.:.:.:.:-0.197241
+chr21 36221620 . T G 510.77 PASS SOMATIC;DP=46;AC=1;AN=4;AF=0.5;MQ0=2;BaseQRankSum=1.801;Dels=0.0;FS=1.988;HaplotypeScore=33.0546;MLEAC=1;MLEAF=0.5;MQ=47.01;MQRankSum=-2.77;QD=11.1;ReadPosRankSum=3.093;SOR=1.485 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0106314 0/1:26,19:46:99.0:539,0,872:19:42:45:.:1:.:.:.:.:-0.197241
+chr21 36221629 . CTATA C 644.73 PASS SOMATIC;DP=46;AC=1;AN=4;AF=0.5;MQ0=0;BaseQRankSum=1.829;FS=8.544;MLEAC=1;MLEAF=0.5;MQ=47.47;MQRankSum=-2.688;QD=10.51;RPA=4,2;RU=TA;ReadPosRankSum=3.293;SOR=2.925;STR GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0106314 0/1:24,13:36:99.0:682,0,1282:13:35:37:.:1:.:.:.:.:-0.197241
+chr21 36221656 . A C 101.429 REJECT NS=2;DP=55;DPB=55.0;AC=2;AN=4;AF=0.5;RO=44;AO=11;PRO=0.0;PAO=0.0;QR=1613;QA=414;PQR=0.0;PQA=0.0;SRF=18;SRR=26;SAF=0;SAR=11;SRP=6.16881;SAP=26.8965;AB=0.2;ABP=46.0055;RUN=1;RPP=19.0002;RPPR=10.1169;RPL=10.0;RPR=1.0;EPP=19.0002;EPPR=10.1169;DPRA=0.0;ODDS=8.5599;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=43.5455;MQMR=44.6364;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=2;BaseQRankSum=-1.674;Dels=0.0;FS=14.659;HaplotypeScore=4.6806;MLEAC= [...]
+chr21 36221670 . C G 95.8824 REJECT NS=2;DP=40;DPB=40.0;AC=2;AN=4;AF=0.5;RO=26;AO=13;PRO=0.0;PAO=0.0;QR=929;QA=507;PQR=0.0;PQA=0.0;SRF=9;SRR=17;SAF=5;SAR=8;SRP=8.35546;SAP=4.51363;AB=0.325;ABP=13.6505;RUN=1;RPP=11.1951;RPPR=6.01695;RPL=10.0;RPR=3.0;EPP=16.5402;EPPR=36.4176;DPRA=0.0;ODDS=2.31738;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=25.1538;MQMR=57.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=2;BaseQRankSum=1.17;Dels=0.0;FS=1.462;HaplotypeScore=6.647;MLEAC=1;MLEAF [...]
+chr21 36221704 . A AG 35.2739 REJECT SOMATIC;NS=2;DP=45;DPB=51.0;AC=1;AN=4;AF=0.25;RO=35;AO=8;PRO=4.5;PAO=2.5;QR=1287;QA=223;PQR=118.5;PQA=52.5;SRF=23;SRR=12;SAF=8;SAR=0;SRP=10.5174;SAP=20.3821;AB=0.222222;ABP=27.1378;RUN=1;RPP=4.09604;RPPR=16.9698;RPL=3.0;RPR=5.0;EPP=4.09604;EPPR=10.5174;DPRA=4.0;ODDS=6.64696;GTI=0;TYPE=ins;CIGAR=1M1I2M;NUMALT=1;MEANALT=2.0;LEN=1;MQM=34.625;MQMR=57.3714;PAIRED=1.0;PAIREDR=0.971429;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:Call [...]
+chr21 36221714 . T A 270.855 REJECT NS=2;DP=64;DPB=79.0;AC=2;AN=2;AF=0.0;RO=40;AO=4;PRO=1.5;PAO=1.0;QR=1479;QA=140;PQR=28.6667;PQA=12.6667;SRF=31;SRR=9;SAF=4;SAR=0;SRP=29.2851;SAP=11.6962;AB=0.0816327;ABP=77.5051;RUN=1;RPP=11.6962;RPPR=45.5712;RPL=0.0;RPR=4.0;EPP=11.6962;EPPR=20.5992;DPRA=0.0;ODDS=27.9803;GTI=0;TYPE=snp;CIGAR=1X2M;NUMALT=2;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=58.45;PAIRED=1.0;PAIREDR=0.975;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=2;BaseQRankSum=-2.762;Dels=0.0;FS=0.0;Hap [...]
+chr21 36221714 . T TAA 270.855 REJECT NS=2;DP=64;DPB=79.0;AC=2;AN=4;AF=0.5;RO=40;AO=20;PRO=1.5;PAO=1.5;QR=1479;QA=652;PQR=28.6667;PQA=28.6667;SRF=31;SRR=9;SAF=20;SAR=0;SRP=29.2851;SAP=46.4397;AB=0.3125;ABP=22.5536;RUN=1;RPP=24.2907;RPPR=45.5712;RPL=3.0;RPR=17.0;EPP=24.2907;EPPR=20.5992;DPRA=0.0;ODDS=27.9803;GTI=0;TYPE=ins;CIGAR=1M2I2M;NUMALT=2;MEANALT=1.5;LEN=2;MQM=47.3;MQMR=58.45;PAIRED=1.0;PAIREDR=0.975;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMI [...]
+chr21 36221730 . T G 677.2 REJECT NS=2;DP=74;DPB=83.0;AC=2;AN=4;AF=0.5;RO=49;AO=34;PRO=0.0;PAO=0.0;QR=1822;QA=1302;PQR=0.0;PQA=0.0;SRF=35;SRR=14;SAF=33;SAR=1;SRP=22.5536;SAP=68.4099;AB=0.409639;ABP=8.89682;RUN=1;RPP=28.557;RPPR=10.4997;RPL=7.0;RPR=27.0;EPP=23.7032;EPPR=3.40914;DPRA=0.0;ODDS=50.0346;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=52.5294;MQMR=58.6939;PAIRED=0.970588;PAIREDR=0.979592;technology.ILLUMINA=1.0;MQ0=2;BaseQRankSum=-0.288;Dels=0.0;FS=12.115;HaplotypeScore [...]
+chr21 36221741 . C A 668.43 REJECT NS=2;DP=70;DPB=79.0;AC=2;AN=4;AF=0.5;RO=43;AO=32;PRO=0.0;PAO=0.0;QR=1421;QA=1206;PQR=0.0;PQA=0.0;SRF=29;SRR=14;SAF=30;SAR=2;SRP=14.3727;SAP=56.2114;AB=0.405063;ABP=9.19487;RUN=1;RPP=56.2114;RPPR=4.27278;RPL=2.0;RPR=30.0;EPP=42.0968;EPPR=9.12072;DPRA=0.0;ODDS=44.7226;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=2;MEANALT=2.0;LEN=1;MQM=58.625;MQMR=59.8605;PAIRED=0.96875;PAIREDR=0.976744;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=2;BaseQRankSum=1.857;Dels=0.0;FS=11.4 [...]
+chr21 36221741 . C T 668.43 REJECT NS=2;DP=79;DPB=79.0;AC=2;AN=2;AF=0.0;RO=43;AO=4;PRO=0.0;PAO=0.0;QR=1421;QA=64;PQR=0.0;PQA=0.0;SRF=29;SRR=14;SAF=4;SAR=0;SRP=14.3727;SAP=11.6962;AB=0.0506329;ABP=141.572;RUN=1;RPP=5.18177;RPPR=4.27278;RPL=3.0;RPR=1.0;EPP=5.18177;EPPR=9.12072;DPRA=0.0;ODDS=44.7226;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=2;MEANALT=2.0;LEN=1;MQM=55.0;MQMR=59.8605;PAIRED=1.0;PAIREDR=0.976744;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC [...]
+chr21 36221760 . GTA G 861.934 REJECT NS=2;DP=82;DPB=91.1538;AC=2;AN=4;AF=0.5;RO=44;AO=38;PRO=8.5;PAO=5.5;QR=1559;QA=1359;PQR=284.0;PQA=201.0;SRF=31;SRR=13;SAF=36;SAR=2;SRP=19.0002;SAP=69.0688;AB=0.422222;ABP=7.73928;RUN=1;RPP=3.0103;RPPR=4.78696;RPL=19.0;RPR=19.0;EPP=3.9246;EPPR=3.79993;DPRA=0.0;ODDS=61.8949;GTI=0;TYPE=del;CIGAR=1M2D10M;NUMALT=1;MEANALT=3.5;LEN=2;MQM=58.0526;MQMR=59.5;PAIRED=0.973684;PAIREDR=0.977273;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1235;FS=11.8515;MLEAC=1;M [...]
+chr21 36222139 . T A 10088.385 REJECT NS=2;DP=435;DPB=490.0;AC=3;AN=4;AF=0.75;RO=143;AO=347;PRO=0.0;PAO=0.0;QR=5534;QA=13424;PQR=0.0;PQA=0.0;SRF=61;SRR=82;SAF=175;SAR=172;SRP=9.70694;SAP=3.06662;AB=0.625654;ABP=55.3985;RUN=1;RPP=3.31693;RPPR=3.14697;RPL=177.0;RPR=170.0;EPP=6.3207;EPPR=3.02549;DPRA=0.0;ODDS=68.387;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994236;PAIREDR=0.993007;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.462;Dels=0.0;FS=5.6995;Haplot [...]
+chr21 36222258 . G A 5334.48 REJECT NS=2;DP=357;DPB=405.0;AC=2;AN=4;AF=0.5;RO=214;AO=191;PRO=0.0;PAO=0.0;QR=8048;QA=7234;PQR=0.0;PQA=0.0;SRF=115;SRR=99;SAF=105;SAR=86;SRP=5.60795;SAP=7.1145;AB=0.471605;ABP=5.84662;RUN=1;RPP=11.2983;RPPR=12.1427;RPL=82.0;RPR=109.0;EPP=8.02401;EPPR=3.17265;DPRA=0.0;ODDS=284.852;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.9424;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990654;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.305;Dels=0.0;FS=0.207;HaplotypeScor [...]
+chr21 36222324 . AAAC A 4903.62 REJECT NS=2;DP=305;DPB=373.696;AC=2;AN=4;AF=0.5;RO=138;AO=159;PRO=103.0;PAO=90.0;QR=5250;QA=5868;PQR=3739.0;PQA=3271.0;SRF=67;SRR=71;SAF=75;SAR=84;SRP=3.26206;SAP=4.11652;AB=0.521311;ABP=4.21351;RUN=1;RPP=3.35173;RPPR=7.03854;RPL=77.0;RPR=82.0;EPP=3.6795;EPPR=3.57677;DPRA=0.0;ODDS=220.4;GTI=0;TYPE=del;CIGAR=1M3D19M;NUMALT=1;MEANALT=5.0;LEN=3;MQM=60.5031;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=36222327;HOMLEN=11;HOMSEQ=AACAACAACAA [...]
+chr21 36222447 . T C 5850.530000000001 REJECT NS=2;DP=380;DPB=435.0;AC=2;AN=4;AF=0.5;RO=222;AO=211;PRO=0.0;PAO=0.0;QR=7831;QA=7980;PQR=0.0;PQA=0.0;SRF=114;SRR=108;SAF=97;SAR=114;SRP=3.36243;SAP=5.9845;AB=0.485057;ABP=3.85393;RUN=1;RPP=3.8439;RPPR=8.64439;RPL=110.0;RPR=101.0;EPP=12.9003;EPPR=3.0103;DPRA=0.0;ODDS=329.339;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990521;PAIREDR=0.990991;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.118;Dels=0.0;FS=3.8445; [...]
+chr21 36222560 . T C 4922.905000000001 REJECT NS=2;DP=300;DPB=346.0;AC=2;AN=4;AF=0.5;RO=171;AO=175;PRO=0.0;PAO=0.0;QR=6432;QA=6720;PQR=0.0;PQA=0.0;SRF=78;SRR=93;SAF=98;SAR=77;SRP=5.8675;SAP=8.48241;AB=0.50578;ABP=3.11071;RUN=1;RPP=9.57435;RPPR=6.68022;RPL=76.0;RPR=99.0;EPP=3.32051;EPPR=4.03889;DPRA=0.0;ODDS=291.398;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994286;PAIREDR=0.988304;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.823;Dels=0.0;FS=6.961;Haplo [...]
+chr21 36222713 . G C 5010.89 REJECT NS=2;DP=325;DPB=370.0;AC=2;AN=4;AF=0.5;RO=192;AO=178;PRO=0.0;PAO=0.0;QR=7219;QA=6772;PQR=0.0;PQA=0.0;SRF=101;SRR=91;SAF=85;SAR=93;SRP=4.14128;SAP=3.79105;AB=0.481081;ABP=4.16059;RUN=1;RPP=22.5292;RPPR=7.5342;RPL=69.0;RPR=109.0;EPP=3.0591;EPPR=3.41745;DPRA=0.0;ODDS=243.476;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.601;Dels=0.0;FS=2.395;HaplotypeScore=1.9997;M [...]
+chr21 36222741 . A G 5495.37 REJECT NS=2;DP=345;DPB=390.0;AC=2;AN=4;AF=0.5;RO=194;AO=195;PRO=0.0;PAO=0.0;QR=7413;QA=7353;PQR=0.0;PQA=0.0;SRF=98;SRR=96;SAF=100;SAR=95;SRP=3.05507;SAP=3.28869;AB=0.5;ABP=3.0103;RUN=1;RPP=7.03031;RPPR=4.12962;RPL=88.0;RPR=107.0;EPP=4.35773;EPPR=3.41325;DPRA=0.0;ODDS=255.145;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.9795;MQMR=60.0;PAIRED=0.994872;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.287;Dels=0.0;FS=0.3955;HaplotypeScore=14. [...]
+chr21 36222862 . T C 5933.955 REJECT NS=2;DP=374;DPB=426.0;AC=2;AN=4;AF=0.5;RO=218;AO=208;PRO=0.0;PAO=0.0;QR=8418;QA=8115;PQR=0.0;PQA=0.0;SRF=114;SRR=104;SAF=108;SAR=100;SRP=4.00639;SAP=3.67845;AB=0.488263;ABP=3.52004;RUN=1;RPP=3.05206;RPPR=4.44467;RPL=105.0;RPR=103.0;EPP=3.38613;EPPR=5.56029;DPRA=0.0;ODDS=340.736;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995413;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.287;Dels=0.0;FS=0.5735;HaplotypeS [...]
+chr21 36223096 . TA T 15.3844 REJECT NS=2;DP=340;DPB=385.6;AC=1;AN=4;AF=0.25;RO=289;AO=25;PRO=59.5;PAO=43.5;QR=10945;QA=933;PQR=2077.0;PQA=1510.0;SRF=149;SRR=140;SAF=10;SAR=15;SRP=3.61891;SAP=5.18177;AB=0.0978261;ABP=132.26;RUN=1;RPP=3.09716;RPPR=25.7394;RPL=13.0;RPR=12.0;EPP=5.18177;EPPR=3.61891;DPRA=0.0;ODDS=3.51302;GTI=0;TYPE=del;CIGAR=1M1D13M;NUMALT=1;MEANALT=7.5;LEN=1;MQM=60.4;MQMR=60.0;PAIRED=1.0;PAIREDR=0.986159;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV: [...]
+chr21 36223234 . T C 5698.52 REJECT NS=2;DP=361;DPB=405.0;AC=2;AN=4;AF=0.5;RO=199;AO=205;PRO=0.0;PAO=0.0;QR=7538;QA=7757;PQR=0.0;PQA=0.0;SRF=113;SRR=86;SAF=110;SAR=95;SRP=10.9651;SAP=5.39362;AB=0.506173;ABP=3.14434;RUN=1;RPP=4.292;RPPR=4.33064;RPL=97.0;RPR=108.0;EPP=3.8683;EPPR=4.33064;DPRA=0.0;ODDS=227.049;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.980488;PAIREDR=0.994975;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.764;Dels=0.0;FS=4.9065;HaplotypeSco [...]
+chr21 36223627 . G A 2248.4 REJECT NS=2;DP=400;DPB=456.0;AC=2;AN=4;AF=0.5;RO=341;AO=115;PRO=0.0;PAO=0.0;QR=13122;QA=4358;PQR=0.0;PQA=0.0;SRF=137;SRR=204;SAF=54;SAR=61;SRP=31.596;SAP=3.93554;AB=0.252193;ABP=246.234;RUN=1;RPP=7.25883;RPPR=3.1695;RPL=50.0;RPR=65.0;EPP=3.93554;EPPR=14.7846;DPRA=0.0;ODDS=257.943;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991304;PAIREDR=0.997067;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.386;Dels=0.0;FS=8.284;HaplotypeScor [...]
+chr21 36223744 . C T 6396.245000000001 REJECT NS=2;DP=414;DPB=472.0;AC=2;AN=4;AF=0.5;RO=243;AO=229;PRO=0.0;PAO=0.0;QR=9296;QA=8775;PQR=0.0;PQA=0.0;SRF=124;SRR=119;SAF=132;SAR=97;SRP=3.2337;SAP=14.6263;AB=0.485169;ABP=3.91201;RUN=1;RPP=4.15767;RPPR=6.23623;RPL=120.0;RPR=109.0;EPP=17.433;EPPR=5.02092;DPRA=0.0;ODDS=375.572;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.9869;PAIREDR=0.995885;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.929;Dels=0.0;FS=4.3175;H [...]
+chr21 36223886 . G A 5769.620000000001 REJECT NS=2;DP=369;DPB=420.0;AC=2;AN=4;AF=0.5;RO=194;AO=216;PRO=0.0;PAO=0.0;QR=7237;QA=8105;PQR=0.0;PQA=0.0;SRF=95;SRR=99;SAF=101;SAR=115;SRP=3.18939;SAP=4.98071;AB=0.514286;ABP=3.7548;RUN=1;RPP=3.6537;RPPR=7.48756;RPL=104.0;RPR=112.0;EPP=17.527;EPPR=3.41325;DPRA=0.0;ODDS=302.612;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990741;PAIREDR=0.994845;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7275;Dels=0.0;FS=0.937;H [...]
+chr21 36223906 . T C 6386.465 REJECT NS=2;DP=382;DPB=439.0;AC=2;AN=4;AF=0.5;RO=204;AO=233;PRO=0.0;PAO=0.0;QR=7665;QA=8728;PQR=0.0;PQA=0.0;SRF=106;SRR=98;SAF=122;SAR=111;SRP=3.69155;SAP=4.13797;AB=0.530752;ABP=6.61623;RUN=1;RPP=3.24329;RPPR=4.07475;RPL=114.0;RPR=119.0;EPP=11.9665;EPPR=3.05288;DPRA=0.0;ODDS=317.831;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995708;PAIREDR=0.995098;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.3095;Dels=0.0;FS=0.204;Haplot [...]
+chr21 36224276 . T C 1704.05 REJECT NS=2;DP=120;DPB=139.0;AC=2;AN=4;AF=0.5;RO=70;AO=69;PRO=0.0;PAO=0.0;QR=2720;QA=2517;PQR=0.0;PQA=0.0;SRF=15;SRR=55;SAF=13;SAR=56;SRP=52.644;SAP=61.1995;AB=0.496403;ABP=3.02592;RUN=1;RPP=6.81824;RPPR=6.1124;RPL=40.0;RPR=29.0;EPP=12.1053;EPPR=20.8784;DPRA=0.0;ODDS=109.756;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=57.913;MQMR=60.0;PAIRED=0.971014;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.081;Dels=0.0;FS=0.0;HaplotypeScore=2.8909 [...]
+chr21 36224466 . AAAAAC A 1328.24 REJECT NS=2;DP=107;DPB=247.446;AC=2;AN=4;AF=0.5;RO=61;AO=42;PRO=156.0;PAO=133.0;QR=2334;QA=1500;PQR=5684.5;PQA=4775.5;SRF=51;SRR=10;SAF=36;SAR=6;SRP=62.8504;SAP=49.5419;AB=0.392523;ABP=13.7459;RUN=1;RPP=16.2459;RPPR=9.02635;RPL=13.0;RPR=29.0;EPP=16.2459;EPPR=3.0459;DPRA=0.0;ODDS=68.4317;GTI=0;TYPE=del;CIGAR=1M5D50M;NUMALT=1;MEANALT=3.0;LEN=5;MQM=61.1905;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=36224471;HOMLEN=27;HOMSEQ=AAAACAAAA [...]
+chr21 36224963 . C G 6169.8150000000005 REJECT NS=2;DP=381;DPB=431.0;AC=2;AN=4;AF=0.5;RO=212;AO=218;PRO=0.0;PAO=0.0;QR=8137;QA=8445;PQR=0.0;PQA=0.0;SRF=96;SRR=116;SAF=100;SAR=118;SRP=7.10742;SAP=6.23763;AB=0.5058;ABP=3.13626;RUN=1;RPP=4.96263;RPPR=4.03458;RPL=102.0;RPR=116.0;EPP=3.05014;EPPR=3.05127;DPRA=0.0;ODDS=268.384;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990826;PAIREDR=0.995283;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.0005;Dels=0.0;FS=3.46 [...]
+chr21 36224983 . T C 1684.76 REJECT NS=2;DP=372;DPB=418.0;AC=2;AN=4;AF=0.5;RO=328;AO=90;PRO=0.0;PAO=0.0;QR=12734;QA=3430;PQR=0.0;PQA=0.0;SRF=145;SRR=183;SAF=45;SAR=45;SRP=12.5701;SAP=3.0103;AB=0.215311;ABP=297.271;RUN=1;RPP=3.39634;RPPR=6.82362;RPL=47.0;RPR=43.0;EPP=5.42305;EPPR=3.03678;DPRA=0.0;ODDS=160.829;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.988889;PAIREDR=0.990854;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4395;Dels=0.0;FS=6.1365;Haplotype [...]
+chr21 36226112 . A C 472.324 REJECT NS=2;DP=156;DPB=226.286;AC=2;AN=2;AF=0.0;RO=48;AO=6;PRO=34.6786;PAO=7.09524;QR=1717;QA=90;PQR=1239.55;PQA=230.548;SRF=12;SRR=36;SAF=0;SAR=6;SRP=29.068;SAP=16.0391;AB=0.0508475;ABP=209.779;RUN=1;RPP=8.80089;RPPR=21.1059;RPL=5.0;RPR=1.0;EPP=8.80089;EPPR=3.73412;DPRA=0.0;ODDS=43.4815;GTI=0;TYPE=snp;CIGAR=1X20M;NUMALT=6;MEANALT=16.0;LEN=1;MQM=59.6667;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr21 36226112 . A T 472.324 REJECT NS=2;DP=156;DPB=226.286;AC=2;AN=2;AF=0.0;RO=48;AO=23;PRO=34.6786;PAO=6.09524;QR=1717;QA=332;PQR=1239.55;PQA=215.548;SRF=12;SRR=36;SAF=0;SAR=23;SRP=29.068;SAP=52.9542;AB=0.147436;ABP=171.439;RUN=1;RPP=5.3706;RPPR=21.1059;RPL=9.0;RPR=14.0;EPP=5.3706;EPPR=3.73412;DPRA=0.0;ODDS=43.4815;GTI=0;TYPE=snp;CIGAR=1X20M;NUMALT=6;MEANALT=11.5;LEN=1;MQM=56.8261;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr21 36226112 . A AT 472.324 REJECT NS=2;DP=156;DPB=226.286;AC=2;AN=4;AF=0.5;RO=48;AO=26;PRO=34.6786;PAO=32.1786;QR=1717;QA=655;PQR=1239.55;PQA=1081.55;SRF=12;SRR=36;SAF=7;SAR=19;SRP=29.068;SAP=15.0369;AB=0.166667;ABP=153.566;RUN=1;RPP=6.01695;RPPR=21.1059;RPL=16.0;RPR=10.0;EPP=4.34659;EPPR=3.73412;DPRA=0.0;ODDS=43.4815;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=6;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.8395;FS [...]
+chr21 36226112 . A TT 472.324 REJECT NS=2;DP=156;DPB=226.286;AC=2;AN=2;AF=0.0;RO=48;AO=10;PRO=34.6786;PAO=7.09524;QR=1717;QA=116;PQR=1239.55;PQA=229.548;SRF=12;SRR=36;SAF=0;SAR=10;SRP=29.068;SAP=24.725;AB=0.0847458;ABP=179.746;RUN=1;RPP=24.725;RPPR=21.1059;RPL=0.0;RPR=10.0;EPP=24.725;EPPR=3.73412;DPRA=0.0;ODDS=43.4815;GTI=0;TYPE=complex;CIGAR=1X1I20M;NUMALT=6;MEANALT=16.0;LEN=22;MQM=70.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr21 36226112 . A ATT 472.324 REJECT NS=2;DP=156;DPB=226.286;AC=2;AN=2;AF=0.0;RO=48;AO=5;PRO=34.6786;PAO=26.1786;QR=1717;QA=137;PQR=1239.55;PQA=939.548;SRF=12;SRR=36;SAF=2;SAR=3;SRP=29.068;SAP=3.44459;AB=0.0320513;ABP=299.723;RUN=1;RPP=6.91895;RPPR=21.1059;RPL=4.0;RPR=1.0;EPP=3.44459;EPPR=3.73412;DPRA=0.0;ODDS=43.4815;GTI=0;TYPE=ins;CIGAR=1M2I20M;NUMALT=6;MEANALT=11.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr21 36226112 . AT A 472.324 PASS SOMATIC;NS=2;DP=156;DPB=226.286;AC=2;AN=2;AF=0.0;RO=48;AO=15;PRO=34.6786;PAO=23.6786;QR=1717;QA=372;PQR=1239.55;PQA=810.714;SRF=12;SRR=36;SAF=1;SAR=14;SRP=29.068;SAP=27.4756;AB=0.0961538;ABP=223.999;RUN=1;RPP=3.15506;RPPR=21.1059;RPL=7.0;RPR=8.0;EPP=4.31318;EPPR=3.73412;DPRA=0.0;ODDS=43.4815;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=6;MEANALT=11.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr21 36226892 . G GA 11.8354 REJECT NS=2;DP=215;DPB=294.852;AC=2;AN=2;AF=0.0;RO=152;AO=13;PRO=65.5;PAO=55.5;QR=5426;QA=454;PQR=2265.67;PQA=1891.67;SRF=114;SRR=38;SAF=12;SAR=1;SRP=85.5263;SAP=23.2217;AB=0.0961538;ABP=76.6733;RUN=1;RPP=7.18621;RPPR=65.2401;RPL=4.0;RPR=9.0;EPP=4.51363;EPPR=28.2108;DPRA=0.0;ODDS=2.65059;GTI=0;TYPE=ins;CIGAR=1M1I26M;NUMALT=2;MEANALT=17.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993421;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr21 36226892 . GA G 11.8354 REJECT NS=2;DP=215;DPB=294.852;AC=2;AN=3;AF=0.25;RO=152;AO=12;PRO=65.5;PAO=57.0;QR=5426;QA=409;PQR=2265.67;PQA=1953.67;SRF=114;SRR=38;SAF=8;SAR=4;SRP=85.5263;SAP=5.9056;AB=0.0961538;ABP=76.6733;RUN=1;RPP=3.73412;RPPR=65.2401;RPL=5.0;RPR=7.0;EPP=9.52472;EPPR=28.2108;DPRA=0.0;ODDS=2.65059;GTI=0;TYPE=del;CIGAR=1M1D25M;NUMALT=2;MEANALT=17.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.993421;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr21 36227745 . C T 1113.77 PASS SOMATIC;NS=2;DP=164;DPB=164.0;AC=1;AN=3;AF=0.25;RO=117;AO=47;PRO=0.0;PAO=0.0;QR=4536;QA=1714;PQR=0.0;PQA=0.0;SRF=25;SRR=92;SAF=7;SAR=40;SRP=86.3243;SAP=53.3238;AB=0.391667;ABP=15.2429;RUN=1;RPP=4.16534;RPPR=6.14687;RPL=26.0;RPR=21.0;EPP=3.0565;EPPR=7.18621;DPRA=2.72727;ODDS=28.4919;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.7872;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.113;Dels=0.0;FS=0.0;Haplot [...]
+chr21 36228360 . C T 2805.21 PASS SOMATIC;NS=2;DP=413;DPB=413.0;AC=1;AN=3;AF=0.25;RO=305;AO=107;PRO=0.0;PAO=0.0;QR=11654;QA=4117;PQR=0.0;PQA=0.0;SRF=160;SRR=145;SAF=53;SAR=54;SRP=4.61221;SAP=3.03059;AB=0.341853;ABP=71.0058;RUN=1;RPP=3.51765;RPPR=4.61221;RPL=56.0;RPR=51.0;EPP=3.51765;EPPR=7.46004;DPRA=3.13;ODDS=63.375;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990654;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=2.673;Dels=0.0;FS=0.907;H [...]
+chr21 36228390 . A T 14376.4 REJECT NS=2;DP=380;DPB=431.0;AC=4;AN=4;AF=1.0;RO=0;AO=431;PRO=0.0;PAO=0.0;QR=0;QA=16452;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=250;SAR=181;SRP=0.0;SAP=26.9973;AB=0.0;ABP=0.0;RUN=1;RPP=13.2127;RPPR=0.0;RPL=193.0;RPR=238.0;EPP=3.61992;EPPR=0.0;DPRA=0.0;ODDS=66.6948;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9861;MQMR=0.0;PAIRED=0.99536;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9997;MLEAC=2;MLEAF=1.0;MQ=59.99;QD=31.145;SO [...]
+chr21 36229637 . G A 6591.635 REJECT NS=2;DP=438;DPB=493.0;AC=2;AN=4;AF=0.5;RO=259;AO=234;PRO=0.0;PAO=0.0;QR=9850;QA=8955;PQR=0.0;PQA=0.0;SRF=143;SRR=116;SAF=114;SAR=120;SRP=9.12228;SAP=3.34437;AB=0.474645;ABP=5.76318;RUN=1;RPP=11.3621;RPPR=3.01868;RPL=102.0;RPR=132.0;EPP=13.7377;EPPR=6.70767;DPRA=0.0;ODDS=365.153;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.987179;PAIREDR=0.992278;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.1045;Dels=0.0;FS=7.9915;Hapl [...]
+chr21 36229941 . C T 5836.825000000001 REJECT NS=2;DP=395;DPB=451.0;AC=2;AN=4;AF=0.5;RO=240;AO=211;PRO=0.0;PAO=0.0;QR=9239;QA=8079;PQR=0.0;PQA=0.0;SRF=119;SRR=121;SAF=114;SAR=97;SRP=3.04649;SAP=5.9845;AB=0.467849;ABP=7.05954;RUN=1;RPP=8.45442;RPPR=3.15506;RPL=94.0;RPR=117.0;EPP=3.8439;EPPR=9.12661;DPRA=0.0;ODDS=356.101;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995833;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.369;Dels=0.0;FS=2.907;Haplot [...]
+chr21 36229995 . C A 6981.8150000000005 REJECT NS=2;DP=442;DPB=512.0;AC=2;AN=4;AF=0.5;RO=265;AO=247;PRO=0.0;PAO=0.0;QR=9981;QA=9544;PQR=0.0;PQA=0.0;SRF=139;SRR=126;SAF=135;SAR=112;SRP=4.39513;SAP=7.66094;AB=0.482422;ABP=4.38443;RUN=1;RPP=4.98836;RPPR=7.34505;RPL=116.0;RPR=131.0;EPP=4.49604;EPPR=4.39513;DPRA=0.0;ODDS=412.878;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995951;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.0535;Dels=0.0;FS=2.016; [...]
+chr21 36231159 . A C 9810.835 REJECT NS=2;DP=421;DPB=478.0;AC=3;AN=4;AF=0.75;RO=135;AO=342;PRO=0.0;PAO=0.0;QR=5201;QA=13173;PQR=0.0;PQA=0.0;SRF=65;SRR=70;SAF=171;SAR=171;SRP=3.41242;SAP=3.0103;AB=0.628415;ABP=55.4342;RUN=1;RPP=4.63573;RPPR=11.5193;RPL=179.0;RPR=163.0;EPP=3.0357;EPPR=5.72866;DPRA=0.0;ODDS=70.8062;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991228;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.831;Dels=0.0;FS=2.4115;HaplotypeSco [...]
+chr21 36231175 . C T 6204.015 REJECT NS=2;DP=411;DPB=463.0;AC=2;AN=4;AF=0.5;RO=242;AO=221;PRO=0.0;PAO=0.0;QR=9130;QA=8487;PQR=0.0;PQA=0.0;SRF=120;SRR=122;SAF=123;SAR=98;SRP=3.04619;SAP=9.15134;AB=0.477322;ABP=5.07859;RUN=1;RPP=19.5272;RPPR=14.6393;RPL=131.0;RPR=90.0;EPP=3.80618;EPPR=17.3671;DPRA=0.0;ODDS=325.394;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99095;PAIREDR=0.991736;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=3.2965;Dels=0.0;FS=4.2375;Haploty [...]
+chr21 36410869 . CCTCTCT C 10430.6 REJECT NS=2;DP=135;DPB=211.795;AC=1;AN=3;AF=0.25;RO=0;AO=6;PRO=18.781;PAO=18.781;QR=0;QA=152;PQR=678.101;PQA=678.101;SRF=0;SRR=0;SAF=2;SAR=4;SRP=0.0;SAP=4.45795;AB=0.0444444;ABP=246.36;RUN=1;RPP=16.0391;RPPR=0.0;RPL=6.0;RPR=0.0;EPP=4.45795;EPPR=0.0;DPRA=0.0;ODDS=3.55542;GTI=1;TYPE=del;CIGAR=1M6D37M;NUMALT=11;MEANALT=20.5;LEN=6;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV: [...]
+chr21 36410869 . CCTCTCTCT C 10430.6 REJECT SOMATIC;NS=2;DP=135;DPB=211.795;AC=1;AN=3;AF=0.25;RO=0;AO=6;PRO=18.781;PAO=17.681;QR=0;QA=181;PQR=678.101;PQA=637.001;SRF=0;SRR=0;SAF=4;SAR=2;SRP=0.0;SAP=4.45795;AB=0.0444444;ABP=246.36;RUN=1;RPP=16.0391;RPPR=0.0;RPL=6.0;RPR=0.0;EPP=4.45795;EPPR=0.0;DPRA=0.0;ODDS=3.55542;GTI=1;TYPE=del;CIGAR=1M8D35M;NUMALT=11;MEANALT=20.5;LEN=8;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr21 36410869 . CCTCTCTCTCTCTCTCT C 10430.6 REJECT NS=2;DP=135;DPB=211.795;AC=0;AN=4;AF=0.0;RO=0;AO=5;PRO=18.781;PAO=15.5143;QR=0;QA=166;PQR=678.101;PQA=555.834;SRF=0;SRR=0;SAF=3;SAR=2;SRP=0.0;SAP=3.44459;AB=0.037037;ABP=254.338;RUN=1;RPP=13.8677;RPPR=0.0;RPL=5.0;RPR=0.0;EPP=3.44459;EPPR=0.0;DPRA=0.0;ODDS=3.55542;GTI=1;TYPE=del;CIGAR=1M16D27M;NUMALT=11;MEANALT=20.5;LEN=16;MQM=56.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr21 36410869 . CCTCTCTCTCTCTCTCTCT C 10430.6 REJECT SOMATIC;NS=2;DP=135;DPB=211.795;AC=1;AN=4;AF=0.0;RO=0;AO=20;PRO=18.781;PAO=15.05;QR=0;QA=547;PQR=678.101;PQA=538.977;SRF=0;SRR=0;SAF=9;SAR=11;SRP=0.0;SAP=3.44459;AB=0.148148;ABP=148.177;RUN=1;RPP=38.1882;RPPR=0.0;RPL=19.0;RPR=1.0;EPP=4.74748;EPPR=0.0;DPRA=0.0;ODDS=3.55542;GTI=1;TYPE=del;CIGAR=1M18D25M;NUMALT=11;MEANALT=20.5;LEN=18;MQM=58.95;MQMR=0.0;PAIRED=0.95;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1 [...]
+chr21 36410892 . CTCTCTCTCTCTCTCTCTC GTGTG 10430.6 REJECT NS=2;DP=135;DPB=211.795;AC=0;AN=4;AF=0.0;RO=0;AO=7;PRO=18.781;PAO=27.0286;QR=0;QA=217;PQR=678.101;PQA=950.545;SRF=0;SRR=0;SAF=5;SAR=2;SRP=0.0;SAP=5.80219;AB=0.0518519;ABP=238.511;RUN=1;RPP=3.32051;RPPR=0.0;RPL=3.0;RPR=4.0;EPP=3.32051;EPPR=0.0;DPRA=0.0;ODDS=3.55542;GTI=1;TYPE=complex;CIGAR=1M14D22M1X1M1X1M1X2M;NUMALT=11;MEANALT=20.5;LEN=30;MQM=42.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:R [...]
+chr21 36410894 . CTCTCTCTCTCTCTCTC G 10430.6 REJECT NS=2;DP=135;DPB=211.795;AC=0;AN=4;AF=0.0;RO=0;AO=5;PRO=18.781;PAO=19.5119;QR=0;QA=145;PQR=678.101;PQA=701.739;SRF=0;SRR=0;SAF=3;SAR=2;SRP=0.0;SAP=3.44459;AB=0.037037;ABP=254.338;RUN=1;RPP=3.44459;RPPR=0.0;RPL=3.0;RPR=2.0;EPP=6.91895;EPPR=0.0;DPRA=0.0;ODDS=3.55542;GTI=1;TYPE=complex;CIGAR=1M16D24M1X2M;NUMALT=11;MEANALT=20.5;LEN=28;MQM=54.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr21 36410894 . CTCTCTCTCTCTCTCTC GTG 10430.6 REJECT NS=2;DP=135;DPB=211.795;AC=0;AN=4;AF=0.0;RO=0;AO=8;PRO=18.781;PAO=39.6119;QR=0;QA=212;PQR=678.101;PQA=1354.94;SRF=0;SRR=0;SAF=8;SAR=0;SRP=0.0;SAP=20.3821;AB=0.0592593;ABP=230.79;RUN=1;RPP=4.09604;RPPR=0.0;RPL=3.0;RPR=5.0;EPP=4.09604;EPPR=0.0;DPRA=0.0;ODDS=3.55542;GTI=1;TYPE=complex;CIGAR=1M14D24M1X1M1X2M;NUMALT=11;MEANALT=20.5;LEN=30;MQM=33.625;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO [...]
+chr21 36410894 . CTCTCTCTCTCTCTCTC GTGTG 10430.6 REJECT SOMATIC;NS=2;DP=135;DPB=211.795;AC=1;AN=3;AF=0.25;RO=0;AO=32;PRO=18.781;PAO=33.6119;QR=0;QA=873;PQR=678.101;PQA=1193.27;SRF=0;SRR=0;SAF=22;SAR=10;SRP=0.0;SAP=12.7819;AB=0.237037;ABP=84.0947;RUN=1;RPP=56.2114;RPPR=0.0;RPL=2.0;RPR=30.0;EPP=12.7819;EPPR=0.0;DPRA=0.0;ODDS=3.55542;GTI=1;TYPE=complex;CIGAR=1M12D24M1X1M1X1M1X2M;NUMALT=11;MEANALT=20.5;LEN=32;MQM=38.3125;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLEL [...]
+chr21 36410906 . C G 1805.77 PASS DP=153;AC=2;AN=4;AF=0.5;MQ0=0;ALERT;BaseQRankSum=-1.9005;Dels=0.0;FS=5.761;HaplotypeScore=91.2287;MLEAC=1;MLEAF=0.5;MQ=51.335;MQRankSum=-3.7935;QD=10.48;ReadPosRankSum=4.594;SOR=1.092;ClippingRankSum=0.46 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:18,23:41:99.0:695,0,437:23:56:41:1:.:.:.:.:.:-0.0106314 0/1:99,104:204:99.0:2973,0,3098:104:51:203:.:1:.:.:.:.:-0.02803
+chr21 36410906 . CTCTC G 10430.6 REJECT NS=2;DP=135;DPB=211.795;AC=0;AN=4;AF=0.0;RO=0;AO=2;PRO=18.781;PAO=22.0762;QR=0;QA=52;PQR=678.101;PQA=797.03;SRF=0;SRR=0;SAF=1;SAR=1;SRP=0.0;SAP=3.0103;AB=0.05;ABP=73.366;RUN=1;RPP=7.35324;RPPR=0.0;RPL=0.0;RPR=2.0;EPP=3.0103;EPPR=0.0;DPRA=0.0;ODDS=3.55542;GTI=1;TYPE=complex;CIGAR=1M4D36M1X2M;NUMALT=11;MEANALT=14.0;LEN=40;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:Ca [...]
+chr21 36410906 . CTCTC GTGTG 10430.6 REJECT NS=2;DP=135;DPB=211.795;AC=1;AN=3;AF=0.25;RO=0;AO=11;PRO=18.781;PAO=36.1762;QR=0;QA=404;PQR=678.101;PQA=1288.56;SRF=0;SRR=0;SAF=7;SAR=4;SRP=0.0;SAP=4.78696;AB=0.0814815;ABP=208.399;RUN=1;RPP=26.8965;RPPR=0.0;RPL=0.0;RPR=11.0;EPP=4.78696;EPPR=0.0;DPRA=0.0;ODDS=3.55542;GTI=1;TYPE=complex;CIGAR=37M1X1M1X1M1X2M;NUMALT=11;MEANALT=20.5;LEN=44;MQM=44.4545;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr21 36410906 . CTCTC GTGTGTGTGTG 10430.6 REJECT NS=2;DP=135;DPB=211.795;AC=0;AN=4;AF=0.0;RO=0;AO=2;PRO=18.781;PAO=29.1762;QR=0;QA=52;PQR=678.101;PQA=987.896;SRF=0;SRR=0;SAF=2;SAR=0;SRP=0.0;SAP=7.35324;AB=0.05;ABP=73.366;RUN=1;RPP=7.35324;RPPR=0.0;RPL=0.0;RPR=2.0;EPP=7.35324;EPPR=0.0;DPRA=0.0;ODDS=3.55542;GTI=1;TYPE=complex;CIGAR=36M6I1M1X1M1X1M1X2M;NUMALT=11;MEANALT=14.0;LEN=50;MQM=27.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr21 36410908 . C G 3011.7700000000004 PASS DP=151;AC=2;AN=4;AF=0.5;MQ0=0;ALERT;BaseQRankSum=-1.0005;Dels=0.0;FS=3.815;HaplotypeScore=91.2287;MLEAC=1;MLEAF=0.5;MQ=51.205;MQRankSum=-4.246;QD=17.81;ReadPosRankSum=4.676;SOR=1.2495;ClippingRankSum=-1.365 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:5,34:39:33.0:1178,0,33:34:87:39:1:.:.:.:.:.:-0.0106314 0/1:62,142:204:99.0:4902,0,1915:142:70:204:.:1:.:.:.:.:-0.02803
+chr21 36410910 . C G 3943.75 PASS DP=151;AC=3;AN=4;AF=0.75;MQ0=0;ALERT;BaseQRankSum=1.291;Dels=0.0;FS=3.7045;HaplotypeScore=88.3292;MLEAC=1;MLEAF=0.75;MQ=51.225;MQRankSum=-2.836;QD=25.625;ReadPosRankSum=3.8925;SOR=1.147;ClippingRankSum=-0.908 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:1,59:60:99.0:2369,169,0:59:98:60:1:.:.:.:.:.:-0.0106314 0/1:51,156:207:99.0:5584,0,1311:156:75:207:.:1:.:.:.:.:-0.02803
+chr21 36410948 . T TAG 472.556 REJECT NS=2;DP=272;DPB=374.87;AC=2;AN=3;AF=0.25;RO=169;AO=31;PRO=75.1667;PAO=75.1667;QR=6259;QA=983;PQR=2550.5;PQA=2550.5;SRF=83;SRR=86;SAF=14;SAR=17;SRP=3.12594;SAP=3.64073;AB=0.113971;ABP=355.076;RUN=1;RPP=28.2974;RPPR=3.12594;RPL=6.0;RPR=25.0;EPP=3.08035;EPPR=17.0028;DPRA=0.0;ODDS=30.0072;GTI=0;TYPE=ins;CIGAR=1M2I22M;NUMALT=2;MEANALT=12.5;LEN=2;MQM=56.2258;MQMR=57.2781;PAIRED=1.0;PAIREDR=0.994083;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.8 [...]
+chr21 36410948 . TAG T 472.556 REJECT NS=2;DP=272;DPB=374.87;AC=2;AN=3;AF=0.25;RO=169;AO=38;PRO=75.1667;PAO=66.6667;QR=6259;QA=1183;PQR=2550.5;PQA=2247.0;SRF=83;SRR=86;SAF=14;SAR=24;SRP=3.12594;SAP=8.7247;AB=0.139706;ABP=309.699;RUN=1;RPP=3.9246;RPPR=3.12594;RPL=21.0;RPR=17.0;EPP=6.66752;EPPR=17.0028;DPRA=0.0;ODDS=30.0072;GTI=0;TYPE=del;CIGAR=1M2D20M;NUMALT=2;MEANALT=12.5;LEN=2;MQM=52.5;MQMR=57.2781;PAIRED=1.0;PAIREDR=0.994083;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:Q [...]
+chr21 36411127 . C T 1566.96 REJECT NS=2;DP=347;DPB=396.0;AC=2;AN=4;AF=0.5;RO=309;AO=87;PRO=0.0;PAO=0.0;QR=11760;QA=3336;PQR=0.0;PQA=0.0;SRF=84;SRR=225;SAF=30;SAR=57;SRP=142.722;SAP=21.2057;AB=0.219697;ABP=273.26;RUN=1;RPP=4.23331;RPPR=21.2886;RPL=47.0;RPR=40.0;EPP=18.61;EPPR=6.10939;DPRA=0.0;ODDS=160.011;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.977011;PAIREDR=0.996764;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8655;Dels=0.0;FS=3.347;HaplotypeScore [...]
+chr21 39764211 . T A 917.672 REJECT NS=2;DP=173;DPB=201.0;AC=2;AN=4;AF=0.5;RO=153;AO=48;PRO=0.0;PAO=0.0;QR=5796;QA=1805;PQR=0.0;PQA=0.0;SRF=127;SRR=26;SAF=36;SAR=12;SRP=147.789;SAP=29.068;AB=0.238806;ABP=122.117;RUN=1;RPP=14.5915;RPPR=82.8438;RPL=16.0;RPR=32.0;EPP=5.9056;EPPR=20.3963;DPRA=0.0;ODDS=77.455;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.4455;Dels=0.0;FS=3.8345;HaplotypeScore=1.9972;M [...]
+chr21 39870310 . G A 13849.099999999999 REJECT NS=2;DP=362;DPB=415.0;AC=4;AN=4;AF=1.0;RO=0;AO=415;PRO=0.0;PAO=0.0;QR=0;QA=16036;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=178;SAR=237;SRP=0.0;SAP=21.2245;AB=0.0;ABP=0.0;RUN=1;RPP=42.6148;RPPR=0.0;RPL=251.0;RPR=164.0;EPP=3.14111;EPPR=0.0;DPRA=0.0;ODDS=69.2071;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99759;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.04 [...]
+chr21 40525287 . G A 4921.745000000001 REJECT NS=2;DP=305;DPB=356.0;AC=2;AN=4;AF=0.5;RO=180;AO=176;PRO=0.0;PAO=0.0;QR=6944;QA=6832;PQR=0.0;PQA=0.0;SRF=49;SRR=131;SAF=54;SAR=122;SRP=84.1269;SAP=60.0608;AB=0.494382;ABP=3.10789;RUN=1;RPP=38.9876;RPPR=33.1696;RPL=115.0;RPR=61.0;EPP=7.00778;EPPR=3.20332;DPRA=0.0;ODDS=314.82;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994318;PAIREDR=0.994444;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=2.1295;Dels=0.0;FS=5.1935 [...]
+chr21 42845383 . A G 1291.53 REJECT NS=1;DP=101;DPB=101.0;AC=1;AN=4;AF=0.5;RO=55;AO=46;PRO=0.0;PAO=0.0;QR=2048;QA=1804;PQR=0.0;PQA=0.0;SRF=18;SRR=37;SAF=15;SAR=31;SRP=17.2631;SAP=15.095;AB=0.455446;ABP=4.75178;RUN=1;RPP=3.76559;RPPR=4.94488;RPL=21.0;RPR=25.0;EPP=4.70971;EPPR=3.04978;DPRA=0.0;ODDS=297.385;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.981818;technology.ILLUMINA=1.0;BaseQRankSum=1.073;FS=1.81;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=0 [...]
