[med-svn] [freebayes] 02/03: Add manpages

Fri Jan 13 20:57:48 UTC 2017

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository freebayes.

commit 7d20c04d5e111b0e2ef6d980d0fe2091dca579fa
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jan 13 21:50:15 2017 +0100

    Add manpages
---
 debian/bamleftalign.1 |  27 +++
 debian/freebayes.1    | 459 ++++++++++++++++++++++++++++++++++++++++++++++++++
 debian/manpages       |   1 +
 3 files changed, 487 insertions(+)

diff --git a/debian/bamleftalign.1 b/debian/bamleftalign.1
new file mode 100644
index 0000000..db395a7
--- /dev/null
+++ b/debian/bamleftalign.1
@@ -0,0 +1,27 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
+.TH BAMLEFTALIGN "1" "January 2017" "bamleftalign 1.0.2" "User Commands"
+.SH NAME
+bamleftalign \- Left\-aligns and merges the insertions and deletions in all alignments
+.SH SYNOPSIS
+[BAM data stream] | \fBbamleftalign\fR [options]
+.SH DESCRIPTION
+Left\-aligns and merges the insertions and deletions in all alignments in stdin.
+Iterates until each alignment is stable through a left\-realignment step.
+.SH OPTIONS
+.TP
+\fB\-f\fR \fB\-\-fasta\-reference\fR FILE
+FASTA reference file to use for realignment (required)
+.TP
+\fB\-d\fR \fB\-\-debug\fR
+Print debugging information about realignment process
+.TP
+\fB\-s\fR \fB\-\-suppress\-output\fR
+Don't write BAM output stream (for debugging)
+.TP
+\fB\-m\fR \fB\-\-max\-iterations\fR N
+Iterate the left\-realignment no more than this many times
+.TP
+\fB\-c\fR \fB\-\-compressed\fR
+Write compressed BAM on stdout, default is uncompressed
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/freebayes.1 b/debian/freebayes.1
new file mode 100644
index 0000000..70b8157
--- /dev/null
+++ b/debian/freebayes.1
@@ -0,0 +1,459 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
+.TH FREEBAYES "1" "January 2017" "freebayes 1.0.2" "User Commands"
+.SH NAME
+freebayes \- Bayesian haplotype\-based polymorphism discovery
+.SH SYNOPSIS
+.B  freebayes
+\fB\-f\fR [REFERENCE] [OPTIONS] [BAM FILES] >[OUTPUT]
+.SH DESCRIPTION
+FreeBayes is a Bayesian genetic variant detector designed to find
+small polymorphisms, specifically SNPs (single-nucleotide
+polymorphisms), indels (insertions and deletions), MNPs
+(multi-nucleotide polymorphisms), and complex events (composite
+insertion and substitution events) smaller than the length of a
+short-read sequencing alignment.
+.SS Overview:
+To call variants from aligned short\-read sequencing data, supply BAM files and
+a reference.  FreeBayes will provide VCF output on standard out describing SNPs,
+indels, and complex variants in samples in the input alignments.
+.PP
+By default, FreeBayes will consider variants supported by at least 2
+observations in a single sample (\fB\-C\fR) and also by at least 20% of the reads from
+a single sample (\fB\-F\fR).  These settings are suitable to low to high depth
+sequencing in haploid and diploid samples, but users working with polyploid or
+pooled samples may wish to adjust them depending on the characteristics of
+their sequencing data.
+.IP
+FreeBayes is capable of calling variant haplotypes shorter than a read length
+where multiple polymorphisms segregate on the same read.  The maximum distance
+between polymorphisms phased in this way is determined by the
+\fB\-\-max\-complex\-gap\fR, which defaults to 3bp.  In practice, this can comfortably be
+set to half the read length.
+.IP
+Ploidy may be set to any level (\fB\-p\fR), but by default all samples are assumed to
+be diploid.  FreeBayes can model per\-sample and per\-region variation in
+copy\-number (\fB\-A\fR) using a copy\-number variation map.
+.IP
+FreeBayes can act as a frequency\-based pooled caller and describe variants
+and haplotypes in terms of observation frequency rather than called genotypes.
+To do so, use \fB\-\-pooled\-continuous\fR and set input filters to a suitable level.
+Allele observation counts will be described by AO and RO fields in the VCF output.
+.SH Examples
+.TP
+# call variants assuming a diploid sample
+freebayes \fB\-f\fR ref.fa aln.bam >var.vcf
+.TP
+# call variants assuming a diploid sample, providing gVCF output
+freebayes \fB\-f\fR ref.fa \fB\-\-gvcf\fR aln.bam >var.gvcf
+.TP
+# require at least 5 supporting observations to consider a variant
+freebayes \fB\-f\fR ref.fa \fB\-C\fR 5 aln.bam >var.vcf
+.TP
+# use a different ploidy
+freebayes \fB\-f\fR ref.fa \fB\-p\fR 4 aln.bam >var.vcf
+.TP
+# assume a pooled sample with a known number of genome copies
+freebayes \fB\-f\fR ref.fa \fB\-p\fR 20 \fB\-\-pooled\-discrete\fR aln.bam >var.vcf
+.TP
+# generate frequency\-based calls for all variants passing input thresholds
+freebayes \fB\-f\fR ref.fa \fB\-F\fR 0.01 \fB\-C\fR 1 \fB\-\-pooled\-continuous\fR aln.bam >var.vcf
+.TP
+# use an input VCF (bgzipped + tabix indexed) to force calls at particular alleles
+freebayes \fB\-f\fR ref.fa \-@ in.vcf.gz aln.bam >var.vcf
+.TP
+# generate long haplotype calls over known variants
+freebayes \fB\-f\fR ref.fa \fB\-\-haplotype\-basis\-alleles\fR in.vcf.gz \fB\-\-haplotype\-length\fR 50 aln.bam
+.TP
+# naive variant calling: simply annotate observation counts of SNPs and indels
+freebayes \fB\-f\fR ref.fa \fB\-\-haplotype\-length\fR 0 \fB\-\-min\-alternate\-count\fR 1 \fB\-\-min\-alternate\-fraction\fR 0 \fB\-\-pooled\-continuous\fR \fB\-\-report\-monomorphic\fR >var.vcf
+.SH OPTIONS
+.TP
+\fB\-h\fR \fB\-\-help\fR
+Prints this help dialog.
+.TP
+\fB\-\-version\fR
+Prints the release number and the git commit id.
+.SS input
+.TP
+\fB\-b\fR \fB\-\-bam\fR FILE
+Add FILE to the set of BAM files to be analyzed.
+.HP
+\fB\-L\fR \fB\-\-bam\-list\fR FILE
+.IP
+A file containing a list of BAM files to be analyzed.
+.TP
+\fB\-c\fR \fB\-\-stdin\fR
+Read BAM input on stdin.
+.HP
+\fB\-f\fR \fB\-\-fasta\-reference\fR FILE
+.IP
+Use FILE as the reference sequence for analysis.
+An index file (FILE.fai) will be created if none exists.
+If neither \fB\-\-targets\fR nor \fB\-\-region\fR are specified, FreeBayes
+will analyze every position in this reference.
+.HP
+\fB\-t\fR \fB\-\-targets\fR FILE
+.IP
+Limit analysis to targets listed in the BED\-format FILE.
+.HP
+\fB\-r\fR \fB\-\-region\fR <chrom>:<start_position>\-<end_position>
+.IP
+Limit analysis to the specified region, 0\-base coordinates,
+end_position not included (same as BED format).
+Either '\-' or '..' maybe used as a separator.
+.HP
+\fB\-s\fR \fB\-\-samples\fR FILE
+.IP
+Limit analysis to samples listed (one per line) in the FILE.
+By default FreeBayes will analyze all samples in its input
+BAM files.
+.HP
+\fB\-\-populations\fR FILE
+.IP
+Each line of FILE should list a sample and a population which
+it is part of.  The population\-based bayesian inference model
+will then be partitioned on the basis of the populations.
+.HP
+\fB\-A\fR \fB\-\-cnv\-map\fR FILE
+.IP
+Read a copy number map from the BED file FILE, which has
+the format:
+.IP
+reference sequence, start, end, sample name, copy number
+.IP
+\&... for each region in each sample which does not have the
+default copy number as set by \fB\-\-ploidy\fR.
+.SS output
+.TP
+\fB\-v\fR \fB\-\-vcf\fR FILE
+Output VCF\-format results to FILE. (default: stdout)
+.HP
+\fB\-\-gvcf\fR
+.IP
+Write gVCF output, which indicates coverage in uncalled regions.