+chr21 42848560 . CAG C 11771.8 REJECT NS=2;DP=326;DPB=185.75;AC=4;AN=4;AF=1.0;RO=0;AO=365;PRO=6.5;PAO=6.5;QR=0;QA=13229;PQR=176.5;PQA=176.5;SRF=0;SRR=0;SAF=138;SAR=227;SRP=0.0;SAP=50.1342;AB=0.0;ABP=0.0;RUN=1;RPP=16.1522;RPPR=0.0;RPL=206.0;RPR=159.0;EPP=31.3346;EPPR=0.0;DPRA=0.0;ODDS=58.45;GTI=0;TYPE=del;CIGAR=1M2D1M;NUMALT=1;MEANALT=1.0;LEN=2;MQM=60.4384;MQMR=0.0;PAIRED=0.989041;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=42848562;HOMLEN=0;SVLEN=-2;SVTYPE=DEL;FS=0.0;MLEAC=2;MLEAF=1.0; [...]
+chr21 42860307 . C T 9317.895 REJECT NS=2;DP=252;DPB=288.0;AC=4;AN=4;AF=1.0;RO=0;AO=287;PRO=0.0;PAO=0.0;QR=0;QA=10834;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=207;SAR=80;SRP=0.0;SAP=125.044;AB=0.0;ABP=0.0;RUN=1;RPP=50.2304;RPPR=0.0;RPL=104.0;RPR=183.0;EPP=11.2498;EPPR=0.0;DPRA=0.0;ODDS=48.5976;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993031;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.235;SOR=1 [...]
+chr21 42866994 . CA C 1280.02 REJECT NS=2;DP=117;DPB=204.472;AC=2;AN=2;AF=0.25;RO=9;AO=47;PRO=57.7833;PAO=46.7833;QR=324;QA=1459;PQR=2078.95;PQA=1672.45;SRF=5;SRR=4;SAF=29;SAR=18;SRP=3.25157;SAP=8.60069;AB=0.401709;ABP=12.8283;RUN=1;RPP=36.6912;RPPR=14.8328;RPL=10.0;RPR=37.0;EPP=3.42611;EPPR=5.18177;DPRA=0.0;ODDS=10.1092;GTI=0;TYPE=del;CIGAR=1M1D34M;NUMALT=4;MEANALT=16.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.978723;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.07 [...]
+chr21 42866994 . CAA C 1280.02 REJECT NS=2;DP=117;DPB=204.472;AC=2;AN=3;AF=0.5;RO=9;AO=26;PRO=57.7833;PAO=46.6167;QR=324;QA=832;PQR=2078.95;PQA=1662.95;SRF=5;SRR=4;SAF=20;SAR=6;SRP=3.25157;SAP=19.3799;AB=0.222222;ABP=81.4246;RUN=1;RPP=15.0369;RPPR=14.8328;RPL=7.0;RPR=19.0;EPP=3.0103;EPPR=5.18177;DPRA=0.0;ODDS=10.1092;GTI=0;TYPE=del;CIGAR=1M2D33M;NUMALT=4;MEANALT=16.5;LEN=2;MQM=60.3846;MQMR=60.0;PAIRED=0.961538;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.19 [...]
+chr21 42866994 . CAAA C 1280.02 REJECT NS=2;DP=117;DPB=204.472;AC=1;AN=3;AF=0.0;RO=9;AO=7;PRO=57.7833;PAO=44.2;QR=324;QA=220;PQR=2078.95;PQA=1579.45;SRF=5;SRR=4;SAF=6;SAR=1;SRP=3.25157;SAP=10.7656;AB=0.0598291;ABP=199.909;RUN=1;RPP=3.32051;RPPR=14.8328;RPL=3.0;RPR=4.0;EPP=3.32051;EPPR=5.18177;DPRA=0.0;ODDS=10.1092;GTI=0;TYPE=del;CIGAR=1M3D32M;NUMALT=4;MEANALT=16.5;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr21 42867010 . AGTAATAGAAAAGAAGAGGT GTAATAGAAAAGAAGAGGA 1280.02 REJECT NS=2;DP=117;DPB=204.472;AC=1;AN=3;AF=0.0;RO=9;AO=3;PRO=57.7833;PAO=8.61667;QR=324;QA=48;PQR=2078.95;PQA=314.2;SRF=5;SRR=4;SAF=3;SAR=0;SRP=3.25157;SAP=9.52472;AB=0.025641;ABP=231.683;RUN=1;RPP=3.73412;RPPR=14.8328;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=5.18177;DPRA=0.0;ODDS=10.1092;GTI=0;TYPE=complex;CIGAR=1M1D33M1X;NUMALT=4;MEANALT=16.5;LEN=35;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALL [...]
+chr21 42867553 . C CA 334.181 REJECT NS=2;DP=101;DPB=167.44;AC=2;AN=3;AF=0.25;RO=19;AO=15;PRO=37.4833;PAO=33.9833;QR=660;QA=486;PQR=1308.95;PQA=1157.95;SRF=14;SRR=5;SAF=13;SAR=2;SRP=12.2676;SAP=20.5268;AB=0.148515;ABP=111.39;RUN=1;RPP=14.7363;RPPR=36.0395;RPL=3.0;RPR=12.0;EPP=14.7363;EPPR=16.8392;DPRA=0.0;ODDS=17.4211;GTI=0;TYPE=ins;CIGAR=1M1I24M;NUMALT=4;MEANALT=17.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.762;FS=3.522;MLE [...]
+chr21 42867553 . CA C 334.181 REJECT NS=2;DP=101;DPB=167.44;AC=2;AN=3;AF=0.25;RO=19;AO=27;PRO=37.4833;PAO=23.3167;QR=660;QA=775;PQR=1308.95;PQA=799.617;SRF=14;SRR=5;SAF=20;SAR=7;SRP=12.2676;SAP=16.6021;AB=0.267327;ABP=50.5032;RUN=1;RPP=9.52472;RPPR=36.0395;RPL=9.0;RPR=18.0;EPP=6.95112;EPPR=16.8392;DPRA=0.0;ODDS=17.4211;GTI=0;TYPE=del;CIGAR=1M1D23M;NUMALT=4;MEANALT=17.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.37;FS=1.5 [...]
+chr21 42867553 . CAA C 334.181 REJECT NS=2;DP=101;DPB=167.44;AC=2;AN=2;AF=0.0;RO=19;AO=4;PRO=37.4833;PAO=22.15;QR=660;QA=78;PQR=1308.95;PQA=756.45;SRF=14;SRR=5;SAF=2;SAR=2;SRP=12.2676;SAP=3.0103;AB=0.039604;ABP=188.961;RUN=1;RPP=3.0103;RPPR=36.0395;RPL=2.0;RPR=2.0;EPP=3.0103;EPPR=16.8392;DPRA=0.0;ODDS=17.4211;GTI=0;TYPE=del;CIGAR=1M2D22M;NUMALT=4;MEANALT=17.5;LEN=2;MQM=51.75;MQMR=60.0;PAIRED=0.75;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF: [...]
+chr21 42867569 . AC A 334.181 REJECT NS=2;DP=101;DPB=167.44;AC=2;AN=2;AF=0.0;RO=19;AO=4;PRO=37.4833;PAO=22.0667;QR=660;QA=44;PQR=1308.95;PQA=762.033;SRF=14;SRR=5;SAF=4;SAR=0;SRP=12.2676;SAP=11.6962;AB=0.0506329;ABP=141.572;RUN=1;RPP=11.6962;RPPR=36.0395;RPL=4.0;RPR=0.0;EPP=11.6962;EPPR=16.8392;DPRA=0.0;ODDS=17.4211;GTI=0;TYPE=del;CIGAR=17M1D7M;NUMALT=4;MEANALT=27.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr21 42867842 . T TA 533.3620000000001 REJECT NS=2;DP=302;DPB=392.9;AC=2;AN=4;AF=0.5;RO=158;AO=46;PRO=50.8333;PAO=41.3333;QR=5761;QA=1454;PQR=1749.5;PQA=1412.0;SRF=77;SRR=81;SAF=23;SAR=23;SRP=3.2302;SAP=3.0103;AB=0.149837;ABP=329.969;RUN=1;RPP=12.2627;RPPR=18.8978;RPL=16.0;RPR=30.0;EPP=15.095;EPPR=29.6177;DPRA=0.0;ODDS=18.4627;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=3;MEANALT=19.0;LEN=1;MQM=60.4348;MQMR=59.9557;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRank [...]
+chr21 42867842 . T TAA 706.994 REJECT NS=2;DP=307;DPB=392.9;AC=2;AN=2;AF=0.0;RO=158;AO=17;PRO=50.8333;PAO=41.3333;QR=5761;QA=486;PQR=1749.5;PQA=1412.0;SRF=77;SRR=81;SAF=8;SAR=9;SRP=3.2302;SAP=3.13803;AB=0.0553746;ABP=530.169;RUN=1;RPP=4.1599;RPPR=18.8978;RPL=7.0;RPR=10.0;EPP=3.13803;EPPR=29.6177;DPRA=0.0;ODDS=18.4627;GTI=0;TYPE=ins;CIGAR=1M2I19M;NUMALT=3;MEANALT=19.0;LEN=2;MQM=60.0;MQMR=59.9557;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr21 42867842 . TA T 706.994 REJECT NS=2;DP=307;DPB=392.9;AC=2;AN=2;AF=0.0;RO=158;AO=35;PRO=50.8333;PAO=33.5;QR=5761;QA=1166;PQR=1749.5;PQA=1134.5;SRF=77;SRR=81;SAF=12;SAR=23;SRP=3.2302;SAP=10.5174;AB=0.114007;ABP=400.305;RUN=1;RPP=3.56868;RPPR=18.8978;RPL=19.0;RPR=16.0;EPP=3.07234;EPPR=29.6177;DPRA=0.0;ODDS=18.4627;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=3;MEANALT=19.0;LEN=1;MQM=60.0;MQMR=59.9557;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr21 42868206 . T C 3300.06 PASS SOMATIC;NS=2;DP=463;DPB=463.0;AC=1;AN=3;AF=0.25;RO=337;AO=126;PRO=0.0;PAO=0.0;QR=12985;QA=4757;PQR=0.0;PQA=0.0;SRF=157;SRR=180;SAF=66;SAR=60;SRP=6.41893;SAP=3.63072;AB=0.369501;ABP=53.4509;RUN=1;RPP=3.63072;RPPR=3.06829;RPL=66.0;RPR=60.0;EPP=3.63072;EPPR=10.9036;DPRA=2.79508;ODDS=77.1136;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997033;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.451;Dels=0.0;FS=6. [...]
+chr21 42868876 . G A 543.1904999999999 REJECT NS=2;DP=77;DPB=93.0;AC=2;AN=4;AF=0.5;RO=55;AO=35;PRO=0.0;PAO=0.0;QR=1769;QA=1015;PQR=0.0;PQA=0.0;SRF=22;SRR=33;SAF=16;SAR=19;SRP=7.78754;SAP=3.56868;AB=0.376344;ABP=15.362;RUN=1;RPP=3.07234;RPPR=3.99733;RPL=18.0;RPR=17.0;EPP=4.56135;EPPR=3.99733;DPRA=0.0;ODDS=48.6446;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=59.8;MQMR=59.8182;PAIRED=1.0;PAIREDR=0.981818;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.2215;Dels=0.0;FS=1.3555;Haploty [...]
+chr21 42868888 . C T 1294.21 REJECT NS=2;DP=71;DPB=87.3333;AC=2;AN=4;AF=0.5;RO=32;AO=50;PRO=5.0;PAO=1.0;QR=971;QA=1676;PQR=53.5;PQA=21.5;SRF=15;SRR=17;SAF=22;SAR=28;SRP=3.28173;SAP=4.57376;AB=0.588235;ABP=8.75832;RUN=1;RPP=3.18402;RPPR=4.09604;RPL=26.0;RPR=24.0;EPP=3.18402;EPPR=16.3106;DPRA=0.0;ODDS=44.9581;GTI=0;TYPE=snp;CIGAR=2M1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=58.6562;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.6285;Dels=0.0;FS=0.511;HaplotypeScore=12 [...]
+chr21 42868997 . A C 675.967 REJECT NS=2;DP=124;DPB=143.0;AC=2;AN=4;AF=0.5;RO=106;AO=37;PRO=0.0;PAO=0.0;QR=3927;QA=1405;PQR=0.0;PQA=0.0;SRF=98;SRR=8;SAF=36;SAR=1;SRP=168.944;SAP=74.9036;AB=0.258741;ABP=75.3067;RUN=1;RPP=12.9286;RPPR=7.02548;RPL=12.0;RPR=25.0;EPP=16.2152;EPPR=9.64763;DPRA=0.0;ODDS=65.4713;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.8396;PAIRED=0.972973;PAIREDR=0.990566;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.6385;Dels=0.0;FS=0.0;HaplotypeScor [...]
+chr21 42869063 . A G 6584.705 REJECT NS=2;DP=181;DPB=209.0;AC=4;AN=4;AF=1.0;RO=0;AO=209;PRO=0.0;PAO=0.0;QR=0;QA=7822;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=172;SAR=37;SRP=0.0;SAP=192.365;AB=0.0;ABP=0.0;RUN=1;RPP=22.2211;RPPR=0.0;RPL=83.0;RPR=126.0;EPP=5.34801;EPPR=0.0;DPRA=0.0;ODDS=37.4092;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.985646;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.875;SOR=2.848 [...]
+chr21 42871273 . T C 6523.33 REJECT NS=2;DP=414;DPB=476.0;AC=2;AN=4;AF=0.5;RO=238;AO=238;PRO=0.0;PAO=0.0;QR=9252;QA=9070;PQR=0.0;PQA=0.0;SRF=93;SRR=145;SAF=96;SAR=142;SRP=27.6811;SAP=22.3163;AB=0.5;ABP=3.0103;RUN=1;RPP=5.96642;RPPR=3.33876;RPL=128.0;RPR=110.0;EPP=3.92268;EPPR=31.6226;DPRA=0.0;ODDS=385.938;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.7983;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995798;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3465;Dels=0.0;FS=0.731;HaplotypeScore= [...]
+chr21 42871545 . A AT 2036.93 REJECT NS=2;DP=398;DPB=442.778;AC=2;AN=4;AF=0.5;RO=295;AO=97;PRO=39.5;PAO=34.5;QR=11125;QA=3499;PQR=1287.0;PQA=1143.0;SRF=160;SRR=135;SAF=50;SAR=47;SRP=7.61088;SAP=3.21178;AB=0.243719;ABP=230.066;RUN=1;RPP=5.71904;RPPR=11.0263;RPL=43.0;RPR=54.0;EPP=9.47994;EPPR=10.0841;DPRA=0.0;ODDS=134.561;GTI=0;TYPE=ins;CIGAR=1M1I8M;NUMALT=1;MEANALT=3.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989691;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.506;FS=1.625;MLEAC=1;MLEAF=0 [...]
+chr21 42871941 . G C 13330.1 REJECT NS=2;DP=358;DPB=396.0;AC=4;AN=4;AF=1.0;RO=0;AO=395;PRO=0.0;PAO=0.0;QR=0;QA=14906;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=159;SAR=236;SRP=0.0;SAP=35.6044;AB=0.0;ABP=0.0;RUN=1;RPP=6.44617;RPPR=0.0;RPL=210.0;RPR=185.0;EPP=4.59905;EPPR=0.0;DPRA=0.0;ODDS=51.6625;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=4.857;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.66;SOR=1.171 GT [...]
+chr21 42872897 . G C 15662.599999999999 REJECT NS=2;DP=423;DPB=481.0;AC=4;AN=4;AF=1.0;RO=0;AO=479;PRO=0.0;PAO=0.0;QR=0;QA=17905;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=247;SAR=232;SRP=0.0;SAP=4.0303;AB=0.0;ABP=0.0;RUN=1;RPP=3.01483;RPPR=0.0;RPL=239.0;RPR=240.0;EPP=5.84364;EPPR=0.0;DPRA=0.0;ODDS=75.2645;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.987474;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.835;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=32. [...]
+chr21 42873550 . AAAAAAAAA G 443.934 REJECT NS=2;DP=25;DPB=92.3673;AC=2;AN=4;AF=0.5;RO=1;AO=9;PRO=109.5;PAO=78.5;QR=37;QA=165;PQR=3722.0;PQA=2554.0;SRF=0;SRR=1;SAF=6;SAR=3;SRP=5.18177;SAP=5.18177;AB=0.36;ABP=7.26639;RUN=1;RPP=5.18177;RPPR=5.18177;RPL=3.0;RPR=6.0;EPP=5.18177;EPPR=5.18177;DPRA=0.0;ODDS=25.8644;GTI=0;TYPE=complex;CIGAR=1M8D14M1X25M;NUMALT=1;MEANALT=8.5;LEN=41;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallH [...]
+chr21 42873558 . A G 445.27 PASS DP=52;AC=2;AN=4;AF=0.5;MQ0=0;BaseQRankSum=-1.823;Dels=0.02;FS=6.0775;HaplotypeScore=49.187;MLEAC=1;MLEAF=0.5;MQ=56.845;MQRankSum=1.185;QD=13.87;ReadPosRankSum=-0.098;SOR=1.5385;ClippingRankSum=-0.331 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/1:4,16:20:55.0:508,0,55:16:80:20:1:.:.:.:.:.:-0.0106314 0/1:59,23:82:99.0:439,0,1902:23:28:82:.:1:.:.:.:.:-0.02803
+chr21 42873605 . G A 2642.76 REJECT NS=2;DP=225;DPB=262.0;AC=2;AN=4;AF=0.5;RO=150;AO=112;PRO=0.0;PAO=0.0;QR=5311;QA=4076;PQR=0.0;PQA=0.0;SRF=108;SRR=42;SAF=88;SAR=24;SRP=66.0699;SAP=82.4241;AB=0.427481;ABP=14.9783;RUN=1;RPP=98.0122;RPPR=48.4085;RPL=21.0;RPR=91.0;EPP=77.5383;EPPR=3.93679;DPRA=0.0;ODDS=122.851;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.2143;MQMR=59.7467;PAIRED=0.928571;PAIREDR=0.993333;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.934;Dels=0.0;FS=7.119;Haplot [...]
+chr21 42875004 . C T 5281.485000000001 REJECT NS=2;DP=368;DPB=424.0;AC=2;AN=4;AF=0.5;RO=224;AO=200;PRO=0.0;PAO=0.0;QR=8379;QA=7464;PQR=0.0;PQA=0.0;SRF=90;SRR=134;SAF=77;SAR=123;SRP=21.778;SAP=25.9845;AB=0.471698;ABP=5.96022;RUN=1;RPP=3.40116;RPPR=6.15118;RPL=97.0;RPR=103.0;EPP=4.57376;EPPR=4.91034;DPRA=0.0;ODDS=346.27;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995;PAIREDR=0.986607;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.405;Dels=0.0;FS=5.3185;Hapl [...]
+chr21 42876400 . C T 5651.115 REJECT NS=2;DP=415;DPB=476.0;AC=2;AN=4;AF=0.5;RO=255;AO=221;PRO=0.0;PAO=0.0;QR=9820;QA=8281;PQR=0.0;PQA=0.0;SRF=134;SRR=121;SAF=115;SAR=106;SRP=4.44943;SAP=3.80618;AB=0.464286;ABP=8.28388;RUN=1;RPP=3.09873;RPPR=3.22319;RPL=109.0;RPR=112.0;EPP=17.9551;EPPR=3.08694;DPRA=0.0;ODDS=343.319;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995475;PAIREDR=0.996078;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.0235;Dels=0.0;FS=0.194;Hapl [...]
+chr21 42877542 . C A 5319.035 REJECT NS=2;DP=342;DPB=396.0;AC=2;AN=4;AF=0.5;RO=202;AO=193;PRO=0.0;PAO=0.0;QR=7752;QA=7384;PQR=0.0;PQA=0.0;SRF=104;SRR=98;SAF=107;SAR=86;SRP=3.3973;SAP=7.97206;AB=0.487374;ABP=3.55865;RUN=1;RPP=4.37169;RPPR=3.0103;RPL=91.0;RPR=102.0;EPP=3.02155;EPPR=11.4382;DPRA=0.0;ODDS=339.564;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994819;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.589;Dels=0.0;FS=2.6895;HaplotypeScore= [...]
+chr21 42878126 . A C 1637.94 REJECT NS=2;DP=401;DPB=459.0;AC=2;AN=4;AF=0.5;RO=372;AO=87;PRO=0.0;PAO=0.0;QR=14293;QA=3274;PQR=0.0;PQA=0.0;SRF=175;SRR=197;SAF=41;SAR=46;SRP=5.83555;SAP=3.63429;AB=0.189542;ABP=387.276;RUN=1;RPP=12.0207;RPPR=6.37258;RPL=53.0;RPR=34.0;EPP=3.23494;EPPR=4.15441;DPRA=0.0;ODDS=49.0098;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.997312;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.837;Dels=0.0;FS=1.9525;HaplotypeScore [...]
+chr21 42879403 . A T 1482.37 PASS SOMATIC;NS=2;DP=270;DPB=270.0;AC=1;AN=3;AF=0.25;RO=209;AO=61;PRO=0.0;PAO=0.0;QR=7835;QA=2247;PQR=0.0;PQA=0.0;SRF=139;SRR=70;SAF=30;SAR=31;SRP=52.4762;SAP=3.0459;AB=0.337017;ABP=44.7722;RUN=1;RPP=3.90025;RPPR=6.01296;RPL=33.0;RPR=28.0;EPP=3.0459;EPPR=6.01296;DPRA=2.03371;ODDS=56.5222;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995215;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.278;Dels=0.0;FS=14.985;H [...]
+chr21 42879604 . C A 4779.58 REJECT NS=2;DP=309;DPB=358.0;AC=2;AN=4;AF=0.5;RO=181;AO=177;PRO=0.0;PAO=0.0;QR=6923;QA=6701;PQR=0.0;PQA=0.0;SRF=89;SRR=92;SAF=75;SAR=102;SRP=3.11827;SAP=11.9538;AB=0.494413;ABP=3.10735;RUN=1;RPP=3.31701;RPPR=6.47746;RPL=91.0;RPR=86.0;EPP=8.42058;EPPR=3.31023;DPRA=0.0;ODDS=308.13;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.6475;Dels=0.0;FS=3.738;HaplotypeScore=8.7986 [...]
+chr21 42879909 . C A 1136.84 REJECT NS=2;DP=84;DPB=100.0;AC=2;AN=4;AF=0.5;RO=54;AO=46;PRO=0.0;PAO=0.0;QR=2081;QA=1666;PQR=0.0;PQA=0.0;SRF=19;SRR=35;SAF=12;SAR=34;SRP=13.3047;SAP=25.858;AB=0.46;ABP=4.40004;RUN=1;RPP=15.095;RPPR=3.6537;RPL=31.0;RPR=15.0;EPP=9.80795;EPPR=10.8919;DPRA=0.0;ODDS=47.2391;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-1.795;Dels=0.0;FS=3.184;HaplotypeScore=1.933;MLEAC=1;MLE [...]
+chr21 45056085 . GAAAGAAAAGA G 3319.47 REJECT NS=2;DP=49;DPB=415.632;AC=2;AN=3;AF=0.5;RO=7;AO=14;PRO=204.333;PAO=191.833;QR=261;QA=490;PQR=7560.92;PQA=7080.92;SRF=7;SRR=0;SAF=14;SAR=0;SRP=18.2106;SAP=33.4109;AB=0.285714;ABP=22.5536;RUN=1;RPP=3.63072;RPPR=3.32051;RPL=8.0;RPR=6.0;EPP=3.63072;EPPR=3.32051;DPRA=0.0;ODDS=23.1436;GTI=0;TYPE=del;CIGAR=1M10D84M;NUMALT=3;MEANALT=4.0;LEN=10;MQM=66.4286;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;END=45056095;HOMLEN=5 [...]
+chr21 45056089 . GAAAAGA AAAAAG 3319.47 REJECT NS=2;DP=49;DPB=415.632;AC=1;AN=3;AF=0.0;RO=7;AO=5;PRO=204.333;PAO=153.167;QR=261;QA=164;PQR=7560.92;PQA=5491.58;SRF=7;SRR=0;SAF=5;SAR=0;SRP=18.2106;SAP=13.8677;AB=0.147059;ABP=39.7976;RUN=1;RPP=3.44459;RPPR=3.32051;RPL=2.0;RPR=3.0;EPP=3.44459;EPPR=3.32051;DPRA=0.0;ODDS=23.1436;GTI=0;TYPE=complex;CIGAR=4M1X5M1D84M;NUMALT=3;MEANALT=7.0;LEN=94;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO: [...]
+chr21 45056149 . GAAAAA G 3319.47 PASS SOMATIC;NS=2;DP=49;DPB=415.632;AC=2;AN=3;AF=0.25;RO=7;AO=19;PRO=204.333;PAO=235.667;QR=261;QA=645;PQR=7560.92;PQA=8119.58;SRF=7;SRR=0;SAF=19;SAR=0;SRP=18.2106;SAP=44.2683;AB=0.558824;ABP=4.03217;RUN=1;RPP=4.03889;RPPR=3.32051;RPL=11.0;RPR=8.0;EPP=4.03889;EPPR=3.32051;DPRA=0.0;ODDS=23.1436;GTI=0;TYPE=del;CIGAR=65M5D25M;NUMALT=3;MEANALT=7.0;LEN=5;MQM=59.1579;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;END=45056154; [...]
+chr22 21337415 . C G 9713.54 REJECT NS=2;DP=260;DPB=291.0;AC=4;AN=4;AF=1.0;RO=0;AO=290;PRO=0.0;PAO=0.0;QR=0;QA=11102;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=92;SAR=198;SRP=0.0;SAP=87.1436;AB=0.0;ABP=0.0;RUN=1;RPP=145.609;RPPR=0.0;RPL=214.0;RPR=76.0;EPP=5.43636;EPPR=0.0;DPRA=0.0;ODDS=42.3625;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.835;SOR=2.286 GT [...]
+chr22 21340088 . T C 3462.87 REJECT NS=2;DP=221;DPB=253.0;AC=2;AN=4;AF=0.5;RO=127;AO=123;PRO=0.0;PAO=0.0;QR=4800;QA=4760;PQR=0.0;PQA=0.0;SRF=90;SRR=37;SAF=79;SAR=44;SRP=51.0392;SAP=24.6368;AB=0.486166;ABP=3.43086;RUN=1;RPP=68.7018;RPPR=29.0167;RPL=31.0;RPR=92.0;EPP=3.16919;EPPR=3.84811;DPRA=0.0;ODDS=189.882;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.633;Dels=0.0;FS=3.981;HaplotypeScore=5.8324;M [...]
+chr22 21343965 . GGAGGAGGTGAGGGGCGTGGGGAGCCAGGGCGCAGGTA G 1600.69 REJECT NS=2;DP=190;DPB=240.103;AC=1;AN=3;AF=0.0;RO=48;AO=51;PRO=71.0;PAO=3.0;QR=1781;QA=1345;PQR=2555.75;PQA=108.75;SRF=13;SRR=35;SAF=16;SAR=35;SRP=24.906;SAP=18.3809;AB=0.268421;ABP=91.5149;RUN=1;RPP=113.755;RPPR=29.068;RPL=0.0;RPR=51.0;EPP=18.3809;EPPR=11.8771;DPRA=0.0;ODDS=1.44437;GTI=0;TYPE=del;CIGAR=1M37D1M;NUMALT=3;MEANALT=6.0;LEN=37;MQM=60.1569;MQMR=60.0;PAIRED=1.0;PAIREDR=0.979167;technology.ILLUMINA=1.0;SPLITMULTI [...]
+chr22 21343995 . CGCAGGTA TGCAGGTG 1600.69 REJECT NS=2;DP=190;DPB=240.103;AC=2;AN=3;AF=0.5;RO=48;AO=55;PRO=71.0;PAO=62.0;QR=1781;QA=1928;PQR=2555.75;PQA=2232.75;SRF=13;SRR=35;SAF=31;SAR=24;SRP=24.906;SAP=4.94488;AB=0.289474;ABP=76.1546;RUN=1;RPP=122.441;RPPR=29.068;RPL=55.0;RPR=0.0;EPP=4.94488;EPPR=11.8771;DPRA=0.0;ODDS=1.44437;GTI=0;TYPE=complex;CIGAR=30M1X6M1X1M;NUMALT=3;MEANALT=6.0;LEN=39;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.979167;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP [...]
+chr22 21344002 . A G 1600.69 PASS SOMATIC;NS=2;DP=190;DPB=240.103;AC=2;AN=2;AF=0.25;RO=48;AO=29;PRO=71.0;PAO=54.0;QR=1781;QA=1082;PQR=2555.75;PQA=1958.75;SRF=13;SRR=35;SAF=11;SAR=18;SRP=24.906;SAP=6.67934;AB=0.211679;ABP=101.931;RUN=1;RPP=57.5966;RPPR=29.068;RPL=28.0;RPR=1.0;EPP=9.07545;EPPR=11.8771;DPRA=0.0;ODDS=1.44437;GTI=0;TYPE=snp;CIGAR=37M1X1M;NUMALT=3;MEANALT=7.0;LEN=1;MQM=59.069;MQMR=60.0;PAIRED=1.0;PAIREDR=0.979167;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:G [...]
+chr22 21346485 . T C 5846.57 REJECT NS=2;DP=223;DPB=262.0;AC=2;AN=4;AF=0.5;RO=64;AO=198;PRO=0.0;PAO=0.0;QR=2404;QA=7558;PQR=0.0;PQA=0.0;SRF=46;SRR=18;SAF=146;SAR=52;SRP=29.6108;SAP=99.915;AB=0.755725;ABP=151.831;RUN=1;RPP=80.3937;RPPR=29.6108;RPL=57.0;RPR=141.0;EPP=7.39711;EPPR=3.0103;DPRA=0.0;ODDS=44.6686;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994949;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.646;Dels=0.0;FS=1.1135;HaplotypeScore=0.0 [...]
+chr22 21400282 . G C 2025.765 REJECT NS=2;DP=351;DPB=405.0;AC=2;AN=4;AF=0.5;RO=309;AO=96;PRO=0.0;PAO=0.0;QR=11730;QA=3710;PQR=0.0;PQA=0.0;SRF=176;SRR=133;SAF=46;SAR=50;SRP=16.004;SAP=3.37221;AB=0.237037;ABP=246.263;RUN=1;RPP=7.44372;RPPR=29.1593;RPL=41.0;RPR=55.0;EPP=10.339;EPPR=6.10939;DPRA=0.0;ODDS=149.747;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996764;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.9785;Dels=0.0;FS=6.7795;HaplotypeScore= [...]
+chr22 21403869 . GG AA 9299.85 REJECT NS=2;DP=286;DPB=317.0;AC=4;AN=4;AF=1.0;RO=0;AO=315;PRO=0.0;PAO=2.0;QR=0;QA=11355;PQR=0.0;PQA=74.0;SRF=0;SRR=0;SAF=219;SAR=96;SRP=0.0;SAP=107.303;AB=0.0;ABP=0.0;RUN=1;RPP=4.56135;RPPR=0.0;RPL=150.0;RPR=165.0;EPP=48.239;EPPR=0.0;DPRA=0.0;ODDS=47.8254;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=1;MEANALT=1.5;LEN=2;MQM=44.4889;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=12;JOINED;Dels=0.0;FS=0.0;HaplotypeScore=5.8632;MLEAC=2;MLEAF=1.0;MQ=46.76;QD=27.2 [...]
+chr22 21403912 . G T 12458.9 REJECT NS=2;DP=364;DPB=398.0;AC=4;AN=4;AF=1.0;RO=0;AO=398;PRO=0.0;PAO=0.0;QR=0;QA=15238;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=230;SAR=168;SRP=0.0;SAP=23.983;AB=0.0;ABP=0.0;RUN=1;RPP=25.3579;RPPR=0.0;RPL=167.0;RPR=231.0;EPP=3.79596;EPPR=0.0;DPRA=0.0;ODDS=54.0512;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=42.5729;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=13;Dels=0.0;FS=0.0;HaplotypeScore=4.8634;MLEAC=2;MLEAF=1.0;MQ=43.71;QD=27.97;SOR=1.1 [...]
+chr22 21403971 . C A 15621.2 REJECT NS=2;DP=421;DPB=469.0;AC=4;AN=4;AF=1.0;RO=0;AO=468;PRO=0.0;PAO=0.0;QR=0;QA=17903;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=262;SAR=206;SRP=0.0;SAP=17.561;AB=0.0;ABP=0.0;RUN=1;RPP=3.02886;RPPR=0.0;RPL=233.0;RPR=235.0;EPP=3.47429;EPPR=0.0;DPRA=0.0;ODDS=62.1767;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=53.1068;MQMR=0.0;PAIRED=0.99359;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=9.7984;MLEAC=2;MLEAF=1.0;MQ=54.02;QD=33.0;SOR=1 [...]
+chr22 21404113 . A G 2126.54 REJECT NS=2;DP=355;DPB=411.0;AC=2;AN=4;AF=0.5;RO=311;AO=100;PRO=0.0;PAO=0.0;QR=12040;QA=3862;PQR=0.0;PQA=0.0;SRF=140;SRR=171;SAF=39;SAR=61;SRP=9.72022;SAP=13.5202;AB=0.243309;ABP=238.232;RUN=1;RPP=13.5202;RPPR=13.6303;RPL=61.0;RPR=39.0;EPP=6.13722;EPPR=28.9912;DPRA=0.0;ODDS=151.365;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.5035;Dels=0.0;FS=2.7055;HaplotypeScore=4.8 [...]
+chr22 24029646 . T G 6712.0650000000005 REJECT NS=2;DP=393;DPB=448.0;AC=2;AN=4;AF=0.5;RO=215;AO=233;PRO=0.0;PAO=0.0;QR=7953;QA=8950;PQR=0.0;PQA=0.0;SRF=100;SRR=115;SAF=113;SAR=120;SRP=5.28277;SAP=3.46696;AB=0.520089;ABP=4.58074;RUN=1;RPP=14.4268;RPPR=4.71718;RPL=134.0;RPR=99.0;EPP=14.4268;EPPR=15.3826;DPRA=0.0;ODDS=341.204;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995708;PAIREDR=0.995349;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.8375;Dels=0.0;FS=1. [...]
+chr22 24030367 . A G 8828.12 REJECT NS=2;DP=358;DPB=413.0;AC=2;AN=4;AF=0.5;RO=119;AO=294;PRO=0.0;PAO=0.0;QR=4470;QA=11149;PQR=0.0;PQA=0.0;SRF=53;SRR=66;SAF=139;SAR=155;SRP=6.09416;SAP=4.90111;AB=0.711864;ABP=164.03;RUN=1;RPP=6.5851;RPPR=6.09416;RPL=136.0;RPR=158.0;EPP=17.3095;EPPR=7.11603;DPRA=0.0;ODDS=222.004;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989796;PAIREDR=0.991597;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.031;Dels=0.0;FS=6.191;Haplotype [...]
+chr22 24030799 . T C 10507.8 REJECT NS=2;DP=364;DPB=413.0;AC=2;AN=4;AF=0.5;RO=71;AO=342;PRO=0.0;PAO=0.0;QR=2693;QA=13001;PQR=0.0;PQA=0.0;SRF=43;SRR=28;SAF=182;SAR=160;SRP=9.89173;SAP=6.08338;AB=0.828087;ABP=389.149;RUN=1;RPP=3.64523;RPPR=14.0512;RPL=166.0;RPR=176.0;EPP=4.25477;EPPR=3.04088;DPRA=0.0;ODDS=45.7636;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.1825;Dels=0.0;FS=1.6355;HaplotypeScore=7. [...]
+chr22 24031712 . G T 5883.085 REJECT NS=2;DP=364;DPB=420.0;AC=2;AN=4;AF=0.5;RO=204;AO=216;PRO=0.0;PAO=0.0;QR=7888;QA=8184;PQR=0.0;PQA=0.0;SRF=80;SRR=124;SAF=103;SAR=113;SRP=23.618;SAP=4.01561;AB=0.514286;ABP=3.7548;RUN=1;RPP=5.5839;RPPR=12.5903;RPL=100.0;RPR=116.0;EPP=3.05051;EPPR=12.5903;DPRA=0.0;ODDS=311.488;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.99537;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3535;Dels=0.0;FS=6.188;HaplotypeScore [...]
+chr22 24143502 . C G 11464.05 REJECT NS=2;DP=307;DPB=355.0;AC=4;AN=4;AF=1.0;RO=0;AO=355;PRO=0.0;PAO=0.0;QR=0;QA=13378;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=157;SAR=198;SRP=0.0;SAP=13.2927;AB=0.0;ABP=0.0;RUN=1;RPP=20.1925;RPPR=0.0;RPL=204.0;RPR=151.0;EPP=3.50576;EPPR=0.0;DPRA=0.0;ODDS=63.5606;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.994366;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=7.7642;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=26.7;SOR=0. [...]
+chr22 24270585 . G A 11474.349999999999 REJECT NS=2;DP=304;DPB=352.0;AC=4;AN=4;AF=1.0;RO=0;AO=352;PRO=0.0;PAO=0.0;QR=0;QA=13424;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=214;SAR=138;SRP=0.0;SAP=38.6422;AB=0.0;ABP=0.0;RUN=1;RPP=31.5356;RPPR=0.0;RPL=142.0;RPR=210.0;EPP=11.0053;EPPR=0.0;DPRA=0.0;ODDS=63.5819;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997159;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.8799;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=2 [...]
+chr22 24270732 . GG CA 12515.55 REJECT NS=2;DP=327;DPB=375.0;AC=4;AN=4;AF=1.0;RO=0;AO=370;PRO=0.0;PAO=10.0;QR=0;QA=13990;PQR=0.0;PQA=360.0;SRF=0;SRR=0;SAF=162;SAR=208;SRP=0.0;SAP=15.4288;AB=0.0;ABP=0.0;RUN=1;RPP=11.4849;RPPR=0.0;RPL=204.0;RPR=166.0;EPP=4.16059;EPPR=0.0;DPRA=0.0;ODDS=61.694;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=1;MEANALT=1.0;LEN=2;MQM=59.9135;MQMR=0.0;PAIRED=0.994595;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;JOINED;Dels=0.0;FS=0.0;HaplotypeScore=5.8966;MLEAC=2;MLEAF=1.0;MQ=59.96 [...]
+chr22 24270777 . C T 11367.55 REJECT NS=2;DP=303;DPB=345.0;AC=4;AN=4;AF=1.0;RO=1;AO=344;PRO=0.0;PAO=0.0;QR=16;QA=13129;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=109;SAR=235;SRP=5.18177;SAP=103.226;AB=0.0;ABP=0.0;RUN=1;RPP=9.47422;RPPR=5.18177;RPL=188.0;RPR=156.0;EPP=18.7913;EPPR=5.18177;DPRA=0.0;ODDS=54.908;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997093;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.69;Dels=0.0;FS=0.0;HaplotypeScore=2.8995;MLEAC=2;M [...]
+chr22 24273325 . TG T 16242.0 REJECT NS=2;DP=445;DPB=414.2;AC=4;AN=4;AF=1.0;RO=0;AO=499;PRO=14.0;PAO=19.0;QR=0;QA=18287;PQR=439.0;PQA=622.0;SRF=0;SRR=0;SAF=274;SAR=225;SRP=0.0;SAP=13.4586;AB=0.0;ABP=0.0;RUN=1;RPP=3.74573;RPPR=0.0;RPL=243.0;RPR=256.0;EPP=43.955;EPPR=0.0;DPRA=0.0;ODDS=84.1161;GTI=0;TYPE=del;CIGAR=1M1D3M;NUMALT=1;MEANALT=2.5;LEN=1;MQM=60.1583;MQMR=0.0;PAIRED=0.991984;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=24273326;HOMLEN=1;HOMSEQ=G;SVLEN=-1;SVTYPE=DEL;FS=0.0;MLEAC=2; [...]
+chr22 29669693 . T C 4707.42 REJECT NS=2;DP=185;DPB=211.0;AC=2;AN=4;AF=0.5;RO=50;AO=161;PRO=0.0;PAO=0.0;QR=1829;QA=6173;PQR=0.0;PQA=0.0;SRF=36;SRR=14;SAF=105;SAR=56;SRP=24.0302;SAP=35.3936;AB=0.763033;ABP=129.81;RUN=1;RPP=169.189;RPPR=47.4821;RPL=25.0;RPR=136.0;EPP=10.1451;EPPR=5.78978;DPRA=0.0;ODDS=97.1079;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.102;Dels=0.0;FS=3.8395;HaplotypeScore=1.933;M [...]
+chr22 29674493 . TG T 4257.2 REJECT NS=2;DP=133;DPB=134.143;AC=4;AN=4;AF=1.0;RO=0;AO=145;PRO=8.5;PAO=12.5;QR=0;QA=5183;PQR=299.5;PQA=422.5;SRF=0;SRR=0;SAF=2;SAR=143;SRP=0.0;SAP=300.742;AB=0.0;ABP=0.0;RUN=1;RPP=51.6663;RPPR=0.0;RPL=101.0;RPR=44.0;EPP=51.6663;EPPR=0.0;DPRA=0.0;ODDS=28.5628;GTI=0;TYPE=del;CIGAR=1M1D5M;NUMALT=1;MEANALT=1.5;LEN=1;MQM=59.7793;MQMR=0.0;PAIRED=0.993103;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.035;QD=31.645;RPA=3,2;RU=G;SOR=7.291;S [...]
+chr22 29674528 . T A 3357.09 REJECT NS=2;DP=103;DPB=116.0;AC=4;AN=4;AF=1.0;RO=0;AO=116;PRO=0.0;PAO=0.0;QR=0;QA=4202;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=3;SAR=113;SRP=0.0;SAP=229.517;AB=0.0;ABP=0.0;RUN=1;RPP=32.9616;RPPR=0.0;RPL=78.0;RPR=38.0;EPP=36.0317;EPPR=0.0;DPRA=0.0;ODDS=19.6333;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.0948;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=2.8936;MLEAC=2;MLEAF=1.0;MQ=58.975;QD=29.975;SOR=6.6495 [...]
+chr22 29674534 . G C 3043.77 PASS SOMATIC;DP=73;AC=2;AN=4;AF=1.0;MQ0=0;ALERT;Dels=0.0;FS=0.0;HaplotypeScore=2.9108;MLEAC=2;MLEAF=1.0;MQ=57.83;QD=34.48;SOR=6.358 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0124524 1/1:0,73:73:99.0:3072,217,0:73:100:73:.:1:.:.:.:.:-0.068504
+chr22 29674534 . GG CA 2521.9 REJECT NS=2;DP=89;DPB=89.5;AC=4;AN=4;AF=1.0;RO=0;AO=89;PRO=0.0;PAO=1.0;QR=0;QA=3101;PQR=0.0;PQA=35.0;SRF=0;SRR=0;SAF=3;SAR=86;SRP=0.0;SAP=171.092;AB=0.0;ABP=0.0;RUN=1;RPP=10.0615;RPPR=0.0;RPL=53.0;RPR=36.0;EPP=11.8182;EPPR=0.0;DPRA=0.0;ODDS=13.988;GTI=0;TYPE=mnp;CIGAR=2X;NUMALT=1;MEANALT=1.0;LEN=2;MQM=56.8539;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;JOINED;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=56.5;QD=32.45;SOR=4.892 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chr22 29674535 . G A 2911.77 PASS SOMATIC;DP=73;AC=2;AN=4;AF=1.0;MQ0=0;ALERT;Dels=0.0;FS=0.0;HaplotypeScore=2.8603;MLEAC=2;MLEAF=1.0;MQ=57.83;QD=29.83;SOR=6.358 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:-0.0124524 1/1:0,73:73:99.0:2940,211,0:73:100:73:.:1:.:.:.:.:-0.068504
+chr22 29674813 . C CA 98.5048 REJECT NS=2;DP=70;DPB=98.8148;AC=2;AN=2;AF=0.0;RO=43;AO=4;PRO=21.9167;PAO=19.9167;QR=1511;QA=148;PQR=711.167;PQA=625.167;SRF=41;SRR=2;SAF=4;SAR=0;SRP=79.8198;SAP=11.6962;AB=0.0571429;ABP=122.255;RUN=1;RPP=3.0103;RPPR=9.12072;RPL=2.0;RPR=2.0;EPP=3.0103;EPPR=14.3727;DPRA=0.0;ODDS=10.6593;GTI=0;TYPE=ins;CIGAR=1M1I26M;NUMALT=3;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr22 29674813 . CA C 98.5048 REJECT NS=2;DP=70;DPB=98.8148;AC=2;AN=4;AF=0.5;RO=43;AO=11;PRO=21.9167;PAO=19.9167;QR=1511;QA=354;PQR=711.167;PQA=636.167;SRF=41;SRR=2;SAF=11;SAR=0;SRP=79.8198;SAP=26.8965;AB=0.157143;ABP=74.4828;RUN=1;RPP=12.6832;RPPR=9.12072;RPL=2.0;RPR=9.0;EPP=12.6832;EPPR=14.3727;DPRA=0.0;ODDS=10.6593;GTI=0;TYPE=del;CIGAR=1M1D25M;NUMALT=3;MEANALT=6.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr22 29674827 . T A 98.5048 REJECT NS=2;DP=70;DPB=98.8148;AC=2;AN=2;AF=0.0;RO=43;AO=4;PRO=21.9167;PAO=12.25;QR=1511;QA=76;PQR=711.167;PQA=371.5;SRF=41;SRR=2;SAF=4;SAR=0;SRP=79.8198;SAP=11.6962;AB=0.0784314;ABP=81.7368;RUN=1;RPP=3.0103;RPPR=9.12072;RPL=2.0;RPR=2.0;EPP=3.0103;EPPR=14.3727;DPRA=0.0;ODDS=10.6593;GTI=0;TYPE=snp;CIGAR=14M1X12M;NUMALT=3;MEANALT=9.0;LEN=1;MQM=55.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GM [...]
+chr22 29674983 . C CA 527.915 REJECT NS=2;DP=273;DPB=366.0;AC=2;AN=2;AF=0.0;RO=131;AO=34;PRO=49.6333;PAO=51.1333;QR=4713;QA=1017;PQR=1748.12;PQA=1779.12;SRF=74;SRR=57;SAF=16;SAR=18;SRP=7.8008;SAP=3.26577;AB=0.124542;ABP=337.282;RUN=1;RPP=19.3602;RPPR=42.8096;RPL=9.0;RPR=25.0;EPP=3.0103;EPPR=4.35297;DPRA=0.0;ODDS=7.70733;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=4;MEANALT=19.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMU [...]
+chr22 29674983 . CA C 527.915 REJECT NS=2;DP=273;DPB=366.0;AC=2;AN=4;AF=0.5;RO=131;AO=38;PRO=49.6333;PAO=44.1333;QR=4713;QA=1292;PQR=1748.12;PQA=1556.87;SRF=74;SRR=57;SAF=28;SAR=10;SRP=7.8008;SAP=21.525;AB=0.139194;ABP=311.701;RUN=1;RPP=11.239;RPPR=42.8096;RPL=13.0;RPR=25.0;EPP=3.9246;EPPR=4.35297;DPRA=0.0;ODDS=7.70733;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=4;MEANALT=19.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr22 29674998 . GT AGG 527.915 REJECT NS=2;DP=273;DPB=366.0;AC=2;AN=2;AF=0.0;RO=131;AO=8;PRO=49.6333;PAO=18.3;QR=4713;QA=120;PQR=1748.12;PQA=591.45;SRF=74;SRR=57;SAF=8;SAR=0;SRP=7.8008;SAP=20.3821;AB=0.029304;ABP=528.371;RUN=1;RPP=7.35324;RPPR=42.8096;RPL=2.0;RPR=6.0;EPP=7.35324;EPPR=4.35297;DPRA=0.0;ODDS=7.70733;GTI=0;TYPE=complex;CIGAR=1M1I15M1X7M;NUMALT=4;MEANALT=19.5;LEN=25;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr22 29674999 . T G 527.915 REJECT NS=2;DP=273;DPB=366.0;AC=2;AN=2;AF=0.0;RO=131;AO=18;PRO=49.6333;PAO=23.8;QR=4713;QA=270;PQR=1748.12;PQA=723.45;SRF=74;SRR=57;SAF=18;SAR=0;SRP=7.8008;SAP=42.0968;AB=0.0659341;ABP=449.785;RUN=1;RPP=3.49285;RPPR=42.8096;RPL=10.0;RPR=8.0;EPP=3.49285;EPPR=4.35297;DPRA=0.0;ODDS=7.70733;GTI=0;TYPE=snp;CIGAR=16M1X7M;NUMALT=4;MEANALT=19.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr22 29675401 . A G 14492.8 REJECT NS=2;DP=527;DPB=596.0;AC=2;AN=4;AF=0.5;RO=124;AO=471;PRO=0.0;PAO=0.0;QR=4684;QA=17990;PQR=0.0;PQA=0.0;SRF=54;SRR=70;SAF=253;SAR=218;SRP=7.49334;SAP=8.65797;AB=0.790268;ABP=439.185;RUN=1;RPP=6.8876;RPPR=4.76149;RPL=250.0;RPR=221.0;EPP=4.04763;EPPR=11.486;DPRA=0.0;ODDS=156.445;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997877;PAIREDR=0.991935;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.094;Dels=0.0;FS=2.5495;Haplotype [...]
+chr22 29675936 . T A 12315.6 REJECT NS=2;DP=463;DPB=528.0;AC=2;AN=4;AF=0.5;RO=115;AO=413;PRO=0.0;PAO=0.0;QR=4306;QA=15363;PQR=0.0;PQA=0.0;SRF=51;SRR=64;SAF=200;SAR=213;SRP=6.20142;SAP=3.89887;AB=0.782197;ABP=368.229;RUN=1;RPP=11.0074;RPPR=5.29507;RPL=187.0;RPR=226.0;EPP=3.14175;EPPR=7.25883;DPRA=0.0;ODDS=199.874;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990315;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.7285;Dels=0.0;FS=3.2835;HaplotypeSc [...]
+chr22 29676663 . G T 251.54 REJECT NS=2;DP=205;DPB=295.625;AC=2;AN=2;AF=0.0;RO=114;AO=15;PRO=59.25;PAO=6.5;QR=4008;QA=270;PQR=2124.2;PQA=246.7;SRF=26;SRR=88;SAF=0;SAR=15;SRP=76.2308;SAP=35.5824;AB=0.0731707;ABP=327.407;RUN=1;RPP=3.15506;RPPR=10.6295;RPL=7.0;RPR=8.0;EPP=3.15506;EPPR=10.6295;DPRA=0.0;ODDS=24.269;GTI=0;TYPE=snp;CIGAR=1X23M;NUMALT=4;MEANALT=12.0;LEN=1;MQM=58.8667;MQMR=59.2193;PAIRED=1.0;PAIREDR=0.982456;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr22 29676663 . G GT 251.54 REJECT NS=2;DP=205;DPB=295.625;AC=2;AN=4;AF=0.5;RO=114;AO=27;PRO=59.25;PAO=47.25;QR=4008;QA=663;PQR=2124.2;PQA=1594.2;SRF=26;SRR=88;SAF=9;SAR=18;SRP=76.2308;SAP=9.52472;AB=0.131707;ABP=244.531;RUN=1;RPP=12.7417;RPPR=10.6295;RPL=19.0;RPR=8.0;EPP=6.95112;EPPR=10.6295;DPRA=0.0;ODDS=24.269;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=4;MEANALT=12.0;LEN=1;MQM=59.4074;MQMR=59.2193;PAIRED=0.925926;PAIREDR=0.982456;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=1.187; [...]
+chr22 29676663 . GT G 251.54 REJECT NS=2;DP=205;DPB=295.625;AC=2;AN=2;AF=0.0;RO=114;AO=21;PRO=59.25;PAO=38.25;QR=4008;QA=506;PQR=2124.2;PQA=1345.2;SRF=26;SRR=88;SAF=6;SAR=15;SRP=76.2308;SAP=11.386;AB=0.102439;ABP=284.444;RUN=1;RPP=3.94093;RPPR=10.6295;RPL=9.0;RPR=12.0;EPP=15.5221;EPPR=10.6295;DPRA=0.0;ODDS=24.269;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=4;MEANALT=12.0;LEN=1;MQM=60.0;MQMR=59.2193;PAIRED=0.952381;PAIREDR=0.982456;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chr22 29676663 . GTT G 251.54 REJECT NS=2;DP=205;DPB=295.625;AC=2;AN=2;AF=0.0;RO=114;AO=9;PRO=59.25;PAO=28.75;QR=4008;QA=180;PQR=2124.2;PQA=1041.7;SRF=26;SRR=88;SAF=1;SAR=8;SRP=76.2308;SAP=14.8328;AB=0.0439024;ABP=373.421;RUN=1;RPP=5.18177;RPPR=10.6295;RPL=3.0;RPR=6.0;EPP=9.04217;EPPR=10.6295;DPRA=0.0;ODDS=24.269;GTI=0;TYPE=del;CIGAR=1M2D21M;NUMALT=4;MEANALT=12.0;LEN=2;MQM=60.0;MQMR=59.2193;PAIRED=1.0;PAIREDR=0.982456;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr22 29676695 . T A 3474.8450000000003 REJECT NS=2;DP=180;DPB=215.0;AC=2;AN=4;AF=0.5;RO=45;AO=168;PRO=0.0;PAO=0.0;QR=1539;QA=4866;PQR=0.0;PQA=0.0;SRF=8;SRR=37;SAF=27;SAR=141;SRP=43.5927;SAP=170.989;AB=0.781395;ABP=150.883;RUN=1;RPP=28.0339;RPPR=13.8677;RPL=106.0;RPR=62.0;EPP=4.30284;EPPR=3.05855;DPRA=0.0;ODDS=2.3095;GTI=1;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=59.1786;MQMR=58.6667;PAIRED=0.982143;PAIREDR=0.977778;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.818;Dels=0.0;FS=0. [...]
+chr22 29677352 . G A 69.0039 REJECT SOMATIC;NS=1;DP=3;DPB=3.0;AC=2;AN=4;AF=1.0;RO=0;AO=3;PRO=0.0;PAO=0.0;QR=0;QA=103;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=3;SAR=0;SRP=0.0;SAP=9.52472;AB=0.0;ABP=0.0;RUN=1;RPP=9.52472;RPPR=0.0;RPL=3.0;RPR=0.0;EPP=9.52472;EPPR=0.0;DPRA=0.0;ODDS=6.54477;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=24.87;SOR=2.303 GT:GQ:DP:RO: [...]
+chr22 29677357 . CT C 39.8779 REJECT SOMATIC;NS=1;DP=2;DPB=1.33333;AC=2;AN=4;AF=1.0;RO=0;AO=2;PRO=0.0;PAO=0.0;QR=0;QA=61;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=2;SAR=0;SRP=0.0;SAP=7.35324;AB=0.0;ABP=0.0;RUN=1;RPP=7.35324;RPPR=0.0;RPL=2.0;RPR=0.0;EPP=7.35324;EPPR=0.0;DPRA=0.0;ODDS=5.91987;GTI=0;TYPE=del;CIGAR=1M1D1M;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.0;PAIREDR=0.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR [...]
+chr22 29677746 . T C 2689.01 REJECT NS=2;DP=116;DPB=130.0;AC=2;AN=4;AF=0.5;RO=28;AO=102;PRO=0.0;PAO=0.0;QR=983;QA=3791;PQR=0.0;PQA=0.0;SRF=28;SRR=0;SAF=101;SAR=1;SRP=63.8115;SAP=215.9;AB=0.784615;ABP=94.4794;RUN=1;RPP=22.1704;RPPR=5.80219;RPL=36.0;RPR=66.0;EPP=24.8102;EPPR=5.80219;DPRA=0.0;ODDS=42.5205;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=58.9286;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.135;Dels=0.0;FS=0.0;HaplotypeScore=9.865;MLEAC [...]
+chr22 29678749 . C T 564.18 REJECT NS=2;DP=130;DPB=212.455;AC=2;AN=2;AF=0.0;RO=56;AO=17;PRO=55.1833;PAO=7.08333;QR=1961;QA=328;PQR=1933.27;PQA=215.017;SRF=17;SRR=39;SAF=0;SAR=17;SRP=21.778;SAP=39.9253;AB=0.130769;ABP=156.951;RUN=1;RPP=18.4661;RPPR=21.778;RPL=3.0;RPR=14.0;EPP=18.4661;EPPR=3.63072;DPRA=0.0;ODDS=22.1196;GTI=0;TYPE=snp;CIGAR=1X21M;NUMALT=5;MEANALT=13.0;LEN=1;MQM=58.4118;MQMR=59.25;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr22 29678749 . C CT 564.18 REJECT NS=2;DP=130;DPB=212.455;AC=2;AN=2;AF=0.0;RO=56;AO=12;PRO=55.1833;PAO=30.1833;QR=1961;QA=288;PQR=1933.27;PQA=1045.27;SRF=17;SRR=39;SAF=3;SAR=9;SRP=21.778;SAP=9.52472;AB=0.0923077;ABP=190.692;RUN=1;RPP=3.73412;RPPR=21.778;RPL=5.0;RPR=7.0;EPP=3.0103;EPPR=3.63072;DPRA=0.0;ODDS=22.1196;GTI=0;TYPE=ins;CIGAR=1M1I21M;NUMALT=5;MEANALT=13.0;LEN=1;MQM=59.9167;MQMR=59.25;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr22 29678749 . CT C 564.18 REJECT NS=2;DP=130;DPB=212.455;AC=2;AN=4;AF=0.5;RO=56;AO=17;PRO=55.1833;PAO=31.6833;QR=1961;QA=459;PQR=1933.27;PQA=1094.27;SRF=17;SRR=39;SAF=5;SAR=12;SRP=21.778;SAP=9.26925;AB=0.130769;ABP=156.951;RUN=1;RPP=4.1599;RPPR=21.778;RPL=10.0;RPR=7.0;EPP=4.1599;EPPR=3.63072;DPRA=0.0;ODDS=22.1196;GTI=0;TYPE=del;CIGAR=1M1D20M;NUMALT=5;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=59.25;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr22 29678749 . CTT C 564.18 REJECT NS=2;DP=130;DPB=212.455;AC=2;AN=2;AF=0.0;RO=56;AO=7;PRO=55.1833;PAO=27.4333;QR=1961;QA=157;PQR=1933.27;PQA=951.767;SRF=17;SRR=39;SAF=0;SAR=7;SRP=21.778;SAP=18.2106;AB=0.0538462;ABP=227.774;RUN=1;RPP=10.7656;RPPR=21.778;RPL=6.0;RPR=1.0;EPP=10.7656;EPPR=3.63072;DPRA=0.0;ODDS=22.1196;GTI=0;TYPE=del;CIGAR=1M2D19M;NUMALT=5;MEANALT=13.0;LEN=2;MQM=60.0;MQMR=59.25;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr22 29678764 . T C 564.18 REJECT NS=2;DP=130;DPB=212.455;AC=2;AN=2;AF=0.0;RO=56;AO=3;PRO=55.1833;PAO=27.4333;QR=1961;QA=112;PQR=1933.27;PQA=941.417;SRF=17;SRR=39;SAF=1;SAR=2;SRP=21.778;SAP=3.73412;AB=0.0230769;ABP=259.845;RUN=1;RPP=3.73412;RPPR=21.778;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=3.63072;DPRA=0.0;ODDS=22.1196;GTI=0;TYPE=snp;CIGAR=15M1X6M;NUMALT=5;MEANALT=13.0;LEN=1;MQM=60.0;MQMR=59.25;PAIRED=1.0;PAIREDR=0.964286;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr22 29679683 . AT A 57.0504 REJECT NS=2;DP=4;DPB=6.0;AC=3;AN=3;AF=0.75;RO=0;AO=3;PRO=2.16667;PAO=1.66667;QR=0;QA=106;PQR=75.3333;PQA=56.3333;SRF=0;SRR=0;SAF=0;SAR=3;SRP=0.0;SAP=9.52472;AB=0.666667;ABP=3.73412;RUN=1;RPP=3.73412;RPPR=0.0;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=0.0;DPRA=0.0;ODDS=0.218731;GTI=1;TYPE=del;CIGAR=1M1D23M;NUMALT=2;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.666667;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallH [...]
+chr22 29679703 . A T 57.0504 REJECT NS=2;DP=4;DPB=6.0;AC=1;AN=3;AF=0.25;RO=0;AO=1;PRO=2.16667;PAO=2.16667;QR=0;QA=16;PQR=75.3333;PQA=75.3333;SRF=0;SRR=0;SAF=0;SAR=1;SRP=0.0;SAP=5.18177;AB=0.333333;ABP=3.73412;RUN=1;RPP=5.18177;RPPR=0.0;RPL=1.0;RPR=0.0;EPP=5.18177;EPPR=0.0;DPRA=3.0;ODDS=0.218731;GTI=1;TYPE=snp;CIGAR=20M1X4M;NUMALT=2;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallU [...]
+chr22 29681216 . A G 277.342 REJECT NS=2;DP=46;DPB=54.0;AC=2;AN=4;AF=0.5;RO=40;AO=14;PRO=0.0;PAO=0.0;QR=1503;QA=541;PQR=0.0;PQA=0.0;SRF=38;SRR=2;SAF=12;SAR=2;SRP=73.366;SAP=18.5208;AB=0.259259;ABP=30.1939;RUN=1;RPP=8.59409;RPPR=4.96463;RPL=10.0;RPR=4.0;EPP=3.63072;EPPR=4.96463;DPRA=0.0;ODDS=10.0683;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.95;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.26;Dels=0.0;FS=1.568;HaplotypeScore=1.9157;MLEAC=1;ML [...]
+chr22 29682675 . CA C 186.06 REJECT NS=2;DP=78;DPB=169.868;AC=2;AN=3;AF=0.5;RO=8;AO=5;PRO=51.4583;PAO=50.7917;QR=278;QA=148;PQR=1783.75;PQA=1695.75;SRF=7;SRR=1;SAF=4;SAR=1;SRP=12.7819;SAP=6.91895;AB=0.0641026;ABP=131.74;RUN=1;RPP=3.44459;RPPR=7.35324;RPL=2.0;RPR=3.0;EPP=3.44459;EPPR=4.09604;DPRA=0.0;ODDS=1.52304;GTI=0;TYPE=del;CIGAR=1M1D36M;NUMALT=7;MEANALT=13.5;LEN=1;MQM=60.0;MQMR=54.375;PAIRED=0.8;PAIREDR=0.875;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chr22 29682675 . CAA C 186.06 REJECT SOMATIC;NS=2;DP=78;DPB=169.868;AC=1;AN=3;AF=0.0;RO=8;AO=12;PRO=51.4583;PAO=45.7083;QR=278;QA=324;PQR=1783.75;PQA=1576.5;SRF=7;SRR=1;SAF=10;SAR=2;SRP=12.7819;SAP=14.5915;AB=0.153846;ABP=84.19;RUN=1;RPP=14.5915;RPPR=7.35324;RPL=2.0;RPR=10.0;EPP=14.5915;EPPR=4.09604;DPRA=0.0;ODDS=1.52304;GTI=0;TYPE=del;CIGAR=1M2D35M;NUMALT=7;MEANALT=13.5;LEN=2;MQM=60.0;MQMR=54.375;PAIRED=0.916667;PAIREDR=0.875;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum= [...]
+chr22 29682675 . CAAA C 186.06 REJECT NS=2;DP=78;DPB=169.868;AC=2;AN=2;AF=0.25;RO=8;AO=8;PRO=51.4583;PAO=46.875;QR=278;QA=278;PQR=1783.75;PQA=1614.5;SRF=7;SRR=1;SAF=8;SAR=0;SRP=12.7819;SAP=20.3821;AB=0.102564;ABP=110.025;RUN=1;RPP=7.35324;RPPR=7.35324;RPL=6.0;RPR=2.0;EPP=7.35324;EPPR=4.09604;DPRA=0.0;ODDS=1.52304;GTI=0;TYPE=del;CIGAR=1M3D34M;NUMALT=7;MEANALT=13.5;LEN=3;MQM=59.75;MQMR=54.375;PAIRED=1.0;PAIREDR=0.875;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chr22 29682699 . AAATTTTTTTG TTTTTTTT 186.06 REJECT SOMATIC;NS=2;DP=78;DPB=169.868;AC=1;AN=3;AF=0.0;RO=8;AO=4;PRO=51.4583;PAO=10.7917;QR=278;QA=56;PQR=1783.75;PQA=291.25;SRF=7;SRR=1;SAF=4;SAR=0;SRP=12.7819;SAP=11.6962;AB=0.0666667;ABP=100.871;RUN=1;RPP=3.0103;RPPR=7.35324;RPL=2.0;RPR=2.0;EPP=3.0103;EPPR=4.09604;DPRA=0.0;ODDS=1.52304;GTI=0;TYPE=complex;CIGAR=1M3D30M1X3M;NUMALT=7;MEANALT=19.0;LEN=35;MQM=60.0;MQMR=54.375;PAIRED=1.0;PAIREDR=0.875;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT: [...]
+chr22 29682700 . AATTTTTTTG TTTTTTTT 186.06 REJECT SOMATIC;NS=2;DP=78;DPB=169.868;AC=1;AN=3;AF=0.0;RO=8;AO=8;PRO=51.4583;PAO=12.125;QR=278;QA=113;PQR=1783.75;PQA=326.25;SRF=7;SRR=1;SAF=8;SAR=0;SRP=12.7819;SAP=20.3821;AB=0.102564;ABP=110.025;RUN=1;RPP=3.0103;RPPR=7.35324;RPL=4.0;RPR=4.0;EPP=3.0103;EPPR=4.09604;DPRA=0.0;ODDS=1.52304;GTI=0;TYPE=complex;CIGAR=1M2D31M1X3M;NUMALT=7;MEANALT=13.5;LEN=36;MQM=61.0;MQMR=54.375;PAIRED=1.0;PAIREDR=0.875;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ [...]
+chr22 29682701 . ATTTTTTTG TTTTTTTT 186.06 REJECT SOMATIC;NS=2;DP=78;DPB=169.868;AC=1;AN=3;AF=0.0;RO=8;AO=12;PRO=51.4583;PAO=14.2083;QR=278;QA=162;PQR=1783.75;PQA=374.0;SRF=7;SRR=1;SAF=12;SAR=0;SRP=12.7819;SAP=29.068;AB=0.153846;ABP=84.19;RUN=1;RPP=3.73412;RPPR=7.35324;RPL=5.0;RPR=7.0;EPP=3.73412;EPPR=4.09604;DPRA=0.0;ODDS=1.52304;GTI=0;TYPE=complex;CIGAR=1M1D32M1X3M;NUMALT=7;MEANALT=13.5;LEN=37;MQM=56.0;MQMR=54.375;PAIRED=1.0;PAIREDR=0.875;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ [...]
+chr22 29682701 . ATTTTTTTG TTTTTTTTT 186.06 REJECT SOMATIC;NS=2;DP=78;DPB=169.868;AC=1;AN=3;AF=0.0;RO=8;AO=3;PRO=51.4583;PAO=12.0417;QR=278;QA=44;PQR=1783.75;PQA=334.0;SRF=7;SRR=1;SAF=3;SAR=0;SRP=12.7819;SAP=9.52472;AB=0.05;ABP=108.544;RUN=1;RPP=3.73412;RPPR=7.35324;RPL=1.0;RPR=2.0;EPP=3.73412;EPPR=4.09604;DPRA=0.0;ODDS=1.52304;GTI=0;TYPE=complex;CIGAR=26M1X7M1X3M;NUMALT=7;MEANALT=19.0;LEN=38;MQM=53.3333;MQMR=54.375;PAIRED=1.0;PAIREDR=0.875;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ [...]
+chr22 29682881 . C CT 679.496 REJECT NS=2;DP=329;DPB=512.484;AC=2;AN=2;AF=0.0;RO=208;AO=27;PRO=172.333;PAO=103.333;QR=7521;QA=986;PQR=6192.83;PQA=3713.83;SRF=97;SRR=111;SAF=13;SAR=14;SRP=5.0565;SAP=3.09072;AB=0.0820669;ABP=502.152;RUN=1;RPP=3.73412;RPPR=4.51363;RPL=15.0;RPR=12.0;EPP=5.02092;EPPR=4.05428;DPRA=0.0;ODDS=51.6615;GTI=0;TYPE=ins;CIGAR=1M1I30M;NUMALT=2;MEANALT=21.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990385;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:Q [...]
+chr22 29682881 . CT C 679.496 REJECT NS=2;DP=329;DPB=512.484;AC=2;AN=4;AF=0.5;RO=208;AO=46;PRO=172.333;PAO=99.3333;QR=7521;QA=1637;PQR=6192.83;PQA=3570.33;SRF=97;SRR=111;SAF=21;SAR=25;SRP=5.0565;SAP=3.76559;AB=0.139818;ABP=373.738;RUN=1;RPP=4.70971;RPPR=4.51363;RPL=20.0;RPR=26.0;EPP=15.095;EPPR=4.05428;DPRA=0.0;ODDS=51.6615;GTI=0;TYPE=del;CIGAR=1M1D29M;NUMALT=2;MEANALT=21.0;LEN=1;MQM=60.2174;MQMR=60.0;PAIRED=1.0;PAIREDR=0.990385;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-1.3 [...]
+chr22 29685711 . C T 2564.37 REJECT NS=2;DP=475;DPB=544.0;AC=2;AN=4;AF=0.5;RO=415;AO=128;PRO=0.0;PAO=0.0;QR=15853;QA=4843;PQR=0.0;PQA=0.0;SRF=236;SRR=179;SAF=76;SAR=52;SRP=20.0106;SAP=12.7819;AB=0.235294;ABP=334.096;RUN=1;RPP=3.07816;RPPR=3.26669;RPL=63.0;RPR=65.0;EPP=3.62103;EPPR=3.43413;DPRA=0.0;ODDS=214.126;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992188;PAIREDR=0.99759;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.801;Dels=0.0;FS=2.5565;Haplotype [...]
+chr22 29688751 . C CT 385.769 REJECT NS=2;DP=108;DPB=204.731;AC=2;AN=2;AF=0.0;RO=15;AO=8;PRO=41.9;PAO=38.9;QR=528;QA=215;PQR=1484.93;PQA=1336.93;SRF=4;SRR=11;SAF=2;SAR=6;SRP=10.1038;SAP=7.35324;AB=0.0740741;ABP=173.189;RUN=1;RPP=7.35324;RPPR=14.7363;RPL=6.0;RPR=2.0;EPP=3.0103;EPPR=3.15506;DPRA=0.0;ODDS=2.58624;GTI=0;TYPE=ins;CIGAR=2M1I24M;NUMALT=5;MEANALT=15.5;LEN=1;MQM=60.0;MQMR=54.4;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr22 29688751 . CT C 385.769 REJECT NS=2;DP=108;DPB=204.731;AC=2;AN=4;AF=0.5;RO=15;AO=31;PRO=41.9;PAO=35.9;QR=528;QA=734;PQR=1484.93;PQA=1243.6;SRF=4;SRR=11;SAF=2;SAR=29;SRP=10.1038;SAP=54.0749;AB=0.287037;ABP=45.5551;RUN=1;RPP=23.254;RPPR=14.7363;RPL=24.0;RPR=7.0;EPP=14.8483;EPPR=3.15506;DPRA=0.0;ODDS=2.58624;GTI=0;TYPE=del;CIGAR=2M1D23M;NUMALT=5;MEANALT=15.5;LEN=1;MQM=58.9355;MQMR=54.4;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr22 29688751 . CTT C 385.769 REJECT NS=2;DP=108;DPB=204.731;AC=2;AN=2;AF=0.0;RO=15;AO=13;PRO=41.9;PAO=27.8167;QR=528;QA=343;PQR=1484.93;PQA=967.933;SRF=4;SRR=11;SAF=3;SAR=10;SRP=10.1038;SAP=11.1951;AB=0.12037;ABP=138.205;RUN=1;RPP=23.2217;RPPR=14.7363;RPL=12.0;RPR=1.0;EPP=16.5402;EPPR=3.15506;DPRA=0.0;ODDS=2.58624;GTI=0;TYPE=del;CIGAR=2M2D22M;NUMALT=5;MEANALT=15.5;LEN=2;MQM=60.0;MQMR=54.4;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.921;FS=1.263 [...]
+chr22 29688751 . CTTT C 385.769 REJECT NS=2;DP=108;DPB=204.731;AC=2;AN=2;AF=0.0;RO=15;AO=10;PRO=41.9;PAO=23.3667;QR=528;QA=246;PQR=1484.93;PQA=807.533;SRF=4;SRR=11;SAF=2;SAR=8;SRP=10.1038;SAP=10.8276;AB=0.0925926;ABP=158.713;RUN=1;RPP=10.8276;RPPR=14.7363;RPL=8.0;RPR=2.0;EPP=3.87889;EPPR=3.15506;DPRA=0.0;ODDS=2.58624;GTI=0;TYPE=del;CIGAR=2M3D21M;NUMALT=5;MEANALT=15.5;LEN=3;MQM=59.0;MQMR=54.4;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chr22 29688770 . TG T 385.769 REJECT NS=2;DP=108;DPB=204.731;AC=2;AN=2;AF=0.0;RO=15;AO=6;PRO=41.9;PAO=29.1167;QR=528;QA=48;PQR=1484.93;PQA=1024.07;SRF=4;SRR=11;SAF=6;SAR=0;SRP=10.1038;SAP=16.0391;AB=0.0681818;ABP=145.538;RUN=1;RPP=16.0391;RPPR=14.7363;RPL=6.0;RPR=0.0;EPP=16.0391;EPPR=3.15506;DPRA=0.0;ODDS=2.58624;GTI=0;TYPE=del;CIGAR=21M1D4M;NUMALT=5;MEANALT=23.0;LEN=1;MQM=55.1667;MQMR=54.4;PAIRED=0.833333;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr22 29689837 . A G 730.115 REJECT NS=2;DP=31;DPB=36.0;AC=2;AN=4;AF=0.5;RO=9;AO=27;PRO=0.0;PAO=0.0;QR=321;QA=981;PQR=0.0;PQA=0.0;SRF=2;SRR=7;SAF=15;SAR=12;SRP=9.04217;SAP=3.73412;AB=0.75;ABP=22.5536;RUN=1;RPP=3.73412;RPPR=9.04217;RPL=12.0;RPR=15.0;EPP=12.7417;EPPR=9.04217;DPRA=0.0;ODDS=4.70096;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1895;Dels=0.0;FS=4.67;HaplotypeScore=2.8995;MLEAC=1;MLEAF [...]
+chr22 29689868 . G A 1347.47 REJECT NS=2;DP=38;DPB=43.0;AC=4;AN=4;AF=1.0;RO=0;AO=43;PRO=0.0;PAO=0.0;QR=0;QA=1565;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=29;SAR=14;SRP=0.0;SAP=14.3727;AB=0.0;ABP=0.0;RUN=1;RPP=3.46479;RPPR=0.0;RPL=20.0;RPR=23.0;EPP=29.7245;EPPR=0.0;DPRA=0.0;ODDS=9.97225;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.31;SOR=1.7555 GT:GQ:DP [...]
+chr22 29690345 . T C 1118.95 REJECT NS=2;DP=220;DPB=247.0;AC=2;AN=4;AF=0.5;RO=189;AO=58;PRO=0.0;PAO=0.0;QR=7252;QA=2219;PQR=0.0;PQA=0.0;SRF=27;SRR=162;SAF=7;SAR=51;SRP=212.402;SAP=75.4926;AB=0.234818;ABP=153.879;RUN=1;RPP=5.40641;RPPR=12.6728;RPL=33.0;RPR=25.0;EPP=4.35811;EPPR=10.1911;DPRA=0.0;ODDS=90.8373;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=51.9655;MQMR=57.3651;PAIRED=0.982759;PAIREDR=0.994709;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.5825;Dels=0.0;FS=4.5845;Haplot [...]
+chr22 29690593 . C CA 7.51042 REJECT SOMATIC;NS=2;DP=18;DPB=20.75;AC=1;AN=4;AF=0.25;RO=9;AO=4;PRO=4.5;PAO=4.5;QR=327;QA=82;PQR=152.0;PQA=152.0;SRF=2;SRR=7;SAF=2;SAR=2;SRP=9.04217;SAP=3.0103;AB=0.266667;ABP=10.1038;RUN=1;RPP=5.18177;RPPR=3.25157;RPL=1.0;RPR=3.0;EPP=5.18177;EPPR=9.04217;DPRA=5.0;ODDS=1.35526;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=1;MEANALT=4.0;LEN=1;MQM=50.5;MQMR=59.6667;PAIRED=0.75;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG [...]
+chr22 29690900 . C CA 240.696 REJECT NS=2;DP=136;DPB=179.55;AC=2;AN=3;AF=0.25;RO=87;AO=15;PRO=28.25;PAO=24.25;QR=3195;QA=500;PQR=963.667;PQA=816.667;SRF=56;SRR=31;SAF=11;SAR=4;SRP=18.61;SAP=10.1038;AB=0.110294;ABP=182.412;RUN=1;RPP=6.62942;RPPR=24.0012;RPL=5.0;RPR=10.0;EPP=3.15506;EPPR=10.2236;DPRA=0.0;ODDS=8.22174;GTI=0;TYPE=ins;CIGAR=1M1I19M;NUMALT=3;MEANALT=8.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.977011;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chr22 29690900 . CA C 240.696 REJECT NS=2;DP=136;DPB=179.55;AC=2;AN=3;AF=0.25;RO=87;AO=18;PRO=28.25;PAO=22.25;QR=3195;QA=650;PQR=963.667;PQA=745.667;SRF=56;SRR=31;SAF=16;SAR=2;SRP=18.61;SAP=26.6552;AB=0.132353;ABP=162.677;RUN=1;RPP=10.7311;RPPR=24.0012;RPL=5.0;RPR=13.0;EPP=4.9405;EPPR=10.2236;DPRA=0.0;ODDS=8.22174;GTI=0;TYPE=del;CIGAR=1M1D18M;NUMALT=3;MEANALT=8.0;LEN=1;MQM=60.5556;MQMR=60.0;PAIRED=1.0;PAIREDR=0.977011;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.636;FS=1.983; [...]
+chr22 29690900 . CAA C 240.696 REJECT NS=2;DP=136;DPB=179.55;AC=2;AN=2;AF=0.0;RO=87;AO=5;PRO=28.25;PAO=21.25;QR=3195;QA=180;PQR=963.667;PQA=707.0;SRF=56;SRR=31;SAF=3;SAR=2;SRP=18.61;SAP=3.44459;AB=0.0367647;ABP=256.498;RUN=1;RPP=6.91895;RPPR=24.0012;RPL=1.0;RPR=4.0;EPP=3.44459;EPPR=10.2236;DPRA=0.0;ODDS=8.22174;GTI=0;TYPE=del;CIGAR=1M2D17M;NUMALT=3;MEANALT=8.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.977011;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chr22 29691382 . A T 2100.075 REJECT NS=2;DP=327;DPB=377.0;AC=2;AN=4;AF=0.5;RO=279;AO=97;PRO=0.0;PAO=0.0;QR=10590;QA=3692;PQR=0.0;PQA=0.0;SRF=150;SRR=129;SAF=47;SAR=50;SRP=6.44263;SAP=3.21178;AB=0.257294;ABP=195.903;RUN=1;RPP=3.56996;RPPR=3.01808;RPL=51.0;RPR=46.0;EPP=9.47994;EPPR=12.5445;DPRA=0.0;ODDS=150.29;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989691;PAIREDR=0.989247;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.2045;Dels=0.0;FS=8.1755;Haplotyp [...]
+chr22 29691521 . AG A 17769.550000000003 REJECT NS=2;DP=495;DPB=490.0;AC=4;AN=4;AF=1.0;RO=0;AO=557;PRO=22.5;PAO=25.5;QR=0;QA=20715;PQR=667.5;PQA=774.5;SRF=0;SRR=0;SAF=314;SAR=243;SRP=0.0;SAP=22.6627;AB=0.0;ABP=0.0;RUN=1;RPP=3.32608;RPPR=0.0;RPL=283.0;RPR=274.0;EPP=14.8033;EPPR=0.0;DPRA=0.0;ODDS=94.0223;GTI=0;TYPE=del;CIGAR=1M1D4M;NUMALT=1;MEANALT=3.5;LEN=1;MQM=60.1436;MQMR=0.0;PAIRED=0.991023;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=29691522;HOMLEN=2;HOMSEQ=GG;SVLEN=-1;SVTYPE=DEL;FS [...]
+chr22 29692488 . G T 13346.0 REJECT NS=2;DP=486;DPB=540.0;AC=2;AN=4;AF=0.5;RO=103;AO=437;PRO=0.0;PAO=0.0;QR=3962;QA=16559;PQR=0.0;PQA=0.0;SRF=52;SRR=51;SAF=227;SAR=210;SRP=3.03138;SAP=4.44635;AB=0.809259;ABP=451.604;RUN=1;RPP=14.941;RPPR=3.03138;RPL=243.0;RPR=194.0;EPP=9.81292;EPPR=4.04333;DPRA=0.0;ODDS=51.6049;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995423;PAIREDR=0.990291;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.069;Dels=0.0;FS=0.3715;Haplotyp [...]
+chr22 29692497 . G T 13717.9 REJECT NS=2;DP=494;DPB=551.0;AC=2;AN=4;AF=0.5;RO=107;AO=444;PRO=0.0;PAO=0.0;QR=4135;QA=17000;PQR=0.0;PQA=0.0;SRF=52;SRR=55;SAF=231;SAR=213;SRP=3.19295;SAP=4.59489;AB=0.805808;ABP=450.582;RUN=1;RPP=12.4787;RPPR=3.19295;RPL=244.0;RPR=200.0;EPP=6.31642;EPPR=4.00471;DPRA=0.0;ODDS=64.4009;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.995495;PAIREDR=0.990654;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4895;Dels=0.0;FS=3.4335;Haplot [...]
+chr22 29694312 . G A 601.636 REJECT NS=2;DP=147;DPB=168.0;AC=2;AN=4;AF=0.5;RO=133;AO=35;PRO=0.0;PAO=0.0;QR=5101;QA=1305;PQR=0.0;PQA=0.0;SRF=27;SRR=106;SAF=5;SAR=30;SRP=104.906;SAP=41.7866;AB=0.208333;ABP=127.146;RUN=1;RPP=8.03571;RPPR=7.72876;RPL=22.0;RPR=13.0;EPP=6.05036;EPPR=23.0107;DPRA=0.0;ODDS=22.6098;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=51.6857;MQMR=59.4812;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4375;Dels=0.0;FS=0.6695;HaplotypeScore=0 [...]
+chr22 29694483 . T C 620.041 REJECT NS=2;DP=174;DPB=202.0;AC=2;AN=4;AF=0.5;RO=161;AO=41;PRO=0.0;PAO=0.0;QR=5818;QA=1414;PQR=0.0;PQA=0.0;SRF=140;SRR=21;SAF=36;SAR=5;SRP=194.005;SAP=53.9075;AB=0.20297;ABP=157.808;RUN=1;RPP=3.48696;RPPR=3.34749;RPL=22.0;RPR=19.0;EPP=7.30028;EPPR=6.04497;DPRA=0.0;ODDS=0.485759;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=58.4878;MQMR=59.1925;PAIRED=0.97561;PAIREDR=0.993789;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1705;Dels=0.0;FS=0.8575;Haplot [...]
+chr22 29694497 . C CA 148.673 REJECT NS=2;DP=162;DPB=244.08;AC=2;AN=2;AF=0.0;RO=58;AO=15;PRO=33.15;PAO=30.15;QR=2102;QA=499;PQR=1138.28;PQA=975.775;SRF=48;SRR=10;SAF=13;SAR=2;SRP=57.0725;SAP=20.5268;AB=0.0925926;ABP=236.564;RUN=1;RPP=10.1038;RPPR=51.5315;RPL=4.0;RPR=11.0;EPP=20.5268;EPPR=24.5753;DPRA=0.0;ODDS=2.9851;GTI=1;TYPE=ins;CIGAR=1M1I24M;NUMALT=7;MEANALT=18.0;LEN=1;MQM=60.0;MQMR=59.6552;PAIRED=0.933333;PAIREDR=0.982759;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chr22 29694497 . CA C 148.673 REJECT NS=2;DP=162;DPB=244.08;AC=2;AN=4;AF=0.5;RO=58;AO=18;PRO=33.15;PAO=23.15;QR=2102;QA=628;PQR=1138.28;PQA=765.108;SRF=48;SRR=10;SAF=14;SAR=4;SRP=57.0725;SAP=15.074;AB=0.111111;ABP=215.815;RUN=1;RPP=20.3821;RPPR=51.5315;RPL=3.0;RPR=15.0;EPP=20.3821;EPPR=24.5753;DPRA=0.0;ODDS=2.9851;GTI=1;TYPE=del;CIGAR=1M1D23M;NUMALT=7;MEANALT=18.0;LEN=1;MQM=60.0;MQMR=59.6552;PAIRED=1.0;PAIREDR=0.982759;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr22 29694497 . CAA C 148.673 REJECT NS=2;DP=162;DPB=244.08;AC=2;AN=2;AF=0.0;RO=58;AO=4;PRO=33.15;PAO=17.9833;QR=2102;QA=151;PQR=1138.28;PQA=598.875;SRF=48;SRR=10;SAF=4;SAR=0;SRP=57.0725;SAP=11.6962;AB=0.0246914;ABP=320.903;RUN=1;RPP=5.18177;RPPR=51.5315;RPL=1.0;RPR=3.0;EPP=5.18177;EPPR=24.5753;DPRA=0.0;ODDS=2.9851;GTI=1;TYPE=del;CIGAR=1M2D22M;NUMALT=7;MEANALT=18.0;LEN=2;MQM=60.0;MQMR=59.6552;PAIRED=1.0;PAIREDR=0.982759;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr22 29694497 . CAAA C 148.673 REJECT NS=2;DP=162;DPB=244.08;AC=2;AN=2;AF=0.0;RO=58;AO=3;PRO=33.15;PAO=16.7333;QR=2102;QA=84;PQR=1138.28;PQA=553.708;SRF=48;SRR=10;SAF=3;SAR=0;SRP=57.0725;SAP=9.52472;AB=0.0185185;ABP=329.214;RUN=1;RPP=3.73412;RPPR=51.5315;RPL=2.0;RPR=1.0;EPP=3.73412;EPPR=24.5753;DPRA=0.0;ODDS=2.9851;GTI=1;TYPE=del;CIGAR=1M3D21M;NUMALT=7;MEANALT=18.0;LEN=3;MQM=60.0;MQMR=59.6552;PAIRED=1.0;PAIREDR=0.982759;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chr22 29694497 . CAAAA C 148.673 REJECT NS=2;DP=162;DPB=244.08;AC=2;AN=2;AF=0.0;RO=58;AO=2;PRO=33.15;PAO=16.3333;QR=2102;QA=70;PQR=1138.28;PQA=539.708;SRF=48;SRR=10;SAF=1;SAR=1;SRP=57.0725;SAP=3.0103;AB=0.0487805;ABP=75.5163;RUN=1;RPP=7.35324;RPPR=51.5315;RPL=2.0;RPR=0.0;EPP=3.0103;EPPR=24.5753;DPRA=0.0;ODDS=2.9851;GTI=1;TYPE=del;CIGAR=1M4D20M;NUMALT=7;MEANALT=15.0;LEN=4;MQM=60.0;MQMR=59.6552;PAIRED=1.0;PAIREDR=0.982759;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr22 29694515 . ATTGT TTGG 148.673 REJECT NS=2;DP=162;DPB=244.08;AC=2;AN=2;AF=0.0;RO=58;AO=7;PRO=33.15;PAO=8.5;QR=2102;QA=96;PQR=1138.28;PQA=259.442;SRF=48;SRR=10;SAF=7;SAR=0;SRP=57.0725;SAP=18.2106;AB=0.0432099;ABP=296.615;RUN=1;RPP=5.80219;RPPR=51.5315;RPL=5.0;RPR=2.0;EPP=5.80219;EPPR=24.5753;DPRA=0.0;ODDS=2.9851;GTI=1;TYPE=complex;CIGAR=1M1D20M1X2M;NUMALT=7;MEANALT=18.0;LEN=24;MQM=59.5714;MQMR=59.6552;PAIRED=1.0;PAIREDR=0.982759;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:Q [...]
+chr22 29694519 . T G 148.673 REJECT NS=2;DP=162;DPB=244.08;AC=2;AN=2;AF=0.0;RO=58;AO=25;PRO=33.15;PAO=22.0;QR=2102;QA=270;PQR=1138.28;PQA=717.108;SRF=48;SRR=10;SAF=25;SAR=0;SRP=57.0725;SAP=57.2971;AB=0.154321;ABP=171.152;RUN=1;RPP=10.0459;RPPR=51.5315;RPL=17.0;RPR=8.0;EPP=10.0459;EPPR=24.5753;DPRA=0.0;ODDS=2.9851;GTI=1;TYPE=snp;CIGAR=22M1X2M;NUMALT=7;MEANALT=18.0;LEN=1;MQM=60.0;MQMR=59.6552;PAIRED=1.0;PAIREDR=0.982759;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr22 29899735 . G GA 2073.62 REJECT NS=2;DP=322;DPB=397.136;AC=2;AN=2;AF=0.0;RO=135;AO=17;PRO=51.75;PAO=42.75;QR=4701;QA=580;PQR=1751.58;PQA=1476.58;SRF=97;SRR=38;SAF=14;SAR=3;SRP=59.0021;SAP=18.4661;AB=0.052795;ABP=562.36;RUN=1;RPP=9.26925;RPPR=38.542;RPL=5.0;RPR=12.0;EPP=3.13803;EPPR=3.79846;DPRA=0.0;ODDS=137.817;GTI=0;TYPE=ins;CIGAR=1M1I21M;NUMALT=3;MEANALT=22.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.985185;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIM [...]
+chr22 29899735 . GA G 1657.675 REJECT NS=2;DP=300;DPB=397.136;AC=2;AN=4;AF=0.5;RO=135;AO=92;PRO=51.75;PAO=37.75;QR=4701;QA=3189;PQR=1751.58;PQA=1276.58;SRF=97;SRR=38;SAF=69;SAR=23;SRP=59.0021;SAP=52.9542;AB=0.285714;ABP=131.437;RUN=1;RPP=33.5997;RPPR=38.542;RPL=28.0;RPR=64.0;EPP=5.3706;EPPR=3.79846;DPRA=0.0;ODDS=137.817;GTI=0;TYPE=del;CIGAR=1M1D20M;NUMALT=3;MEANALT=22.5;LEN=1;MQM=60.5435;MQMR=60.0;PAIRED=0.98913;PAIREDR=0.985185;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSu [...]
+chr22 29899735 . GAA G 2073.62 REJECT NS=2;DP=322;DPB=397.136;AC=2;AN=2;AF=0.0;RO=135;AO=19;PRO=51.75;PAO=31.75;QR=4701;QA=663;PQR=1751.58;PQA=1082.25;SRF=97;SRR=38;SAF=13;SAR=6;SRP=59.0021;SAP=8.61041;AB=0.0590062;ABP=546.93;RUN=1;RPP=5.8675;RPPR=38.542;RPL=12.0;RPR=7.0;EPP=12.2676;EPPR=3.79846;DPRA=0.0;ODDS=137.817;GTI=0;TYPE=del;CIGAR=1M2D19M;NUMALT=3;MEANALT=22.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.985185;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chr22 29902192 . A C 1998.39 REJECT NS=2;DP=403;DPB=464.0;AC=2;AN=4;AF=0.5;RO=364;AO=100;PRO=0.0;PAO=0.0;QR=13897;QA=3868;PQR=0.0;PQA=0.0;SRF=218;SRR=146;SAF=52;SAR=48;SRP=33.9359;SAP=3.35774;AB=0.215517;ABP=329.18;RUN=1;RPP=13.5202;RPPR=23.0785;RPL=39.0;RPR=61.0;EPP=13.5202;EPPR=8.37933;DPRA=0.0;ODDS=139.772;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994505;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.163;Dels=0.0;FS=4.1115;HaplotypeScore= [...]
+chr22 30038152 . A C 1080.275 REJECT NS=2;DP=220;DPB=245.0;AC=2;AN=4;AF=0.5;RO=187;AO=58;PRO=0.0;PAO=0.0;QR=7068;QA=2176;PQR=0.0;PQA=0.0;SRF=120;SRR=67;SAF=28;SAR=30;SRP=35.6288;SAP=3.16006;AB=0.236735;ABP=150.502;RUN=1;RPP=62.913;RPPR=75.4817;RPL=9.0;RPR=49.0;EPP=3.60933;EPPR=3.3006;DPRA=0.0;ODDS=101.786;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.994652;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.791;Dels=0.0;FS=7.958;HaplotypeScore=4.865 [...]
+chr22 33229804 . G A 2600.26 PASS SOMATIC;NS=2;DP=394;DPB=394.0;AC=1;AN=3;AF=0.25;RO=291;AO=103;PRO=0.0;PAO=0.0;QR=11275;QA=3892;PQR=0.0;PQA=0.0;SRF=145;SRR=146;SAF=51;SAR=52;SRP=3.01776;SAP=3.03138;AB=0.336634;ABP=73.2499;RUN=1;RPP=4.71796;RPPR=3.37594;RPL=47.0;RPR=56.0;EPP=5.56125;EPPR=42.7759;DPRA=0.0;ODDS=52.3686;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.996564;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=0.729;Dels=0.0;FS=0.0;Hap [...]
+chr22 33229830 . A G 8094.93 REJECT NS=2;DP=332;DPB=380.0;AC=3;AN=4;AF=0.75;RO=94;AO=286;PRO=0.0;PAO=0.0;QR=3601;QA=10926;PQR=0.0;PQA=0.0;SRF=38;SRR=56;SAF=114;SAR=172;SRP=10.4949;SAP=28.5517;AB=0.672535;ABP=76.4428;RUN=1;RPP=8.14287;RPPR=3.37991;RPL=156.0;RPR=130.0;EPP=40.2138;EPPR=4.48875;DPRA=0.0;ODDS=57.4013;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.7915;Dels=0.0;FS=2.091;HaplotypeScore=0. [...]
+chr22 36688178 . G A 1877.79 REJECT NS=2;DP=358;DPB=416.0;AC=2;AN=4;AF=0.5;RO=322;AO=92;PRO=0.0;PAO=0.0;QR=12364;QA=3531;PQR=0.0;PQA=0.0;SRF=153;SRR=169;SAF=42;SAR=50;SRP=4.73669;SAP=4.52089;AB=0.221154;ABP=283.965;RUN=1;RPP=3.0103;RPPR=14.9062;RPL=46.0;RPR=46.0;EPP=6.40913;EPPR=27.2876;DPRA=0.0;ODDS=103.381;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4095;Dels=0.0;FS=1.559;HaplotypeScore=3.9327 [...]
+chr22 36690113 . G A 7084.32 REJECT NS=2;DP=189;DPB=212.0;AC=4;AN=4;AF=1.0;RO=0;AO=212;PRO=0.0;PAO=0.0;QR=0;QA=8157;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=154;SAR=58;SRP=0.0;SAP=97.4079;AB=0.0;ABP=0.0;RUN=1;RPP=105.438;RPPR=0.0;RPL=56.0;RPR=156.0;EPP=19.3988;EPPR=0.0;DPRA=0.0;ODDS=33.0727;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.695;SOR=1.9525 GT:GQ [...]
+chr22 36691607 . A C 12616.05 REJECT NS=2;DP=342;DPB=393.0;AC=4;AN=4;AF=1.0;RO=4;AO=387;PRO=0.0;PAO=0.0;QR=109;QA=14732;PQR=0.0;PQA=0.0;SRF=2;SRR=2;SAF=238;SAR=149;SRP=3.0103;SAP=47.4553;AB=0.0;ABP=0.0;RUN=1;RPP=3.15058;RPPR=5.18177;RPL=196.0;RPR=191.0;EPP=3.95857;EPPR=5.18177;DPRA=0.0;ODDS=60.1973;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.994832;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.469;Dels=0.0;FS=0.0;HaplotypeScore=5.9312;MLEAC=2 [...]
+chr22 36700175 . A G 6140.185 REJECT NS=2;DP=403;DPB=460.0;AC=2;AN=4;AF=0.5;RO=241;AO=219;PRO=0.0;PAO=0.0;QR=9194;QA=8325;PQR=0.0;PQA=0.0;SRF=122;SRR=119;SAF=104;SAR=115;SRP=3.09139;SAP=4.21006;AB=0.476087;ABP=5.29507;RUN=1;RPP=9.20742;RPPR=5.03761;RPL=122.0;RPR=97.0;EPP=3.09954;EPPR=3.74013;DPRA=0.0;ODDS=325.565;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.03;Dels=0.0;FS=0.9625;HaplotypeScore=8 [...]
+chr22 36708084 . C T 4465.91 REJECT NS=2;DP=300;DPB=344.0;AC=2;AN=4;AF=0.5;RO=181;AO=162;PRO=0.0;PAO=0.0;QR=6896;QA=6155;PQR=0.0;PQA=0.0;SRF=113;SRR=68;SAF=115;SAR=47;SRP=27.3044;SAP=64.9911;AB=0.47093;ABP=5.53527;RUN=1;RPP=16.7362;RPPR=19.4343;RPL=65.0;RPR=97.0;EPP=9.49791;EPPR=11.7562;DPRA=0.0;ODDS=233.561;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.222;Dels=0.0;FS=5.8385;HaplotypeScore=4.9233 [...]