+.HP
+\fB\-\-gvcf\-chunk\fR NUM
+.IP
+When writing gVCF output emit a record for every NUM bases.
+.HP
+\-@ \fB\-\-variant\-input\fR VCF
+.IP
+Use variants reported in VCF file as input to the algorithm.
+Variants in this file will included in the output even if
+there is not enough support in the data to pass input filters.
+.HP
+\fB\-l\fR \fB\-\-only\-use\-input\-alleles\fR
+.IP
+Only provide variant calls and genotype likelihoods for sites
+and alleles which are provided in the VCF input, and provide
+output in the VCF for all input alleles, not just those which
+have support in the data.
+.HP
+\fB\-\-haplotype\-basis\-alleles\fR VCF
+.IP
+When specified, only variant alleles provided in this input
+VCF will be used for the construction of complex or haplotype
+alleles.
+.HP
+\fB\-\-report\-all\-haplotype\-alleles\fR
+.IP
+At sites where genotypes are made over haplotype alleles,
+provide information about all alleles in output, not only
+those which are called.
+.HP
+\fB\-\-report\-monomorphic\fR
+.IP
+Report even loci which appear to be monomorphic, and report all
+considered alleles, even those which are not in called genotypes.
+Loci which do not have any potential alternates have '.' for ALT.
+.TP
+\fB\-P\fR \fB\-\-pvar\fR N
+Report sites if the probability that there is a polymorphism
+at the site is greater than N.  default: 0.0.  Note that postfiltering is generally recommended over the use of this parameter.
+.SS population model
+.TP
+\fB\-T\fR \fB\-\-theta\fR N
+The expected mutation rate or pairwise nucleotide diversity
+among the population under analysis.  This serves as the
+single parameter to the Ewens Sampling Formula prior model
+default: 0.001
+.TP
+\fB\-p\fR \fB\-\-ploidy\fR N
+Sets the default ploidy for the analysis to N.  default: 2
+.HP
+\fB\-J\fR \fB\-\-pooled\-discrete\fR
+.IP
+Assume that samples result from pooled sequencing.
+Model pooled samples using discrete genotypes across pools.
+When using this flag, set \fB\-\-ploidy\fR to the number of
+alleles in each sample or use the \fB\-\-cnv\-map\fR to define
+per\-sample ploidy.
+.HP
+\fB\-K\fR \fB\-\-pooled\-continuous\fR
+.IP
+Output all alleles which pass input filters, regardles of
+genotyping outcome or model.
+.SS reference allele
+.HP
+\fB\-Z\fR \fB\-\-use\-reference\-allele\fR
+.IP
+This flag includes the reference allele in the analysis as
+if it is another sample from the same population.
+.HP
+\fB\-\-reference\-quality\fR MQ,BQ
+.IP
+Assign mapping quality of MQ to the reference allele at each
+site and base quality of BQ.  default: 100,60
+.SS allele scope
+.TP
+\fB\-I\fR \fB\-\-no\-snps\fR
+Ignore SNP alleles.
+.TP
+\fB\-i\fR \fB\-\-no\-indels\fR
+Ignore insertion and deletion alleles.
+.TP
+\fB\-X\fR \fB\-\-no\-mnps\fR
+Ignore multi\-nuceotide polymorphisms, MNPs.
+.HP
+\fB\-u\fR \fB\-\-no\-complex\fR Ignore complex events (composites of other classes).
+.HP
+\fB\-n\fR \fB\-\-use\-best\-n\-alleles\fR N
+.IP
+Evaluate only the best N SNP alleles, ranked by sum of
+supporting quality scores.  (Set to 0 to use all; default: all)
+.HP
+\fB\-E\fR \fB\-\-max\-complex\-gap\fR N
+.HP
+\fB\-\-haplotype\-length\fR N
+.IP
+Allow haplotype calls with contiguous embedded matches of up
+to this length.  (default: 3)
+.HP
+\fB\-\-min\-repeat\-size\fR N
+.IP
+When assembling observations across repeats, require the total repeat
+length at least this many bp.  (default: 5)
+.HP
+\fB\-\-min\-repeat\-entropy\fR N
+.IP
+To detect interrupted repeats, build across sequence until it has
+entropy > N bits per bp.  (default: 0, off)
+.HP
+\fB\-\-no\-partial\-observations\fR
+.IP
+Exclude observations which do not fully span the dynamically\-determined
+detection window.  (default, use all observations, dividing partial
+support across matching haplotypes when generating haplotypes.)