+chr22 36710183 . T C 5116.13 REJECT NS=2;DP=313;DPB=362.0;AC=2;AN=4;AF=0.5;RO=178;AO=184;PRO=0.0;PAO=0.0;QR=6899;QA=7006;PQR=0.0;PQA=0.0;SRF=108;SRR=70;SAF=120;SAR=64;SRP=20.6261;SAP=40.0197;AB=0.508287;ABP=3.22625;RUN=1;RPP=64.1892;RPPR=28.824;RPL=56.0;RPR=128.0;EPP=15.095;EPPR=38.5834;DPRA=0.0;ODDS=291.223;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.3945;Dels=0.0;FS=2.547;HaplotypeScore=3.957 [...]
+chr22 38369976 . A G 4431.8 REJECT NS=2;DP=307;DPB=347.0;AC=2;AN=4;AF=0.5;RO=183;AO=164;PRO=0.0;PAO=0.0;QR=6972;QA=6159;PQR=0.0;PQA=0.0;SRF=104;SRR=79;SAF=67;SAR=97;SRP=10.4265;SAP=14.9269;AB=0.472622;ABP=5.26938;RUN=1;RPP=13.391;RPPR=6.43957;RPL=68.0;RPR=96.0;EPP=7.30028;EPPR=3.11709;DPRA=0.0;ODDS=254.753;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993902;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.309;Dels=0.0;FS=23.3185;HaplotypeScore=8. [...]
+chr22 39632920 . C G 14202.0 REJECT NS=2;DP=376;DPB=429.0;AC=4;AN=4;AF=1.0;RO=1;AO=428;PRO=0.0;PAO=0.0;QR=2;QA=16291;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=203;SAR=225;SRP=5.18177;SAP=5.46589;AB=0.0;ABP=0.0;RUN=1;RPP=6.44001;RPPR=5.18177;RPL=201.0;RPR=227.0;EPP=5.03971;EPPR=5.18177;DPRA=0.0;ODDS=68.5248;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990654;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=6.8322;MLEAC=2;MLEAF=1.0;MQ=60.0;QD [...]
+chr22 39632931 . A G 14561.7 REJECT NS=2;DP=386;DPB=441.0;AC=4;AN=4;AF=1.0;RO=1;AO=440;PRO=0.0;PAO=0.0;QR=40;QA=16761;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=196;SAR=244;SRP=5.18177;SAP=14.3809;AB=0.0;ABP=0.0;RUN=1;RPP=5.39892;RPPR=5.18177;RPL=209.0;RPR=231.0;EPP=11.7159;EPPR=5.18177;DPRA=0.0;ODDS=70.9933;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993182;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.115;Dels=0.0;FS=1.6625;HaplotypeScore=5.8654;MLEA [...]
+chr22 39633622 . C T 14153.15 REJECT NS=2;DP=390;DPB=449.0;AC=4;AN=4;AF=1.0;RO=0;AO=448;PRO=0.0;PAO=0.0;QR=0;QA=16498;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=226;SAR=222;SRP=0.0;SAP=3.08785;AB=0.0;ABP=0.0;RUN=1;RPP=3.70827;RPPR=0.0;RPL=218.0;RPR=230.0;EPP=4.94911;EPPR=0.0;DPRA=0.0;ODDS=76.3373;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993304;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=11.6231;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.32;SOR= [...]
+chr22 39633749 . T C 13910.95 REJECT NS=2;DP=367;DPB=415.0;AC=4;AN=4;AF=1.0;RO=1;AO=414;PRO=0.0;PAO=0.0;QR=39;QA=15854;PQR=0.0;PQA=0.0;SRF=0;SRR=1;SAF=202;SAR=212;SRP=5.18177;SAP=3.53481;AB=0.0;ABP=0.0;RUN=1;RPP=3.53481;RPPR=5.18177;RPL=202.0;RPR=212.0;EPP=3.19912;EPPR=5.18177;DPRA=0.0;ODDS=62.9657;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.997585;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=7.7792;MLEAC=2;MLEAF=1.0;MQ=60.0; [...]
+chr22 39634434 . A C 21393.75 REJECT NS=2;DP=566;DPB=648.0;AC=4;AN=4;AF=1.0;RO=0;AO=648;PRO=0.0;PAO=0.0;QR=0;QA=24736;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=310;SAR=338;SRP=0.0;SAP=5.63751;AB=0.0;ABP=0.0;RUN=1;RPP=10.1011;RPPR=0.0;RPL=347.0;RPR=301.0;EPP=4.09604;EPPR=0.0;DPRA=0.0;ODDS=106.585;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993827;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=8.7207;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.725;SOR= [...]
+chr22 39634923 . A G 13423.849999999999 REJECT NS=2;DP=353;DPB=405.0;AC=4;AN=4;AF=1.0;RO=0;AO=405;PRO=0.0;PAO=0.0;QR=0;QA=15577;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=231;SAR=174;SRP=0.0;SAP=20.4303;AB=0.0;ABP=0.0;RUN=1;RPP=3.65906;RPPR=0.0;RPL=197.0;RPR=208.0;EPP=3.05855;EPPR=0.0;DPRA=0.0;ODDS=69.2211;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.995062;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=3 [...]
+chr22 39635858 . G GCA 7752.764999999999 REJECT NS=2;DP=236;DPB=336.786;AC=4;AN=4;AF=1.0;RO=6;AO=232;PRO=41.0;PAO=50.0;QR=232;QA=8627;PQR=1416.0;PQA=1716.0;SRF=3;SRR=3;SAF=125;SAR=107;SRP=3.0103;SAP=6.04287;AB=0.0;ABP=0.0;RUN=1;RPP=6.04287;RPPR=4.45795;RPL=125.0;RPR=107.0;EPP=4.35811;EPPR=8.80089;DPRA=0.0;ODDS=35.7342;GTI=0;TYPE=ins;CIGAR=1M2I13M;NUMALT=1;MEANALT=5.0;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=0.99569;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.0505;FS=0.886;MLEAC=2;ML [...]
+chr22 39636354 . C CT 1393.6 REJECT NS=2;DP=428;DPB=496.235;AC=2;AN=2;AF=0.0;RO=295;AO=25;PRO=60.5;PAO=52.5;QR=10973;QA=791;PQR=2134.83;PQA=1814.83;SRF=101;SRR=194;SAF=8;SAR=17;SRP=66.6749;SAP=10.0459;AB=0.0584112;ABP=727.937;RUN=1;RPP=3.09716;RPPR=3.01766;RPL=12.0;RPR=13.0;EPP=3.79203;EPPR=4.66651;DPRA=0.0;ODDS=91.2565;GTI=0;TYPE=ins;CIGAR=1M1I16M;NUMALT=2;MEANALT=14.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.979661;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chr22 39636354 . CT C 1393.6 REJECT NS=2;DP=428;DPB=496.235;AC=2;AN=4;AF=0.5;RO=295;AO=73;PRO=60.5;PAO=47.0;QR=10973;QA=2774;PQR=2134.83;PQA=1635.33;SRF=101;SRR=194;SAF=31;SAR=42;SRP=66.6749;SAP=6.60959;AB=0.170561;ABP=406.478;RUN=1;RPP=3.27802;RPPR=3.01766;RPL=35.0;RPR=38.0;EPP=3.04005;EPPR=4.66651;DPRA=0.0;ODDS=91.2565;GTI=0;TYPE=del;CIGAR=1M1D15M;NUMALT=2;MEANALT=14.0;LEN=1;MQM=60.411;MQMR=60.0;PAIRED=0.986301;PAIREDR=0.979661;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=2.7 [...]
+chr22 39636510 . T TG 8730.22 REJECT NS=2;DP=279;DPB=374.444;AC=4;AN=4;AF=1.0;RO=0;AO=301;PRO=25.5;PAO=31.5;QR=0;QA=10770;PQR=889.5;PQA=1069.5;SRF=0;SRR=0;SAF=159;SAR=142;SRP=0.0;SAP=5.0952;AB=0.0;ABP=0.0;RUN=1;RPP=3.19065;RPPR=0.0;RPL=153.0;RPR=148.0;EPP=8.26945;EPPR=0.0;DPRA=0.0;ODDS=54.7542;GTI=0;TYPE=ins;CIGAR=1M1I8M;NUMALT=1;MEANALT=4.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996678;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.14;QD=29.48;RPA=6,7;RU=G;SOR=0.831; [...]
+chr22 39636586 . C G 13094.3 REJECT NS=2;DP=350;DPB=407.0;AC=4;AN=4;AF=1.0;RO=0;AO=407;PRO=0.0;PAO=0.0;QR=0;QA=15335;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=255;SAR=152;SRP=0.0;SAP=59.6126;AB=0.0;ABP=0.0;RUN=1;RPP=3.27173;RPPR=0.0;RPL=200.0;RPR=207.0;EPP=9.54606;EPPR=0.0;DPRA=0.0;ODDS=75.2889;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.1229;MQMR=0.0;PAIRED=0.992629;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8983;MLEAC=2;MLEAF=1.0;MQ=60.15;QD=32.16;SO [...]
+chr22 39636762 . G A 3676.96 PASS SOMATIC;NS=2;DP=537;DPB=537.0;AC=1;AN=3;AF=0.25;RO=395;AO=141;PRO=0.0;PAO=0.0;QR=15102;QA=5345;PQR=0.0;PQA=0.0;SRF=184;SRR=211;SAF=58;SAR=83;SRP=7.0179;SAP=12.6356;AB=0.359694;ABP=70.0379;RUN=1;RPP=11.1572;RPPR=8.99697;RPL=82.0;RPR=59.0;EPP=3.0257;EPPR=8.99697;DPRA=2.70345;ODDS=91.3915;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=2.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992908;PAIREDR=0.989873;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.26;Dels=0.0;FS= [...]
+chr22 39636899 . GTC G 367.312 PASS SOMATIC;NS=2;DP=286;DPB=361.227;AC=1;AN=4;AF=0.25;RO=222;AO=39;PRO=92.0;PAO=79.0;QR=8094;QA=1207;PQR=3030.5;PQA=2568.5;SRF=98;SRR=124;SAF=14;SAR=25;SRP=9.62253;SAP=9.74743;AB=0.164319;ABP=211.482;RUN=1;RPP=7.52028;RPPR=3.36243;RPL=24.0;RPR=15.0;EPP=7.52028;EPPR=11.8136;DPRA=0.0;ODDS=14.9326;GTI=0;TYPE=del;CIGAR=1M2D19M;NUMALT=1;MEANALT=11.0;LEN=2;MQM=59.4872;MQMR=62.4324;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIM [...]
+chr22 39636918 . TCAGATGCGCACACACA AGATGCGCGCG . PASS SOMATIC;AC=1;AN=4;END=39636934;HOMLEN=0;SVLEN=-17;SVTYPE=RPL;NTLEN=11 GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:-0.0124524 0/1:47,21:21:31:68:.:.:.:1:.:.:-0.068504
+chr22 39636928 . A G 6099.285 PASS DP=171;AC=4;AN=4;AF=1.0;MQ0=0;ALERT;BaseQRankSum=0.9925;Dels=0.03;FS=1.093;HaplotypeScore=47.5877;MLEAC=2;MLEAF=1.0;MQ=61.925;MQRankSum=-0.569;QD=26.775;ReadPosRankSum=-0.35;SOR=0.375;ClippingRankSum=0.109 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:3,53:56:64.0:1851,64,0:53:95:56:1:.:.:.:.:.:-0.0124524 1/1:1,249:250:99.0:10404,728,0:249:100:250:.:1:.:.:.:.:-0.068504
+chr22 39636928 . ACA GCG 10554.8 REJECT NS=2;DP=327;DPB=332.333;AC=4;AN=4;AF=1.0;RO=1;AO=318;PRO=0.0;PAO=9.0;QR=35;QA=11498;PQR=0.0;PQA=314.0;SRF=1;SRR=0;SAF=157;SAR=161;SRP=5.18177;SAP=3.11956;AB=0.0;ABP=0.0;RUN=1;RPP=3.25613;RPPR=5.18177;RPL=162.0;RPR=156.0;EPP=8.36387;EPPR=5.18177;DPRA=0.0;ODDS=49.3574;GTI=0;TYPE=complex;CIGAR=1X1M1X;NUMALT=1;MEANALT=2.0;LEN=3;MQM=61.4717;MQMR=60.0;PAIRED=0.993711;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC: [...]
+chr22 39636930 . A G 6249.77 PASS DP=172;AC=4;AN=4;AF=1.0;MQ0=0;ALERT;BaseQRankSum=0.9805;Dels=0.02;FS=3.38;HaplotypeScore=47.579;MLEAC=2;MLEAF=1.0;MQ=62.12;MQRankSum=-0.175;QD=32.98;ReadPosRankSum=-0.7895;SOR=0.3485;ClippingRankSum=1.299 GT:AD:DP:GQ:PL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 1/1:1,71:72:99.0:2609,178,0:71:99:72:1:.:.:.:.:.:-0.0124524 1/1:7,248:255:99.0:9947,509,0:248:97:255:.:1:.:.:.:.:-0.068504
+chr22 39636944 . ACACT A 8427.7 REJECT NS=2;DP=323;DPB=192.0;AC=4;AN=4;AF=0.75;RO=14;AO=301;PRO=6.0;PAO=11.0;QR=480;QA=9696;PQR=183.0;PQA=347.0;SRF=4;SRR=10;SAF=147;SAR=154;SRP=8.59409;SAP=3.3638;AB=0.0;ABP=0.0;RUN=1;RPP=3.3638;RPPR=8.59409;RPL=154.0;RPR=147.0;EPP=3.59465;EPPR=3.63072;DPRA=0.0;ODDS=19.4238;GTI=0;TYPE=del;CIGAR=1M4D3M;NUMALT=3;MEANALT=5.0;LEN=4;MQM=63.9801;MQMR=60.0;PAIRED=0.996678;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;END=39636948;HOMLEN=1;HOMSEQ=C; [...]
+chr22 39636944 . ACACTCT A 8427.7 REJECT SOMATIC;NS=2;DP=355;DPB=192.0;AC=1;AN=3;AF=0.0;RO=14;AO=13;PRO=6.0;PAO=2.0;QR=480;QA=393;PQR=183.0;PQA=44.5;SRF=4;SRR=10;SAF=5;SAR=8;SRP=8.59409;SAP=4.51363;AB=0.0;ABP=0.0;RUN=1;RPP=7.18621;RPPR=8.59409;RPL=9.0;RPR=4.0;EPP=3.17734;EPPR=3.63072;DPRA=0.0;ODDS=19.4238;GTI=0;TYPE=del;CIGAR=1M6D1M;NUMALT=3;MEANALT=5.0;LEN=6;MQM=60.0;MQMR=60.0;PAIRED=0.923077;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.79;FS=0.0;MLEAC=1;ML [...]
+chr22 39636946 . ACTCT A 8427.7 REJECT NS=2;DP=355;DPB=192.0;AC=0;AN=4;AF=0.0;RO=14;AO=16;PRO=6.0;PAO=4.0;QR=480;QA=477;PQR=183.0;PQA=118.5;SRF=4;SRR=10;SAF=11;SAR=5;SRP=8.59409;SAP=7.89611;AB=0.0;ABP=0.0;RUN=1;RPP=29.6108;RPPR=8.59409;RPL=1.0;RPR=15.0;EPP=5.18177;EPPR=3.63072;DPRA=0.0;ODDS=19.4238;GTI=0;TYPE=del;CIGAR=3M4D1M;NUMALT=3;MEANALT=5.0;LEN=4;MQM=60.625;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC [...]
+chr22 39639257 . GTCTCTC G 6845.43 REJECT NS=2;DP=136;DPB=211.085;AC=3;AN=3;AF=0.75;RO=0;AO=97;PRO=38.0833;PAO=75.5833;QR=0;QA=2935;PQR=1326.25;PQA=2562.75;SRF=0;SRR=0;SAF=43;SAR=54;SRP=0.0;SAP=5.71904;AB=0.698113;ABP=39.1469;RUN=1;RPP=5.71904;RPPR=0.0;RPL=54.0;RPR=43.0;EPP=6.79359;EPPR=0.0;DPRA=0.0;ODDS=5.9259;GTI=0;TYPE=del;CIGAR=1M6D40M;NUMALT=3;MEANALT=10.5;LEN=6;MQM=60.6804;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.6635;FS=0.0;MLE [...]
+chr22 39639257 . GTCTCTCTC G 6845.43 REJECT NS=2;DP=136;DPB=211.085;AC=0;AN=4;AF=0.0;RO=0;AO=6;PRO=38.0833;PAO=45.0833;QR=0;QA=169;PQR=1326.25;PQA=1569.42;SRF=0;SRR=0;SAF=4;SAR=2;SRP=0.0;SAP=4.45795;AB=0.0566038;ABP=184.021;RUN=1;RPP=8.80089;RPPR=0.0;RPL=1.0;RPR=5.0;EPP=8.80089;EPPR=0.0;DPRA=3.53333;ODDS=5.9259;GTI=0;TYPE=del;CIGAR=1M8D38M;NUMALT=3;MEANALT=14.0;LEN=8;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:G [...]
+chr22 39639271 . CTCTCTCTT C . PASS SOMATIC;AC=1;AN=4;END=39639279;HOMLEN=7;HOMSEQ=TCTCTCT;SVLEN=-8;SVTYPE=DEL GT:AD:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU:LR 0/0:.:.:.:.:.:.:.:.:.:.:-0.0124524 0/1:16,28:28:64:44:.:.:.:1:.:.:-0.068504
+chr22 39639273 . CTCTCTTTC T 6845.43 REJECT SOMATIC;NS=2;DP=136;DPB=211.085;AC=1;AN=3;AF=0.25;RO=0;AO=13;PRO=38.0833;PAO=70.25;QR=0;QA=450;PQR=1326.25;PQA=2304.58;SRF=0;SRR=0;SAF=5;SAR=8;SRP=0.0;SAP=4.51363;AB=0.103774;ABP=147.557;RUN=1;RPP=4.51363;RPPR=0.0;RPL=8.0;RPR=5.0;EPP=7.18621;EPPR=0.0;DPRA=0.0;ODDS=5.9259;GTI=0;TYPE=complex;CIGAR=15M8D1M1X22M;NUMALT=3;MEANALT=10.5;LEN=39;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chr22 39639853 . G T 7985.695000000001 REJECT NS=2;DP=219;DPB=250.0;AC=4;AN=4;AF=1.0;RO=0;AO=250;PRO=0.0;PAO=0.0;QR=0;QA=9291;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=70;SAR=180;SRP=0.0;SAP=108.11;AB=0.0;ABP=0.0;RUN=1;RPP=16.9077;RPPR=0.0;RPL=145.0;RPR=105.0;EPP=4.26107;EPPR=0.0;DPRA=0.0;ODDS=42.936;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.29;SOR [...]
+chr22 41513727 . G A 3130.01 PASS SOMATIC;NS=2;DP=402;DPB=402.0;AC=1;AN=3;AF=0.25;RO=285;AO=117;PRO=0.0;PAO=0.0;QR=10887;QA=4438;PQR=0.0;PQA=0.0;SRF=142;SRR=143;SAF=60;SAR=57;SRP=3.01792;SAP=3.17734;AB=0.392617;ABP=32.8571;RUN=1;RPP=4.51363;RPPR=4.72462;RPL=54.0;RPR=63.0;EPP=3.47429;EPPR=4.29794;DPRA=2.86538;ODDS=65.8392;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.991453;PAIREDR=0.989474;technology.ILLUMINA=1.0;MQ0=0;VT=SNP;BaseQRankSum=-0.589;Dels=0.0; [...]
+chr22 41537234 . G T 11342.2 REJECT NS=2;DP=299;DPB=339.0;AC=4;AN=4;AF=1.0;RO=0;AO=339;PRO=0.0;PAO=0.0;QR=0;QA=13035;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=89;SAR=250;SRP=0.0;SAP=169.048;AB=0.0;ABP=0.0;RUN=1;RPP=39.0414;RPPR=0.0;RPL=207.0;RPR=132.0;EPP=5.32269;EPPR=0.0;DPRA=0.0;ODDS=53.6194;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.9941;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.8711;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=30.315;SOR=2.34 [...]
+chr22 41548008 . A G 6159.82 REJECT NS=2;DP=432;DPB=482.0;AC=2;AN=4;AF=0.5;RO=263;AO=219;PRO=0.0;PAO=0.0;QR=10205;QA=8400;PQR=0.0;PQA=0.0;SRF=115;SRR=148;SAF=95;SAR=124;SRP=12.0017;SAP=11.3492;AB=0.454357;ABP=11.7322;RUN=1;RPP=9.20742;RPPR=3.21671;RPL=97.0;RPR=122.0;EPP=18.0916;EPPR=5.39644;DPRA=0.0;ODDS=296.669;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990868;PAIREDR=0.996198;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.7215;Dels=0.0;FS=2.205;Haplot [...]
+chr22 41551039 . T A 4743.015 REJECT NS=2;DP=343;DPB=390.0;AC=2;AN=4;AF=0.5;RO=202;AO=188;PRO=0.0;PAO=0.0;QR=7640;QA=6846;PQR=0.0;PQA=0.0;SRF=136;SRR=66;SAF=123;SAR=65;SRP=55.6846;SAP=41.8658;AB=0.482051;ABP=4.1016;RUN=1;RPP=17.9796;RPPR=8.21323;RPL=76.0;RPR=112.0;EPP=8.60069;EPPR=15.4371;DPRA=0.0;ODDS=278.634;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.989362;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.163;Dels=0.0;FS=0.732;HaplotypeScore [...]
+chr22 41568480 . T C 4093.48 REJECT NS=2;DP=234;DPB=267.0;AC=2;AN=4;AF=0.5;RO=118;AO=149;PRO=0.0;PAO=0.0;QR=4574;QA=5637;PQR=0.0;PQA=0.0;SRF=78;SRR=40;SAF=112;SAR=37;SRP=29.5832;SAP=84.987;AB=0.558052;ABP=10.826;RUN=1;RPP=103.408;RPPR=45.4092;RPL=33.0;RPR=116.0;EPP=9.43728;EPPR=5.66023;DPRA=0.0;ODDS=199.511;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.1445;Dels=0.0;FS=5.2565;HaplotypeScore=1.933 [...]
+chr22 41572541 . C T 1966.03 REJECT NS=2;DP=311;DPB=358.0;AC=2;AN=4;AF=0.5;RO=264;AO=94;PRO=0.0;PAO=0.0;QR=10117;QA=3542;PQR=0.0;PQA=0.0;SRF=119;SRR=145;SAF=45;SAR=49;SRP=8.57059;SAP=3.37991;AB=0.26257;ABP=178.305;RUN=1;RPP=12.2506;RPPR=32.6213;RPL=57.0;RPR=37.0;EPP=10.4949;EPPR=8.57059;DPRA=0.0;ODDS=135.248;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.8905;Dels=0.0;FS=3.6545;HaplotypeScore=7.87 [...]
+chr22 41574969 . TGTA T 3413.48 REJECT NS=2;DP=258;DPB=246.25;AC=2;AN=4;AF=0.5;RO=147;AO=130;PRO=23.0;PAO=15.0;QR=5528;QA=4795;PQR=784.5;PQA=510.5;SRF=47;SRR=100;SAF=38;SAR=92;SRP=44.5046;SAP=51.7181;AB=0.467626;ABP=5.54108;RUN=1;RPP=24.6582;RPPR=23.2331;RPL=83.0;RPR=47.0;EPP=3.0103;EPPR=4.20683;DPRA=0.0;ODDS=204.58;GTI=0;TYPE=del;CIGAR=1M3D4M;NUMALT=1;MEANALT=1.5;LEN=3;MQM=60.2308;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;END=41574972;HOMLEN=3;HOMSEQ=GTA;SVLEN=-3;SV [...]
+chrX 15818114 . AT A 6466.995 REJECT NS=2;DP=188;DPB=196.444;AC=4;AN=4;AF=1.0;RO=0;AO=197;PRO=16.0;PAO=28.0;QR=0;QA=7517;PQR=589.5;PQA=1028.5;SRF=0;SRR=0;SAF=78;SAR=119;SRP=0.0;SAP=21.5395;AB=0.0;ABP=0.0;RUN=1;RPP=148.786;RPPR=0.0;RPL=156.0;RPR=41.0;EPP=7.87131;EPPR=0.0;DPRA=0.0;ODDS=36.1829;GTI=0;TYPE=del;CIGAR=1M1D7M;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.969543;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;END=15818115;HOMLEN=3;HOMSEQ=TTT;SVLEN=-1;SVTYPE=DEL;FS=0.0;MLEAC=2; [...]
+chrX 15838366 . C T 13989.599999999999 REJECT NS=2;DP=367;DPB=423.0;AC=4;AN=4;AF=1.0;RO=0;AO=423;PRO=0.0;PAO=0.0;QR=0;QA=16281;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=235;SAR=188;SRP=0.0;SAP=14.3502;AB=0.0;ABP=0.0;RUN=1;RPP=3.26184;RPPR=0.0;RPL=208.0;RPR=215.0;EPP=36.6912;EPPR=0.0;DPRA=0.0;ODDS=74.2366;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.9409;MQMR=0.0;PAIRED=0.990544;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=5.8324;MLEAC=2;MLEAF=1.0;MQ=59.945; [...]
+chrX 22505654 . C T 9759.52 REJECT NS=2;DP=398;DPB=455.0;AC=2;AN=4;AF=0.5;RO=134;AO=321;PRO=0.0;PAO=0.0;QR=5139;QA=12316;PQR=0.0;PQA=0.0;SRF=57;SRR=77;SAF=137;SAR=184;SRP=9.49231;SAP=17.9535;AB=0.705495;ABP=169.899;RUN=1;RPP=9.51119;RPPR=3.0103;RPL=176.0;RPR=145.0;EPP=4.53236;EPPR=6.18648;DPRA=0.0;ODDS=290.08;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.993769;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.073;Dels=0.0;FS=2.365;HaplotypeScore=2 [...]
+chrX 37513172 . G GA 400.494 REJECT NS=2;DP=300;DPB=354.905;AC=2;AN=3;AF=0.25;RO=203;AO=31;PRO=45.6667;PAO=40.6667;QR=7337;QA=1070;PQR=1585.67;PQA=1431.67;SRF=136;SRR=67;SAF=23;SAR=8;SRP=53.9383;SAP=18.771;AB=0.103333;ABP=413.013;RUN=1;RPP=3.08035;RPPR=56.9334;RPL=16.0;RPR=15.0;EPP=8.68415;EPPR=8.66896;DPRA=0.0;ODDS=6.46598;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=2;MEANALT=14.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995074;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA [...]
+chrX 37513172 . GA G 256.112 REJECT NS=2;DP=271;DPB=354.905;AC=2;AN=3;AF=0.375;RO=203;AO=33;PRO=45.6667;PAO=39.6667;QR=7337;QA=1166;PQR=1585.67;PQA=1383.67;SRF=136;SRR=67;SAF=24;SAR=9;SRP=53.9383;SAP=17.8158;AB=0.11;ABP=399.347;RUN=1;RPP=8.34028;RPPR=56.9334;RPL=12.0;RPR=21.0;EPP=4.65535;EPPR=8.66896;DPRA=0.0;ODDS=6.46598;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=2;MEANALT=14.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995074;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=1.8 [...]
+chrX 39930433 . G GA 128.534 REJECT NS=2;DP=111;DPB=129.0;AC=2;AN=2;AF=0.0;RO=69;AO=15;PRO=19.1667;PAO=10.1667;QR=2563;QA=446;PQR=675.417;PQA=352.417;SRF=8;SRR=61;SAF=3;SAR=12;SRP=91.4113;SAP=14.7363;AB=0.135135;ABP=131.362;RUN=1;RPP=6.62942;RPPR=50.8771;RPL=10.0;RPR=5.0;EPP=3.15506;EPPR=19.6583;DPRA=0.0;ODDS=1.17068;GTI=1;TYPE=ins;CIGAR=1M1I22M;NUMALT=3;MEANALT=6.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chrX 39930433 . G GAA 128.534 REJECT NS=2;DP=111;DPB=129.0;AC=2;AN=2;AF=0.0;RO=69;AO=3;PRO=19.1667;PAO=11.1667;QR=2563;QA=48;PQR=675.417;PQA=368.417;SRF=8;SRR=61;SAF=0;SAR=3;SRP=91.4113;SAP=9.52472;AB=0.027027;ABP=218.69;RUN=1;RPP=9.52472;RPPR=50.8771;RPL=3.0;RPR=0.0;EPP=9.52472;EPPR=19.6583;DPRA=0.0;ODDS=1.17068;GTI=1;TYPE=ins;CIGAR=1M2I22M;NUMALT=3;MEANALT=6.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chrX 39930433 . GA G 128.534 REJECT NS=2;DP=111;DPB=129.0;AC=2;AN=4;AF=0.5;RO=69;AO=14;PRO=19.1667;PAO=11.5;QR=2563;QA=475;PQR=675.417;PQA=387.75;SRF=8;SRR=61;SAF=0;SAR=14;SRP=91.4113;SAP=33.4109;AB=0.126126;ABP=137.779;RUN=1;RPP=8.59409;RPPR=50.8771;RPL=10.0;RPR=4.0;EPP=8.59409;EPPR=19.6583;DPRA=0.0;ODDS=1.17068;GTI=1;TYPE=del;CIGAR=1M1D21M;NUMALT=3;MEANALT=6.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=0.774;FS=0.0;MLEAC=1;MLE [...]
+chrX 39933339 . A G 8110.51 REJECT NS=2;DP=324;DPB=373.0;AC=2;AN=4;AF=0.5;RO=105;AO=268;PRO=0.0;PAO=0.0;QR=4001;QA=10225;PQR=0.0;PQA=0.0;SRF=55;SRR=50;SAF=133;SAR=135;SRP=3.52732;SAP=3.04271;AB=0.718499;ABP=157.686;RUN=1;RPP=5.63551;RPPR=3.03098;RPL=125.0;RPR=143.0;EPP=15.9743;EPPR=3.19643;DPRA=0.0;ODDS=271.069;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.327;Dels=0.0;FS=1.949;HaplotypeScore=8.8 [...]
+chrX 42030736 . C T 14645.55 REJECT NS=2;DP=382;DPB=439.0;AC=4;AN=4;AF=1.0;RO=0;AO=438;PRO=0.0;PAO=0.0;QR=0;QA=16992;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=247;SAR=191;SRP=0.0;SAP=18.5576;AB=0.0;ABP=0.0;RUN=1;RPP=30.1587;RPPR=0.0;RPL=256.0;RPR=182.0;EPP=10.9426;EPPR=0.0;DPRA=0.0;ODDS=72.37;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.5;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.993151;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=1.9243;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.005;SOR=1.0 [...]
+chrX 42030761 . C T 13535.55 REJECT NS=2;DP=358;DPB=409.0;AC=4;AN=4;AF=1.0;RO=0;AO=409;PRO=0.0;PAO=0.0;QR=0;QA=15631;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=189;SAR=220;SRP=0.0;SAP=8.11246;AB=0.0;ABP=0.0;RUN=1;RPP=24.0826;RPPR=0.0;RPL=236.0;RPR=173.0;EPP=21.4917;EPPR=0.0;DPRA=0.0;ODDS=66.7106;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.99511;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=27.65;SOR=0.8655 [...]
+chrX 44921996 . G A 960.249 REJECT NS=1;DP=78;DPB=78.0;AC=1;AN=4;AF=0.5;RO=42;AO=36;PRO=0.0;PAO=0.0;QR=1625;QA=1372;PQR=0.0;PQA=0.0;SRF=14;SRR=28;SAF=12;SAR=24;SRP=13.1438;SAP=11.6962;AB=0.461538;ABP=4.01252;RUN=1;RPP=11.6962;RPPR=16.2459;RPL=24.0;RPR=12.0;EPP=3.0103;EPPR=3.0103;DPRA=0.0;ODDS=221.106;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=0.865;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0.907;QD=1 [...]
+chrX 44938563 . G A 7759.46 REJECT NS=2;DP=332;DPB=381.0;AC=2;AN=4;AF=0.5;RO=124;AO=257;PRO=0.0;PAO=0.0;QR=4735;QA=9893;PQR=0.0;PQA=0.0;SRF=52;SRR=72;SAF=94;SAR=163;SRP=10.015;SAP=43.2375;AB=0.674541;ABP=103.827;RUN=1;RPP=3.08634;RPPR=10.015;RPL=130.0;RPR=127.0;EPP=8.29112;EPPR=5.53201;DPRA=0.0;ODDS=244.832;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.992218;PAIREDR=0.991935;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.535;Dels=0.0;FS=4.524;HaplotypeScor [...]
+chrX 45037023 . G A 6468.38 REJECT NS=2;DP=262;DPB=301.0;AC=2;AN=4;AF=0.5;RO=85;AO=216;PRO=0.0;PAO=0.0;QR=3300;QA=8293;PQR=0.0;PQA=0.0;SRF=50;SRR=35;SAF=147;SAR=69;SRP=8.75832;SAP=64.1734;AB=0.717608;ABP=126.813;RUN=1;RPP=39.2015;RPPR=10.3933;RPL=78.0;RPR=138.0;EPP=20.744;EPPR=30.8307;DPRA=0.0;ODDS=224.865;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9294;PAIRED=0.990741;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=-0.677;Dels=0.0;FS=6.594;HaplotypeScore= [...]
+chrX 48888074 . T C 11833.05 REJECT NS=2;DP=313;DPB=352.0;AC=4;AN=4;AF=1.0;RO=0;AO=352;PRO=0.0;PAO=0.0;QR=0;QA=13399;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=148;SAR=204;SRP=0.0;SAP=22.3561;AB=0.0;ABP=0.0;RUN=1;RPP=4.21942;RPPR=0.0;RPL=183.0;RPR=169.0;EPP=5.00904;EPPR=0.0;DPRA=0.0;ODDS=51.7396;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.991477;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.97;SOR=1. [...]
+chrX 48892468 . G GT 461.189 REJECT NS=2;DP=223;DPB=321.08;AC=2;AN=3;AF=0.25;RO=148;AO=19;PRO=98.1667;PAO=65.1667;QR=5312;QA=682;PQR=3442.5;PQA=2234.5;SRF=40;SRR=108;SAF=8;SAR=11;SRP=70.8541;SAP=4.03889;AB=0.0852018;ABP=336.278;RUN=1;RPP=8.61041;RPPR=3.24505;RPL=13.0;RPR=6.0;EPP=16.8392;EPPR=11.4614;DPRA=0.0;ODDS=30.6329;GTI=0;TYPE=ins;CIGAR=1M1I24M;NUMALT=2;MEANALT=13.0;LEN=1;MQM=59.4737;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:G [...]
+chrX 48892468 . GT G 461.189 REJECT NS=2;DP=223;DPB=321.08;AC=2;AN=3;AF=0.25;RO=148;AO=28;PRO=98.1667;PAO=52.6667;QR=5312;QA=898;PQR=3442.5;PQA=1774.0;SRF=40;SRR=108;SAF=9;SAR=19;SRP=70.8541;SAP=10.7656;AB=0.125561;ABP=274.581;RUN=1;RPP=7.97367;RPPR=3.24505;RPL=18.0;RPR=10.0;EPP=3.32051;EPPR=11.4614;DPRA=0.0;ODDS=30.6329;GTI=0;TYPE=del;CIGAR=1M1D23M;NUMALT=2;MEANALT=13.0;LEN=1;MQM=60.3571;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-1.195;FS=2. [...]
+chrX 48892694 . A G 913.26 REJECT NS=2;DP=27;DPB=33.0;AC=4;AN=4;AF=1.0;RO=0;AO=33;PRO=0.0;PAO=0.0;QR=0;QA=1196;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=2;SAR=31;SRP=0.0;SAP=58.3499;AB=0.0;ABP=0.0;RUN=1;RPP=3.0761;RPPR=0.0;RPL=17.0;RPR=16.0;EPP=4.65535;EPPR=0.0;DPRA=0.0;ODDS=11.2459;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.909091;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=31.38;SOR=4.123 GT:GQ:DP:RO [...]
+chrX 48895224 . G GA 417.723 REJECT;LowQual NS=2;DP=157;DPB=256.429;AC=2;AN=3;AF=0.25;RO=53;AO=20;PRO=45.3333;PAO=44.3333;QR=1806;QA=588;PQR=1546.28;PQA=1519.78;SRF=41;SRR=12;SAF=15;SAR=5;SRP=37.4671;SAP=13.8677;AB=0.127389;ABP=192.343;RUN=1;RPP=9.95901;RPPR=24.6841;RPL=6.0;RPR=14.0;EPP=3.44459;EPPR=7.96781;DPRA=0.0;ODDS=15.3061;GTI=0;TYPE=ins;CIGAR=1M1I27M;NUMALT=5;MEANALT=21.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=- [...]
+chrX 48895224 . GA G 417.723 REJECT NS=2;DP=157;DPB=256.429;AC=2;AN=3;AF=0.25;RO=53;AO=25;PRO=45.3333;PAO=38.3333;QR=1806;QA=793;PQR=1546.28;PQA=1288.78;SRF=41;SRR=12;SAF=18;SAR=7;SRP=37.4671;SAP=13.5202;AB=0.159236;ABP=161.362;RUN=1;RPP=5.18177;RPPR=24.6841;RPL=10.0;RPR=15.0;EPP=3.09716;EPPR=7.96781;DPRA=0.0;ODDS=15.3061;GTI=0;TYPE=del;CIGAR=1M1D26M;NUMALT=5;MEANALT=21.5;LEN=1;MQM=59.2;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMI [...]
+chrX 48895224 . GAA G 417.723 REJECT NS=2;DP=157;DPB=256.429;AC=2;AN=2;AF=0.0;RO=53;AO=7;PRO=45.3333;PAO=34.5;QR=1806;QA=208;PQR=1546.28;PQA=1158.78;SRF=41;SRR=12;SAF=5;SAR=2;SRP=37.4671;SAP=5.80219;AB=0.044586;ABP=285.841;RUN=1;RPP=3.32051;RPPR=24.6841;RPL=3.0;RPR=4.0;EPP=10.7656;EPPR=7.96781;DPRA=0.0;ODDS=15.3061;GTI=0;TYPE=del;CIGAR=1M2D25M;NUMALT=5;MEANALT=21.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chrX 48895224 . GAAA G 417.723 REJECT NS=2;DP=157;DPB=256.429;AC=2;AN=2;AF=0.0;RO=53;AO=4;PRO=45.3333;PAO=31.6;QR=1806;QA=95;PQR=1546.28;PQA=1057.33;SRF=41;SRR=12;SAF=3;SAR=1;SRP=37.4671;SAP=5.18177;AB=0.0254777;ABP=310.073;RUN=1;RPP=3.0103;RPPR=24.6841;RPL=2.0;RPR=2.0;EPP=5.18177;EPPR=7.96781;DPRA=0.0;ODDS=15.3061;GTI=0;TYPE=del;CIGAR=1M3D24M;NUMALT=5;MEANALT=21.5;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chrX 48895250 . A C 417.723 REJECT NS=2;DP=157;DPB=256.429;AC=2;AN=2;AF=0.0;RO=53;AO=3;PRO=45.3333;PAO=15.9;QR=1806;QA=48;PQR=1546.28;PQA=516.033;SRF=41;SRR=12;SAF=3;SAR=0;SRP=37.4671;SAP=9.52472;AB=0.0191083;ABP=318.372;RUN=1;RPP=9.52472;RPPR=24.6841;RPL=3.0;RPR=0.0;EPP=9.52472;EPPR=7.96781;DPRA=0.0;ODDS=15.3061;GTI=0;TYPE=snp;CIGAR=26M1X1M;NUMALT=5;MEANALT=21.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chrX 48898183 . C G 17127.1 REJECT NS=2;DP=465;DPB=536.0;AC=4;AN=4;AF=1.0;RO=0;AO=536;PRO=0.0;PAO=0.0;QR=0;QA=19997;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=259;SAR=277;SRP=0.0;SAP=4.32291;AB=0.0;ABP=0.0;RUN=1;RPP=4.32291;RPPR=0.0;RPL=259.0;RPR=277.0;EPP=3.59368;EPPR=0.0;DPRA=0.0;ODDS=94.0069;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.996269;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.01;FS=0.0;HaplotypeScore=17.2645;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.865;SOR= [...]
+chrX 48898463 . C CT 232.198 REJECT NS=2;DP=231;DPB=313.667;AC=2;AN=3;AF=0.25;RO=108;AO=23;PRO=43.4;PAO=32.0667;QR=3780;QA=509;PQR=1534.75;PQA=1126.75;SRF=31;SRR=77;SAF=6;SAR=17;SRP=45.5551;SAP=14.4341;AB=0.0995671;ABP=324.736;RUN=1;RPP=14.4341;RPPR=12.7417;RPL=17.0;RPR=6.0;EPP=3.86001;EPPR=14.5915;DPRA=0.0;ODDS=10.6108;GTI=0;TYPE=ins;CIGAR=1M1I20M;NUMALT=4;MEANALT=19.5;LEN=1;MQM=58.7826;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GM [...]
+chrX 48898463 . C CTT 232.198 REJECT NS=2;DP=231;DPB=313.667;AC=2;AN=2;AF=0.0;RO=108;AO=10;PRO=43.4;PAO=31.0667;QR=3780;QA=267;PQR=1534.75;PQA=1086.75;SRF=31;SRR=77;SAF=3;SAR=7;SRP=45.5551;SAP=6.48466;AB=0.04329;ABP=421.522;RUN=1;RPP=6.48466;RPPR=12.7417;RPL=7.0;RPR=3.0;EPP=3.87889;EPPR=14.5915;DPRA=0.0;ODDS=10.6108;GTI=0;TYPE=ins;CIGAR=1M2I20M;NUMALT=4;MEANALT=19.5;LEN=2;MQM=53.4;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GM [...]
+chrX 48898463 . CT C 232.198 REJECT NS=2;DP=231;DPB=313.667;AC=2;AN=3;AF=0.25;RO=108;AO=30;PRO=43.4;PAO=28.4;QR=3780;QA=783;PQR=1534.75;PQA=991.75;SRF=31;SRR=77;SAF=5;SAR=25;SRP=45.5551;SAP=31.9633;AB=0.12987;ABP=277.885;RUN=1;RPP=13.4334;RPPR=12.7417;RPL=21.0;RPR=9.0;EPP=5.61607;EPPR=14.5915;DPRA=0.0;ODDS=10.6108;GTI=0;TYPE=del;CIGAR=1M1D19M;NUMALT=4;MEANALT=19.5;LEN=1;MQM=59.1333;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:G [...]
+chrX 48898479 . G T 232.198 REJECT NS=2;DP=231;DPB=313.667;AC=2;AN=2;AF=0.0;RO=108;AO=9;PRO=43.4;PAO=24.0667;QR=3780;QA=146;PQR=1534.75;PQA=774.0;SRF=31;SRR=77;SAF=9;SAR=0;SRP=45.5551;SAP=22.5536;AB=0.038961;ABP=429.493;RUN=1;RPP=9.04217;RPPR=12.7417;RPL=7.0;RPR=2.0;EPP=9.04217;EPPR=14.5915;DPRA=0.0;ODDS=10.6108;GTI=0;TYPE=snp;CIGAR=16M1X4M;NUMALT=4;MEANALT=19.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chrX 48898809 . TAC T 246.314 REJECT NS=2;DP=281;DPB=333.947;AC=2;AN=4;AF=0.5;RO=234;AO=32;PRO=63.0;PAO=54.0;QR=8854;QA=1176;PQR=2270.0;PQA=1927.0;SRF=173;SRR=61;SAF=24;SAR=8;SRP=119.416;SAP=20.3821;AB=0.113879;ABP=366.898;RUN=1;RPP=3.28173;RPPR=38.6818;RPL=15.0;RPR=17.0;EPP=3.28173;EPPR=8.35546;DPRA=0.0;ODDS=15.5097;GTI=0;TYPE=del;CIGAR=1M2D16M;NUMALT=1;MEANALT=6.0;LEN=2;MQM=61.25;MQMR=60.0;PAIRED=1.0;PAIREDR=0.995726;technology.ILLUMINA=1.0;BaseQRankSum=-0.632;FS=7.065;MLEAC=1;MLEAF=0. [...]
+chrX 53228148 . C A 13115.849999999999 REJECT NS=2;DP=354;DPB=405.0;AC=4;AN=4;AF=1.0;RO=1;AO=404;PRO=0.0;PAO=0.0;QR=16;QA=15180;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=213;SAR=191;SRP=5.18177;SAP=5.61177;AB=0.0;ABP=0.0;RUN=1;RPP=3.0963;RPPR=5.18177;RPL=200.0;RPR=204.0;EPP=3.2038;EPPR=5.18177;DPRA=0.0;ODDS=66.6391;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990099;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.641;Dels=0.0;FS=0.0;HaplotypeScore=3.8993; [...]
+chrX 53449568 . G A 5191.26 REJECT NS=2;DP=207;DPB=235.0;AC=2;AN=4;AF=0.5;RO=61;AO=174;PRO=0.0;PAO=0.0;QR=2302;QA=6677;PQR=0.0;PQA=0.0;SRF=28;SRR=33;SAF=60;SAR=114;SRP=3.90025;SAP=39.4012;AB=0.740426;ABP=121.0;RUN=1;RPP=75.0932;RPPR=37.2199;RPL=125.0;RPR=49.0;EPP=12.7944;EPPR=18.709;DPRA=0.0;ODDS=142.215;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.62;Dels=0.0;FS=5.6635;HaplotypeScore=2.9133;MLEA [...]
+chrX 66676395 . C T 1323.53 REJECT NS=1;DP=88;DPB=88.0;AC=1;AN=4;AF=0.5;RO=38;AO=50;PRO=0.0;PAO=0.0;QR=1405;QA=1801;PQR=0.0;PQA=0.0;SRF=16;SRR=22;SAF=24;SAR=26;SRP=5.06748;SAP=3.18402;AB=0.568182;ABP=6.56362;RUN=1;RPP=14.1282;RPPR=3.23888;RPL=33.0;RPR=17.0;EPP=3.0103;EPPR=3.23888;DPRA=0.0;ODDS=225.109;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=0.973684;technology.ILLUMINA=1.0;BaseQRankSum=-0.234;FS=1.807;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0 [...]
+chrX 66765158 . T A 1028.52 REJECT SOMATIC;NS=2;DP=68;DPB=232.549;AC=1;AN=3;AF=0.0;RO=1;AO=11;PRO=84.1167;PAO=27.3667;QR=39;QA=396;PQR=3097.87;PQA=998.7;SRF=0;SRR=1;SAF=4;SAR=7;SRP=5.18177;SAP=4.78696;AB=0.161765;ABP=70.5814;RUN=1;RPP=26.8965;RPPR=5.18177;RPL=0.0;RPR=11.0;EPP=4.78696;EPPR=5.18177;DPRA=0.0;ODDS=1.39504;GTI=0;TYPE=snp;CIGAR=1X70M;NUMALT=5;MEANALT=8.5;LEN=1;MQM=58.2727;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chrX 66765158 . T TGCAGCA 1028.52 REJECT NS=2;DP=68;DPB=232.549;AC=2;AN=2;AF=0.25;RO=1;AO=5;PRO=84.1167;PAO=84.1167;QR=39;QA=192;PQR=3097.87;PQA=3097.87;SRF=0;SRR=1;SAF=0;SAR=5;SRP=5.18177;SAP=13.8677;AB=0.0735294;ABP=110.434;RUN=1;RPP=6.91895;RPPR=5.18177;RPL=1.0;RPR=4.0;EPP=6.91895;EPPR=5.18177;DPRA=0.0;ODDS=1.39504;GTI=0;TYPE=ins;CIGAR=1M6I70M;NUMALT=5;MEANALT=8.5;LEN=6;MQM=59.6;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=1.999;FS=2.881;MLEA [...]
+chrX 66765158 . TGCAGCA T 1028.52 REJECT NS=2;DP=68;DPB=232.549;AC=2;AN=3;AF=0.5;RO=1;AO=35;PRO=84.1167;PAO=75.7833;QR=39;QA=1284;PQR=3097.87;PQA=2790.87;SRF=0;SRR=1;SAF=16;SAR=19;SRP=5.18177;SAP=3.56868;AB=0.514706;ABP=3.13803;RUN=1;RPP=8.03571;RPPR=5.18177;RPL=22.0;RPR=13.0;EPP=4.56135;EPPR=5.18177;DPRA=0.0;ODDS=1.39504;GTI=0;TYPE=del;CIGAR=1M6D64M;NUMALT=5;MEANALT=8.5;LEN=6;MQM=61.7143;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=1.999;FS=2.8 [...]
+chrX 66765158 . TGCAGCAGCA T 1028.52 REJECT SOMATIC;NS=2;DP=68;DPB=232.549;AC=1;AN=3;AF=0.0;RO=1;AO=5;PRO=84.1167;PAO=68.5833;QR=39;QA=155;PQR=3097.87;PQA=2515.0;SRF=0;SRR=1;SAF=0;SAR=5;SRP=5.18177;SAP=13.8677;AB=0.0735294;ABP=110.434;RUN=1;RPP=3.44459;RPPR=5.18177;RPL=3.0;RPR=2.0;EPP=3.44459;EPPR=5.18177;DPRA=0.0;ODDS=1.39504;GTI=0;TYPE=del;CIGAR=1M9D61M;NUMALT=5;MEANALT=8.5;LEN=9;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chrX 66765161 . AGCA TGCT 1028.52 REJECT SOMATIC;NS=2;DP=68;DPB=232.549;AC=1;AN=3;AF=0.0;RO=1;AO=2;PRO=84.1167;PAO=29.0333;QR=39;QA=74;PQR=3097.87;PQA=1050.7;SRF=0;SRR=1;SAF=2;SAR=0;SRP=5.18177;SAP=7.35324;AB=0.1;ABP=30.8051;RUN=1;RPP=7.35324;RPPR=5.18177;RPL=0.0;RPR=2.0;EPP=7.35324;EPPR=5.18177;DPRA=0.0;ODDS=1.39504;GTI=0;TYPE=complex;CIGAR=3M1X2M1X64M;NUMALT=5;MEANALT=7.0;LEN=71;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chrX 66766356 . T TGGC 1890.32 REJECT NS=2;DP=116;DPB=231.13;AC=2;AN=2;AF=0.375;RO=4;AO=14;PRO=86.0833;PAO=86.0833;QR=151;QA=461;PQR=3117.25;PQA=3117.25;SRF=2;SRR=2;SAF=8;SAR=6;SRP=3.0103;SAP=3.63072;AB=0.12069;ABP=147.975;RUN=1;RPP=12.937;RPPR=5.18177;RPL=11.0;RPR=3.0;EPP=5.49198;EPPR=5.18177;DPRA=0.0;ODDS=1.87233;GTI=1;TYPE=ins;CIGAR=1M3I53M;NUMALT=3;MEANALT=10.5;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=0.024;FS=1.55;M [...]
+chrX 66766356 . TGGCGGCGGCGGC T 1890.32 REJECT NS=2;DP=116;DPB=231.13;AC=2;AN=2;AF=0.5;RO=4;AO=74;PRO=86.0833;PAO=76.5833;QR=151;QA=2271;PQR=3117.25;PQA=2760.75;SRF=2;SRR=2;SAF=50;SAR=24;SRP=3.0103;SAP=22.847;AB=0.637931;ABP=22.1792;RUN=1;RPP=3.47981;RPPR=5.18177;RPL=39.0;RPR=35.0;EPP=3.47981;EPPR=5.18177;DPRA=0.0;ODDS=1.87233;GTI=1;TYPE=del;CIGAR=1M12D41M;NUMALT=3;MEANALT=10.5;LEN=12;MQM=60.9459;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSu [...]
+chrX 66766356 . TGGCGGCGGCGGCGGC T 1890.32 REJECT NS=2;DP=116;DPB=231.13;AC=1;AN=3;AF=0.0;RO=4;AO=7;PRO=86.0833;PAO=66.25;QR=151;QA=199;PQR=3117.25;PQA=2373.75;SRF=2;SRR=2;SAF=4;SAR=3;SRP=3.0103;SAP=3.32051;AB=0.0603448;ABP=197.769;RUN=1;RPP=3.32051;RPPR=5.18177;RPL=3.0;RPR=4.0;EPP=10.7656;EPPR=5.18177;DPRA=0.0;ODDS=1.87233;GTI=1;TYPE=del;CIGAR=1M15D38M;NUMALT=3;MEANALT=10.5;LEN=15;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL [...]
+chrX 69001530 . G T 8134.6 REJECT NS=2;DP=338;DPB=390.0;AC=2;AN=4;AF=0.5;RO=124;AO=266;PRO=0.0;PAO=0.0;QR=4776;QA=10294;PQR=0.0;PQA=0.0;SRF=57;SRR=67;SAF=121;SAR=145;SRP=4.76149;SAP=7.71244;AB=0.682051;ABP=115.281;RUN=1;RPP=5.10014;RPPR=3.0103;RPL=141.0;RPR=125.0;EPP=3.04295;EPPR=6.44263;DPRA=0.0;ODDS=310.925;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.439;Dels=0.0;FS=2.717;HaplotypeScore=0.9665 [...]
+chrX 70341169 . A C 7131.5 REJECT NS=2;DP=290;DPB=329.0;AC=2;AN=4;AF=0.5;RO=87;AO=242;PRO=0.0;PAO=0.0;QR=3303;QA=9118;PQR=0.0;PQA=0.0;SRF=54;SRR=33;SAF=151;SAR=91;SRP=14.0174;SAP=35.3132;AB=0.735562;ABP=161.581;RUN=1;RPP=85.7057;RPPR=6.03039;RPL=73.0;RPR=169.0;EPP=4.76901;EPPR=3.03526;DPRA=0.0;ODDS=222.293;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.2479;MQMR=60.0;PAIRED=0.991736;PAIREDR=0.988506;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.3925;Dels=0.0;FS=0.0;HaplotypeSco [...]
+chrX 70347330 . G A 2017.44 REJECT NS=2;DP=266;DPB=295.0;AC=2;AN=4;AF=0.5;RO=201;AO=94;PRO=0.0;PAO=0.0;QR=7547;QA=3585;PQR=0.0;PQA=0.0;SRF=68;SRR=133;SAF=32;SAR=62;SRP=48.6544;SAP=23.801;AB=0.318644;ABP=87.2855;RUN=1;RPP=23.801;RPPR=57.47;RPL=62.0;RPR=32.0;EPP=7.53805;EPPR=6.13247;DPRA=0.0;ODDS=132.732;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=59.9801;PAIRED=0.989362;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.186;Dels=0.0;FS=0.2975;HaplotypeScore=7.79 [...]
+chrX 70349947 . A C 9510.16 REJECT NS=2;DP=402;DPB=457.0;AC=2;AN=4;AF=0.5;RO=146;AO=311;PRO=0.0;PAO=0.0;QR=5562;QA=12045;PQR=0.0;PQA=0.0;SRF=59;SRR=87;SAF=140;SAR=171;SRP=14.6708;SAP=9.72022;AB=0.680525;ABP=132.372;RUN=1;RPP=17.1493;RPPR=3.06979;RPL=178.0;RPR=133.0;EPP=5.53088;EPPR=11.5772;DPRA=0.0;ODDS=332.397;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.990354;PAIREDR=0.993151;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=1.7585;Dels=0.0;FS=1.2935;Haploty [...]
+chrX 70361967 . G A 9732.51 REJECT NS=2;DP=259;DPB=295.0;AC=4;AN=4;AF=1.0;RO=0;AO=295;PRO=0.0;PAO=0.0;QR=0;QA=11217;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=167;SAR=128;SRP=0.0;SAP=14.2063;AB=0.0;ABP=0.0;RUN=1;RPP=114.374;RPPR=0.0;RPL=86.0;RPR=209.0;EPP=10.0841;EPPR=0.0;DPRA=0.0;ODDS=48.5976;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.635;SOR=0.946 GT:GQ [...]
+chrX 76937963 . G C 2422.425 REJECT NS=2;DP=352;DPB=402.0;AC=2;AN=4;AF=0.5;RO=283;AO=119;PRO=0.0;PAO=0.0;QR=10730;QA=4485;PQR=0.0;PQA=0.0;SRF=151;SRR=132;SAF=68;SAR=51;SRP=5.78027;SAP=8.28388;AB=0.29602;ABP=148.294;RUN=1;RPP=3.90444;RPPR=3.38628;RPL=63.0;RPR=56.0;EPP=3.46649;EPPR=11.3662;DPRA=0.0;ODDS=324.108;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.983193;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.4565;Dels=0.0;FS=2.442;HaplotypeScore= [...]
+chrX 100615023 . T G 530.784 REJECT NS=1;DP=54;DPB=54.0;AC=1;AN=4;AF=0.5;RO=32;AO=22;PRO=0.0;PAO=0.0;QR=1243;QA=846;PQR=0.0;PQA=0.0;SRF=17;SRR=15;SAF=14;SAR=8;SRP=3.28173;SAP=6.56362;AB=0.407407;ABP=7.03155;RUN=1;RPP=34.9902;RPPR=42.0968;RPL=2.0;RPR=20.0;EPP=6.56362;EPPR=3.28173;DPRA=0.0;ODDS=122.218;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.954545;PAIREDR=1.0;technology.ILLUMINA=1.0;BaseQRankSum=-0.695;FS=2.418;MLEAC=1;MLEAF=0.5;MQ=60.0;MQRankSum=-0. [...]
+chrX 118514315 . G A 8734.84 REJECT NS=2;DP=383;DPB=432.0;AC=2;AN=4;AF=0.5;RO=142;AO=290;PRO=0.0;PAO=0.0;QR=5458;QA=11149;PQR=0.0;PQA=0.0;SRF=55;SRR=87;SAF=117;SAR=173;SRP=18.6694;SAP=26.4922;AB=0.671296;ABP=113.112;RUN=1;RPP=37.6341;RPPR=6.92507;RPL=179.0;RPR=111.0;EPP=5.43636;EPPR=3.56081;DPRA=0.0;ODDS=274.051;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.996552;PAIREDR=1.0;technology.ILLUMINA=1.0;MQ0=0;BaseQRankSum=0.8085;Dels=0.0;FS=3.868;HaplotypeSco [...]
+chrX 129147079 . T C 11646.15 REJECT NS=2;DP=303;DPB=343.0;AC=4;AN=4;AF=1.0;RO=0;AO=343;PRO=0.0;PAO=0.0;QR=0;QA=13245;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=203;SAR=140;SRP=0.0;SAP=28.1373;AB=0.0;ABP=0.0;RUN=1;RPP=3.16857;RPPR=0.0;RPL=174.0;RPR=169.0;EPP=4.08021;EPPR=0.0;DPRA=0.0;ODDS=53.6287;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=60.0;MQMR=0.0;PAIRED=0.997085;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;Dels=0.0;FS=0.0;HaplotypeScore=3.9652;MLEAC=2;MLEAF=1.0;MQ=60.0;QD=28.765;SOR= [...]
+chrX 132838305 . G GA 134.813 REJECT NS=1;DP=62;DPB=77.5417;AC=1;AN=3;AF=0.0;RO=34;AO=6;PRO=14.6667;PAO=8.66667;QR=1247;QA=154;PQR=520.333;PQA=304.333;SRF=4;SRR=30;SAF=1;SAR=5;SRP=46.1843;SAP=8.80089;AB=0.0967742;ABP=90.5697;RUN=1;RPP=4.45795;RPPR=4.03217;RPL=4.0;RPR=2.0;EPP=3.0103;EPPR=4.03217;DPRA=0.0;ODDS=31.0418;GTI=0;TYPE=ins;CIGAR=1M1I23M;NUMALT=2;MEANALT=7.0;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMI [...]
+chrX 132838305 . GA G 134.813 REJECT NS=1;DP=62;DPB=77.5417;AC=1;AN=4;AF=0.5;RO=34;AO=13;PRO=14.6667;PAO=6.66667;QR=1247;QA=390;PQR=520.333;PQA=221.333;SRF=4;SRR=30;SAF=4;SAR=9;SRP=46.1843;SAP=7.18621;AB=0.209677;ABP=48.4011;RUN=1;RPP=3.17734;RPPR=4.03217;RPL=7.0;RPR=6.0;EPP=11.1951;EPPR=4.03217;DPRA=0.0;ODDS=31.0418;GTI=0;TYPE=del;CIGAR=1M1D22M;NUMALT=2;MEANALT=7.0;LEN=1;MQM=60.7692;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;BaseQRankSum=-0.423;FS=3.375;M [...]
+chrX 132888207 . T A 208.351 REJECT NS=2;DP=112;DPB=143.419;AC=2;AN=2;AF=0.0;RO=46;AO=3;PRO=28.7167;PAO=0.0;QR=1732;QA=44;PQR=989.467;PQA=0.0;SRF=0;SRR=46;SAF=0;SAR=3;SRP=102.898;SAP=9.52472;AB=0.0267857;ABP=220.856;RUN=1;RPP=3.73412;RPPR=4.70971;RPL=1.0;RPR=2.0;EPP=3.73412;EPPR=4.70971;DPRA=0.0;ODDS=9.3745;GTI=0;TYPE=snp;CIGAR=1X30M;NUMALT=5;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV [...]
+chrX 132888207 . T TA 208.351 REJECT NS=2;DP=112;DPB=143.419;AC=2;AN=3;AF=0.25;RO=46;AO=18;PRO=28.7167;PAO=15.7167;QR=1732;QA=428;PQR=989.467;PQA=533.467;SRF=0;SRR=46;SAF=0;SAR=18;SRP=102.898;SAP=42.0968;AB=0.160714;ABP=114.996;RUN=1;RPP=3.49285;RPPR=4.70971;RPL=10.0;RPR=8.0;EPP=3.49285;EPPR=4.70971;DPRA=0.0;ODDS=9.3745;GTI=0;TYPE=ins;CIGAR=1M1I30M;NUMALT=5;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.944444;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL: [...]
+chrX 132888207 . TA T 208.351 REJECT NS=2;DP=112;DPB=143.419;AC=2;AN=3;AF=0.25;RO=46;AO=20;PRO=28.7167;PAO=15.7167;QR=1732;QA=439;PQR=989.467;PQA=507.967;SRF=0;SRR=46;SAF=1;SAR=19;SRP=102.898;SAP=38.1882;AB=0.178571;ABP=103.518;RUN=1;RPP=3.44459;RPPR=4.70971;RPL=11.0;RPR=9.0;EPP=4.74748;EPPR=4.70971;DPRA=0.0;ODDS=9.3745;GTI=0;TYPE=del;CIGAR=1M1D29M;NUMALT=5;MEANALT=12.5;LEN=1;MQM=60.0;MQMR=60.0;PAIRED=0.95;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC;MQ0=0;BaseQRankSum=-0.03;FS= [...]
+chrX 132888207 . TAA T 208.351 REJECT NS=2;DP=112;DPB=143.419;AC=2;AN=2;AF=0.0;RO=46;AO=6;PRO=28.7167;PAO=11.05;QR=1732;QA=114;PQR=989.467;PQA=364.3;SRF=0;SRR=46;SAF=1;SAR=5;SRP=102.898;SAP=8.80089;AB=0.0535714;ABP=196.892;RUN=1;RPP=3.0103;RPPR=4.70971;RPL=3.0;RPR=3.0;EPP=4.45795;EPPR=4.70971;DPRA=0.0;ODDS=9.3745;GTI=0;TYPE=del;CIGAR=1M2D28M;NUMALT=5;MEANALT=12.5;LEN=2;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMA [...]
+chrX 132888207 . TAAA T 208.351 REJECT NS=2;DP=112;DPB=143.419;AC=2;AN=2;AF=0.0;RO=46;AO=3;PRO=28.7167;PAO=9.8;QR=1732;QA=60;PQR=989.467;PQA=319.8;SRF=0;SRR=46;SAF=0;SAR=3;SRP=102.898;SAP=9.52472;AB=0.0267857;ABP=220.856;RUN=1;RPP=3.73412;RPPR=4.70971;RPL=1.0;RPR=2.0;EPP=3.73412;EPPR=4.70971;DPRA=0.0;ODDS=9.3745;GTI=0;TYPE=del;CIGAR=1M3D27M;NUMALT=5;MEANALT=12.5;LEN=3;MQM=60.0;MQMR=60.0;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF [...]
+chrX 148500282 . CAC TAT 10619.2 REJECT NS=2;DP=290;DPB=335.333;AC=4;AN=4;AF=1.0;RO=0;AO=327;PRO=0.0;PAO=10.0;QR=0;QA=11975;PQR=0.0;PQA=363.0;SRF=0;SRR=0;SAF=257;SAR=70;SRP=0.0;SAP=235.225;AB=0.0;ABP=0.0;RUN=1;RPP=31.0668;RPPR=0.0;RPL=131.0;RPR=196.0;EPP=3.81381;EPPR=0.0;DPRA=0.0;ODDS=53.6126;GTI=0;TYPE=complex;CIGAR=1X1M1X;NUMALT=1;MEANALT=2.0;LEN=3;MQM=60.0612;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=0;JOINED;BaseQRankSum=1.622;Dels=0.0;FS=0.0;HaplotypeScore=4.8325;M [...]
+chrX 150872315 . T C 3371.12 REJECT NS=1;DP=110;DPB=110.0;AC=2;AN=4;AF=1.0;RO=0;AO=110;PRO=0.0;PAO=0.0;QR=0;QA=4016;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=62;SAR=48;SRP=0.0;SAP=6.87947;AB=0.0;ABP=0.0;RUN=1;RPP=177.439;RPPR=0.0;RPL=102.0;RPR=8.0;EPP=3.08926;EPPR=0.0;DPRA=0.0;ODDS=73.058;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=59.4727;MQMR=0.0;PAIRED=0.981818;PAIREDR=0.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID:CallMU: [...]
+chrX 150872329 . G T 2325.3 REJECT NS=1;DP=83;DPB=83.0;AC=2;AN=4;AF=1.0;RO=1;AO=82;PRO=0.0;PAO=0.0;QR=2;QA=3011;PQR=0.0;PQA=0.0;SRF=1;SRR=0;SAF=57;SAR=25;SRP=5.18177;SAP=30.1272;AB=0.0;ABP=0.0;RUN=1;RPP=118.363;RPPR=5.18177;RPL=74.0;RPR=8.0;EPP=18.2636;EPPR=5.18177;DPRA=0.0;ODDS=56.5748;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=54.9024;MQMR=6.0;PAIRED=0.97561;PAIREDR=1.0;technology.ILLUMINA=1.0 GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT:GMIMAF:GMICOV:CallHC:CallUG:CallFB:CallPI:CallSID: [...]
+chrX 150872385 . TGTGTGTG T 119.803 REJECT NS=1;DP=52;DPB=32.6923;AC=1;AN=4;AF=0.5;RO=11;AO=20;PRO=9.5;PAO=2.5;QR=379;QA=383;PQR=204.333;PQA=64.3333;SRF=0;SRR=11;SAF=4;SAR=16;SRP=26.8965;SAP=18.6449;AB=0.384615;ABP=9.02361;RUN=1;RPP=46.4397;RPPR=19.0002;RPL=0.0;RPR=20.0;EPP=18.6449;EPPR=19.0002;DPRA=0.0;ODDS=10.8666;GTI=0;TYPE=del;CIGAR=1M7D5M;NUMALT=3;MEANALT=5.0;LEN=7;MQM=58.65;MQMR=43.6364;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chrX 150872385 . TGTGTGTGTG T 119.803 REJECT NS=1;DP=52;DPB=32.6923;AC=1;AN=3;AF=0.0;RO=11;AO=13;PRO=9.5;PAO=2.5;QR=379;QA=275;PQR=204.333;PQA=73.3333;SRF=0;SRR=11;SAF=1;SAR=12;SRP=26.8965;SAP=23.2217;AB=0.25;ABP=31.2394;RUN=1;RPP=31.2394;RPPR=19.0002;RPL=0.0;RPR=13.0;EPP=23.2217;EPPR=19.0002;DPRA=0.0;ODDS=10.8666;GTI=0;TYPE=del;CIGAR=1M9D3M;NUMALT=3;MEANALT=5.0;LEN=9;MQM=56.9231;MQMR=43.6364;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT: [...]
+chrX 150872385 . TGTGTGTGTGTG T 119.803 REJECT NS=1;DP=52;DPB=32.6923;AC=1;AN=3;AF=0.0;RO=11;AO=6;PRO=9.5;PAO=0.5;QR=379;QA=132;PQR=204.333;PQA=0.0;SRF=0;SRR=11;SAF=0;SAR=6;SRP=26.8965;SAP=16.0391;AB=0.115385;ABP=69.8248;RUN=1;RPP=16.0391;RPPR=19.0002;RPL=0.0;RPR=6.0;EPP=16.0391;EPPR=19.0002;DPRA=0.0;ODDS=10.8666;GTI=0;TYPE=del;CIGAR=1M11D1M;NUMALT=3;MEANALT=5.0;LEN=11;MQM=56.6667;MQMR=43.6364;PAIRED=1.0;PAIREDR=1.0;technology.ILLUMINA=1.0;SPLITMULTIALLELIC GT:GQ:DP:RO:QR:AO:QA:GL:GMIMUT [...]
+chrX 153629155 . A G 9236.215 REJECT NS=2;DP=277;DPB=316.0;AC=4;AN=4;AF=1.0;RO=0;AO=316;PRO=0.0;PAO=0.0;QR=0;QA=11984;PQR=0.0;PQA=0.0;SRF=0;SRR=0;SAF=215;SAR=101;SRP=0.0;SAP=92.3155;AB=0.0;ABP=0.0;RUN=1;RPP=3.45009;RPPR=0.0;RPL=162.0;RPR=154.0;EPP=7.6556;EPPR=0.0;DPRA=0.0;ODDS=71.4974;GTI=0;TYPE=snp;CIGAR=1X;NUMALT=1;MEANALT=1.0;LEN=1;MQM=39.4557;MQMR=0.0;PAIRED=1.0;PAIREDR=0.0;technology.ILLUMINA=1.0;MQ0=30;Dels=0.0;FS=0.0;HaplotypeScore=1.9997;MLEAC=2;MLEAF=1.0;MQ=38.525;QD=29.06;SOR=1 [...]
diff --git a/test/formats/nosample.vcf b/test/formats/nosample.vcf
new file mode 100644
index 0000000..fe22d98
--- /dev/null
+++ b/test/formats/nosample.vcf
@@ -0,0 +1,140 @@
+##fileformat=VCFv4.2
+##fileDate=20150729
+##source=SNV-Unifier
+##reference=file:///home/dnanexus/genome.fa
+##phasing=none
+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic event">
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
+##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
+##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
+##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
+##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
+##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
+##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
+##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
+##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
+##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
+##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
+##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without.">
+##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
+##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
+##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
+##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
+##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
+##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
+##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
+##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
+##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
+##INFO=<ID=technology.ILLUMINA,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from ILLUMINA">
+##INFO=<ID=SPLITMULTIALLELIC,Number=0,Type=Flag,Description="Variant represents one alternate allele from a multiallelic variant call.">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=VT,Number=1,Type=String,Description="Variant type, can be SNP, MNP, INS or DEL">
+##INFO=<ID=JOINED,Number=0,Type=Flag,Description="Variant is the result of joining adjacent SNPs/MNPs. Please use caution when interpreting sample-specific values.">
+##INFO=<ID=ALERT,Number=0,Type=Flag,Description="Variant is adjacent to other variants, but case was too complex for joinAdjacentSNPs to handle. Please review.">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=PF,Number=1,Type=Integer,Description="The number of samples carry the variant">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=NTLEN,Number=.,Type=Integer,Description="Number of bases inserted in place of deleted code">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
+##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
+##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
+##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
+##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)">
+##INFO=<ID=ADERROR,Number=0,Type=Flag,Description="The AD field from the original variant caller VCF has an error at this locus. Please use caution when interpreting AD, GMIMAF, and GMICOV.">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+##FORMAT=<ID=BQ,Number=A,Type=Float,Description="Average base quality for reads supporting alleles">
+##FORMAT=<ID=FA,Number=A,Type=Float,Description="Allele fraction of the alternate allele with regard to reference">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal,0=wildtype,1=germline,2=somatic,3=LOH,4=post-transcriptional modification,5=unknown">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Reference depth, how many reads support the reference">
+##FORMAT=<ID=GMIMUT,Number=A,Type=Integer,Description="GMI-derived mutant read count: the number of reads observed at the variant locus that support each ALT allele.">
+##FORMAT=<ID=GMIMAF,Number=A,Type=Integer,Description="GMI-derived MAF: the proportion of reads observed at the variant locus that support each ALT allele.">
+##FORMAT=<ID=GMICOV,Number=1,Type=Integer,Description="GMI-derived coverage: total read depth at the variant locus.">
+##FORMAT=<ID=AD,Number=2,Type=Integer,Description="# of reads supporting consensus reference/indel at the site">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total coverage at the site">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MM,Number=2,Type=Float,Description="Average # of mismatches per ref-/consensus indel-supporting read">
+##FORMAT=<ID=MQS,Number=2,Type=Float,Description="Average mapping qualities of ref-/consensus indel-supporting reads">
+##FORMAT=<ID=NQSBQ,Number=2,Type=Float,Description="Within NQS window: average quality of bases in ref-/consensus indel-supporting reads">
+##FORMAT=<ID=NQSMM,Number=2,Type=Float,Description="Within NQS window: fraction of mismatching bases in ref/consensus indel-supporting reads">
+##FORMAT=<ID=REnd,Number=2,Type=Integer,Description="Median/mad of indel offsets from the ends of the reads">
+##FORMAT=<ID=RStart,Number=2,Type=Integer,Description="Median/mad of indel offsets from the starts of the reads">
+##FORMAT=<ID=SC,Number=4,Type=Integer,Description="Strandness: counts of forward-/reverse-aligned reference and indel-supporting reads (FwdRef,RevRef,FwdIndel,RevIndel)">
+##FORMAT=<ID=CallHC,Number=1,Type=Integer,Description="Variant was called by HaplotypeCaller">
+##FORMAT=<ID=CallUG,Number=1,Type=Integer,Description="Variant was called by UnifiedGenotyper">
+##FORMAT=<ID=CallFB,Number=1,Type=Integer,Description="Variant was called by freeBayes">
+##FORMAT=<ID=CallPI,Number=1,Type=Integer,Description="Variant was called by pindel">
+##FORMAT=<ID=CallSID,Number=1,Type=Integer,Description="Variant was called by SomaticIndelDetector">
+##FORMAT=<ID=CallMU,Number=1,Type=Integer,Description="Variant was called by MuTect">
+##FORMAT=<ID=LR,Number=1,Type=Float,Description="CNV log2 ratio">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=REJECT,Description="Not somatic due to normal call frequency or phred likelihoods: tumor: 35, normal 35.">
+##contig=<ID=chrM,length=16571>
+##contig=<ID=chr1,length=249250621>
+##contig=<ID=chr2,length=243199373>
+##contig=<ID=chr3,length=198022430>
+##contig=<ID=chr4,length=191154276>
+##contig=<ID=chr5,length=180915260>
+##contig=<ID=chr6,length=171115067>
+##contig=<ID=chr7,length=159138663>
+##contig=<ID=chr8,length=146364022>
+##contig=<ID=chr9,length=141213431>
+##contig=<ID=chr10,length=135534747>
+##contig=<ID=chr11,length=135006516>
+##contig=<ID=chr12,length=133851895>
+##contig=<ID=chr13,length=115169878>
+##contig=<ID=chr14,length=107349540>
+##contig=<ID=chr15,length=102531392>
+##contig=<ID=chr16,length=90354753>
+##contig=<ID=chr17,length=81195210>
+##contig=<ID=chr18,length=78077248>
+##contig=<ID=chr19,length=59128983>
+##contig=<ID=chr20,length=63025520>
+##contig=<ID=chr21,length=48129895>
+##contig=<ID=chr22,length=51304566>
+##contig=<ID=chrX,length=155270560>
+##contig=<ID=chrY,length=59373566>
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
diff --git a/test/formats/p2-20_1.cnr b/test/formats/p2-20_1.cnr
new file mode 100644
index 0000000..4d85f62
--- /dev/null
+++ b/test/formats/p2-20_1.cnr
@@ -0,0 +1,19090 @@
+chromosome start end gene log2 depth weight
+chr1 464423 664483 Background -1.1692 0.063131 0.297196
+chr1 676306 876366 Background -0.296369 0.625912 0.872633
+chr1 882963 1083008 Background -0.0910526 1.12911 0.982855
+chr1 1086530 1286590 Background -0.243692 1.02254 0.958583
+chr1 1508981 1509154 SSU72 -0.240325 280.636 0.465659
+chr1 1512177 1712224 Background -0.363181 0.804786 0.932087
+chr1 1715329 1915389 Background -0.295251 0.842607 0.947215
+chr1 1919111 2119169 Background -0.0793628 1.20299 0.95786
+chr1 2123226 2323286 Background -0.0648468 1.31114 0.913927
+chr1 2407978 2408183 PLCH2 -0.0556597 101.351 0.456289
+chr1 2409866 2410095 PLCH2 -0.111898 150.803 0.472758
+chr1 2411123 2411451 PLCH2 -0.582245 68.372 0.443161
+chr1 2411574 2411784 PLCH2 -0.0045977 151.619 0.437032
+chr1 2415834 2416097 PLCH2 -0.11198 132.369 0.394863
+chr1 2418292 2418472 PLCH2 -0.251859 147.228 0.4518
+chr1 2418560 2418846 PLCH2 -0.250291 130.874 0.448932
+chr1 2418986 2419185 PLCH2 -0.0236917 190.095 0.414784
+chr1 2420594 2420846 PLCH2 -0.164083 170.734 0.450697
+chr1 2421147 2421341 PLCH2 -0.313618 175.835 0.477494
+chr1 2422583 2422802 PLCH2 0.196428 182.772 0.436826
+chr1 2426243 2426422 PLCH2 -0.136084 115.648 0.428418
+chr1 2426870 2427049 PLCH2 -0.27876 89.2402 0.450138
+chr1 2427997 2428175 PLCH2 -0.0936396 133.938 0.476787
+chr1 2428224 2428479 PLCH2 -0.108165 128.741 0.42957
+chr1 2428888 2429083 PLCH2 -0.300335 99.0923 0.387024
+chr1 2429914 2430119 PLCH2 -0.0031316 56.639 0.351328
+chr1 2430126 2430312 PLCH2 0.0592653 104.532 0.384614
+chr1 2430471 2430703 PLCH2 -0.238224 111.461 0.449213
+chr1 2431021 2431202 PLCH2 -0.0330987 123.591 0.346201
+chr1 2433502 2433878 PLCH2 -0.43321 58.4681 0.356728
+chr1 2435318 2436685 PLCH2 -0.292787 56.9342 0.379282
+chr1 2441137 2641183 Background -0.264743 0.881912 0.945866
+chr1 2645892 2845952 Background -0.103727 0.836519 0.994728
+chr1 3003377 3003530 PRDM16 -0.0842387 207.412 0.437736
+chr1 3006394 3206454 Background 0.17249 1.36469 0.983423
+chr1 3208886 3408946 Background -0.0957203 1.10409 0.998696
+chr1 3412493 3612540 Background -0.113825 1.18094 0.932067
+chr1 3629030 3829090 Background -0.0450996 1.0933 0.979829
+chr1 3904252 4104312 Background 0.118094 0.544817 0.769104
+chr1 4107699 4307759 Background -0.00769879 0.792102 0.883772
+chr1 4510012 4510179 CGH -0.193363 222.701 0.448106
+chr1 4513384 4713444 Background -0.0241348 0.847096 0.944443
+chr1 4716231 4916280 Background 0.0892775 1.10299 0.999767
+chr1 4922738 5122798 Background 0.144887 0.905658 0.975315
+chr1 5136120 5336180 Background -0.178576 0.597936 0.942836
+chr1 5384800 5584860 Background -0.0709448 1.08071 0.939644
+chr1 5591951 5792011 Background -0.0911128 0.874103 0.982292
+chr1 5796817 5996871 Background 0.00339431 1.11153 0.993756
+chr1 6011253 6011428 NPHP4 -0.271154 258.389 0.437252
+chr1 6016405 6216465 Background 0.113585 1.24746 0.994012
+chr1 6218728 6418779 Background 0.0666423 1.24816 0.986901
+chr1 6424137 6624197 Background -0.514604 0.776487 0.973373
+chr1 6627129 6827189 Background -0.22962 0.703959 0.881694
+chr1 6830183 7030243 Background -0.00721869 0.861806 0.965558
+chr1 7032211 7232271 Background -0.137678 0.863726 0.998723
+chr1 7237734 7437794 Background -0.22193 0.727382 0.986497
+chr1 7503170 7503355 CAMTA1 -0.092038 231.503 0.453221
+chr1 7508101 7708161 Background -0.0204966 1.12915 0.996613
+chr1 7710999 7911059 Background -0.290406 0.718315 0.986936
+chr1 7915416 8115476 Background -0.125738 0.723413 0.982755
+chr1 8121018 8321078 Background -0.161895 0.730101 0.95156
+chr1 8325583 8525643 Background -0.0410958 1.00413 0.935734
+chr1 8527277 8727337 Background -0.377503 0.43369 0.959969
+chr1 8730201 8930261 Background -0.299204 0.53249 0.960635
+chr1 9032922 9033104 CA6 -0.0980039 272.94 0.477324
+chr1 9036433 9236493 Background -0.223151 0.811377 0.955863
+chr1 9240549 9440594 Background -0.0977308 1.27562 0.90373
+chr1 9446821 9646881 Background -0.286064 0.827927 0.99875
+chr1 9651373 9851431 Background -0.210591 0.871722 0.945843
+chr1 9856374 10056434 Background -0.372008 0.614021 0.882774
+chr1 10061041 10261101 Background -0.329637 0.50154 0.870985
+chr1 10264889 10464949 Background -0.342055 0.533725 0.971116
+chr1 10517836 10517977 CGH -0.234247 263.496 0.475868
+chr1 10525315 10725375 Background -0.176903 0.900415 0.961947
+chr1 10727711 10927771 Background -0.327432 1.09646 0.919175
+chr1 10930297 11130353 Background -0.372862 0.763726 0.943352
+chr1 11167450 11167630 MTOR -0.144238 284.483 0.461559
+chr1 11168190 11168371 MTOR -0.101737 272.254 0.48083
+chr1 11169288 11169470 MTOR -0.185679 244.654 0.42517
+chr1 11169646 11169824 MTOR -0.21089 251.73 0.470858
+chr1 11172844 11173024 MTOR -0.263946 356.1 0.478074
+chr1 11174327 11174549 MTOR -0.391457 228.973 0.453436
+chr1 11174809 11174986 MTOR -0.212783 284.825 0.470387
+chr1 11175391 11175570 MTOR -0.345604 229.257 0.479902
+chr1 11177004 11177187 MTOR -0.149946 292.339 0.466662
+chr1 11181252 11181456 MTOR -0.129233 257.73 0.475038
+chr1 11181984 11182210 MTOR 0.0627399 268.531 0.403569
+chr1 11184503 11184720 MTOR -0.106964 250.931 0.473603
+chr1 11186626 11186882 MTOR -0.0520266 245.938 0.459842
+chr1 11187018 11187237 MTOR -0.272438 227.256 0.47895
+chr1 11187633 11187899 MTOR -0.0441649 268.947 0.471889
+chr1 11188012 11188214 MTOR -0.022604 284.213 0.470493
+chr1 11188463 11188644 MTOR -0.25132 264.983 0.471006
+chr1 11188862 11189042 MTOR -0.221595 255.456 0.464367
+chr1 11189742 11189930 MTOR -0.0220399 286.697 0.476198
+chr1 11190533 11190864 MTOR 0.0706792 304.344 0.445365
+chr1 11193084 11193287 MTOR -0.145904 258.887 0.472293
+chr1 11194359 11194554 MTOR -0.154351 239.759 0.479601
+chr1 11199312 11199514 MTOR -0.0127131 268.441 0.479926
+chr1 11199542 11199749 MTOR -0.285255 230.329 0.461867
+chr1 11204656 11204846 MTOR -0.302064 215.153 0.479079
+chr1 11204966 11205140 MTOR 0.04377 277.707 0.465055
+chr1 11206682 11206861 MTOR -0.363734 241.151 0.475886
+chr1 11210130 11210310 MTOR -0.589197 228.45 0.432189
+chr1 11217156 11217373 MTOR -0.29818 238.101 0.479473
+chr1 11227439 11227613 MTOR -0.294746 209.92 0.472081
+chr1 11259262 11259494 MTOR -0.185108 216.091 0.470083
+chr1 11259548 11259797 MTOR -0.132123 259.036 0.473922
+chr1 11264565 11264797 MTOR -0.286866 279.556 0.431721
+chr1 11269321 11269545 MTOR -0.0159846 260.714 0.437182
+chr1 11270814 11270998 MTOR 0.0173782 306.777 0.475582
+chr1 11272317 11272564 MTOR -0.273679 234.587 0.481663
+chr1 11272800 11273003 MTOR -0.423453 225.65 0.477572
+chr1 11273408 11273657 MTOR -0.0206346 274.932 0.478826
+chr1 11276149 11276328 MTOR -0.284342 252.955 0.442383
+chr1 11288674 11289013 MTOR -0.017829 240.944 0.456356
+chr1 11290934 11291136 MTOR -0.221015 252.183 0.47686
+chr1 11291308 11291528 MTOR -0.27151 240.559 0.429583
+chr1 11292436 11292620 MTOR -0.145511 270.946 0.480735
+chr1 11293402 11293572 MTOR -0.268868 284.2 0.459704
+chr1 11294151 11294353 MTOR -0.293579 232.5 0.481031
+chr1 11297852 11298136 MTOR -0.302707 214.602 0.48196
+chr1 11298408 11298707 MTOR -0.27844 229.749 0.482976
+chr1 11300321 11300638 MTOR -0.0839634 258.726 0.460485
+chr1 11301558 11301779 MTOR -0.265927 211.602 0.478662
+chr1 11303118 11303391 MTOR -0.352336 218.341 0.467761
+chr1 11307632 11308191 MTOR -0.10673 233.664 0.486561
+chr1 11313846 11314070 MTOR -0.136023 283.701 0.476566
+chr1 11315996 11316280 MTOR -0.218472 244.489 0.483763
+chr1 11316937 11317256 MTOR -0.126023 255.426 0.481938
+chr1 11318494 11318684 MTOR -0.0836712 281.426 0.480985
+chr1 11319252 11319500 MTOR -0.172708 294.512 0.44658
+chr1 11329519 11529579 Background -0.214542 0.903609 0.97078
+chr1 11538462 11738519 Background -0.0755338 0.910361 0.897317
+chr1 11743082 11943142 Background -0.0919337 1.13092 0.975277
+chr1 12042647 12042826 MFN2 -0.135053 300.341 0.466827
+chr1 12046349 12246409 Background 0.0732802 1.29981 0.954588
+chr1 12250263 12450323 Background -0.179392 0.665395 0.996807
+chr1 12453842 12653902 Background -0.190092 0.756408 0.990769
+chr1 12656494 12856554 Background -0.234648 0.641323 0.933098
+chr1 13082310 13282370 Background -0.734541 0.079321 0.395095
+chr1 13801713 13801869 LRRC38 -0.187091 244.673 0.453611
+chr1 13806369 14006427 Background -0.180269 0.63828 0.905023
+chr1 14012990 14213050 Background -0.297748 0.630911 0.970509
+chr1 14217258 14417318 Background -0.37482 0.693222 0.890642
+chr1 14421647 14621707 Background -0.173999 0.570734 0.947313
+chr1 14633878 14833938 Background -0.345001 0.591837 0.950298
+chr1 15011426 15011610 KAZN -0.168314 231.804 0.477324
+chr1 15015479 15215538 Background -0.408126 0.769818 0.963181
+chr1 15218358 15418409 Background -0.287309 1.01704 0.957464
+chr1 15423185 15623245 Background -0.191923 0.972903 0.925574
+chr1 15626086 15826146 Background -0.418636 0.759742 0.977301
+chr1 15829563 16029623 Background -0.524786 0.468055 0.880298
+chr1 16035376 16235436 Background -0.443125 0.53342 0.85612
+chr1 16237207 16437267 Background -0.432823 0.876067 0.989012
+chr1 16517097 16517252 CGH -1.0497 179.884 0.478653
+chr1 16520955 16721015 Background -0.352854 0.667855 0.953961
+chr1 16731934 16931985 Background -0.306583 0.850623 0.882817
+chr1 16948731 17148791 Background 0.249012 1.35115 0.749004
+chr1 17151966 17352023 Background -0.156221 1.34197 0.729822
+chr1 17355788 17555848 Background -0.0204955 1.04051 0.984857
+chr1 17557769 17757818 Background -0.203272 0.909487 0.968982
+chr1 17760246 17960305 Background -0.220699 0.892747 0.950307
+chr1 18026101 18026277 CGH -0.0859931 261.324 0.469443
+chr1 18030195 18230255 Background -0.0155587 0.998241 0.973343
+chr1 18236487 18436547 Background 0.00386601 1.03646 0.987976
+chr1 18438173 18638233 Background 0.18293 1.19491 0.99179
+chr1 18644708 18844768 Background 0.121752 1.06618 0.985898
+chr1 18847638 19047698 Background 0.295426 1.5675 0.912457
+chr1 19052992 19253041 Background 0.0598512 1.27921 0.951724
+chr1 19264435 19464495 Background -0.18157 0.941178 0.950273
+chr1 19504013 19504193 UBR4 -0.237916 277.089 0.467827
+chr1 19510377 19710437 Background -0.0378936 0.991408 0.99295
+chr1 19717435 19917495 Background -0.100749 0.806663 0.975096
+chr1 19921975 20122035 Background 0.0127435 1.02431 0.995008
+chr1 20124216 20324276 Background -0.113408 0.704614 0.963993
+chr1 20327622 20527676 Background -0.097487 0.816275 0.997321
+chr1 20530474 20730531 Background 0.157645 1.12855 0.984442
+chr1 20732674 20932734 Background -0.132895 0.798735 0.933352
+chr1 21016504 21016620 KIF17 -0.11138 265.603 0.474593
+chr1 21019843 21219903 Background 0.0233662 0.731865 0.95021
+chr1 21221453 21421513 Background -0.257534 0.46524 0.960205
+chr1 21424320 21624380 Background -0.130461 0.712516 0.932653
+chr1 21663884 21863930 Background -0.0954227 0.839292 0.97393
+chr1 21870126 22070186 Background 0.112071 1.08217 0.957422
+chr1 22075632 22275678 Background 0.0283018 1.22034 0.98169
+chr1 22404948 22405110 CDC42 0.0615463 324.66 0.459801
+chr1 22408148 22408336 CDC42 0.000760297 326.213 0.463872
+chr1 22412888 22412991 CDC42 -0.296945 310.087 0.476751
+chr1 22412994 22413069 CDC42 -0.135284 355.88 0.426756
+chr1 22413113 22413393 CDC42 -0.119304 327.436 0.467895
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diff --git a/test/formats/p2-20_2.cnr b/test/formats/p2-20_2.cnr
new file mode 100644
index 0000000..a05bffa
--- /dev/null
+++ b/test/formats/p2-20_2.cnr
@@ -0,0 +1,19090 @@
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+chrY 13892303 14092363 Background -5.81753 0.003529 0.952647
+chrY 14105695 14305755 Background -6.28437 0.002524 0.999119
+chrY 14311781 14511841 Background -5.39609 0.005048 0.899287
+chrY 14519834 14719894 Background -7.69654 0.00101 0.91824
+chrY 14721312 14921372 Background -2.01841 0.047366 0.932864
+chrY 15007106 15007258 CGH -5.4547 2.64474 0.490503
+chrY 15035272 15235322 Background -7.54932 0.00101 0.953052
+chrY 15243779 15443839 Background -2.5628 0.03218 0.916079
+chrY 15454400 15654460 Background -1.98303 0.047346 0.919315
+chrY 15664504 15864564 Background -18.8247 0 0.997359
+chrY 15866292 16066352 Background -5.79653 0.003534 0.978292
+chrY 16074764 16274824 Background -18.8059 0 0.963098
+chrY 16289899 16489959 Background -18.8063 0 0.95736
+chrY 16504317 16504496 CGH -6.26247 1.59218 0.492878
+chrY 16508873 16708933 Background -8.58055 0.000505 0.985274
+chrY 16710165 16910225 Background -6.97703 0.00151 0.915313
+chrY 16912563 17112623 Background -7.53452 0.00101 0.916625
+chrY 17125255 17325315 Background -6.2349 0.002524 0.917823
+chrY 17334482 17534542 Background -18.8443 0 0.983455
+chrY 17544681 17744741 Background -6.26749 0.002524 0.995398
+chrY 17748364 17948424 Background -18.7753 0 0.925008
+chrY 18022728 18022918 CGH -7.60248 0.631579 0.493679
+chrY 18037695 18237755 Background -18.7785 0 0.929835
+chrY 18289803 18489863 Background -8.53192 0.000505 0.91886
+chrY 18498222 18698282 Background -7.5395 0.00101 0.864842
+chrY 18707140 18907200 Background -18.7928 0 0.889541
+chrY 18912088 19112148 Background -7.56194 0.00101 0.930885
+chrY 19122475 19322535 Background -8.60497 0.0005 0.971418
+chrY 19506484 19506650 CGH -5.09082 3.39759 0.492657
+chrY 20704594 20904654 Background -18.7993 0 0.955395
+chrY 21033917 21034071 CGH -19.0917 0 0.491148
+chrY 21035683 21235743 Background -4.40102 0.009292 0.986116
+chrY 21253931 21453991 Background -7.60688 0.00101 0.9839
+chrY 21517265 21717325 Background -8.58758 0.000505 0.958676
+chrY 21735973 21936033 Background -6.62302 0.001944 0.928853
+chrY 21983942 22184002 Background -8.56721 0.0005 0.890524
+chrY 22554203 22554385 CGH -4.92975 3.70879 0.491301
+chrY 22557559 22757619 Background -18.7746 0 0.922307
+chrY 22762602 22962661 Background -7.61942 0.00101 0.993059
+chrY 22968227 23168287 Background -6.59668 0.002019 0.962744
+chrY 23171308 23371368 Background -7.60753 0.00101 0.993987
+chrY 23376094 23576148 Background -6.20944 0.002524 0.918778
+chrY 23647930 23847985 Background -7.01435 0.001515 0.975335
+chrY 24000592 24000773 CGH -5.77275 2.11602 0.490815
+chrY 24259406 24459466 Background -18.8312 0 0.994939
+chrY 27228274 27428334 Background -18.8242 0 0.996423
+chrY 28462976 28463157 CGH -6.05074 1.82873 0.492811
+chrY 28463434 28463622 CGH -5.61955 2.5266 0.493306
+chrY 28514032 28514208 CGH -6.97549 0.960227 0.493413
+chrY 28522911 28722971 Background -3.9991 0.012106 0.955341
diff --git a/test/formats/refflat-mini.txt b/test/formats/refflat-mini.txt
new file mode 100644
index 0000000..1f77ade
--- /dev/null
+++ b/test/formats/refflat-mini.txt
@@ -0,0 +1,100 @@
+DDX11L1 NR_046018 chr1 + 11873 14409 14409 14409 3 11873,12612,13220, 12227,12721,14409,
+WASH7P NR_024540 chr1 - 14361 29370 29370 29370 11 14361,14969,15795,16606,16857,17232,17605,17914,18267,24737,29320, 14829,15038,15947,16765,17055,17368,17742,18061,18366,24891,29370,
+MIR6859-1 NR_106918 chr1 - 17368 17436 17436 17436 1 17368, 17436,
+MIR6859-2 NR_107062 chr1 - 17368 17436 17436 17436 1 17368, 17436,
+MIR6859-3 NR_107063 chr1 - 17368 17436 17436 17436 1 17368, 17436,
+MIR6859-4 NR_128720 chr1 - 17368 17436 17436 17436 1 17368, 17436,
+MIR1302-2 NR_036051 chr1 + 30365 30503 30503 30503 1 30365, 30503,
+MIR1302-9 NR_036266 chr1 + 30365 30503 30503 30503 1 30365, 30503,
+MIR1302-10 NR_036267 chr1 + 30365 30503 30503 30503 1 30365, 30503,
+MIR1302-11 NR_036268 chr1 + 30365 30503 30503 30503 1 30365, 30503,
+FBXL22 NM_203373 chr15 + 63889551 63894620 63889591 63893885 2 63889551,63893494, 63889944,63894620,
+LOC729737 NR_039983 chr1 - 134772 140566 140566 140566 3 134772,139789,140074, 139696,139847,140566,
+LOC100132287 NR_028322 chr1 + 323891 328581 328581 328581 3 323891,324287,324438, 324060,324345,328581,
+LOC100132062 NR_028325 chr1 + 323891 328581 328581 328581 3 323891,324287,324438, 324060,324345,328581,
+LOC100133331 NR_028327 chr1 + 323891 328581 328581 328581 4 323891,324287,324438,327035, 324060,324345,326938,328581,
+LOC101928626 NR_125957 chr1 - 562759 564389 564389 564389 3 562759,563340,564298, 563203,563603,564389,
+MIR6723 NR_106781 chr1 - 567704 567793 567793 567793 1 567704, 567793,
+ADGRG1 NM_001145770 chr16 + 57653909 57698951 57684199 57697494 15 57653909,57675502,57684164,57685111,57687114,57687897,57689310,57689787,57690137,57690425,57691284,57693324,57694679,57695608,57697363, 57654048,57675620,57684263,57685534,57687247,57688045,57689442,57689904,57690183,57690529,57691403,57693593,57694788,57695877,57698951,
+TBC1D3 NM_001123391 chr17 + 36284004 36295098 36285544 36294600 14 36284004,36285543,36285778,36287147,36287669,36288193,36288630,36289993,36290585,36291419,36291898,36292427,36292897,36294031, 36284115,36285616,36285864,36287187,36287750,36288301,36288740,36290042,36290706,36291514,36291964,36292527,36293050,36295098,
+LOC100133331 NR_028327 chr1 - 661138 665731 665731 665731 3 661138,665277,665562, 665184,665335,665731,
+LOC100288069 NR_033908 chr1 - 700244 714068 714068 714068 7 700244,701708,703927,704876,708355,709550,713663, 700627,701767,703993,705092,708487,709660,714068,
+LINC01128 NR_047526 chr1 + 762970 778984 778984 778984 3 762970,764382,776579, 763155,764484,778984,
+LINC01128 NR_047519 chr1 + 762970 794826 794826 794826 6 762970,764382,783033,787306,788050,788770, 763155,764484,783186,787490,788146,794826,
+LINC01128 NR_047521 chr1 + 762970 794826 794826 794826 5 762970,764382,787306,788050,788770, 763155,764484,787490,788146,794826,
+LINC01128 NR_047523 chr1 + 762970 794826 794826 794826 4 762970,764382,787306,788770, 763155,764484,787490,794826,
+LINC01128 NR_047524 chr1 + 762970 794826 794826 794826 4 762970,764382,788050,788770, 763155,764484,788146,794826,
+LINC01128 NR_047525 chr1 + 763177 794826 794826 794826 5 763177,764382,787306,788050,788770, 763229,764484,787490,788146,794826,
+CLEC4A NM_194447 chr12 + 8276227 8291203 8276474 8290883 5 8276227,8281859,8288180,8289383,8290735, 8276556,8281958,8288332,8289499,8291203,
+LOC100130417 NR_026874 chr1 - 852197 855072 855072 855072 4 852197,853401,854204,854714, 853100,853555,854295,855072,
+LOC100130417 NR_122045 chr1 - 852197 855072 855072 855072 4 852197,853401,854204,854714, 853100,853495,854295,855072,
+SAMD11 NM_152486 chr1 + 861120 879961 861321 879533 14 861120,861301,865534,866418,871151,874419,874654,876523,877515,877789,877938,878632,879077,879287, 861180,861393,865716,866469,871276,874509,874840,876686,877631,877868,878438,878757,879188,879961,
+NELFE NM_002904 chr6_cox_hap2 - 3429619 3436620 3429833 3435979 11 3429619,3431261,3431612,3431830,3432087,3432591,3432751,3434225,3434473,3435904,3436424, 3429931,3431364,3431667,3431975,3432425,3432629,3432826,3434371,3434543,3435987,3436620,
+KCNJ11 NM_001166290 chr11 - 17406795 17410878 17408465 17409377 2 17406795,17410720, 17409393,17410878,
+DLG3 NM_020730 chrX + 69672154 69725339 69672471 69722119 14 69672154,69673486,69674063,69698999,69711956,69712370,69713225,69717029,69718369,69719025,69719726,69720320,69720747,69722012, 69672605,69673643,69674166,69699114,69712133,69712446,69713325,69717071,69718420,69719127,69719899,69720430,69720839,69725339,
+PERM1 NM_001291366 chr1 - 910578 917497 911551 916409 4 910578,911878,914260,917444, 911649,912004,916427,917497,
+PERM1 NM_001291367 chr1 - 910578 917497 911551 917497 5 910578,911878,914260,916516,917444, 911649,912004,916037,916553,917497,
+HES4 NM_021170 chr1 - 934341 935552 934438 935353 4 934341,934905,935071,935245, 934812,934993,935167,935552,
+HES4 NM_001142467 chr1 - 934343 935552 934438 935353 3 934343,934905,935071, 934812,934993,935552,
+AGRN NM_001305275 chr1 + 955502 991499 955552 990361 39 955502,957580,970656,976044,976552,976857,977335,978618,978917,979202,979488,979713,980540,980738,981112,981343,981539,981776,982199,982706,982952,983155,983391,984246,984615,984945,985282,985612,985806,986105,986621,986630,986832,987107,987372,988840,989132,989827,990203, 955753,957842,970704,976260,976777,977082,977542,978837,979112,979403,979637,979819,980657,980903,981256,981468,981645,982115,982337,982834,983067,983275,983745,9 [...]