+.SS indel realignment
+.HP
+\fB\-O\fR \fB\-\-dont\-left\-align\-indels\fR
+.IP
+Turn off left\-alignment of indels, which is enabled by default.
+.SS input filters
+.HP
+\fB\-4\fR \fB\-\-use\-duplicate\-reads\fR
+.IP
+Include duplicate\-marked alignments in the analysis.
+default: exclude duplicates marked as such in alignments
+.HP
+\fB\-m\fR \fB\-\-min\-mapping\-quality\fR Q
+.IP
+Exclude alignments from analysis if they have a mapping
+quality less than Q.  default: 1
+.HP
+\fB\-q\fR \fB\-\-min\-base\-quality\fR Q
+.IP
+Exclude alleles from analysis if their supporting base
+quality is less than Q.  default: 0
+.HP
+\fB\-R\fR \fB\-\-min\-supporting\-allele\-qsum\fR Q
+.IP
+Consider any allele in which the sum of qualities of supporting
+observations is at least Q.  default: 0
+.HP
+\fB\-Y\fR \fB\-\-min\-supporting\-mapping\-qsum\fR Q
+.IP
+Consider any allele in which and the sum of mapping qualities of
+supporting reads is at least Q.  default: 0
+.HP
+\fB\-Q\fR \fB\-\-mismatch\-base\-quality\-threshold\fR Q
+.IP
+Count mismatches toward \fB\-\-read\-mismatch\-limit\fR if the base
+quality of the mismatch is >= Q.  default: 10
+.HP
+\fB\-U\fR \fB\-\-read\-mismatch\-limit\fR N
+.IP
+Exclude reads with more than N mismatches where each mismatch
+has base quality >= mismatch\-base\-quality\-threshold.
+default: ~unbounded
+.HP
+\fB\-z\fR \fB\-\-read\-max\-mismatch\-fraction\fR N
+.IP
+Exclude reads with more than N [0,1] fraction of mismatches where
+each mismatch has base quality >= mismatch\-base\-quality\-threshold
+default: 1.0
+.HP
+\-$ \fB\-\-read\-snp\-limit\fR N
+.IP
+Exclude reads with more than N base mismatches, ignoring gaps
+with quality >= mismatch\-base\-quality\-threshold.
+default: ~unbounded
+.HP
+\fB\-e\fR \fB\-\-read\-indel\-limit\fR N
+.IP
+Exclude reads with more than N separate gaps.
+default: ~unbounded
+.TP
+\fB\-0\fR \fB\-\-standard\-filters\fR
+Use stringent input base and mapping quality filters
+.IP
+Equivalent to \fB\-m\fR 30 \fB\-q\fR 20 \fB\-R\fR 0 \fB\-S\fR 0
+.HP
+\fB\-F\fR \fB\-\-min\-alternate\-fraction\fR N
+.IP
+Require at least this fraction of observations supporting
+an alternate allele within a single individual in the
+in order to evaluate the position.  default: 0.2
+.HP
+\fB\-C\fR \fB\-\-min\-alternate\-count\fR N
+.IP
+Require at least this count of observations supporting
+an alternate allele within a single individual in order
+to evaluate the position.  default: 2
+.HP
+\fB\-3\fR \fB\-\-min\-alternate\-qsum\fR N
+.IP
+Require at least this sum of quality of observations supporting
+an alternate allele within a single individual in order
+to evaluate the position.  default: 0
+.HP
+\fB\-G\fR \fB\-\-min\-alternate\-total\fR N
+.IP
+Require at least this count of observations supporting
+an alternate allele within the total population in order
+to use the allele in analysis.  default: 1
+.HP
+\fB\-\-min\-coverage\fR N
+.IP
+Require at least this coverage to process a site. default: 0
+.HP
+\fB\-\-max\-coverage\fR N
+.IP
+Do not process sites with greater than this coverage. default: no limit
+.SS population priors
+.HP
+\fB\-k\fR \fB\-\-no\-population\-priors\fR
+.IP
+Equivalent to \fB\-\-pooled\-discrete\fR \fB\-\-hwe\-priors\-off\fR and removal of
+Ewens Sampling Formula component of priors.