+AGRN NM_198576 chr1 + 955502 991499 955552 990361 36 955502,957580,970656,976044,976552,976857,977335,978618,978917,979202,979488,979713,980540,980738,981112,981343,981539,981776,982199,982706,982952,983155,983391,984246,984615,984945,985282,985612,985806,986105,986632,986832,987107,989132,989827,990203, 955753,957842,970704,976260,976777,977082,977542,978837,979112,979403,979637,979819,980657,980903,981256,981468,981645,982115,982337,982834,983067,983275,983745,984439,984831,985175,9854 [...]
+RNF223 NM_001205252 chr1 - 1007125 1009687 1007196 1007946 2 1007125,1009395, 1007955,1009687,
+TUBB3 NM_006086 chr16 + 89989686 90002505 89989809 90002212 4 89989686,89998978,89999875,90001136, 89989866,89999087,89999986,90002505,
+LINC01342 NR_038869 chr1 + 1072396 1079434 1079434 1079434 3 1072396,1076204,1078118, 1072490,1076412,1079434,
+MIR200B NR_029639 chr1 + 1102483 1102578 1102578 1102578 1 1102483, 1102578,
+MIR200A NR_029834 chr1 + 1103242 1103332 1103332 1103332 1 1103242, 1103332,
+MIR429 NR_029957 chr1 + 1104384 1104467 1104467 1104467 1 1104384, 1104467,
+PGAP2 NM_001145438 chr11 + 3819048 3847601 3819073 3846688 7 3819048,3829523,3832479,3845112,3845499,3846249,3846557, 3819212,3829545,3832654,3845365,3845594,3846358,3847601,
+TREX1 NM_033629 chr3 + 48506918 48509044 48508054 48508999 2 48506918,48508028, 48507708,48509044,
+CEACAM21 NM_033543 chr19 + 42082530 42093197 42082626 42092224 7 42082530,42083551,42085705,42090702,42091795,42092192,42092816, 42082690,42083911,42085981,42090796,42091848,42092224,42093197,
+TPD52L3 NM_033516 chr9 + 6328348 6330918 6328595 6329018 1 6328348, 6330918,
+FKBP1A NM_054014 chr20 - 1352355 1373816 1352755 1373642 4 1352355,1356134,1373477,1373605, 1352884,1356247,1373525,1373816,
+MLXIPL NM_032952 chr7 - 73007523 73038870 73008194 73038822 17 73007523,73008603,73009966,73010171,73010482,73010693,73010968,73011194,73011511,73013855,73020017,73020239,73021303,73021660,73021919,73030400,73038529, 73008313,73008733,73010090,73010242,73010602,73010809,73011119,73011262,73012043,73014025,73020098,73020441,73021348,73021750,73022002,73030507,73038870,
+PURB NM_033224 chr7 - 44915891 44924984 44924008 44924947 1 44915891, 44924984,
+HIF3A NM_152796 chr19 + 46801632 46841797 46807189 46841563 12 46801632,46807154,46811477,46811919,46812407,46815417,46815762,46823699,46825032,46828791,46838203,46841483, 46801771,46807345,46811562,46812032,46812616,46815524,46815910,46823818,46825223,46828896,46838243,46841797,
+PRSS33 NM_152891 chr16 - 2833953 2836708 2834644 2836548 6 2833953,2835002,2835375,2835799,2836089,2836502, 2834803,2835172,2835647,2835962,2836122,2836708,
+AFG3L1P NR_003227 chr16 + 90038987 90063028 90063028 90063028 10 90038987,90044085,90045217,90046649,90048180,90050938,90057273,90059128,90060175,90061166, 90039173,90044210,90045286,90046744,90048331,90051007,90057411,90059236,90060301,90063028,
+AFG3L1P NR_003226 chr16 + 90038987 90063028 90063028 90063028 11 90038987,90044012,90045217,90046649,90048180,90050938,90055259,90057273,90059128,90060175,90061100, 90039173,90044210,90045286,90046744,90048331,90051007,90055359,90057411,90059236,90060301,90063028,
+LOC148709 NR_002929 chr1 + 202830881 202844369 202844369 202844369 3 202830881,202841327,202842184, 202830937,202841407,202844369,
+UBE2MP1 NR_002837 chr16 - 34403801 34404762 34404762 34404762 1 34403801, 34404762,
+MIR6726 NR_106784 chr1 - 1231489 1231550 1231550 1231550 1 1231489, 1231550,
+CPSF3L NM_001256456 chr1 - 1246964 1260067 1247238 1257333 19 1246964,1247397,1247605,1247819,1247972,1248166,1248414,1248888,1249111,1249680,1250203,1250783,1250899,1254675,1255835,1256375,1257287,1258271,1259960, 1247304,1247527,1247748,1247881,1248080,1248329,1248504,1248972,1249301,1249745,1250342,1250818,1250998,1254904,1255909,1256473,1257364,1258667,1260067,
+CPSF3L NM_001256460 chr1 - 1246964 1260067 1247238 1256414 18 1246964,1247397,1247605,1247819,1247972,1248166,1248414,1248888,1249111,1249680,1250203,1250783,1250899,1254675,1255835,1256375,1258560,1259960, 1247304,1247527,1247748,1247881,1248080,1248329,1248504,1248972,1249301,1249745,1250342,1250818,1250998,1254904,1255909,1256473,1258667,1260067,
+CPSF3L NM_001256462 chr1 - 1246964 1260067 1247238 1259988 15 1246964,1247397,1247605,1247819,1247972,1248166,1248414,1248888,1249111,1249680,1250203,1250783,1250899,1258556,1259960, 1247304,1247527,1247748,1247881,1248080,1248329,1248504,1248972,1249301,1249745,1250342,1250818,1250994,1258667,1260067,
+CPSF3L NM_001256463 chr1 - 1246964 1260067 1247238 1259988 15 1246964,1247397,1247605,1247819,1247972,1248166,1248414,1248888,1249111,1249680,1250203,1250783,1250899,1256375,1259960, 1247304,1247527,1247748,1247881,1248080,1248329,1248504,1248972,1249301,1249745,1250342,1250818,1250998,1256473,1260067,
+CPSF3L NM_017871 chr1 - 1246964 1260067 1247238 1259988 17 1246964,1247397,1247605,1247819,1247972,1248166,1248414,1248888,1249111,1249680,1250203,1250783,1250899,1254675,1255835,1256375,1259960, 1247304,1247527,1247748,1247881,1248080,1248329,1248504,1248972,1249301,1249745,1250342,1250818,1250998,1254904,1255909,1256473,1260067,
+MIR6727 NR_106785 chr1 - 1247881 1247946 1247946 1247946 1 1247881, 1247946,
+CPTP NM_001029885 chr1 + 1260142 1264276 1262290 1263143 3 1260142,1262215,1262620, 1260482,1262412,1264276,
+TAS1R3 NM_152228 chr1 + 1266725 1270700 1266725 1269844 6 1266725,1267017,1267403,1268300,1268638,1268885, 1266916,1267318,1268186,1268504,1268759,1270700,
+FBXL18 NM_001321213 chr7 - 5528808 5553429 5529437 5553305 5 5528808,5530861,5540118,5545042,5553287, 5529843,5531080,5541662,5545261,5553429,
+MIR6808 NR_106866 chr1 - 1275029 1275088 1275088 1275088 1 1275029, 1275088,
+MXRA8 NM_001282585 chr1 - 1288068 1293927 1288680 1293884 10 1288068,1289227,1289409,1289572,1289733,1290061,1290623,1290829,1292060,1293835, 1288712,1289326,1289486,1289612,1289889,1290532,1290725,1291132,1292084,1293927,
+MXRA8 NM_001282584 chr1 - 1288068 1294174 1288983 1293884 9 1288068,1289227,1289409,1289572,1289733,1290061,1290623,1292060,1293835, 1289009,1289308,1289486,1289612,1289889,1290532,1290725,1292084,1294174,
+MXRA8 NM_032348 chr1 - 1288068 1294174 1288983 1293884 10 1288068,1289227,1289409,1289572,1289733,1290061,1290623,1290829,1292060,1293835, 1289009,1289308,1289486,1289612,1289889,1290532,1290725,1291132,1292084,1294174,
+MXRA8 NM_001282583 chr1 - 1288068 1297157 1288983 1296643 10 1288068,1289227,1289409,1289572,1289733,1290061,1290623,1290829,1292060,1296621, 1289009,1289308,1289486,1289612,1289889,1290532,1290725,1291132,1292084,1297157,
+MXRA8 NM_001282582 chr1 - 1288068 1298921 1288983 1293884 11 1288068,1289227,1289409,1289572,1289733,1290061,1290623,1290829,1292060,1293835,1298896, 1289009,1289308,1289486,1289612,1289889,1290532,1290725,1291132,1292084,1293927,1298921,
+AURKAIP1 NM_001127229 chr1 - 1309109 1310580 1309180 1310136 4 1309109,1309379,1310084,1310376, 1309282,1309825,1310170,1310580,
+AURKAIP1 NM_017900 chr1 - 1309109 1310818 1309180 1310136 4 1309109,1309379,1310084,1310533, 1309282,1309825,1310170,1310818,
+AURKAIP1 NM_001127230 chr1 - 1309110 1310562 1309180 1310136 4 1309110,1309379,1310084,1310454, 1309282,1309825,1310170,1310562,
+FAM72B NM_001320149 chr1 + 120839411 120855681 120839833 120854586 4 120839411,120841974,120845994,120854491, 120839865,120842052,120846119,120855681,
+CAMKV NM_001320147 chr3 - 49895413 49907655 49896750 49899821 12 49895413,49897202,49897603,49897903,49898148,49898375,49898612,49898871,49899223,49899477,49899726,49907190, 49897109,49897314,49897691,49897982,49898285,49898451,49898733,49899010,49899298,49899609,49899835,49907655,
+BPIFA2 NM_001319164 chr20 + 31749653 31769223 31756951 31768366 9 31749653,31756936,31760737,31761884,31763212,31765952,31767409,31768325,31769029, 31749704,31757108,31760882,31761992,31763365,31766034,31767473,31768403,31769223,
+SNX22 NM_024798 chr15 + 64443915 64449680 64443974 64446707 7 64443915,64444441,64444836,64445443,64445850,64446133,64446585, 64444049,64444525,64444941,64445538,64445883,64446201,64449680,
+AURKB NR_132730 chr17 - 8108048 8113944 8113944 8113944 9 8108048,8108533,8109808,8110067,8110635,8110888,8111055,8113494,8113847, 8108362,8108708,8109957,8110206,8110685,8110943,8111158,8113567,8113944,
+NXF1 NM_001081491 chr11 - 62559597 62572964 62567793 62572828 20 62559597,62560112,62561729,62562406,62563372,62563537,62563758,62563931,62564654,62564789,62566010,62568565,62568800,62569033,62569210,62569413,62569648,62570890,62571263,62572800, 62559986,62560173,62561912,62562479,62563415,62563653,62563817,62564039,62564710,62564858,62567958,62568673,62568889,62569103,62569291,62569518,62569732,62571044,62571450,62572964,
+LOC148413 NR_015434 chr1 + 1334909 1337426 1337426 1337426 3 1334909,1335537,1335984, 1335069,1335683,1337426,
+MRPL20 NM_017971 chr1 - 1337275 1342693 1337462 1342597 4 1337275,1341188,1342288,1342510, 1337636,1341266,1342399,1342693,
+MRPL20 NM_001318485 chr1 - 1337288 1342693 1337948 1342597 4 1337288,1341188,1342288,1342510, 1337981,1341266,1342399,1342693,
+ANKRD65 NM_001145210 chr1 - 1353799 1356824 1354479 1356385 4 1353799,1355431,1356176,1356512, 1354929,1355972,1356385,1356824,
+ANKRD65 NM_001243535 chr1 - 1353799 1356824 1354613 1356385 3 1353799,1356176,1356512, 1354929,1356385,1356824,
+ANKRD65 NM_001243536 chr1 - 1353799 1356824 1354921 1356385 3 1353799,1356195,1356512, 1354929,1356385,1356824,
+TMEM88B NM_001146685 chr1 + 1361507 1363167 1361507 1363167 2 1361507,1362933, 1361765,1363167,
+LOC102724312 NR_125994 chr1 - 1365536 1369953 1369953 1369953 2 1365536,1369557, 1366334,1369953,
+LOC102724312 NR_125995 chr1 - 1365536 1369953 1369953 1369953 2 1365536,1369557, 1366042,1369953,
+LOC102724312 NR_125996 chr1 - 1365536 1369953 1369953 1369953 2 1365536,1369567, 1366042,1369953,
+VWA1 NM_022834 chr1 + 1370902 1378262 1371128 1375167 3 1370902,1372306,1374460, 1371201,1372864,1378262,
+VWA1 NM_199121 chr1 + 1370902 1378262 1371128 1372823 3 1370902,1372701,1374460, 1371201,1372864,1378262,
+ATAD3C NM_001039211 chr1 + 1385068 1405538 1386063 1403910 12 1385068,1387425,1387744,1389724,1390839,1391170,1391604,1392508,1394540,1396129,1397979,1403763, 1386138,1387502,1387814,1389880,1390899,1391296,1391729,1392560,1394611,1396297,1398088,1405538,
+ATAD3B NM_031921 chr1 + 1407134 1431584 1407264 1431197 16 1407134,1412653,1414023,1414428,1416246,1417517,1417924,1420395,1421161,1421489,1421923,1423242,1424583,1425636,1425942,1430864, 1407469,1412730,1414125,1414488,1416316,1417683,1417994,1420551,1421218,1421615,1422048,1423294,1424654,1425804,1426051,1431584,
+ATAD3B NM_001317238 chr1 + 1413494 1431584 1413879 1431197 14 1413494,1414428,1416246,1417517,1417924,1420395,1421161,1421489,1421923,1423242,1424583,1425636,1425942,1430864, 1414125,1414488,1416316,1417683,1417994,1420551,1421218,1421615,1422048,1423294,1424654,1425804,1426051,1431584,
+ATAD3A NM_001170535 chr1 + 1447522 1470067 1447648 1469452 16 1447522,1451391,1452690,1453095,1454300,1455520,1455927,1458123,1458890,1459218,1459652,1460619,1461840,1463074,1464602,1469305, 1447853,1451468,1452792,1453155,1454370,1455686,1455997,1458279,1458947,1459344,1459777,1460671,1461911,1463242,1464711,1470067,
diff --git a/test/formats/tr95t.cns b/test/formats/tr95t.cns
index 85490d7..3c63de9 100644
--- a/test/formats/tr95t.cns
+++ b/test/formats/tr95t.cns
@@ -1,126 +1,125 @@
-chromosome start end gene log2 probes weight
-chr1 10500 2421341 SSU72,PLCH2 0.134253 27 19.5922
-chr1 2422583 2431202 PLCH2 0.448062 10 6.38648
-chr1 2433502 18617471 PLCH2,PRDM16,NPHP4,CA6,MTOR,MFN2,LRRC38,KAZN 0.0661341 178 132.846
-chr1 18617471 21479562 UBR4,KIF17 -0.407045 21 16.093
-chr1 21479562 121352354 CDC42,ARID1A,PTAFR,PUM1,ZBTB8A,KIAA0319L,MYCL1,CAP1,HIVEP3,MPL,PTCH2,MUTYH,FAF1,CDKN2C,PPAP2B,DAB1,JUN,FGGY,DOCK7,JAK1,SLC35D1,LRRC7,NEGR1,FPGT-TNNI3K,AK5,MCOLN3,CLCA4,LRRC8B,EVI5,ABCA4,DPYD,COL11A1,NTNG1,CLCC1,KCND3,NRAS,WDR3,NOTCH2 -0.0213287 899 682.544
-chr1 142535934 249240121 PDE4DIP,TXNIP,LIX1L,PEX11B,ITGA10,MCL1,CGN,LAMTOR2,SH2D2A,NTRK1,FCRL5,IFI16,FCGR3A,DDR2,MPC2,TNR,ASTN1,ABL2,CEP350,CACNA1E,LAMC1,SMG7,C1orf21,CDC73,CACNA1S,PPP1R12B,SOX13,MDM4,IKBKE,IL19,TRAF5,SMYD2,USH2A,SUSD4,PRSS38,C1orf198,TBCE,MTR,CHRM3,RGS7,SDCCAG8,AKT3,SMYD3 0.323628 954 716.9
-chr2 10500 92267022 TPO,LINC00299,MBOAT2,HPCAL1,MYCN,C2orf43,ATAD2B,DNMT3A,BRE,ALK,TTC27,PRKD3,CYP1B1,SLC8A1,THADA,MSH2,MSH6,NRXN1,GPR75-ASB3,CCDC88A,VRK2,REL,USP34,EHBP1,ARHGAP25,SNRPG,TCF7L1 0.011528 794 601.241
-chr2 95326671 237943201 LOC442028,DUSP2,FAM178B,AFF3,LOC100287010,NCK2,EDAR,BUB1,ANAPC1,IL36A,PAX8,DPP10,STEAP3,MAP3K2,NCKAP5,UBXN4,THSD7B,NXPH2,ARHGAP15,DKFZp686O1327,LYPD6B,STAM2,CCDC148-AS1,KCNH7,CSRNP3,LRP2,METTL8,ZAK,WIPF1,HOXD-AS2,PDE11A,SESTD1,ITGAV,ANKRD44,SF3B1,TMEM237,NBEAL1,PARD3B,NRP2,NDUFS1,IDH1,CPS1,ERBB4,SPAG16,BARD1,XRCC5,IGFBP2,PAX3,FARSB,NYAP2,COL4A4,GIGYF2,INPP5D,UGT1A8,AGAP1 -0.00117402 1196 903.678
-chr2 237943201 242176790 HDAC4,KIF1A -0.465657 29 22.8255
-chr2 242176790 243188873 - 0.0799059 7 5.31941
-chr3 60500 65409798 CNTN4,GRM7,VHL,ATP2B2,RAF1,FBLN2,NR2C2,RFTN1,PLCL2,KCNH8,NR1D2,RARB,ZCWPW2,RBMS3,TGFBR2,MLH1,ITGA9,CTNNB1,ZDHHC3,MAP4,DAG1,DOCK3,BAP1,NISCH,PBRM1,WNT5A,ARHGEF3,FHIT,ADAMTS9 -0.0147912 627 474.924
-chr3 65409798 66579610 MAGI1 0.536554 8 6.27079
-chr3 66579610 90168173 SUCLG2,MITF,PDZRN3,CADM2,VGLL3,EPHA3 0.0226327 209 157.932
-chr3 93519633 95252544 - -0.350095 16 11.2442
-chr3 95252544 96400715 - 2.40683 9 6.76046
-chr3 96400715 96825973 EPHA6 -0.398751 10 6.97009
-chr3 96825973 96963168 EPHA6 3.18425 5 3.36428
-chr3 96963668 97972088 EPHA6 2.22789 33 21.8018
-chr3 97972088 141877242 ABI3BP,IQCB1,ADCY5,UMPS,ITGB5,MGLL,C3orf37,EPHB1,ARMC8,MRAS,ACPL2 -0.457192 347 262.526
-chr3 141877242 197961930 ATR,TRPC1,MIR548H2,KCNAB1,IQCJ-SCHIP1,EGFEM1P,MYNN,TNIK,NLGN1,NAALADL2,KCNMB2,PIK3CA,SOX2-OT,MCF2L2,DGKG,LOC100131635,BCL6,PYDC2,FGF12,ACAP2,PAK2 -0.0185116 492 375.879
-chr4 13322 49632814 GAK,FGFR3,STX18,SORCS2,CLNK,LOC441009,LDB2,KCNIP4,STIM2,C4orf19,TMEM156,RBM47,CNGA1 0.0268331 392 298.324
-chr4 52660617 67655781 SCFD2,PDGFRA,KIT,KDR,EPHA5 0.0633659 212 157.563
-chr4 67655781 179561500 UGT2A1,CDKL2,ANXA3,MAPK10,ABCG2,FAM190A,BMPR1B,STPG2,MTTP,PPP3CA,NFKB1,TET2,RPL34-AS1,ELOVL6,ANK2,SPRY1,LARP1B,MAML3,LRBA,FBXW7,KIAA0922,MARCH1,SPOCK3,PALLD,AADAT -0.0145253 847 648.477
-chr4 179561500 191025802 - 0.0835995 82 62.3061
-chr5 10500 1295381 TERT 1.44032 30 20.1965
-chr5 1295881 27758999 LPCAT1,ADCY2,FAM134B,CDH18,CDH12,CDH9 -0.438559 190 146.113
-chr5 27758999 29725593 - 0.542628 13 10.4965
-chr5 29725593 32111185 DROSHA 1.43184 18 13.4424
-chr5 32111185 34935473 - -0.290066 20 15.2251
-chr5 34935473 43358297 WDR70,RICTOR 0.458204 103 77.9754
-chr5 43358297 45907753 C5orf34 0.00786783 19 14.8139
-chr5 49555074 180008136 ANKRD55,MAP3K1,PDE4D,ADAMTS6,MAST4,PIK3R1,POC5,SERINC5,SSBP2,XRCC4,RASA1,GPR98,FAM172A,MCTP1,CAST,STARD4-AS1,APC,MCC,COMMD10,DMXL1,PRR16,LOC100505841,ALDH7A1,SLC12A2,ADAMTS19,IL4,SKP1,SPOCK1,RELL2,SPRY4,ARHGAP26,LARS,JAKMIP2-AS1,CSF1R,PDGFRB,GRIA1,SGCD,NPM1,CREBRF,LOC643201,FGFR4,ZNF354C -0.0054079 1238 938.117
-chr5 180008636 180076603 FLT4 0.329968 33 20.5672
-chr5 180077103 180904760 - -0.0654238 6 4.3355
-chr6 60500 31491427 NQO2,NRN1,ATXN1,TPMT,CDKAL1,LRRC16A -0.0159055 240 177.13
-chr6 31491427 32376398 DOM3Z,STK19,NOTCH4 -0.392197 49 22.6737
-chr6 32775421 58745455 PACSIN1,MAPK14,CDKN1A,FOXP4,CCND3,XPO5,NFKBIE,SUPT3H,CYP39A1,PTCHD4,PKHD1,MLIP,ZNF451 0.0306187 318 231.29
-chr6 61944508 171054567 EYS,OGFRL1,KCNQ5,BCKDHB,ME1,GABRR2,EPHA7,KLHL32,POU3F2,LOC728012,GRIK2,CDK19,LAMA4,ROS1,SLC35F1,RSPO3,PTPRK,SAMD3,ENPP3,PDE7B,MAP3K5,TNFAIP3,ADGB,LATS1,ESR1,RGS17,ARID1B,TMEM181,SOD2,IGF2R,SLC22A2,PARK2,PACRG -0.0112598 1035 784.353
-chr7 10500 6426280 CARD11,AIMP2,RAC1 0.12479 72 53.3312
-chr7 6426780 55510241 RAC1,COL28A1,STEAP1B,HOXA3,CREB5,SCRN1,FKBP9,C7orf10,INHBA,GLI3,HECW1,CCM2,IKZF1,EGFR -0.00717592 423 319.927
-chr7 55510741 57938684 - 0.33604 15 9.03152
-chr7 61657308 63386201 - 0.453069 12 6.33337
-chr7 63386701 159128163 CCT6P3,HIP1,MAGI2,PCLO,GRM3,CROT,ABCB1,ZNF804B,GTPBP10,MTERF,CDK6,DYNC1I1,TRRAP,CYP3A5,CYP3A4,EPHB4,MUC12,SRPK2,PIK3CG,NRCAM,IMMP2L,C7orf60,MET,ASZ1,KCND2,POT1,SND1,SMO,AHCYL2,PLXNA4,EXOC4,TBXAS1,BRAF,TMEM178B,EPHB6,EPHA1-AS1,CNTNAP2,EZH2,LRRC61,PRKAG2,PTPRN2 0.00337069 1030 774.777
-chr8 10500 17711900 DLGAP2,CSMD1,TNKS,RP1L1,FAM66D,SGCZ 0.0481852 161 117.883
-chr8 17711900 29536110 CSGALNACT1,BIN3,PTK2B,EXTL3,DUSP4 -0.45971 146 110.218
-chr8 29536110 43398986 MIR548O2,WRN,NRG1,GPR124,FGFR1,TACC1,ADAM32,ZMAT4 0.0571581 195 143.835
-chr8 46950735 146303522 PRKDC,SNTG1,PXDNL,TOX,RAB2A,MYBL1,PREX2,SULF1,KCNB2,PKIA,RALYL,RUNX1T1,LINC00535,MATN2,VPS13B,FBXO43,SNX31,RIMS2,ZFPM2,CSMD3,LINC00536,MTBP,SQLE,MYC,PVT1,ADCY8,KHDRBS3,BOP1 -0.0044328 843 644.393
-chr9 10500 5078278 SMARCA2,SLC1A1,JAK2 -0.0778313 129 98.9505
-chr9 5078278 47317179 JAK2,PTPRD,LOC389705,BNC2,CDKN2A,CDKN2B-AS1,IFT74,LINGO2,PAX5,POLR1E 0.0489359 380 279.65
-chr9 65468179 141152931 LOC642236,PGM5,FAM189A2,TRPM3,PRUNE2,GNAQ,NTRK2,ROR2,WNK2,C9orf3,PTCH1,HSD17B3,COL27A1,TNC,ASTN2,DAB2IP,STRBP,NR6A1,PPP6C,CDK9,ABL1,TSC1,SARDH,OLFM1,GPSM1,NOTCH1,MAN1B1 0.0185149 797 596.14
-chr10 60500 39076015 ADARB2,IL15RA,UPF2,BEND7,PTER,KIAA1217,GPR158,MPP7,SVIL,PARD3 -0.431773 276 210.322
-chr10 42602610 135524247 LOC441666,RET,A1CF,PRKG1,IPMK,M1,CTNNA3,CCAR1,CDH23,FAM149B1,C10orf11,ZMIZ1,NRG3,PTEN,KIF20B,PCGF5,TNKS2,PLCE1,CYP2C8,ENTPD1,HPSE2,CWF19L1,SUFU,SORCS3,RBM20,SHOC2,ATRNL1,INPP5F,FGFR2,UROS,DOCK1,KNDC1 -0.451548 802 606.962
-chr11 60500 51566742 HRAS,MOB2,NAP1L4,OLFML1,NRIP3,PTH,SERGEF,NAV2,NELL1,IMMP1L,WT1,QSER1,ELF5,LDLRAD3,LRRC4C,TTC17,AMBRA1,PTPRJ 0.0196477 380 287.827
-chr11 55028439 134946016 FADS1,SF1,MEN1,YIF1A,GSTP1,ALDH3B1,CCND1,SHANK2,CLPB,MRPL48,TSKU,GAB2,DLG2,SYTL2,GRM5,MRE11A,AMOTL1,MAML2,YAP1,GUCY1A2,ACAT1,ATM,ZBTB16,MLL,CBL,TRIM29,SORL1,CLMP,SIAE,CHEK1,NTM -0.00117398 816 614.453
-chr12 60500 11993912 ERC1,TULP3,CCND2,ANO2,CD163L1,A2ML1,ETV6 0.0307168 122 92.3914
-chr12 11993912 12273512 ETV6 -0.185659 93 71.6682
-chr12 12274012 34431528 LRP6,CDKN1B,MGST1,PLEKHA5,SOX5,KRAS,CCDC91,PKP2 -0.0185943 198 147.425
-chr12 37857194 41701437 - -0.409211 25 18.5549
-chr12 41701437 42901265 - 2.77937 9 6.926
-chr12 42901265 57607768 NELL2,ARID2,TUBA1B,DIP2B,ATF1,ATF7,ERBB3,BAZ2A -0.479329 181 135.552
-chr12 57607768 57914222 DDIT3 3.05428 10 6.95964
-chr12 57914722 58520144 CDK4 3.53273 12 8.57114
-chr12 58520644 60916332 SLC16A7 3.07097 17 12.9918
-chr12 60916332 66908608 SRGAP1 -0.432304 43 33.0768
-chr12 66908608 67954874 - -0.0579432 8 6.26063
-chr12 67954874 69003947 - 2.10195 8 6.11156
-chr12 69004447 69669616 MDM2 2.817 17 12.3802
-chr12 69669616 70541066 - 2.34943 7 5.12415
-chr12 70541566 85204790 SYT1,PTPRQ -0.444059 106 82.5938
-chr12 85204790 88658400 LRRIQ1,CEP290 0.0166753 25 19.4678
-chr12 88658400 89746788 DUSP6 -0.311335 24 17.4608
-chr12 89746788 92702070 DUSP6,ATP2B1,LUM -0.138557 23 17.5832
-chr12 92702070 133841395 UHRF1BP1L,MYBPC1,CHST11,NUAK1,BTBD11,USP30,PPTC7,NAA25,PTPN11,MAP1LC3B2,HNF1A,RSRC2,ZNF664-FAM101A,TMEM132C,ZNF605 0.0261092 328 251.346
-chr13 19020500 105152288 ANKRD26P3,CRYL1,CDK8,FLT3,FLT1,TEX26-AS1,BRCA2,N4BP2L2,RFC3,NBEA,ALG5,EPSTI1,RB1,PCDH9,KLHL1,EDNRB,SPRY2,GPC6,ABCC4,FARP1,CLYBL 0.0119441 804 604.201
-chr13 105152288 107418370 - -0.45566 16 12.5671
-chr13 107418370 110108034 FAM155A,MYO16 0.0555301 20 15.5177
-chr13 110108034 111460835 IRS2,COL4A2 -0.417517 26 18.2627
-chr13 111460835 112353494 - 0.672955 6 4.71689
-chr13 112510573 115109378 GRTP1 -0.393884 17 13.2874
-chr14 19057400 20346012 - 0.497337 13 7.21662
-chr14 20346512 107289040 BCL2L2,THTPA,STXBP6,NOVA1,MIR548AI,AP4S1,AKAP6,RALGAPA1,NKX2-1,SLC25A21,MDGA2,SOS2,ATL1,NID2,SOCS4,C14orf37,CCDC175,SLC38A6,SYNE2,ESR2,FUT8,GPHN,MAP3K9,SIPA1L1,LTBP2,IFT43,SPTLC2,NRXN3,CEP128,TSHR,FOXN3,RPS6KA5,DDX24,GLRX5,HSP90AA1,KLC1,AKT1 0.020917 735 556.033
-chr15 20044632 21398319 NBEAP1 -0.266834 13 6.96087
-chr15 22262614 66511021 LOC727924,HERC2,TJP1,TRPM1,ATPBD4-AS1,SPRED1,FSIP1,PAK6,LTK,MGA,EPB42,SEMA6D,GALK2,SPPL2A,MYO5C,WDR72,RAB27A,ZNF280D,RORA,TLN2,CSNK1G1 -0.456207 432 321.136
-chr15 66511021 102520892 MAP2K1,SMAD3,AAGAB,ANP32A,THSD4,NEO1,LOC729911,BCL2A1,FAM108C1,EFTUD1,AGBL1,NTRK3,RHCG,IDH2,PRC1,C15orf32,LOC145820,FAM169B,IGF1R,ADAMTS17,PCSK6 0.351641 645 498.162
-chr16 60500 35148746 CLCN7,TSC2,PDPK1,KREMEN2,CREBBP,DNAJA3,RBFOX1,USP7,GRIN2A,ATF7IP2,SOCS1,PDXDC1,TMC5,DNAH3,PALB2,SULT1A1,BOLA2B,INO80E,ZNF668,FUS 0.0382109 429 312.9
-chr16 46457168 63157986 ANKRD26P1,CYLD,TOX3,FTO,NLRC5,NDRG4 -0.432499 151 113.232
-chr16 63157986 90294253 CDH5,CDH1,TMCO7,NQO1,PHLPP2,PKD1L3,WDR59,CNTNAP4,VAT1L,NECAB2,ZNF276,DEF8 0.0574363 266 202.965
-chr17 500 22220573 WSCD1,FXR2,TP53,AURKB,NTN1,MAP2K4,HS3ST3A1,DRG2 0.0412136 194 143.626
-chr17 25268559 27481069 - 0.0638443 19 13.4016
-chr17 27481069 30711280 NSRP1,NF1,RHOT1 -0.474127 112 79.2826
-chr17 30711280 81194710 ASIC2,ZNHIT3,DDX52,FBXL20,ERBB2,RARA,STAT3,BRCA1,DCAKD,CRHR1,GOSR2,SKAP1,COL1A1,PPM1E,BRIP1,TANC2,CD79B,PRKCA,MAP2K6,LINC00673,CASKIN2,DNAH17,RPTOR,NPLOC4 0.0132405 585 430.786
-chr18 10500 15381134 C18orf56,TYMS,LPIN2,L3MBTL4,C18orf1 0.0163384 111 82.753
-chr18 18520842 78016748 ROCK1,CDH2,FAM59A,NOL4,INO80C,KIAA1328,RIT2,EPG5,SMAD2,DYM,SMAD4,DCC,RAB27B,TCF4,LMAN1,CDH20,TNFRSF11A,BCL2,DOK6,NETO1,PARD6G 0.0277852 552 414.695
-chr19 60500 24364012 STK11,DOT1L,TLE2,GNA11,GIPC3,MAP2K2,LOC100128568,INSR,ARHGEF18,MUC16,CDC37,KEAP1,SMARCA4,CACNA1A,PODNL1,NOTCH3,EPS15L1,JAK3,SLC5A5,GATAD2A,RPSAP58 0.0590614 380 273.512
-chr19 28263182 59118483 LOC284395,CCNE1,CEBPA,RYR1,ZNF546,AKT2,LOC100505495,CD79A,GSK3A,PSG11,CEACAM20,ERCC2,CCDC61,BCL2L12,LRRC4B,ZNF615,LOC100128252,ZNF606 0.0648454 295 218.048
-chr20 60500 26256532 SIRPD,PTPRA,ITPA,CRLS1,PLCB4,C20orf94,MACROD2,KIF16B,OVOL2,SLC24A3,NINL -0.00373834 192 148.644
-chr20 29420069 62965020 DEFB116,ITCH,SRC,PPP1R16B,TOP1,PLCG1,YWHAB,ELMO2,AURKA,VAPB,GNAS-AS1,GNAS,CDH4,ARFRP1 0.00881644 353 260.977
-chr21 9411693 11185554 - 0.167098 11 5.57339
-chr21 14370291 25345441 LIPI,RBM11,CHODL,NCAM2 -0.0172463 87 64.9672
-chr21 25345441 48119395 RUNX1,CBR3-AS1,KCNJ6,ERG,DSCAM,UMODL1,HSF2BP,SLC19A1 -0.370098 193 145.608
-chr22 16050500 25501410 TPTEP1,ANKRD62P1-PARP4P3,XKR3,CECR2,CLDN5,CRKL,GUSBP11,SMARCB1,KIAA1671 0.0851634 95 66.3061
-chr22 25501910 30061095 CRYBB1,TTC28,CHEK2,EWSR1,NF2 -0.0626938 115 85.8246
-chr22 30064268 39483505 NF2,SYN3,MB,RAC2,SOX10,APOBEC3G 0.0527237 95 72.038
-chr22 39484005 39637713 PDGFB -0.335444 23 17.4422
-chr22 39637713 42059851 PDGFB,TNRC6B,EP300,DESI1,XRCC6 -0.0435486 89 65.3698
-chr22 42060351 51244066 CYP2D6,BIK,LINC00229,FLJ46257,CPT1B 0.0899123 74 56.0008
-chrX 60500 2561647 CRLF2 1.52253 23 12.4313
-chrX 2561647 4653265 XG,ARSF 2.32422 17 12.2041
-chrX 4653265 10942673 NLGN4X 0.951266 45 34.0583
-chrX 10942673 13652870 - 2.40566 20 15.1003
-chrX 13652870 16352969 - 0.917729 19 13.9893
-chrX 16352969 19499971 - 2.45883 23 17.4682
-chrX 19501150 23404334 LOC100873065 2.80571 27 21.338
-chrX 23404334 31504390 KLHL15,DMD 1.15411 60 46.0369
-chrX 31504890 34071142 DMD 2.55621 17 13.0783
-chrX 34071142 40507998 LANCL3 0.924811 46 36.1274
-chrX 40508498 47864357 USP9X,KDM6A,CXorf36,SLC9A7,ARAF 2.11837 155 110.869
-chrX 47864357 55358602 GATA1,PHF8 1.30972 59 41.6211
-chrX 55358602 58180101 SPIN3 0.898777 21 15.3586
-chrX 61931664 80426930 ARHGEF9,AR,OPHN1,EDA,BCYRN1,PIN4,FTX,TBX22 0.910314 177 131.052
-chrX 80426930 94676963 DACH2,PCDH11X 0.772685 101 73.4768
-chrX 94676963 155260060 DIAPH2,LOC442459,BHLHB9,IL1RAPL2,AMMECR1,PAK3,ALG13,HTR2C,XIAP,STAG2,HS6ST2,FMR1-AS1,CD99L2,GABRA3,FAM58A 0.92881 488 360.256
-chrY 10500 2654042 - 1.43559 17 11.0704
-chrY 2654542 28649168 - -3.72105 144 98.5636
-chrY 59099792 59363066 - -0.0244204 2 1.48068
+chromosome start end gene log2 probes weight depth
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+chr1 2422582 2431202 PLCH2 0.448062 10 6.38648 1.37736
+chr1 2433501 18617471 PLCH2,PRDM16,NPHP4,CA6,MTOR,MFN2,LRRC38,KAZN 0.0661341 178 132.846 1.05182
+chr1 18617470 21479562 UBR4,KIF17 -0.407045 21 16.093 0.757367
+chr1 21479561 121352354 CDC42,ARID1A,PTAFR,PUM1,ZBTB8A,KIAA0319L,MYCL1,CAP1,HIVEP3,MPL,PTCH2,MUTYH,FAF1,CDKN2C,PPAP2B,DAB1,JUN,FGGY,DOCK7,JAK1,SLC35D1,LRRC7,NEGR1,FPGT-TNNI3K,AK5,MCOLN3,CLCA4,LRRC8B,EVI5,ABCA4,DPYD,COL11A1,NTNG1,CLCC1,KCND3,NRAS,WDR3,NOTCH2 -0.0213287 899 682.544 0.991427
+chr1 142535933 249240121 PDE4DIP,TXNIP,LIX1L,PEX11B,ITGA10,MCL1,CGN,LAMTOR2,SH2D2A,NTRK1,FCRL5,IFI16,FCGR3A,DDR2,MPC2,TNR,ASTN1,ABL2,CEP350,CACNA1E,LAMC1,SMG7,C1orf21,CDC73,CACNA1S,PPP1R12B,SOX13,MDM4,IKBKE,IL19,TRAF5,SMYD2,USH2A,SUSD4,PRSS38,C1orf198,TBCE,MTR,CHRM3,RGS7,SDCCAG8,AKT3,SMYD3 0.323628 954 716.9 1.25892
+chr2 10500 92267022 TPO,LINC00299,MBOAT2,HPCAL1,MYCN,C2orf43,ATAD2B,DNMT3A,BRE,ALK,TTC27,PRKD3,CYP1B1,SLC8A1,THADA,MSH2,MSH6,NRXN1,GPR75-ASB3,CCDC88A,VRK2,REL,USP34,EHBP1,ARHGAP25,SNRPG,TCF7L1 0.011528 794 601.241 1.01407
+chr2 95326670 237943201 LOC442028,DUSP2,FAM178B,AFF3,LOC100287010,NCK2,EDAR,BUB1,ANAPC1,IL36A,PAX8,DPP10,STEAP3,MAP3K2,NCKAP5,UBXN4,THSD7B,NXPH2,ARHGAP15,DKFZp686O1327,LYPD6B,STAM2,CCDC148-AS1,KCNH7,CSRNP3,LRP2,METTL8,ZAK,WIPF1,HOXD-AS2,PDE11A,SESTD1,ITGAV,ANKRD44,SF3B1,TMEM237,NBEAL1,PARD3B,NRP2,NDUFS1,IDH1,CPS1,ERBB4,SPAG16,BARD1,XRCC5,IGFBP2,PAX3,FARSB,NYAP2,COL4A4,GIGYF2,INPP5D,UGT1A8,AGAP1 -0.00117402 1196 903.678 1.00545
+chr2 237943200 242176790 HDAC4,KIF1A -0.465657 29 22.8255 0.727227
+chr2 242176789 243188873 - 0.0799059 7 5.31941 1.06152
+chr3 60500 65409798 CNTN4,GRM7,VHL,ATP2B2,RAF1,FBLN2,NR2C2,RFTN1,PLCL2,KCNH8,NR1D2,RARB,ZCWPW2,RBMS3,TGFBR2,MLH1,ITGA9,CTNNB1,ZDHHC3,MAP4,DAG1,DOCK3,BAP1,NISCH,PBRM1,WNT5A,ARHGEF3,FHIT,ADAMTS9 -0.0147912 627 474.924 0.996131
+chr3 65409797 66579610 MAGI1 0.536554 8 6.27079 1.45616
+chr3 66579609 90168173 SUCLG2,MITF,PDZRN3,CADM2,VGLL3,EPHA3 0.0226327 209 157.932 1.02111
+chr3 93519632 95252544 - -0.350095 16 11.2442 0.808707
+chr3 95252543 96400715 - 2.40683 9 6.76046 5.53091
+chr3 96400714 96825973 EPHA6 -0.398751 10 6.97009 0.762652
+chr3 96825972 96963168 EPHA6 3.18425 5 3.36428 9.12025
+chr3 96963667 97972088 EPHA6 2.22789 33 21.8018 4.73583
+chr3 97972087 141877242 ABI3BP,IQCB1,ADCY5,UMPS,ITGB5,MGLL,C3orf37,EPHB1,ARMC8,MRAS,ACPL2 -0.457192 347 262.526 0.734085
+chr3 141877241 197961930 ATR,TRPC1,MIR548H2,KCNAB1,IQCJ-SCHIP1,EGFEM1P,MYNN,TNIK,NLGN1,NAALADL2,KCNMB2,PIK3CA,SOX2-OT,MCF2L2,DGKG,LOC100131635,BCL6,PYDC2,FGF12,ACAP2,PAK2 -0.0185116 492 375.879 0.9934
+chr4 13322 49632814 GAK,FGFR3,STX18,SORCS2,CLNK,LOC441009,LDB2,KCNIP4,STIM2,C4orf19,TMEM156,RBM47,CNGA1 0.0268331 392 298.324 1.02661
+chr4 52660616 67655781 SCFD2,PDGFRA,KIT,KDR,EPHA5 0.0633659 212 157.563 1.05042
+chr4 67655780 179561500 UGT2A1,CDKL2,ANXA3,MAPK10,ABCG2,FAM190A,BMPR1B,STPG2,MTTP,PPP3CA,NFKB1,TET2,RPL34-AS1,ELOVL6,ANK2,SPRY1,LARP1B,MAML3,LRBA,FBXW7,KIAA0922,MARCH1,SPOCK3,PALLD,AADAT -0.0145253 847 648.477 0.996519
+chr4 179561499 191025802 - 0.0835995 82 62.3061 1.0665
+chr5 10500 1295381 TERT 1.44032 30 20.1965 2.74749
+chr5 1295880 27758999 LPCAT1,ADCY2,FAM134B,CDH18,CDH12,CDH9 -0.438559 190 146.113 0.74419
+chr5 27758998 29725593 - 0.542628 13 10.4965 1.46849
+chr5 29725592 32111185 DROSHA 1.43184 18 13.4424 2.75829
+chr5 32111184 34935473 - -0.290066 20 15.2251 0.865334
+chr5 34935472 43358297 WDR70,RICTOR 0.458204 103 77.9754 1.39435
+chr5 43358296 45907753 C5orf34 0.00786783 19 14.8139 1.01259
+chr5 49555073 180008136 ANKRD55,MAP3K1,PDE4D,ADAMTS6,MAST4,PIK3R1,POC5,SERINC5,SSBP2,XRCC4,RASA1,GPR98,FAM172A,MCTP1,CAST,STARD4-AS1,APC,MCC,COMMD10,DMXL1,PRR16,LOC100505841,ALDH7A1,SLC12A2,ADAMTS19,IL4,SKP1,SPOCK1,RELL2,SPRY4,ARHGAP26,LARS,JAKMIP2-AS1,CSF1R,PDGFRB,GRIA1,SGCD,NPM1,CREBRF,LOC643201,FGFR4,ZNF354C -0.0054079 1238 938.117 1.00271
+chr5 180008635 180076603 FLT4 0.329968 33 20.5672 1.27176
+chr5 180077102 180904760 - -0.0654238 6 4.3355 0.961004
+chr6 60500 31491427 NQO2,NRN1,ATXN1,TPMT,CDKAL1,LRRC16A -0.0159055 240 177.13 0.994568
+chr6 31491426 32376398 DOM3Z,STK19,NOTCH4 -0.392197 49 22.6737 0.782461
+chr6 32775420 58745455 PACSIN1,MAPK14,CDKN1A,FOXP4,CCND3,XPO5,NFKBIE,SUPT3H,CYP39A1,PTCHD4,PKHD1,MLIP,ZNF451 0.0306187 318 231.29 1.02964
+chr6 61944507 171054567 EYS,OGFRL1,KCNQ5,BCKDHB,ME1,GABRR2,EPHA7,KLHL32,POU3F2,LOC728012,GRIK2,CDK19,LAMA4,ROS1,SLC35F1,RSPO3,PTPRK,SAMD3,ENPP3,PDE7B,MAP3K5,TNFAIP3,ADGB,LATS1,ESR1,RGS17,ARID1B,TMEM181,SOD2,IGF2R,SLC22A2,PARK2,PACRG -0.0112598 1035 784.353 0.998503
+chr7 10500 6426280 CARD11,AIMP2,RAC1 0.12479 72 53.3312 1.09907
+chr7 6426779 55510241 RAC1,COL28A1,STEAP1B,HOXA3,CREB5,SCRN1,FKBP9,C7orf10,INHBA,GLI3,HECW1,CCM2,IKZF1,EGFR -0.00717592 423 319.927 1.00155
+chr7 55510740 57938684 - 0.33604 15 9.03152 1.27525
+chr7 61657307 63386201 - 0.453069 12 6.33337 1.37799
+chr7 63386700 159128163 CCT6P3,HIP1,MAGI2,PCLO,GRM3,CROT,ABCB1,ZNF804B,GTPBP10,MTERF,CDK6,DYNC1I1,TRRAP,CYP3A5,CYP3A4,EPHB4,MUC12,SRPK2,PIK3CG,NRCAM,IMMP2L,C7orf60,MET,ASZ1,KCND2,POT1,SND1,SMO,AHCYL2,PLXNA4,EXOC4,TBXAS1,BRAF,TMEM178B,EPHB6,EPHA1-AS1,CNTNAP2,EZH2,LRRC61,PRKAG2,PTPRN2 0.00337069 1030 774.777 1.00967
+chr8 10500 17711900 DLGAP2,CSMD1,TNKS,RP1L1,FAM66D,SGCZ 0.0481852 161 117.883 1.0463
+chr8 17711899 29536110 CSGALNACT1,BIN3,PTK2B,EXTL3,DUSP4 -0.45971 146 110.218 0.734253
+chr8 29536109 43398986 MIR548O2,WRN,NRG1,GPR124,FGFR1,TACC1,ADAM32,ZMAT4 0.0571581 195 143.835 1.04609
+chr8 46950734 146303522 PRKDC,SNTG1,PXDNL,TOX,RAB2A,MYBL1,PREX2,SULF1,KCNB2,PKIA,RALYL,RUNX1T1,LINC00535,MATN2,VPS13B,FBXO43,SNX31,RIMS2,ZFPM2,CSMD3,LINC00536,MTBP,SQLE,MYC,PVT1,ADCY8,KHDRBS3,BOP1 -0.0044328 843 644.393 1.00289
+chr9 10500 5078278 SMARCA2,SLC1A1,JAK2 -0.0778313 129 98.9505 0.957546
+chr9 5078277 47317179 JAK2,PTPRD,LOC389705,BNC2,CDKN2A,CDKN2B-AS1,IFT74,LINGO2,PAX5,POLR1E 0.0489359 380 279.65 1.04342
+chr9 65468178 141152931 LOC642236,PGM5,FAM189A2,TRPM3,PRUNE2,GNAQ,NTRK2,ROR2,WNK2,C9orf3,PTCH1,HSD17B3,COL27A1,TNC,ASTN2,DAB2IP,STRBP,NR6A1,PPP6C,CDK9,ABL1,TSC1,SARDH,OLFM1,GPSM1,NOTCH1,MAN1B1 0.0185149 797 596.14 1.02064
+chr10 60500 39076015 ADARB2,IL15RA,UPF2,BEND7,PTER,KIAA1217,GPR158,MPP7,SVIL,PARD3 -0.431773 276 210.322 0.747434
+chr10 42602609 135524247 LOC441666,RET,A1CF,PRKG1,IPMK,M1,CTNNA3,CCAR1,CDH23,FAM149B1,C10orf11,ZMIZ1,NRG3,PTEN,KIF20B,PCGF5,TNKS2,PLCE1,CYP2C8,ENTPD1,HPSE2,CWF19L1,SUFU,SORCS3,RBM20,SHOC2,ATRNL1,INPP5F,FGFR2,UROS,DOCK1,KNDC1 -0.451548 802 606.962 0.736925
+chr11 60500 51566742 HRAS,MOB2,NAP1L4,OLFML1,NRIP3,PTH,SERGEF,NAV2,NELL1,IMMP1L,WT1,QSER1,ELF5,LDLRAD3,LRRC4C,TTC17,AMBRA1,PTPRJ 0.0196477 380 287.827 1.01989
+chr11 55028438 134946016 FADS1,SF1,MEN1,YIF1A,GSTP1,ALDH3B1,CCND1,SHANK2,CLPB,MRPL48,TSKU,GAB2,DLG2,SYTL2,GRM5,MRE11A,AMOTL1,MAML2,YAP1,GUCY1A2,ACAT1,ATM,ZBTB16,MLL,CBL,TRIM29,SORL1,CLMP,SIAE,CHEK1,NTM -0.00117398 816 614.453 1.00497
+chr12 60500 11993912 ERC1,TULP3,CCND2,ANO2,CD163L1,A2ML1,ETV6 0.0307168 122 92.3914 1.02728
+chr12 11993911 12273512 ETV6 -0.185659 93 71.6682 0.882144
+chr12 12274011 34431528 LRP6,CDKN1B,MGST1,PLEKHA5,SOX5,KRAS,CCDC91,PKP2 -0.0185943 198 147.425 0.994463
+chr12 37857193 41701437 - -0.409211 25 18.5549 0.760009
+chr12 41701436 42901265 - 2.77937 9 6.926 7.00501
+chr12 42901264 57607768 NELL2,ARID2,TUBA1B,DIP2B,ATF1,ATF7,ERBB3,BAZ2A -0.479329 181 135.552 0.721699
+chr12 57607767 57914222 DDIT3 3.05428 10 6.95964 8.37521
+chr12 57914721 58520144 CDK4 3.53273 12 8.57114 11.5983
+chr12 58520643 60916332 SLC16A7 3.07097 17 12.9918 8.43946
+chr12 60916331 66908608 SRGAP1 -0.432304 43 33.0768 0.745831
+chr12 66908607 67954874 - -0.0579432 8 6.26063 0.966245
+chr12 67954873 69003947 - 2.10195 8 6.11156 4.34939
+chr12 69004446 69669616 MDM2 2.817 17 12.3802 7.06433
+chr12 69669615 70541066 - 2.34943 7 5.12415 5.10572
+chr12 70541565 85204790 SYT1,PTPRQ -0.444059 106 82.5938 0.747667
+chr12 85204789 88658400 LRRIQ1,CEP290 0.0166753 25 19.4678 1.01696
+chr12 88658399 92702070 DUSP6,ATP2B1,LUM -0.224644 47 35.044 0.862747
+chr12 92702069 133841395 UHRF1BP1L,MYBPC1,CHST11,NUAK1,BTBD11,USP30,PPTC7,NAA25,PTPN11,MAP1LC3B2,HNF1A,RSRC2,ZNF664-FAM101A,TMEM132C,ZNF605 0.0261092 328 251.346 1.02341
+chr13 19020500 105152288 ANKRD26P3,CRYL1,CDK8,FLT3,FLT1,TEX26-AS1,BRCA2,N4BP2L2,RFC3,NBEA,ALG5,EPSTI1,RB1,PCDH9,KLHL1,EDNRB,SPRY2,GPC6,ABCC4,FARP1,CLYBL 0.0119441 804 604.201 1.01461
+chr13 105152287 107418370 - -0.45566 16 12.5671 0.734405
+chr13 107418369 110108034 FAM155A,MYO16 0.0555301 20 15.5177 1.05008
+chr13 110108033 111460835 IRS2,COL4A2 -0.417517 26 18.2627 0.755855
+chr13 111460834 112353494 - 0.672955 6 4.71689 1.61703
+chr13 112510572 115109378 GRTP1 -0.393884 17 13.2874 0.770523
+chr14 19057400 20346012 - 0.497337 13 7.21662 1.44168
+chr14 20346511 107289040 BCL2L2,THTPA,STXBP6,NOVA1,MIR548AI,AP4S1,AKAP6,RALGAPA1,NKX2-1,SLC25A21,MDGA2,SOS2,ATL1,NID2,SOCS4,C14orf37,CCDC175,SLC38A6,SYNE2,ESR2,FUT8,GPHN,MAP3K9,SIPA1L1,LTBP2,IFT43,SPTLC2,NRXN3,CEP128,TSHR,FOXN3,RPS6KA5,DDX24,GLRX5,HSP90AA1,KLC1,AKT1 0.020917 735 556.033 1.02182
+chr15 20044632 21398319 NBEAP1 -0.266834 13 6.96087 0.837944
+chr15 22262613 66511021 LOC727924,HERC2,TJP1,TRPM1,ATPBD4-AS1,SPRED1,FSIP1,PAK6,LTK,MGA,EPB42,SEMA6D,GALK2,SPPL2A,MYO5C,WDR72,RAB27A,ZNF280D,RORA,TLN2,CSNK1G1 -0.456207 432 321.136 0.735504
+chr15 66511020 102520892 MAP2K1,SMAD3,AAGAB,ANP32A,THSD4,NEO1,LOC729911,BCL2A1,FAM108C1,EFTUD1,AGBL1,NTRK3,RHCG,IDH2,PRC1,C15orf32,LOC145820,FAM169B,IGF1R,ADAMTS17,PCSK6 0.351641 645 498.162 1.2814
+chr16 60500 35148746 CLCN7,TSC2,PDPK1,KREMEN2,CREBBP,DNAJA3,RBFOX1,USP7,GRIN2A,ATF7IP2,SOCS1,PDXDC1,TMC5,DNAH3,PALB2,SULT1A1,BOLA2B,INO80E,ZNF668,FUS 0.0382109 429 312.9 1.03599
+chr16 46457167 63157986 ANKRD26P1,CYLD,TOX3,FTO,NLRC5,NDRG4 -0.432499 151 113.232 0.745492
+chr16 63157985 90294253 CDH5,CDH1,TMCO7,NQO1,PHLPP2,PKD1L3,WDR59,CNTNAP4,VAT1L,NECAB2,ZNF276,DEF8 0.0574363 266 202.965 1.04681
+chr17 500 22220573 WSCD1,FXR2,TP53,AURKB,NTN1,MAP2K4,HS3ST3A1,DRG2 0.0412136 194 143.626 1.03551
+chr17 25268558 27481069 - 0.0638443 19 13.4016 1.05191
+chr17 27481068 30711280 NSRP1,NF1,RHOT1 -0.474127 112 79.2826 0.723406
+chr17 30711279 81194710 ASIC2,ZNHIT3,DDX52,FBXL20,ERBB2,RARA,STAT3,BRCA1,DCAKD,CRHR1,GOSR2,SKAP1,COL1A1,PPM1E,BRIP1,TANC2,CD79B,PRKCA,MAP2K6,LINC00673,CASKIN2,DNAH17,RPTOR,NPLOC4 0.0132405 585 430.786 1.01651
+chr18 10500 15381134 C18orf56,TYMS,LPIN2,L3MBTL4,C18orf1 0.0163384 111 82.753 1.01884
+chr18 18520841 78016748 ROCK1,CDH2,FAM59A,NOL4,INO80C,KIAA1328,RIT2,EPG5,SMAD2,DYM,SMAD4,DCC,RAB27B,TCF4,LMAN1,CDH20,TNFRSF11A,BCL2,DOK6,NETO1,PARD6G 0.0277852 552 414.695 1.02524
+chr19 60500 24364012 STK11,DOT1L,TLE2,GNA11,GIPC3,MAP2K2,LOC100128568,INSR,ARHGEF18,MUC16,CDC37,KEAP1,SMARCA4,CACNA1A,PODNL1,NOTCH3,EPS15L1,JAK3,SLC5A5,GATAD2A,RPSAP58 0.0590614 380 273.512 1.05042
+chr19 28263181 59118483 LOC284395,CCNE1,CEBPA,RYR1,ZNF546,AKT2,LOC100505495,CD79A,GSK3A,PSG11,CEACAM20,ERCC2,CCDC61,BCL2L12,LRRC4B,ZNF615,LOC100128252,ZNF606 0.0648454 295 218.048 1.05252
+chr20 60500 26256532 SIRPD,PTPRA,ITPA,CRLS1,PLCB4,C20orf94,MACROD2,KIF16B,OVOL2,SLC24A3,NINL -0.00373834 192 148.644 1.00306
+chr20 29420068 62965020 DEFB116,ITCH,SRC,PPP1R16B,TOP1,PLCG1,YWHAB,ELMO2,AURKA,VAPB,GNAS-AS1,GNAS,CDH4,ARFRP1 0.00881644 353 260.977 1.01394
+chr21 9411693 11185554 - 0.167098 11 5.57339 1.14139
+chr21 14370290 25345441 LIPI,RBM11,CHODL,NCAM2 -0.0172463 87 64.9672 0.994992
+chr21 25345440 48119395 RUNX1,CBR3-AS1,KCNJ6,ERG,DSCAM,UMODL1,HSF2BP,SLC19A1 -0.370098 193 145.608 0.779093
+chr22 16050500 25501410 TPTEP1,ANKRD62P1-PARP4P3,XKR3,CECR2,CLDN5,CRKL,GUSBP11,SMARCB1,KIAA1671 0.0851634 95 66.3061 1.07015
+chr22 25501909 30061095 CRYBB1,TTC28,CHEK2,EWSR1,NF2 -0.0626938 115 85.8246 0.96186
+chr22 30064267 39483505 NF2,SYN3,MB,RAC2,SOX10,APOBEC3G 0.0527237 95 72.038 1.04177
+chr22 39484004 39637713 PDGFB -0.335444 23 17.4422 0.794597
+chr22 39637712 42059851 PDGFB,TNRC6B,EP300,DESI1,XRCC6 -0.0435486 89 65.3698 0.976478
+chr22 42060350 51244066 CYP2D6,BIK,LINC00229,FLJ46257,CPT1B 0.0899123 74 56.0008 1.06929
+chrX 60500 2561647 CRLF2 1.52253 23 12.4313 2.97132
+chrX 2561646 4653265 XG,ARSF 2.32422 17 12.2041 5.13739
+chrX 4653264 10942673 NLGN4X 0.951266 45 34.0583 2.14257
+chrX 10942672 13652870 - 2.40566 20 15.1003 5.34066
+chrX 13652869 16352969 - 0.917729 19 13.9893 1.89738
+chrX 16352968 19499971 - 2.45883 23 17.4682 5.66689
+chrX 19501149 23404334 LOC100873065 2.80571 27 21.338 7.02158
+chrX 23404333 31504390 KLHL15,DMD 1.15411 60 46.0369 2.34853
+chrX 31504889 34071142 DMD 2.55621 17 13.0783 5.99214
+chrX 34071141 40507998 LANCL3 0.924811 46 36.1274 1.90599
+chrX 40508497 47864357 USP9X,KDM6A,CXorf36,SLC9A7,ARAF 2.11837 155 110.869 4.38767
+chrX 47864356 55358602 GATA1,PHF8 1.30972 59 41.6211 2.49803
+chrX 55358601 58180101 SPIN3 0.898777 21 15.3586 1.87247
+chrX 61931663 80426930 ARHGEF9,AR,OPHN1,EDA,BCYRN1,PIN4,FTX,TBX22 0.910314 177 131.052 1.89139
+chrX 80426929 94676963 DACH2,PCDH11X 0.772685 101 73.4768 1.72826
+chrX 94676962 155260060 DIAPH2,LOC442459,BHLHB9,IL1RAPL2,AMMECR1,PAK3,ALG13,HTR2C,XIAP,STAG2,HS6ST2,FMR1-AS1,CD99L2,GABRA3,FAM58A 0.92881 488 360.256 1.92276
+chrY 10500 2654042 - 1.43559 17 11.0704 2.86884
+chrY 2654541 28649168 - -3.72105 144 98.5636 0.130802
+chrY 59099791 59363066 - -0.0244204 2 1.48068 0.989748
diff --git a/test/formats/tr95t.segmetrics.cns b/test/formats/tr95t.segmetrics.cns
new file mode 100644
index 0000000..a59613e
--- /dev/null
+++ b/test/formats/tr95t.segmetrics.cns
@@ -0,0 +1,125 @@
+chromosome start end gene log2 depth probes weight mean median mode stdev sem mad mse iqr bivar ci_lo ci_hi pi_lo pi_hi
+chr1 10500 2421341 SSU72,PLCH2 0.134253 1.10244 27 19.5922 0.136947 0.101563 0.101563 0.141581 0.0277662 0.1025 0.020045 0.135183 0.114861 0.09266 0.199236 -0.0814449 0.434447
+chr1 2422582 2431202 PLCH2 0.448062 1.37736 10 6.38648 0.451268 0.421242 0.407133 0.197422 0.0658074 0.202098 0.0389755 0.283794 0.200934 0.344058 0.561994 0.201559 0.813788
+chr1 2433501 18617471 PLCH2,PRDM16,NPHP4,CA6,MTOR,MFN2,LRRC38,KAZN 0.0661341 1.05182 178 132.846 0.0675838 0.0670818 0.0709604 0.141956 0.0106701 0.133833 0.0201515 0.175269 0.139936 0.044368 0.0845963 -0.199943 0.340224
+chr1 18617470 21479562 UBR4,KIF17 -0.407045 0.757367 21 16.093 -0.398992 -0.372617 -0.37124 0.142319 0.0318234 0.0892036 0.0202546 0.129123 0.123425 -0.459451 -0.362187 -0.647213 -0.137312
+chr1 21479561 121352354 CDC42,ARID1A,PTAFR,PUM1,ZBTB8A,KIAA0319L,MYCL1,CAP1,HIVEP3,MPL,PTCH2,MUTYH,FAF1,CDKN2C,PPAP2B,DAB1,JUN,FGGY,DOCK7,JAK1,SLC35D1,LRRC7,NEGR1,FPGT-TNNI3K,AK5,MCOLN3,CLCA4,LRRC8B,EVI5,ABCA4,DPYD,COL11A1,NTNG1,CLCC1,KCND3,NRAS,WDR3,NOTCH2 -0.0213287 0.991427 899 682.544 -0.0198431 -0.0127685 -0.00107655 0.172763 0.00576518 0.151095 0.0298471 0.204504 0.158709 -0.0321178 -0.0130827 -0.364336 0.284609
+chr1 142535933 249240121 PDE4DIP,TXNIP,LIX1L,PEX11B,ITGA10,MCL1,CGN,LAMTOR2,SH2D2A,NTRK1,FCRL5,IFI16,FCGR3A,DDR2,MPC2,TNR,ASTN1,ABL2,CEP350,CACNA1E,LAMC1,SMG7,C1orf21,CDC73,CACNA1S,PPP1R12B,SOX13,MDM4,IKBKE,IL19,TRAF5,SMYD2,USH2A,SUSD4,PRSS38,C1orf198,TBCE,MTR,CHRM3,RGS7,SDCCAG8,AKT3,SMYD3 0.323628 1.25892 954 716.9 0.323066 0.327403 0.326357 0.168162 0.00544729 0.143678 0.0282783 0.192659 0.150713 0.313807 0.331941 -0.0219803 0.624075
+chr2 10500 92267022 TPO,LINC00299,MBOAT2,HPCAL1,MYCN,C2orf43,ATAD2B,DNMT3A,BRE,ALK,TTC27,PRKD3,CYP1B1,SLC8A1,THADA,MSH2,MSH6,NRXN1,GPR75-ASB3,CCDC88A,VRK2,REL,USP34,EHBP1,ARHGAP25,SNRPG,TCF7L1 0.011528 1.01407 794 601.241 0.0144665 0.0203419 0.020938 0.163315 0.00579949 0.146556 0.0266718 0.198345 0.156751 -0.000520578 0.0212597 -0.333387 0.313754
+chr2 95326670 237943201 LOC442028,DUSP2,FAM178B,AFF3,LOC100287010,NCK2,EDAR,BUB1,ANAPC1,IL36A,PAX8,DPP10,STEAP3,MAP3K2,NCKAP5,UBXN4,THSD7B,NXPH2,ARHGAP15,DKFZp686O1327,LYPD6B,STAM2,CCDC148-AS1,KCNH7,CSRNP3,LRP2,METTL8,ZAK,WIPF1,HOXD-AS2,PDE11A,SESTD1,ITGAV,ANKRD44,SF3B1,TMEM237,NBEAL1,PARD3B,NRP2,NDUFS1,IDH1,CPS1,ERBB4,SPAG16,BARD1,XRCC5,IGFBP2,PAX3,FARSB,NYAP2,COL4A4,GIGYF2,INPP5D,UGT1A8,AGAP1 -0.00117402 1.00545 1196 903.678 0.00073752 -0.0023726 -0.0292775 0.170669 0.00493709 0.154421 [...]
+chr2 237943200 242176790 HDAC4,KIF1A -0.465657 0.727227 29 22.8255 -0.463845 -0.460906 -0.438719 0.135276 0.0255647 0.136371 0.0182995 0.178129 0.139402 -0.511261 -0.425293 -0.690058 -0.225472
+chr2 242176789 243188873 - 0.0799059 1.06152 7 5.31941 0.0841879 0.149146 0.153577 0.131008 0.0534838 0.0908932 0.0171631 0.151641 0.136439 -0.0466539 0.175065 -0.135268 0.236331
+chr3 60500 65409798 CNTN4,GRM7,VHL,ATP2B2,RAF1,FBLN2,NR2C2,RFTN1,PLCL2,KCNH8,NR1D2,RARB,ZCWPW2,RBMS3,TGFBR2,MLH1,ITGA9,CTNNB1,ZDHHC3,MAP4,DAG1,DOCK3,BAP1,NISCH,PBRM1,WNT5A,ARHGEF3,FHIT,ADAMTS9 -0.0147912 0.996131 627 474.924 -0.0160971 -0.0146803 -0.0294643 0.17675 0.00706434 0.155039 0.0312405 0.212475 0.157785 -0.0257628 -0.00313019 -0.354306 0.300696
+chr3 65409797 66579610 MAGI1 0.536554 1.45616 8 6.27079 0.53763 0.502897 0.467945 0.125608 0.0474752 0.0929761 0.0157772 0.121084 0.124031 0.468362 0.627855 0.404043 0.76972
+chr3 66579609 90168173 SUCLG2,MITF,PDZRN3,CADM2,VGLL3,EPHA3 0.0226327 1.02111 209 157.932 0.0272914 0.0236744 0.0835237 0.150518 0.0104365 0.157965 0.0226556 0.212935 0.153651 0.0010211 0.0450628 -0.251618 0.307215
+chr3 93519632 95252544 - -0.350095 0.808707 16 11.2442 -0.336148 -0.384988 -0.40457 0.334678 0.0864134 0.274945 0.112009 0.317012 0.301135 -0.494984 -0.165436 -0.799773 0.396892
+chr3 95252543 96400715 - 2.40683 5.53091 9 6.76046 2.43027 2.19677 2.03454 0.418672 0.148023 0.324808 0.175287 0.81606 0.437095 2.16902 2.64948 1.97812 3.01152
+chr3 96400714 96825973 EPHA6 -0.398751 0.762652 10 6.97009 -0.391068 -0.380425 -0.397817 0.151713 0.0505709 0.196264 0.0230167 0.22141 0.157289 -0.478907 -0.285584 -0.591757 -0.146619
+chr3 96825972 96963168 EPHA6 3.18425 9.12025 5 3.36428 3.19353 3.21122 3.21122 0.116131 0.0580653 0.095939 0.0134863 0.12435 0.122911 3.06853 3.29523 3.0114 3.32738
+chr3 96963667 97972088 EPHA6 2.22789 4.73583 33 21.8018 2.23146 2.23718 2.17271 0.222689 0.0393663 0.189802 0.0495905 0.24087 0.211992 2.16474 2.3038 1.8661 2.66105
+chr3 97972087 141877242 ABI3BP,IQCB1,ADCY5,UMPS,ITGB5,MGLL,C3orf37,EPHB1,ARMC8,MRAS,ACPL2 -0.457192 0.734085 347 262.526 -0.454867 -0.463847 -0.492106 0.182679 0.00982091 0.18077 0.0333718 0.24916 0.181922 -0.475649 -0.435249 -0.797172 -0.0924051
+chr3 141877241 197961930 ATR,TRPC1,MIR548H2,KCNAB1,IQCJ-SCHIP1,EGFEM1P,MYNN,TNIK,NLGN1,NAALADL2,KCNMB2,PIK3CA,SOX2-OT,MCF2L2,DGKG,LOC100131635,BCL6,PYDC2,FGF12,ACAP2,PAK2 -0.0185116 0.9934 492 375.879 -0.0151155 -0.0087422 0.0152927 0.166392 0.00750917 0.147704 0.0276864 0.203864 0.158637 -0.0310325 -0.00581183 -0.325829 0.297829
+chr4 13322 49632814 GAK,FGFR3,STX18,SORCS2,CLNK,LOC441009,LDB2,KCNIP4,STIM2,C4orf19,TMEM156,RBM47,CNGA1 0.0268331 1.02661 392 298.324 0.0297994 0.02843 0.019888 0.179597 0.00908259 0.157093 0.0322549 0.209398 0.163531 0.00869258 0.0420851 -0.319125 0.340766
+chr4 52660616 67655781 SCFD2,PDGFRA,KIT,KDR,EPHA5 0.0633659 1.05042 212 157.563 0.0698413 0.0579294 0.0689597 0.167104 0.0115039 0.133965 0.0279238 0.174014 0.141686 0.0448227 0.0799778 -0.205046 0.366236
+chr4 67655780 179561500 UGT2A1,CDKL2,ANXA3,MAPK10,ABCG2,FAM190A,BMPR1B,STPG2,MTTP,PPP3CA,NFKB1,TET2,RPL34-AS1,ELOVL6,ANK2,SPRY1,LARP1B,MAML3,LRBA,FBXW7,KIAA0922,MARCH1,SPOCK3,PALLD,AADAT -0.0145253 0.996519 847 648.477 -0.0124128 -0.0115986 -0.0120613 0.171368 0.00589176 0.166387 0.0293671 0.224853 0.169148 -0.0255608 -0.00375267 -0.336003 0.304433
+chr4 179561499 191025802 - 0.0835995 1.0665 82 62.3061 0.0895735 0.0874189 0.106956 0.165816 0.018424 0.147096 0.0274951 0.203881 0.159902 0.0488678 0.119872 -0.204141 0.501819
+chr5 10500 1295381 TERT 1.44032 2.74749 30 20.1965 1.45682 1.41305 1.37821 0.246378 0.0457513 0.179291 0.0607023 0.224627 0.193689 1.37535 1.51149 1.08963 2.15443
+chr5 1295880 27758999 LPCAT1,ADCY2,FAM134B,CDH18,CDH12,CDH9 -0.438559 0.74419 190 146.113 -0.437785 -0.443532 -0.445048 0.184955 0.0134535 0.173459 0.0342082 0.235422 0.173629 -0.464503 -0.412432 -0.756662 -0.0511494
+chr5 27758998 29725593 - 0.542628 1.46849 13 10.4965 0.543626 0.553525 0.553525 0.185039 0.053416 0.193281 0.0342393 0.240224 0.192594 0.450117 0.635412 0.235567 0.855756
+chr5 29725592 32111185 DROSHA 1.43184 2.75829 18 13.4424 1.431 1.46924 1.51357 0.308518 0.0748265 0.364853 0.0951831 0.509313 0.320169 1.28275 1.57733 0.92378 1.91199
+chr5 32111184 34935473 - -0.290066 0.865334 20 15.2251 -0.296086 -0.456672 -0.457806 0.444378 0.101947 0.257691 0.197471 0.289268 0.251675 -0.473038 -0.113708 -0.690353 0.760622
+chr5 34935472 43358297 WDR70,RICTOR 0.458204 1.39435 103 77.9754 0.452506 0.370331 0.311818 0.239619 0.0237258 0.180053 0.0574172 0.310518 0.230118 0.404335 0.506359 0.138987 1.00654
+chr5 43358296 45907753 C5orf34 0.00786783 1.01259 19 14.8139 0.00837842 0.0130664 0.0130664 0.174777 0.0411954 0.155618 0.0305471 0.190954 0.171242 -0.0636825 0.0795679 -0.369641 0.282739
+chr5 49555073 180008136 ANKRD55,MAP3K1,PDE4D,ADAMTS6,MAST4,PIK3R1,POC5,SERINC5,SSBP2,XRCC4,RASA1,GPR98,FAM172A,MCTP1,CAST,STARD4-AS1,APC,MCC,COMMD10,DMXL1,PRR16,LOC100505841,ALDH7A1,SLC12A2,ADAMTS19,IL4,SKP1,SPOCK1,RELL2,SPRY4,ARHGAP26,LARS,JAKMIP2-AS1,CSF1R,PDGFRB,GRIA1,SGCD,NPM1,CREBRF,LOC643201,FGFR4,ZNF354C -0.0054079 1.00271 1238 938.117 -0.00552678 -0.00901642 -0.0268133 0.168092 0.00477928 0.16435 0.0282549 0.220946 0.162412 -0.0144037 0.0032771 -0.316015 0.316244
+chr5 180008635 180076603 FLT4 0.329968 1.27176 33 20.5672 0.342894 0.345742 0.354668 0.220904 0.0390508 0.203487 0.0487988 0.258274 0.215456 0.265144 0.415763 -0.0010375 0.762983
+chr5 180077102 180904760 - -0.0654238 0.961004 6 4.3355 -0.0646047 -0.0944651 -0.119668 0.151014 0.0675353 0.0854781 0.0228051 0.0990827 0.116263 -0.159851 0.0439335 -0.220574 0.208977
+chr6 60500 31491427 NQO2,NRN1,ATXN1,TPMT,CDKAL1,LRRC16A -0.0159055 0.994568 240 177.13 -0.0126638 -0.0164768 -0.0359206 0.164693 0.0106531 0.146471 0.0271237 0.194988 0.156358 -0.0307344 0.00216784 -0.338251 0.319155
+chr6 31491426 32376398 DOM3Z,STK19,NOTCH4 -0.392197 0.782461 49 22.6737 -0.392543 -0.337732 -0.290335 0.319631 0.0461347 0.243591 0.102164 0.39586 0.289583 -0.484392 -0.299565 -0.942032 0.129062
+chr6 32775420 58745455 PACSIN1,MAPK14,CDKN1A,FOXP4,CCND3,XPO5,NFKBIE,SUPT3H,CYP39A1,PTCHD4,PKHD1,MLIP,ZNF451 0.0306187 1.02964 318 231.29 0.0391144 0.0349209 0.0345477 0.202845 0.0113929 0.164013 0.0411462 0.218182 0.174046 0.0121402 0.0468551 -0.308341 0.49543
+chr6 61944507 171054567 EYS,OGFRL1,KCNQ5,BCKDHB,ME1,GABRR2,EPHA7,KLHL32,POU3F2,LOC728012,GRIK2,CDK19,LAMA4,ROS1,SLC35F1,RSPO3,PTPRK,SAMD3,ENPP3,PDE7B,MAP3K5,TNFAIP3,ADGB,LATS1,ESR1,RGS17,ARID1B,TMEM181,SOD2,IGF2R,SLC22A2,PARK2,PACRG -0.0112598 0.998503 1035 784.353 -0.0128221 -0.0016287 0.0252227 0.183867 0.005718 0.147251 0.0338071 0.198018 0.155965 -0.0207761 -0.00319999 -0.340912 0.294302
+chr7 10500 6426280 CARD11,AIMP2,RAC1 0.12479 1.09907 72 53.3312 0.13815 0.141306 0.141948 0.191731 0.0227543 0.157643 0.036761 0.208283 0.175426 0.0879583 0.171025 -0.221077 0.506295
+chr7 6426779 55510241 RAC1,COL28A1,STEAP1B,HOXA3,CREB5,SCRN1,FKBP9,C7orf10,INHBA,GLI3,HECW1,CCM2,IKZF1,EGFR -0.00717592 1.00155 423 319.927 7.24368e-05 -0.00829665 -0.0050805 0.17322 0.00843224 0.155359 0.0300053 0.209776 0.16666 -0.0230615 0.0087657 -0.315956 0.336879
+chr7 55510740 57938684 - 0.33604 1.27525 15 9.03152 0.36849 0.423131 0.335814 0.221201 0.0591186 0.250098 0.0489301 0.257848 0.226299 0.243905 0.439296 0.0857348 0.802758
+chr7 61657307 63386201 - 0.453069 1.37799 12 6.33337 0.468659 0.448605 0.385545 0.171122 0.0515954 0.191017 0.0292829 0.254317 0.179905 0.364267 0.556531 0.206218 0.744982
+chr7 63386700 159128163 CCT6P3,HIP1,MAGI2,PCLO,GRM3,CROT,ABCB1,ZNF804B,GTPBP10,MTERF,CDK6,DYNC1I1,TRRAP,CYP3A5,CYP3A4,EPHB4,MUC12,SRPK2,PIK3CG,NRCAM,IMMP2L,C7orf60,MET,ASZ1,KCND2,POT1,SND1,SMO,AHCYL2,PLXNA4,EXOC4,TBXAS1,BRAF,TMEM178B,EPHB6,EPHA1-AS1,CNTNAP2,EZH2,LRRC61,PRKAG2,PTPRN2 0.00337069 1.00967 1030 774.777 0.00719318 0.006944 0.0077227 0.184808 0.00576119 0.167676 0.0341539 0.225462 0.173703 -0.00624004 0.0139371 -0.348074 0.359858
+chr8 10500 17711900 DLGAP2,CSMD1,TNKS,RP1L1,FAM66D,SGCZ 0.0481852 1.0463 161 117.883 0.0633752 0.0449979 0.0275304 0.241443 0.0190877 0.17379 0.0582946 0.240643 0.1892 0.0195498 0.0850463 -0.415043 0.672038
+chr8 17711899 29536110 CSGALNACT1,BIN3,PTK2B,EXTL3,DUSP4 -0.45971 0.734253 146 110.218 -0.460899 -0.446082 -0.42804 0.207328 0.0172176 0.204015 0.0429848 0.268269 0.204508 -0.49103 -0.430957 -0.89067 -0.110336
+chr8 29536109 43398986 MIR548O2,WRN,NRG1,GPR124,FGFR1,TACC1,ADAM32,ZMAT4 0.0571581 1.04609 195 143.835 0.0584626 0.0725593 0.0576777 0.152252 0.010931 0.145517 0.0231806 0.197114 0.149786 0.0339823 0.0755077 -0.269758 0.322021
+chr8 46950734 146303522 PRKDC,SNTG1,PXDNL,TOX,RAB2A,MYBL1,PREX2,SULF1,KCNB2,PKIA,RALYL,RUNX1T1,LINC00535,MATN2,VPS13B,FBXO43,SNX31,RIMS2,ZFPM2,CSMD3,LINC00536,MTBP,SQLE,MYC,PVT1,ADCY8,KHDRBS3,BOP1 -0.0044328 1.00289 843 644.393 -0.000893948 -0.0026513 -0.0026513 0.163405 0.00563131 0.148641 0.0267012 0.203568 0.156219 -0.0148895 0.00658124 -0.305722 0.329905
+chr9 10500 5078278 SMARCA2,SLC1A1,JAK2 -0.0778313 0.957546 129 98.9505 -0.0802147 -0.0780898 -0.0697503 0.203042 0.0179465 0.127279 0.0412261 0.172947 0.138301 -0.107717 -0.0435613 -0.39691 0.177355
+chr9 5078277 47317179 JAK2,PTPRD,LOC389705,BNC2,CDKN2A,CDKN2B-AS1,IFT74,LINGO2,PAX5,POLR1E 0.0489359 1.04342 380 279.65 0.0579996 0.0542296 0.0612398 0.206598 0.0106122 0.165075 0.0426827 0.224097 0.177124 0.0332163 0.0673104 -0.292517 0.495561
+chr9 65468178 141152931 LOC642236,PGM5,FAM189A2,TRPM3,PRUNE2,GNAQ,NTRK2,ROR2,WNK2,C9orf3,PTCH1,HSD17B3,COL27A1,TNC,ASTN2,DAB2IP,STRBP,NR6A1,PPP6C,CDK9,ABL1,TSC1,SARDH,OLFM1,GPSM1,NOTCH1,MAN1B1 0.0185149 1.02064 797 596.14 0.0216919 0.0206614 0.0214691 0.19108 0.00677266 0.164807 0.0365116 0.215724 0.168338 0.00635996 0.030514 -0.330394 0.377695
+chr10 60500 39076015 ADARB2,IL15RA,UPF2,BEND7,PTER,KIAA1217,GPR158,MPP7,SVIL,PARD3 -0.431773 0.747434 276 210.322 -0.424388 -0.435433 -0.445231 0.191757 0.0115634 0.191629 0.0367706 0.256259 0.182363 -0.45309 -0.413927 -0.759081 -0.0620835
+chr10 42602609 135524247 LOC441666,RET,A1CF,PRKG1,IPMK,M1,CTNNA3,CCAR1,CDH23,FAM149B1,C10orf11,ZMIZ1,NRG3,PTEN,KIF20B,PCGF5,TNKS2,PLCE1,CYP2C8,ENTPD1,HPSE2,CWF19L1,SUFU,SORCS3,RBM20,SHOC2,ATRNL1,INPP5F,FGFR2,UROS,DOCK1,KNDC1 -0.451548 0.736925 802 606.962 -0.448845 -0.455587 -0.451036 0.18838 0.00665608 0.165122 0.0354871 0.222672 0.175415 -0.462157 -0.440977 -0.790799 -0.0455766
+chr11 60500 51566742 HRAS,MOB2,NAP1L4,OLFML1,NRIP3,PTH,SERGEF,NAV2,NELL1,IMMP1L,WT1,QSER1,ELF5,LDLRAD3,LRRC4C,TTC17,AMBRA1,PTPRJ 0.0196477 1.01989 380 287.827 0.0248287 0.0267299 0.0575824 0.16403 0.00842566 0.153998 0.0269059 0.215254 0.161396 0.00484911 0.0352726 -0.299132 0.357021
+chr11 55028438 134946016 FADS1,SF1,MEN1,YIF1A,GSTP1,ALDH3B1,CCND1,SHANK2,CLPB,MRPL48,TSKU,GAB2,DLG2,SYTL2,GRM5,MRE11A,AMOTL1,MAML2,YAP1,GUCY1A2,ACAT1,ATM,ZBTB16,MLL,CBL,TRIM29,SORL1,CLMP,SIAE,CHEK1,NTM -0.00117398 1.00497 816 614.453 0.00193343 -0.00088435 0.0224834 0.166965 0.00584853 0.142333 0.0278773 0.19203 0.151298 -0.0112655 0.00989041 -0.305743 0.329694
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+chrY 10500 2654042 - 1.43559 2.86884 17 11.0704 1.4338 1.50925 1.50925 0.497117 0.124279 0.409242 0.247125 0.6045 0.453129 1.18361 1.66205 0.308951 2.08908
+chrY 2654541 28649168 - -3.72105 0.130802 144 98.5636 -3.80363 -3.60116 -3.07751 1.92217 0.16074 1.86246 3.69475 2.46601 1.85136 -4.10573 -3.46509 -7.99209 -0.997093
+chrY 59099791 59363066 - -0.0244204 0.989748 2 1.48068 -0.022402 -0.022402 -0.18855 0.166148 0.166148 0.246331 0.0276052 0.166148 0.246331 -0.18855 0.143746 -0.180243 0.135439
diff --git a/test/formats/warning.seg b/test/formats/warning.seg
new file mode 100644
index 0000000..ca03e5b
--- /dev/null
+++ b/test/formats/warning.seg
@@ -0,0 +1,13 @@
+WARNING: ignoring environment value of R_HOME
+"sampleName" "chromosome" "start" "end" "nbrOfLoci" "mean"
+"MySample" "chr1" 10400 40010 146 0.261269921083404
+"MySample" "chr1" 40010 92027 242 -0.265592863407929
+"MySample" "chr1" 92027 142044 249 0.156494661443839
+"MySample" "chr1" 142044 154248 59 -0.440204366407358
+"MySample" "chr1" 154248 174454 99 -0.177414490636111
+"MySample" "chr1" 174454 178256 18 0.0516595860296953
+"MySample" "chr1" 178256 200463 111 0.41853174494091
+"MySample" "chr1" 200463 203264 14 0.159293774926751
+"MySample" "chr1" 203264 258065 23 -0.0203521925601479
+"MySample" "chr1" 258065 261257 16 0.501213680297145
+"MySample" "chr1" 261257 269437 38 0.873232771046872
diff --git a/test/test_cnvlib.py b/test/test_cnvlib.py
index ca0ebad..ba1ce94 100755
--- a/test/test_cnvlib.py
+++ b/test/test_cnvlib.py
@@ -1,130 +1,23 @@
#!/usr/bin/env python
-
"""Unit tests for the CNVkit library, cnvlib."""
from __future__ import absolute_import, division, print_function
import unittest
import numpy as np
-# from Bio._py3k import StringIO
+from skgenome import GenomicArray
import cnvlib
# Import all modules as a smoke test
-from cnvlib import (access, antitarget, commands, core, coverage, diagram,
- export, fix, importers, metrics, ngfrills, params, plots,
- reference, reports, segmentation, smoothing,
- gary, cnary, vary, rary)
-
-
-class GaryTests(unittest.TestCase):
-
- def setUp(self):
- self.ex_cnr = cnvlib.read('formats/reference-tr.cnn')
-
- def test_empty(self):
- """Instantiate from an empty file."""
- garr = gary.GenomicArray.read("formats/empty")
- self.assertEqual(len(garr), 0)
-
- def test_iter(self):
- """Test iteration."""
- rows = iter(self.ex_cnr)
- firstrow = next(rows)
- self.assertEqual(tuple(firstrow), tuple(self.ex_cnr[0]))
- i = 0
- for i, _row in enumerate(rows):
- pass
- self.assertEqual(i + 2, len(self.ex_cnr))
-
- def test_copy(self):
- """Test creation of an independent copy of the object."""
- dupe = self.ex_cnr.copy()
- self.assertEqual(tuple(self.ex_cnr[3]), tuple(dupe[3]))
- self.ex_cnr[3, 'log2'] = -10.0
- self.assertNotEqual(tuple(self.ex_cnr[3]), tuple(dupe[3]))
-
- def test_autosomes(self):
- """Test selection of autosomes."""
- len_all = len(self.ex_cnr)
- len_x = (self.ex_cnr.chromosome == 'chrX').sum()
- len_y = (self.ex_cnr.chromosome == 'chrY').sum()
- auto = self.ex_cnr.autosomes()
- self.assertEqual(len(auto), len_all - len_x - len_y)
- autox = self.ex_cnr.autosomes(also='chrX')
- self.assertEqual(len(autox), len_all - len_y)
- autoy = self.ex_cnr.autosomes(also=['chrY'])
- self.assertEqual(len(autoy), len_all - len_x)
- autoxy = self.ex_cnr.autosomes(also=['chrX', 'chrY'])
- self.assertEqual(len(autoxy), len_all)
-
- def test_by_chromosome(self):
- for fname in ("formats/amplicon.cnr", "formats/cl_seq.cns"):
- cnarr = cnvlib.read(fname)
- row_count = 0
- for _chrom, rows in cnarr.by_chromosome():
- row_count += len(rows)
- self.assertEqual(row_count, len(cnarr))
-
- # def test_concat(self):
-
- def test_ranges(self):
- """Test range methods: by_ranges, in_range, in_ranges."""
- cnarr = cnvlib.read("formats/amplicon.cnr")
- segarr = cnvlib.read("formats/amplicon.cns")
- chrom_segarr = dict(segarr.by_chromosome())
- for chrom, subarr in cnarr.by_chromosome():
- count_segs = 0
- count_bins = 0
- subsegarr = chrom_segarr[chrom]
- for count_segs, (seg, bins) in enumerate(subarr.by_ranges(subsegarr)):
- count_bins += len(bins)
- self.assertEqual(seg.probes, len(bins))
- self.assertEqual(len(bins), len(
- cnarr.in_range(seg.chromosome, seg.start, seg.end,
- mode='outer')))
- self.assertEqual(len(bins), len(
- cnarr.in_range(seg.chromosome, seg.start, seg.end,
- mode='trim')))
- self.assertEqual(len(subsegarr), count_segs + 1)
- self.assertEqual(len(subarr), count_bins)
- self.assertEqual(len(subarr), len(
- cnarr.in_ranges(chrom, subsegarr['start'], subsegarr['end'],
- mode="outer")))
- self.assertEqual(len(subarr), len(
- subarr.in_ranges(starts=subsegarr['start'],
- ends=subsegarr['end'], mode="outer")))
- self.assertEqual(len(subarr), len(
- cnarr.in_ranges(chrom, subsegarr['start'], subsegarr['end'],
- mode="trim")))
- self.assertEqual(len(subarr), len(
- subarr.in_ranges(starts=subsegarr['start'],
- ends=subsegarr['end'], mode="trim")))
-
- def test_select(self):
- """Test sugary selection of a subset of the data array."""
- num_bg_rows = len(self.ex_cnr[self.ex_cnr['gene'] == 'Background'])
- self.assertEqual(len(self.ex_cnr.select(gene='Background')),
- num_bg_rows)
- selector = lambda row: row['gene'] == 'Background'
- self.assertEqual(len(self.ex_cnr.select(selector)), num_bg_rows)
-
- def test_shuffle_sort(self):
- """Test shuffling and re-sorting the data array."""
- orig_cvg = tuple(self.ex_cnr['log2'][:10])
- self.assertEqual(tuple(self.ex_cnr['log2'][:10]), orig_cvg)
- self.ex_cnr.shuffle()
- self.assertNotEqual(tuple(self.ex_cnr['log2'][:10]), orig_cvg)
- self.ex_cnr.sort()
- self.assertEqual(tuple(self.ex_cnr['log2'][:10]), orig_cvg)
-
+from cnvlib import (access, antitarget, autobin, batch, cnary, commands, core,
+ coverage, diagram, export, fix, importers, metrics, params,
+ plots, reference, reports, segmentation, smoothing, tabio,
+ vary)
class CNATests(unittest.TestCase):
"""Tests for the CopyNumArray class."""
- def setUp(self):
- self.ex_cnr = cnvlib.read('formats/reference-tr.cnn')
-
def test_empty(self):
"""Instantiate from an empty file."""
cnarr = cnvlib.read("formats/empty")
@@ -132,25 +25,26 @@ class CNATests(unittest.TestCase):
def test_basic(self):
"""Test basic container functionality and magic methods."""
+ cna = cnvlib.read('formats/reference-tr.cnn')
# Length
- self.assertEqual(len(self.ex_cnr), 27526)
+ self.assertEqual(len(cna),
+ linecount('formats/reference-tr.cnn') - 1)
# Equality
same = cnvlib.read('formats/reference-tr.cnn')
- self.assertEqual(self.ex_cnr, same)
+ self.assertEqual(cna, same)
# Item access
- orig = self.ex_cnr[0]
- self.ex_cnr[0] = orig
- self.ex_cnr[3:4] = self.ex_cnr[3:4]
- self.ex_cnr[6:10] = self.ex_cnr[6:10]
- self.assertEqual(tuple(self.ex_cnr[0]), tuple(same[0]))
- self.assertEqual(self.ex_cnr[3:6], same[3:6])
-
- # def test_by_gene(self):
+ orig = cna[0]
+ cna[0] = orig
+ cna[3:4] = cna[3:4]
+ cna[6:10] = cna[6:10]
+ self.assertEqual(tuple(cna[0]), tuple(same[0]))
+ self.assertEqual(cna[3:6], same[3:6])
def test_center_all(self):
"""Test recentering."""