+.SS mappability priors
+.HP
+\fB\-w\fR \fB\-\-hwe\-priors\-off\fR
+.IP
+Disable estimation of the probability of the combination
+arising under HWE given the allele frequency as estimated
+by observation frequency.
+.HP
+\fB\-V\fR \fB\-\-binomial\-obs\-priors\-off\fR
+.IP
+Disable incorporation of prior expectations about observations.
+Uses read placement probability, strand balance probability,
+and read position (5'\-3') probability.
+.HP
+\fB\-a\fR \fB\-\-allele\-balance\-priors\-off\fR
+.IP
+Disable use of aggregate probability of observation balance between alleles
+as a component of the priors.
+.SS genotype likelihoods
+.HP
+\fB\-\-observation\-bias\fR FILE
+.IP
+Read length\-dependent allele observation biases from FILE.
+The format is [length] [alignment efficiency relative to reference]
+where the efficiency is 1 if there is no relative observation bias.
+.HP
+\fB\-\-base\-quality\-cap\fR Q
+.IP
+Limit estimated observation quality by capping base quality at Q.
+.HP
+\fB\-\-prob\-contamination\fR F
+.TP
+An estimate of contamination to use for all samples.
+default: 10e\-9
+.TP
+\fB\-\-legacy\-gls\fR
+Use legacy (polybayes equivalent) genotype likelihood calculations
+.HP
+\fB\-\-contamination\-estimates\fR FILE
+.IP
+A file containing per\-sample estimates of contamination, such as
+those generated by VerifyBamID.  The format should be:
+.IP
+sample p(read=R|genotype=AR) p(read=A|genotype=AA)
+.IP
+Sample '*' can be used to set default contamination estimates.
+.SS algorithmic features
+.HP
+\fB\-\-report\-genotype\-likelihood\-max\fR
+.IP
+Report genotypes using the maximum\-likelihood estimate provided
+from genotype likelihoods.
+.HP
+\fB\-B\fR \fB\-\-genotyping\-max\-iterations\fR N
+.IP
+Iterate no more than N times during genotyping step. default: 1000.
+.HP
+\fB\-\-genotyping\-max\-banddepth\fR N
+.IP
+Integrate no deeper than the Nth best genotype by likelihood when
+genotyping. default: 6.
+.HP
+\fB\-W\fR \fB\-\-posterior\-integration\-limits\fR N,M
+.IP
+Integrate all genotype combinations in our posterior space
+which include no more than N samples with their Mth best
+data likelihood. default: 1,3.
+.HP
+\fB\-N\fR \fB\-\-exclude\-unobserved\-genotypes\fR
+.IP
+Skip sample genotypings for which the sample has no supporting reads.
+.HP
+\fB\-S\fR \fB\-\-genotype\-variant\-threshold\fR N
+.IP
+Limit posterior integration to samples where the second\-best
+genotype likelihood is no more than log(N) from the highest
+genotype likelihood for the sample.  default: ~unbounded
+.HP
+\fB\-j\fR \fB\-\-use\-mapping\-quality\fR
+.IP
+Use mapping quality of alleles when calculating data likelihoods.
+.HP
+\fB\-H\fR \fB\-\-harmonic\-indel\-quality\fR
+.IP
+Use a weighted sum of base qualities around an indel, scaled by the
+distance from the indel.  By default use a minimum BQ in flanking sequence.
+.HP
+\fB\-D\fR \fB\-\-read\-dependence\-factor\fR N
+.IP
+Incorporate non\-independence of reads by scaling successive
+observations by this factor during data likelihood
+calculations.  default: 0.9
+.HP
+\fB\-=\fR \fB\-\-genotype\-qualities\fR
+.IP
+Calculate the marginal probability of genotypes and report as GQ in
+each sample field in the VCF output.
+.SS debugging
+.TP
+\fB\-d\fR \fB\-\-debug\fR
+Print debugging output.
+.TP
+\fB\-dd\fR
+Print more verbose debugging output (requires "make DEBUG")
+.SH SEE ALSO
+"Haplotype\-based variant detection from short\-read sequencing"
+arXiv:1207.3907 (http://arxiv.org/abs/1207.3907)
+.SH AUTHOR
+Erik Garrison <erik.garrison at bc.edu>, Marth Lab, Boston College, 2010\-2014, Gabor Marth
+.pp
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/freebayes.git