+ cna = cnvlib.read('formats/reference-tr.cnn')
# Median-centering an already median-centered array -> no change
- chr1 = self.ex_cnr.in_range('chr1')
+ chr1 = cna.in_range('chr1')
self.assertAlmostEqual(0, np.median(chr1['log2']), places=1)
chr1.center_all()
orig_chr1_cvg = np.median(chr1['log2'])
@@ -168,13 +62,14 @@ class CNATests(unittest.TestCase):
def test_drop_extra_columns(self):
"""Test removal of optional 'gc' column."""
- self.assertIn('gc', self.ex_cnr)
- cleaned = self.ex_cnr.drop_extra_columns()
+ cna = cnvlib.read('formats/reference-tr.cnn')
+ self.assertIn('gc', cna)
+ cleaned = cna.drop_extra_columns()
self.assertNotIn('gc', cleaned)
- self.assertTrue((cleaned['log2'] == self.ex_cnr['log2']).all())
+ self.assertTrue((cleaned['log2'] == cna['log2']).all())
- def test_gender(self):
- """Guess chromosomal gender from chrX log2 ratio value."""
+ def test_guess_xx(self):
+ """Guess chromosomal sex from chrX log2 ratio value."""
for (fname, sample_is_f, ref_is_m) in (
("formats/f-on-f.cns", True, False),
("formats/f-on-m.cns", True, True),
@@ -185,88 +80,94 @@ class CNATests(unittest.TestCase):
("formats/tr95t.cns", True, True),
("formats/reference-tr.cnn", False, False),
):
- cnarr = cnvlib.read(fname)
- if sample_is_f != cnarr.guess_xx(ref_is_m):
- print("Gender issue:", fname, sample_is_f, ref_is_m)
- self.assertEqual(sample_is_f, cnarr.guess_xx(ref_is_m))
+ guess = cnvlib.read(fname).guess_xx(ref_is_m)
+ self.assertEqual(guess, sample_is_f,
+ "%s: guessed XX %s but is %s"
+ % (fname, guess, sample_is_f))
def test_residuals(self):
cnarr = cnvlib.read("formats/amplicon.cnr")
segments = cnvlib.read("formats/amplicon.cns")
- regions = rary.RegionArray(segments.data).drop_extra_columns()
- for arg in (None, segments, regions):
- resid = cnarr.residuals(arg)
+ regions = GenomicArray(segments.data).drop_extra_columns()
+ for grouping_arg in (None, segments, regions):
+ resid = cnarr.residuals(grouping_arg)
self.assertAlmostEqual(0, resid.mean(), delta=.3)
self.assertAlmostEqual(1, np.percentile(resid, 80), delta=.2)
self.assertAlmostEqual(2, resid.std(), delta=.5)
- # def test_squash_genes(self):
-
-
-
-class RATests(unittest.TestCase):
- """Tests for RegionArray class."""
-
- def test_empty(self):
- """Instantiate from an empty file."""
- regions = rary.RegionArray.read("formats/empty")
- self.assertEqual(len(regions), 0)
-
- def test_read_bed(self):
- """Read the BED format."""
- regions = rary.RegionArray.read("formats/amplicon.bed")
- self.assertEqual(len(regions), 1433)
-
- def test_read_text(self):
- """Read the text region format."""
- regions = rary.RegionArray.read("formats/amplicon.text")
- self.assertEqual(len(regions), 1433)
-
- def test_read_ilist(self):
- """Read the interval list format."""
- regions = rary.RegionArray.read("formats/nv2_baits.interval_list")
- self.assertEqual(len(regions), 6809)
-
-
-
-class ImporterTests(unittest.TestCase):
- """Tests for importers functionality."""
-
- def test_import_picard(self):
- """Test loading a Picard targetcoverage file."""
- fname = 'picard/p2-5_5.antitargetcoverage.csv'
- cna = importers.import_picard_pertargetcoverage(fname)
- self.assertGreater(len(cna), 1)
-
- def test_import_seg(self):
- """Test loading SEG format."""
- for fname, args in (
- # cnvkit.py import-seg cw-tr-log2.seg -p chr -c human -d tmp
- ('formats/cw-tr-log2.seg', ({'23': 'X', '24': 'Y', '25': 'M'}, "chr", False)),
- # cnvkit.py import-seg --from-log10 acgh-log10.seg -d tmp/
- ('formats/acgh-log10.seg', (None, None, True))):
- expect_lines = linecount(fname) - 1
- seen_lines = 0
- for cns in importers.import_seg(fname, *args):
- seen_lines += len(cns)
- self.assertEqual(seen_lines, expect_lines)
-
class CommandTests(unittest.TestCase):
"""Tests for top-level commands."""
+ def test_access(self):
+ fasta = "formats/chrM-Y-trunc.hg19.fa"
+ for min_gap_size, expect_nrows in ((None, 7),
+ (500, 3),
+ (1000, 2)):
+ acc = commands.do_access(fasta, [], min_gap_size)
+ self.assertEqual(len(acc), expect_nrows)
+ excludes = ["formats/dac-my.bed", "formats/my-targets.bed"]
+ for min_gap_size, expect_nrows in ((None, 12),
+ (2, 10),
+ (20, 5),
+ (200, 3),
+ (2000, 2)):
+ commands.do_access(fasta, excludes, min_gap_size)
+
def test_antitarget(self):
"""The 'antitarget' command."""
- baits_fname = "formats/nv2_baits.interval_list"
- access_fname = "../data/access-5k-mappable.hg19.bed"
- self.assertLess(0, len(commands.do_antitarget(baits_fname)))
- self.assertLess(0, len(
- commands.do_antitarget(baits_fname, access_fname)))
- self.assertLess(0, len(
- commands.do_antitarget(baits_fname, access_fname, 200000)))
- self.assertLess(0, len(
- commands.do_antitarget(baits_fname, access_fname, 10000, 5000)))
+ baits = tabio.read_auto('formats/nv2_baits.interval_list')
+ access = tabio.read_auto('../data/access-5k-mappable.hg19.bed')
+ self.assertLess(0, len(commands.do_antitarget(baits)))
+ self.assertLess(0, len(commands.do_antitarget(baits, access)))
+ self.assertLess(0, len(commands.do_antitarget(baits, access, 200000)))
+ self.assertLess(0, len(commands.do_antitarget(baits, access, 10000,
+ 5000)))
+
+ def test_autobin(self):
+ """The 'autobin' command."""
+ bam_fname = "formats/na12878-chrM-Y-trunc.bam"
+ target_bed = "formats/my-targets.bed"
+ targets = tabio.read(target_bed, 'bed')
+ access_bed = "../data/access-5k-mappable.hg19.bed"
+ accessible = tabio.read(access_bed, 'bed').filter(chromosome='chrY')
+ for method in ('amplicon', 'wgs', 'hybrid'):
+ (cov, bs), _ = autobin.do_autobin(bam_fname, method,
+ targets=targets,
+ access=accessible)
+ self.assertGreater(cov, 0)
+ self.assertGreater(bs, 0)
+
+ def test_batch(self):
+ """The 'batch' command."""
+ target_bed = "formats/my-targets.bed"
+ fasta = "formats/chrM-Y-trunc.hg19.fa"
+ bam = "formats/na12878-chrM-Y-trunc.bam"
+ annot = "formats/my-refflat.bed"
+ # Build a single-sample WGS reference
+ ref_fname, tgt_bed_fname, _ = batch.batch_make_reference(
+ [bam], None, None, True, fasta, annot, True, 500, None, None,
+ None, None, 'build', 1, False, "wgs")
+ self.assertEqual(ref_fname, 'build/reference.cnn')
+ refarr = cnvlib.read(ref_fname, 'bed')
+ tgt_regions = tabio.read(tgt_bed_fname, 'bed')
+ self.assertEqual(len(refarr), len(tgt_regions))
+ # Build a single-sample hybrid-capture reference
+ ref_fname, tgt_bed_fname, anti_bed_fname = batch.batch_make_reference(
+ [bam], target_bed, None, True, fasta, None, True, 10, None, 1000,
+ 100, None, 'build', 1, False, "hybrid")
+ self.assertEqual(ref_fname, 'build/reference.cnn')
+ refarr = cnvlib.read(ref_fname, 'bed')
+ tgt_regions = tabio.read(tgt_bed_fname, 'bed')
+ anti_regions = tabio.read(anti_bed_fname, 'bed')
+ self.assertEqual(len(refarr), len(tgt_regions) + len(anti_regions))
+ # Run the same sample
+ batch.batch_run_sample(
+ bam, tgt_bed_fname, anti_bed_fname, ref_fname, 'build', True,
+ True, True, None, False, False, "hybrid", 1)
+ cns = cnvlib.read("build/na12878-chrM-Y-trunc.cns")
+ self.assertGreater(len(cns), 0)
def test_breaks(self):
"""The 'breaks' command."""
@@ -300,7 +201,25 @@ class CommandTests(unittest.TestCase):
is_reference_male=True, is_sample_female=True)
self.assertEqual(len(cl_cns), len(cl_none))
- def test_call_gender(self):
+ def test_call_filter(self):
+ segments = cnvlib.read("formats/tr95t.segmetrics.cns")
+ variants = tabio.read("formats/na12878_na12882_mix.vcf", "vcf")
+ # Each filter individually, then all filters together
+ for filters in (['ampdel'], ['cn'], ['ci'], ['sem'],
+ ['sem', 'cn', 'ampdel'],
+ ['ci', 'cn']):
+ result = commands.do_call(segments, variants, method="threshold",
+ purity=.9, is_reference_male=True,
+ is_sample_female=True, filters=filters)
+ self.assertLessEqual(len(result), len(segments))
+ if 'ampdel' not in filters:
+ # At least 1 segment per chromosome remains
+ self.assertLessEqual(len(segments.chromosome.unique()),
+ len(result))
+ for colname in 'baf', 'cn', 'cn1', 'cn2':
+ self.assertIn(colname, result)
+
+ def test_call_sex(self):
"""Test each 'call' method on allosomes."""
for (fname, sample_is_f, ref_is_m,
chr1_expect, chrx_expect, chry_expect,
@@ -343,40 +262,88 @@ class CommandTests(unittest.TestCase):
is_sample_female=sample_is_f)
test_chrom_means(cns_p99)
- def test_export(self):
- """Run the 'export' command with each format."""
- # SEG
- seg_rows = export.export_seg(["formats/tr95t.cns"])
- self.assertGreater(len(seg_rows), 0)
- seg2_rows = export.export_seg(["formats/tr95t.cns",
- "formats/cl_seq.cns"])
- self.assertGreater(len(seg2_rows), len(seg_rows))
- # THetA2
- cnr = cnvlib.read("formats/tr95t.cns")
- theta_rows = export.export_theta(cnr, None)
- self.assertGreater(len(theta_rows), 0)
- ref = cnvlib.read("formats/reference-tr.cnn")
- theta_rows = export.export_theta(cnr, ref)
- self.assertGreater(len(theta_rows), 0)
- # Formats that calculate absolute copy number
+ def test_coverage(self):
+ """The 'coverage' command."""
+ # fa = 'formats/chrM-Y-trunc.hg19.fa'
+ bed = 'formats/my-targets.bed'
+ bam = 'formats/na12878-chrM-Y-trunc.bam'
+ for by_count in (False, True):
+ for min_mapq in (0, 30):
+ for nprocs in (1, 2):
+ cna = commands.do_coverage(bed, bam,
+ by_count=by_count,
+ min_mapq=min_mapq,
+ processes=nprocs)
+ self.assertEqual(len(cna), 4)
+ self.assertTrue((cna.log2 != 0).any())
+ self.assertGreater(cna.log2.nunique(), 1)
+
+ def test_export_bed_vcf(self):
+ """The 'export' command for formats with absolute copy number."""
for fname, ploidy, is_f in [("tr95t.cns", 2, True),
("cl_seq.cns", 6, True),
("amplicon.cns", 2, False)]:
cns = cnvlib.read("formats/" + fname)
# BED
- self.assertLess(len(export.export_bed(cns, ploidy, True, is_f,
- cns.sample_id, "ploidy")),
- len(cns))
- self.assertLess(len(export.export_bed(cns, ploidy, True, is_f,
- cns.sample_id, "variant")),
- len(cns))
- self.assertEqual(len(export.export_bed(cns, ploidy, True, is_f,
- cns.sample_id, "all")),
- len(cns))
+ for show in ("ploidy", "variant", "all"):
+ tbl_bed = export.export_bed(cns, ploidy, True, is_f,
+ cns.sample_id, show)
+ if show == "all":
+ self.assertEqual(len(tbl_bed), len(cns),
+ "{} {}".format(fname, ploidy))
+ else:
+ self.assertLess(len(tbl_bed), len(cns))
# VCF
_vheader, vcf_body = export.export_vcf(cns, ploidy, True, is_f)
self.assertTrue(0 < len(vcf_body.splitlines()) < len(cns))
+ def test_export_cdt_jtv(self):
+ """The 'export' command for CDT and Java TreeView formats."""
+ fnames = ["formats/p2-20_1.cnr", "formats/p2-20_2.cnr"]
+ sample_ids = list(map(core.fbase, fnames))
+ nrows = linecount(fnames[0]) - 1
+ import sys
+ for fmt_key, header2 in (('cdt', 2), ('jtv', 0)):
+ table = export.merge_samples(fnames)
+ formatter = export.EXPORT_FORMATS[fmt_key]
+ _oh, outrows = formatter(sample_ids, table)
+ self.assertEqual(len(list(outrows)), nrows + header2)
+
+ def test_export_nexus(self):
+ """The 'export nexus-basic' and 'nexus-ogt' commands."""
+ cnr = cnvlib.read("formats/amplicon.cnr")
+ table_nb = export.export_nexus_basic(cnr)
+ self.assertEqual(len(table_nb), len(cnr))
+ varr = commands.load_het_snps("formats/na12878_na12882_mix.vcf",
+ None, None, 15, None)
+ table_ogt = export.export_nexus_ogt(cnr, varr, 0.05)
+ self.assertEqual(len(table_ogt), len(cnr))
+
+ def test_export_seg(self):
+ """The 'export seg' command."""
+ seg_rows = export.export_seg(["formats/tr95t.cns"])
+ self.assertGreater(len(seg_rows), 0)
+ seg2_rows = export.export_seg(["formats/tr95t.cns",
+ "formats/cl_seq.cns"])
+ self.assertGreater(len(seg2_rows), len(seg_rows))
+
+ def test_export_theta(self):
+ """The 'export theta' command."""
+ segarr = cnvlib.read("formats/tr95t.cns")
+ len_seg_auto = len(segarr.autosomes())
+ table_theta = export.export_theta(segarr, None)
+ self.assertEqual(len(table_theta), len_seg_auto)
+ ref = cnvlib.read("formats/reference-tr.cnn")
+ table_theta = export.export_theta(segarr, ref)
+ self.assertEqual(len(table_theta), len_seg_auto)
+ varr = commands.load_het_snps("formats/na12878_na12882_mix.vcf",
+ "NA12882", "NA12878", 15, None)
+ tumor_snps, normal_snps = export.export_theta_snps(varr)
+ self.assertLess(len(tumor_snps), len(varr))
+ self.assertGreater(len(tumor_snps), 0)
+ self.assertLess(len(normal_snps), len(varr))
+ self.assertGreater(len(normal_snps), 0)
+
def test_fix(self):
"""The 'fix' command."""
# Extract fake target/antitarget bins from a combined file
@@ -400,7 +367,7 @@ class CommandTests(unittest.TestCase):
rows = commands.do_gainloss(probes, male_reference=True)
self.assertGreater(len(rows), 0)
segs = cnvlib.read("formats/amplicon.cns")
- rows = commands.do_gainloss(probes, segs, True, 0.3, 4)
+ rows = commands.do_gainloss(probes, segs, 0.3, 4, male_reference=True)
self.assertGreater(len(rows), 0)
def test_import_theta(self):
@@ -414,31 +381,54 @@ class CommandTests(unittest.TestCase):
"""The 'metrics' command."""
cnarr = cnvlib.read("formats/amplicon.cnr")
segments = cnvlib.read("formats/amplicon.cns")
- resids = cnarr.residuals(segments)
- self.assertLessEqual(len(resids), len(cnarr))
- values = metrics.ests_of_scale(resids)
+ result = metrics.do_metrics(cnarr, segments, skip_low=True)
+ self.assertEqual(result.shape, (1, 6))
+ values = result.loc[0, result.columns[1:]]
for val in values:
self.assertGreater(val, 0)
def test_reference(self):
"""The 'reference' command."""
- # Empty antitargets
+ # Empty/unspecified antitargets
+ nlines = linecount("formats/amplicon.cnr") - 1
ref = commands.do_reference(["formats/amplicon.cnr"], ["formats/empty"])
- self.assertGreater(len(ref), 0)
- # Empty antitargets, flat reference
+ self.assertEqual(len(ref), nlines)
+ ref = commands.do_reference(["formats/amplicon.cnr"])
+ self.assertEqual(len(ref), nlines)
+ # Empty/unspecified antitargets, flat reference
+ nlines = linecount("formats/amplicon.bed")
ref = commands.do_reference_flat("formats/amplicon.bed",
"formats/empty")
- self.assertGreater(len(ref), 0)
+ self.assertEqual(len(ref), nlines)
+ ref = commands.do_reference_flat("formats/amplicon.bed")
+ self.assertEqual(len(ref), nlines)
+ # Misc
+ ref = cnvlib.read('formats/reference-tr.cnn')
+ targets, antitargets = reference.reference2regions(ref)
+ self.assertLess(0, len(antitargets))
+ self.assertEqual(len(antitargets), (ref['gene'] == 'Background').sum())
+ self.assertEqual(len(targets), len(ref) - len(antitargets))
def test_segment(self):
"""The 'segment' command."""
cnarr = cnvlib.read("formats/amplicon.cnr")
- # R methods are in another script
+ # NB: R methods are in another script; haar is pure-Python
segments = segmentation.do_segmentation(cnarr, "haar")
self.assertGreater(len(segments), 0)
- segments = segmentation.do_segmentation(cnarr, "haar", threshold=.001,
+ segments = segmentation.do_segmentation(cnarr, "haar", threshold=.0001,
skip_low=True)
self.assertGreater(len(segments), 0)
+ varr = tabio.read("formats/na12878_na12882_mix.vcf", "vcf")
+ segments = segmentation.do_segmentation(cnarr, "haar", variants=varr)
+ self.assertGreater(len(segments), 0)
+
+ def test_segment_parallel(self):
+ """The 'segment' command, in parallel."""
+ cnarr = cnvlib.read("formats/amplicon.cnr")
+ psegments = segmentation.do_segmentation(cnarr, "haar", processes=2)
+ ssegments = segmentation.do_segmentation(cnarr, "haar", processes=1)
+ self.assertEqual(psegments.data.shape, ssegments.data.shape)
+ self.assertEqual(len(psegments.meta), len(ssegments.meta))
def test_segmetrics(self):
"""The 'segmetrics' command."""
@@ -460,12 +450,26 @@ class CommandTests(unittest.TestCase):
def test_target(self):
"""The 'target' command."""
- # ENH: annotate w/ mini-refFlat
- r = commands.do_targets("formats/nv2_baits.interval_list")
- self.assertGreater(len(r), 0)
- r = commands.do_targets("formats/amplicon.bed", do_short_names=True,
- do_split=True, avg_size=100)
- self.assertGreater(len(r), 0)
+ annot_fname = "formats/refflat-mini.txt"
+ for bait_fname in ("formats/nv2_baits.interval_list",
+ "formats/amplicon.bed"):
+ baits = tabio.read_auto(bait_fname)
+ bait_len = len(baits)
+ # No splitting: w/ and w/o re-annotation
+ r1 = commands.do_target(baits)
+ self.assertEqual(len(r1), bait_len)
+ r1a = commands.do_target(baits, do_short_names=True,
+ annotate=annot_fname)
+ self.assertEqual(len(r1a), len(r1))
+ # Splitting
+ r2 = commands.do_target(baits, do_short_names=True, do_split=True,
+ avg_size=100)
+ self.assertGreater(len(r2), len(r1))
+ r2a = commands.do_target(baits, do_short_names=True, do_split=True,
+ avg_size=100, annotate=annot_fname)
+ self.assertEqual(len(r2a), len(r2))
+ # Original regions object should be unmodified
+ self.assertEqual(len(baits), bait_len)
@@ -474,8 +478,8 @@ class OtherTests(unittest.TestCase):
def test_fix_edge(self):
"""Test the 'edge' bias correction calculations."""
- # With no gap, gain and loss should balance out
- # 1. Wide target, no secondary corrections triggered
+ # NB: With no gap, gain and loss should balance out
+ # Wide target, no secondary corrections triggered
insert_size = 250
gap_size = np.zeros(1) # Adjacent
target_size = np.asarray([600])
@@ -483,11 +487,12 @@ class OtherTests(unittest.TestCase):
gain = fix.edge_gains(target_size, gap_size, insert_size)
gain *= 2 # Same on the other side
self.assertAlmostEqual(loss, gain)
- # 2. Trigger 'loss' correction (target_size < 2 * insert_size)
+ # Trigger 'loss' correction (target_size < 2 * insert_size)
target_size = np.asarray([450])
- self.assertAlmostEqual(fix.edge_losses(target_size, insert_size),
- 2 * fix.edge_gains(target_size, gap_size, insert_size))
- # 3. Trigger 'gain' correction (target_size + gap_size < insert_size)
+ self.assertAlmostEqual(
+ fix.edge_losses(target_size, insert_size),
+ 2 * fix.edge_gains(target_size, gap_size, insert_size))
+ # Trigger 'gain' correction (target_size + gap_size < insert_size)
target_size = np.asarray([300])
self.assertAlmostEqual(fix.edge_losses(target_size, insert_size),
2 * fix.edge_gains(target_size, gap_size, insert_size))
@@ -499,7 +504,7 @@ class OtherTests(unittest.TestCase):
# == helpers ==
def linecount(filename):
- i = 0
+ i = -1
with open(filename) as handle:
for i, _line in enumerate(handle):
pass
diff --git a/test/test_genome.py b/test/test_genome.py
new file mode 100755
index 0000000..1083d49
--- /dev/null
+++ b/test/test_genome.py
@@ -0,0 +1,543 @@
+#!/usr/bin/env python
+"""Unit tests for the 'genome' sub-package."""
+from __future__ import absolute_import, division, print_function
+import random
+import unittest
+
+import numpy as np
+import pandas as pd
+
+from cnvlib import read
+from skgenome import chromsort, rangelabel
+from skgenome import tabio, GenomicArray as GA
+
+
+class GaryTests(unittest.TestCase):
+
+ def setUp(self):
+ self.ex_cnr = read('formats/reference-tr.cnn')
+
+ def test_empty(self):
+ """Instantiate from an empty file."""
+ garr = tabio.read("formats/empty")
+ self.assertEqual(len(garr), 0)
+
+ def test_iter(self):
+ """Test iteration."""
+ rows = iter(self.ex_cnr)
+ firstrow = next(rows)
+ self.assertEqual(tuple(firstrow), tuple(self.ex_cnr[0]))
+ i = 0
+ for i, _row in enumerate(rows):
+ pass
+ self.assertEqual(i + 2, len(self.ex_cnr))
+
+ def test_copy(self):
+ """Test creation of an independent copy of the object."""
+ dupe = self.ex_cnr.copy()
+ self.assertEqual(tuple(self.ex_cnr[3]), tuple(dupe[3]))
+ self.ex_cnr[3, 'log2'] = -10.0
+ self.assertNotEqual(tuple(self.ex_cnr[3]), tuple(dupe[3]))
+
+ def test_autosomes(self):
+ """Test selection of autosomes."""
+ len_all = len(self.ex_cnr)
+ len_x = (self.ex_cnr.chromosome == 'chrX').sum()
+ len_y = (self.ex_cnr.chromosome == 'chrY').sum()
+ auto = self.ex_cnr.autosomes()
+ self.assertEqual(len(auto), len_all - len_x - len_y)
+ autox = self.ex_cnr.autosomes(also='chrX')
+ self.assertEqual(len(autox), len_all - len_y)
+ autoy = self.ex_cnr.autosomes(also=['chrY'])
+ self.assertEqual(len(autoy), len_all - len_x)
+ autoxy = self.ex_cnr.autosomes(also=['chrX', 'chrY'])
+ self.assertEqual(len(autoxy), len_all)
+
+ def test_by_chromosome(self):
+ for fname in ("formats/amplicon.cnr", "formats/cl_seq.cns"):
+ cnarr = read(fname)
+ row_count = 0
+ for _chrom, rows in cnarr.by_chromosome():
+ row_count += len(rows)
+ self.assertEqual(row_count, len(cnarr))
+
+ # def test_concat(self):
+
+ def test_filter(self):
+ """Test sugary selection of a subset of the data array."""
+ num_bg_rows = len(self.ex_cnr[self.ex_cnr['gene'] == 'Background'])
+ self.assertEqual(len(self.ex_cnr.filter(gene='Background')),
+ num_bg_rows)
+ selector = lambda row: row['gene'] == 'Background'
+ self.assertEqual(len(self.ex_cnr.filter(selector)), num_bg_rows)
+
+ def test_ranges_by_in(self):
+ """Test range methods: by_ranges, in_range, in_ranges."""
+ cnarr = read("formats/amplicon.cnr")
+ segarr = read("formats/amplicon.cns")
+ chrom_segarr = dict(segarr.by_chromosome())
+ for chrom, subarr in cnarr.by_chromosome():
+ count_segs = 0
+ count_bins = 0
+ subsegarr = chrom_segarr[chrom]
+ for count_segs, (seg, bins) in enumerate(subarr.by_ranges(subsegarr)):
+ count_bins += len(bins)
+ self.assertEqual(seg.probes, len(bins))
+ self.assertEqual(len(bins), len(
+ cnarr.in_range(seg.chromosome, seg.start, seg.end,
+ mode='outer')))
+ self.assertEqual(len(bins), len(
+ cnarr.in_range(seg.chromosome, seg.start, seg.end,
+ mode='trim')))
+ self.assertEqual(len(subsegarr), count_segs + 1)
+ self.assertEqual(len(subarr), count_bins)
+ self.assertEqual(len(subarr), len(
+ cnarr.in_ranges(chrom, subsegarr['start'], subsegarr['end'],
+ mode="outer")))
+ self.assertEqual(len(subarr), len(
+ subarr.in_ranges(starts=subsegarr['start'],
+ ends=subsegarr['end'], mode="outer")))
+ self.assertEqual(len(subarr), len(
+ cnarr.in_ranges(chrom, subsegarr['start'], subsegarr['end'],
+ mode="trim")))
+ self.assertEqual(len(subarr), len(
+ subarr.in_ranges(starts=subsegarr['start'],
+ ends=subsegarr['end'], mode="trim")))
+
+ def test_ranges_into(self):
+ cnarr = read("formats/amplicon.cnr")
+ segarr = read("formats/amplicon.cns")
+ seg_genes = cnarr.into_ranges(segarr, 'gene', '-')
+ self.assertEqual(len(seg_genes), len(segarr))
+ # With a VCF
+ varr = tabio.read("formats/na12878_na12882_mix.vcf", "vcf")
+ seg_baf = varr.into_ranges(segarr, 'alt_freq', np.nan, np.nanmedian)
+ self.assertEqual(len(seg_baf), len(segarr))
+ cna_baf = varr.into_ranges(cnarr, 'alt_freq', 0.0, np.max)
+ self.assertEqual(len(cna_baf), len(cnarr))
+ # Edge cases
+ mtarr = tabio.read("formats/empty")
+ segarr.into_ranges(mtarr, 'start', 0, int)
+ mtarr.into_ranges(segarr, 'end', 0, 0)
+
+ def test_ranges_resize(self):
+ baits_fname = 'formats/nv2_baits.interval_list'
+ chrom_sizes = {'chr1': 249250621,
+ 'chr2': 243199373,
+ 'chr3': 198022430,
+ 'chr4': 191154276,
+ 'chr5': 180915260,
+ 'chr6': 171115067,
+ 'chr7': 159138663,
+ 'chr8': 146364022,
+ 'chr9': 141213431,
+ 'chr10': 135534747,
+ 'chr11': 135006516,
+ 'chr12': 133851895,
+ 'chr13': 115169878,
+ 'chr14': 107349540,
+ 'chr15': 102531392,
+ 'chr16': 90354753,
+ 'chr17': 81195210,
+ 'chr18': 78077248,
+ 'chr19': 59128983,
+ 'chr20': 63025520,
+ 'chr21': 48129895,
+ 'chr22': 51304566,
+ 'chrX': 155270560,
+ 'chrY': 59373566}
+ bins = tabio.read(baits_fname, 'interval')
+ for chrom, arr in bins.resize_ranges(1e7, chrom_sizes).by_chromosome():
+ self.assertLessEqual(0, arr.start.min())
+ self.assertLessEqual(arr.end.max(), chrom_sizes[chrom])
+
+ def test_total_range_size(self):
+ """Test total region coverage calculation."""
+ for fname, area in (
+ ('formats/empty', 0),
+ ('formats/my-targets.bed', 103),
+ ('formats/dac-my.bed', 148),
+ ('formats/example.gff', 7951),
+ ('formats/refflat-mini.txt', 719715),
+ ):
+ regions = tabio.read_auto(fname)
+ self.assertEqual(regions.total_range_size(), area)
+
+ def test_shuffle_sort(self):
+ """Test shuffling and re-sorting the data array."""
+ orig_cvg = tuple(self.ex_cnr['log2'][:10])
+ self.assertEqual(tuple(self.ex_cnr['log2'][:10]), orig_cvg)
+ self.ex_cnr.shuffle()
+ self.assertNotEqual(tuple(self.ex_cnr['log2'][:10]), orig_cvg)
+ self.ex_cnr.sort()
+ self.assertEqual(tuple(self.ex_cnr['log2'][:10]), orig_cvg)
+
+
+
+class IntervalTests(unittest.TestCase):
+ """Interval arithmetic tests."""
+ combiner = {'gene': lambda a: ''.join(a)}
+
+ # Simple: nested, overlapping, & non-overlapping intervals
+ # =A=========================
+ # =B======= =D=== =E======
+ # =C=
+ # 1 3 5 6 8 11 15 19 20 23 <- coordinates
+ region_coords_1 = (
+ (1, 20, 'A'),
+ (3, 8, 'B'),
+ (5, 6, 'C'),
+ (11, 15, 'D'),
+ (19, 23, 'E'),
+ )
+
+ # Semi-realistic: overlapping gene models
+ # =A=============================
+ # =B== =C== =E== =G==
+ # =D=========================
+ # =F== =H== =I==
+ # 3 5 8 11 14 17 19 22 25 28 32 36 39 42
+ region_coords_2 = (
+ (3, 32, 'A'),
+ (5, 8, 'B'),
+ (11, 14, 'C'),
+ (17, 42, 'D'),
+ (19, 22, 'E'),
+ (19, 22, 'F'),
+ (25, 28, 'G'),
+ (25, 28, 'H'),
+ (36, 39, 'I'),
+ )
+
+ @staticmethod
+ def _from_intervals(coords):
+ garr = GA(pd.DataFrame(list(coords),
+ columns=['start', 'end', 'gene'])
+ .assign(chromosome='chr0'))
+ garr.sort_columns()
+ return garr
+
+ def _compare_regions(self, result, expect):
+ self.assertEqual(expect.data.shape, result.data.shape,
+ '\n'.join(["Got:", str(result.data),
+ "Expected:", str(expect.data)]))
+ for col in expect.data.columns:
+ self.assertTrue((expect[col] == result[col]).all(),
+ "Col '{}' differs:\nExpect:\n{}\nGot:\n{}"
+ .format(col, expect.data, result.data))
+
+ def setUp(self):
+ self.regions_1 = self._from_intervals(self.region_coords_1)
+ self.regions_2 = self._from_intervals(self.region_coords_2)
+
+ def test_flatten(self):
+ flat_coords_1 = [
+ (1, 3, 'A'),
+ (3, 5, 'AB'),
+ (5, 6, 'ABC'),
+ (6, 8, 'AB'),
+ (8, 11, 'A'),
+ (11, 15, 'AD'),
+ (15, 19, 'A'),
+ (19, 20, 'AE'),
+ (20, 23, 'E'),
+ ]
+ flat_coords_2 = [
+ (3, 5, 'A'),
+ (5, 8, 'AB'),
+ (8, 11, 'A'),
+ (11, 14, 'AC'),
+ (14, 17, 'A'),
+ (17, 19, 'AD'),
+ (19, 22, 'ADEF'),
+ (22, 25, 'AD'),
+ (25, 28, 'ADGH'),
+ (28, 32, 'AD'),
+ (32, 36, 'D'),
+ (36, 39, 'DI'),
+ (39, 42, 'D'),
+ ]
+ for regions, flat_coords in [
+ (self.regions_1, flat_coords_1),
+ (self.regions_2, flat_coords_2),
+ ]:
+ result = regions.flatten(combine=self.combiner)
+ expect = self._from_intervals(flat_coords)
+ self._compare_regions(result, expect)
+
+ def test_merge(self):
+ merged_coords_1 = [(1, 23, 'ABCDE')]
+ merged_coords_2 = [(3, 42, 'ABCDEFGHI')]
+ for regions, merged_coords in [
+ (self.regions_1, merged_coords_1),
+ (self.regions_2, merged_coords_2),
+ ]:
+ result = regions.merge(combine=self.combiner)
+ expect = self._from_intervals(merged_coords)
+ self._compare_regions(result, expect)
+
+ def test_intersect(self):
+ selections1 = self._from_intervals([
+ (1, 8, ''),
+ (4, 10, ''),
+ (8, 19, ''),
+ (11, 20, ''),
+ (21, 22, ''),
+ ])
+ expectations1 = {
+ 'outer': (
+ # 1-8
+ [(1, 20, 'A'),
+ (3, 8, 'B'),
+ (5, 6, 'C'),
+ ],
+ # 4-10
+ [(1, 20, 'A'),
+ (3, 8, 'B'),
+ (5, 6, 'C'),
+ ],
+ # 8-19
+ [(1, 20, 'A'),
+ (11, 15, 'D')],
+ # 11-20
+ [(1, 20, 'A'),
+ (11, 15, 'D'),
+ (19, 23, 'E')],
+ # 21-22
+ [(19, 23, 'E')],
+ ),
+ 'trim': (
+ # 1-8
+ [(1, 8, 'A'),
+ (3, 8, 'B'),
+ (5, 6, 'C')],
+ # 4-10
+ [(4, 10, 'A'),
+ (4, 8, 'B'),
+ (5, 6, 'C')],
+ # 8-19
+ [(8, 19, 'A'),
+ (11, 15, 'D')],
+ # 11-20
+ [(11, 20, 'A'),
+ (11, 15, 'D'),
+ (19, 20, 'E')],
+ # 21-22
+ [(21, 22, 'E')],
+ ),
+ 'inner': (
+ # 1-8
+ [(3, 8, 'B'),
+ (5, 6, 'C')],
+ # 4-10
+ [(5, 6, 'C')],
+ # 8-19
+ [(11, 15, 'D')],
+ # 11-20
+ [(11, 15, 'D')],
+ # 21-22
+ [],
+ ),
+ }
+
+ selections2 = self._from_intervals([
+ (0, 1, ''),
+ (5, 14, ''),
+ (16, 45, ''),
+ (18, 37, ''),
+ (19, 25, ''),
+ (29, 31, ''),
+ (34, 39, ''),
+ ])
+ expectations2 = {
+ 'outer': (
+ # 0-1
+ [],
+ # 5-14
+ [(3, 32, 'A'),
+ (5, 8, 'B'),
+ (11, 14, 'C')],
+ # 16-45
+ [(3, 32, 'A'),
+ (17, 42, 'D'),
+ (19, 22, 'E'),
+ (19, 22, 'F'),
+ (25, 28, 'G'),
+ (25, 28, 'H'),
+ (36, 39, 'I')],
+ # 18-37
+ [(3, 32, 'A'),
+ (17, 42, 'D'),
+ (19, 22, 'E'),
+ (19, 22, 'F'),
+ (25, 28, 'G'),
+ (25, 28, 'H'),
+ (36, 39, 'I')],
+ # 19-25
+ [(3, 32, 'A'),
+ (17, 42, 'D'),
+ (19, 22, 'E'),
+ (19, 22, 'F')],
+ # 29-31
+ [(3, 32, 'A'),
+ (17, 42, 'D')],
+ # 34-39
+ [(17, 42, 'D'),
+ (36, 39, 'I')],
+ ),
+ 'trim': (
+ # 0-1
+ [],
+ # 5-14
+ [(5, 14, 'A'),
+ (5, 8, 'B'),
+ (11, 14, 'C')],
+ # 16-45
+ [(16, 32, 'A'),
+ (17, 42, 'D'),
+ (19, 22, 'E'),
+ (19, 22, 'F'),
+ (25, 28, 'G'),
+ (25, 28, 'H'),
+ (36, 39, 'I')],
+ # 18-37
+ [(18, 32, 'A'),
+ (18, 37, 'D'),
+ (19, 22, 'E'),
+ (19, 22, 'F'),
+ (25, 28, 'G'),
+ (25, 28, 'H'),
+ (36, 37, 'I')],
+ # 19-25
+ [(19, 25, 'A'),
+ (19, 25, 'D'),
+ (19, 22, 'E'),
+ (19, 22, 'F')],
+ # 29-31
+ [(29, 31, 'A'),
+ (29, 31, 'D')],
+ # 34-39
+ [(34, 39, 'D'),
+ (36, 39, 'I')],
+ ),
+ 'inner': (
+ # 0-1
+ [],
+ # 5-14
+ [(5, 8, 'B'),
+ (11, 14, 'C')],
+ # 16-45
+ [(17, 42, 'D'),
+ (19, 22, 'E'),
+ (19, 22, 'F'),
+ (25, 28, 'G'),
+ (25, 28, 'H'),
+ (36, 39, 'I')],
+ # 18-37
+ [(19, 22, 'E'),
+ (19, 22, 'F'),
+ (25, 28, 'G'),
+ (25, 28, 'H')],
+ # 19-25
+ [(19, 22, 'E'),
+ (19, 22, 'F')],
+ # 29-31
+ [],
+ # 34-39
+ [(36, 39, 'I')],
+ ),
+ }
+
+ for regions, selections, expectations in (
+ (self.regions_1, selections1, expectations1),
+ (self.regions_2, selections2, expectations2),
+ ):
+ for mode in ('outer', 'trim', 'inner'):
+ grouped_results = regions.by_ranges(selections, mode=mode)
+ for (_coord, result), expect in zip(grouped_results,
+ expectations[mode]):
+ self._compare_regions(result, self._from_intervals(expect))
+
+ def test_subtract(self):
+ # Test cases:
+ # | access: ==== ==== ==== ==========
+ # | target: ==== ====== === = == == ===
+ # | expect: == == ===
+ # | invert: = = = = = =
+ # | 1 5 78 2345 7 901234 6 8 1 34
+ # | 0 1 2 3
+
+ access = self._from_intervals([
+ (1, 5, ''),
+ (8, 12, ''),
+ (15, 19, ''),
+ (23, 33, ''),
+ ])
+ target = self._from_intervals([
+ (1, 5, ''),
+ (7, 13, ''),
+ (14, 17, ''),
+ (20, 21, ''),
+ (22, 24, ''),
+ (26, 28, ''),
+ (31, 34, ''),
+ ])
+ expect = self._from_intervals([
+ (17, 19, ''),
+ (24, 26, ''),
+ (28, 31, ''),
+ ])
+ invert = self._from_intervals([
+ (7, 8, ''),
+ (12, 13, ''),
+ (14, 15, ''),
+ (20, 21, ''),
+ (22, 23, ''),
+ (33, 34, ''),
+ ])
+
+ result = access.subtract(target)
+ self._compare_regions(result, expect)
+ iresult = target.subtract(access)
+ self._compare_regions(iresult, invert)
+
+
+
+class OtherTests(unittest.TestCase):
+ """Other small modules & functions in this sub-package."""
+
+ def test_chromsort(self):
+ labels_hg = ["chr1", "chr2", "chr10", "chr19", "chr20",
+ "chrX", "chrY", "chrM"]
+ labels_grc = ["1", "2", "10", "19", "X", "Y", "MT"]
+ for labels in (labels_hg, labels_grc):
+ shuf = labels[:]
+ random.shuffle(shuf)
+ resorted = sorted(labels, key=chromsort.sorter_chrom)
+ self.assertEqual(resorted, labels)
+
+ def test_detect_big_chroms(self):
+ sizes = [1, 20, 30]
+ n_big, thresh = chromsort.detect_big_chroms(sizes)
+ self.assertEqual(n_big, 2)
+ self.assertEqual(thresh, 20)
+
+ def test_rangelabel(self):
+ row = rangelabel.from_label("chr1:123-456", keep_gene=False)
+ self.assertEqual(tuple(row), ("chr1", 122, 456))
+ label = rangelabel.to_label(row)
+ self.assertEqual(label, "chr1:123-456")
+ # unpack_range
+ for region, expect in (
+ ["chr1", ("chr1", None, None)],
+ ["chr1:100-123", ("chr1", 99, 123)],
+ [("chr1", 100, 123), ("chr1", 100, 123)],
+ [("chr1", 100, 123, "A"), ("chr1", 100, 123)],
+ ):
+ result = rangelabel.unpack_range(region)
+ self.assertEqual(result, expect)
+
+
+
+if __name__ == '__main__':
+ unittest.main(verbosity=2)
diff --git a/test/test_io.py b/test/test_io.py
new file mode 100755
index 0000000..519b65b
--- /dev/null
+++ b/test/test_io.py
@@ -0,0 +1,130 @@
+#!/usr/bin/env python
+"""Unit tests for the CNVkit library, cnvlib."""
+from __future__ import absolute_import, division, print_function
+
+import unittest
+
+from skgenome import tabio
+
+
+class IOTests(unittest.TestCase):
+ """Tests for I/O modules."""
+
+ def test_empty(self):
+ """Instantiate from an empty file."""
+ for fmt in ("auto", "bed", #"bed3", "bed4",
+ "interval", "tab", "text"):
+ regions = tabio.read("formats/empty", fmt=fmt)
+ self.assertEqual(len(regions), 0)
+
+ def test_read_auto(self):
+ for fname, nrows in (("formats/empty", 0),
+ ("formats/amplicon.bed", 1433),
+ ("formats/amplicon.text", 1433),
+ ("formats/nv2_baits.interval_list", 6809),
+ ("formats/refflat-mini.txt", 100),
+ ("formats/example.gff", 6),
+ ):
+ self.assertEqual(len(tabio.read_auto(fname)), nrows)
+ with open(fname) as handle:
+ self.assertEqual(len(tabio.read_auto(handle)), nrows)
+
+ def test_read_bed(self):
+ """Read the BED format."""
+ fname = "formats/amplicon.bed"
+ regions = tabio.read(fname, "bed")
+ self.assertEqual(len(regions), linecount(fname))
+ self.assertEqual(regions.sample_id, "amplicon")
+
+ def test_read_gff(self):
+ """Read the GFF format."""
+ fname = 'formats/example.gff'
+ regions = tabio.read(fname, 'gff')
+ self.assertEqual(len(regions), linecount(fname) - 2)
+ self.assertEqual(regions.sample_id, 'example')
+
+ def test_read_ilist(self):
+ """Read the interval list format."""
+ regions = tabio.read("formats/nv2_baits.interval_list", "interval")
+ self.assertEqual(len(regions), 6809)
+ self.assertEqual(regions.sample_id, "nv2_baits")
+
+ def test_read_picardhs(self):
+ """Read Picard CalculateHsMetrics PER_TARGET_COVERAGE format."""
+ fname = "picard/p2-5_5.antitargetcoverage.csv"
+ cna = tabio.read(fname, "picardhs")
+ self.assertEqual(len(cna), linecount(fname) - 1)
+ self.assertEqual(cna.sample_id, "p2-5_5")
+
+ def test_read_refflat(self):
+ """Read the UCSC 'refFlat' format."""
+ fname = "formats/refflat-mini.txt"
+ regions = tabio.read(fname, 'refflat')
+ self.assertEqual(len(regions), linecount(fname))
+ self.assertEqual(13, regions.chromosome.nunique())
+
+ def test_read_seg(self):
+ """Read the SEG format."""
+ for fname, header_len, args in (
+ # Convert integer chrom. IDs to hg19 names
+ ('formats/cw-tr-log2.seg', 1,
+ ({'23': 'X', '24': 'Y', '25': 'M'}, "chr", False)),
+ # Convert segmented array CGH data in log10 scale to log2
+ ('formats/acgh-log10.seg', 1, (None, None, True)),
+ # From PSCBS/DNAcopy, with a stray warning message from R
+ ('formats/warning.seg', 2, (None, None, False)),
+ ):
+ expect_lines = linecount(fname) - header_len
+ seen_lines = 0
+ for _sample_id, dframe in tabio.seg.parse_seg(fname, *args):
+ seen_lines += len(dframe)
+ self.assertEqual(seen_lines, expect_lines)
+
+ def test_read_text(self):
+ """Read the text region format."""
+ fname = "formats/amplicon.text"
+ regions = tabio.read(fname, "text")
+ self.assertEqual(len(regions), linecount(fname))
+ self.assertEqual(regions.sample_id, "amplicon")
+
+ def test_read_vcf(self):
+ """Read the VCF format."""
+ # Paired VCF with full info
+ fname = "formats/na12878_na12882_mix.vcf"
+ v1 = tabio.read(fname, "vcf")
+ self.assertLess(len(v1), linecount(fname))
+ self.assertLess(0, len(v1))
+ for sid in ("NA12882", "NA12878"):
+ v2 = tabio.read(fname, "vcf", sample_id=sid)
+ self.assertEqual(v2.sample_id, sid)
+ self.assertEqual(len(v1), len(v2))
+ for kwarg in ({'min_depth': 100},
+ {'skip_somatic': True},
+ {'skip_reject': True}):
+ v3 = tabio.read(fname, "vcf", **kwarg)
+ self.assertLess(len(v3), len(v1))
+ self.assertLess(0, len(v3),
+ "%d variants left after filter %r"
+ % (len(v3), list(kwarg)[0]))
+ # VCF header, no samples, no records
+ v4 = tabio.read('formats/nosample.vcf', 'vcf')
+ self.assertEqual(len(v4), 0)
+ self.assertEqual(v4.sample_id, 'nosample')
+ # VCF with 1 sample, no records
+ v5 = tabio.read('formats/blank.vcf', 'vcf', sample_id='Blank')
+ self.assertEqual(len(v5), 0)
+ self.assertEqual(v5.sample_id, 'Blank')
+
+
+# == helpers ==
+
+def linecount(filename):
+ i = -1
+ with open(filename) as handle:
+ for i, _line in enumerate(handle):
+ pass
+ return i + 1
+
+
+if __name__ == '__main__':
+ unittest.main(verbosity=2)
diff --git a/test/test_r.py b/test/test_r.py
old mode 100644
new mode 100755
index 1a0ece0..225e841
--- a/test/test_r.py
+++ b/test/test_r.py
@@ -1,5 +1,4 @@
#!/usr/bin/env python
-
"""Unit tests for CNVkit that require an R installation."""
from __future__ import absolute_import, division, print_function
@@ -12,18 +11,32 @@ from cnvlib import segmentation
class RTests(unittest.TestCase):
"""Tests that depend on the R statistical environment."""
- def test_segment(self):
- cnarr = cnvlib.read("formats/amplicon.cnr")
- # Each method
- for method in ("cbs", "flasso"):
- cns = segmentation.do_segmentation(cnarr, method)
- self.assertGreater(len(cns), 0)
- # With the R dataframe
- cns, dframe = segmentation.do_segmentation(cnarr, "flasso", 0.01,
- save_dataframe=True)
- self.assertGreater(len(cns), 0)
- self.assertGreater(len(dframe), 0)
-
+ def setUp(self):
+ self.tas_cnr = cnvlib.read('formats/amplicon.cnr')
+ self.wgs_cnr = cnvlib.read('formats/wgs-chr17.cnr')
+
+ def test_cbs(self):
+ _test_method(self, "cbs")
+
+ def test_flasso(self):
+ _test_method(self, "flasso")
+
+
+def _test_method(self, method):
+ for cnr in (self.tas_cnr,
+ # self.wgs_cnr
+ ):
+ cns, raw_str = segmentation.do_segmentation(cnr, method, processes=1,
+ save_dataframe=True)
+ self.assertGreater(len(cns), 0)
+ self.assertGreater(len(raw_str), 0)
+ # Parallel should produce the same results
+ p_cns, p_raw_str = segmentation.do_segmentation(cnr, method,
+ processes=2,
+ save_dataframe=True)
+ self.assertEqual(cns.data.shape, p_cns.data.shape)
+ self.assertEqual(len(cns.meta), len(p_cns.meta))
+ self.assertEqual(raw_str, p_raw_str)
if __name__ == '__main__':
--
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