[med-svn] [Git][med-team/minimac4][master] Adapt autopkgtest to build time test

Andreas Tille (@tille) gitlab at salsa.debian.org
Tue Jan 24 14:42:19 GMT 2023 


Andreas Tille pushed to branch master at Debian Med / minimac4


Commits:
73be6ef5 by Andreas Tille at 2023-01-24T15:41:37+01:00
Adapt autopkgtest to build time test

- - - - -


15 changed files:

- debian/changelog
- debian/examples
- debian/tests/control
- − debian/tests/output_tests/README
- − debian/tests/output_tests/expected.testRun.dose.vcf
- − debian/tests/output_tests/expected.testRun.info
- debian/tests/run-unit-test
- − debian/upstream.docs/README
- − debian/upstream.docs/refPanel.m3vcf
- − debian/upstream.docs/refPanel.vcf
- − debian/upstream.docs/refPanelChrX.Non.Auto.vcf
- − debian/upstream.docs/sample.txt.filepart
- − debian/upstream.docs/targetStudy.vcf
- − debian/upstream.docs/targetStudyChrX.females.vcf
- − debian/upstream.docs/targetStudyChrX.males.vcf


Changes:

=====================================
debian/changelog
=====================================
@@ -7,6 +7,7 @@ minimac4 (4.1.2-1) UNRELEASED; urgency=medium
   * Rename autopkgtest script to run-unit-test
   * Switch on build tests provided upstream
   * Build-Depends bcftools needed for build tests
+  * Adapt autopkgtest to build time test
 
  -- Andreas Tille <tille at debian.org>  Thu, 22 Sep 2022 09:28:59 +0200
 


=====================================
debian/examples
=====================================
@@ -1,6 +1,3 @@
-# Upstream samples files
-debian/upstream.docs/*
+test/input/*
 
-# Expected outputs and script for autopkgtest
-debian/tests/run-sample-analysis
-debian/tests/output_tests/*
+debian/tests/run-unit-test


=====================================
debian/tests/control
=====================================
@@ -1,2 +1,2 @@
 Tests: run-unit-test
-Depends: @
+Depends: @, bcftools


=====================================
debian/tests/output_tests/README deleted
=====================================
@@ -1,19 +0,0 @@
-# Output files (i.e. expected.testRun.info and expected.testRun.dose.vcf.gz) were generated following:
-
-# Download and extract example files from minimac3 
-wget ftp://share.sph.umich.edu/minimac3/Minimac3.v2.0.1.tar.gz
-tar -xvzf Minimac3.v2.0.1.tar.gz Minimac3/test --strip-components=2
-
-# Download and extract minimac4 binary
-wget https://github.com/statgen/Minimac4/releases/download/v1.0.0/minimac4-1.0.0-Linux.deb
-ar x minimac4-1.0.0-Linux.deb data.tar.gz
-tar -xvzf data.tar.gz ./usr/bin/minimac4 --strip-components=3
-
-# Run example tests
-./minimac4 \
-           --refHaps refPanel.m3vcf.gz \
-           --haps targetStudy.vcf \
-           --prefix testRun
-
-mv testRun.info expected.testRun.info
-zcat testRun.dose.vcf.gz > expected.testRun.dose.vcf


=====================================
debian/tests/output_tests/expected.testRun.dose.vcf deleted
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/tests/output_tests/expected.testRun.info deleted
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/tests/run-unit-test
=====================================
@@ -1,8 +1,6 @@
 #!/bin/sh -e
-# http://dep.debian.net/deps/dep8/
-# Autopkgtest: Test if minimac4 run analysis correctly
-# Author: Dylan Aïssi <daissi at debian.org>
-# Last-Update: 2019-11-05
+# Adapted from build time test
+set -x
 
 pkg=minimac4
 
@@ -13,25 +11,23 @@ fi
 cd $AUTOPKGTEST_TMP
 cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
 
-gzip refPanel.m3vcf
-gzip targetStudy.vcf
-
-set -x
-# asked for help at: https://github.com/statgen/Minimac4/issues/54
-
-minimac4 --update-m3vcf refPanel.m3vcf.gz > refPanel.msav
-
-minimac4 \
-         --refHaps refPanel.msav \
-         --haps targetStudy.vcf.gz \
-         --output testRun
-
-exit
-zcat testRun.dose.vcf.gz > testRun.dose.vcf
-
-# Remove not reproducible headers
-tail -n +15 testRun.dose.vcf > cleaned.testRun.dose.vcf
-tail -n +15 expected.testRun.dose.vcf > cleaned.expected.testRun.dose.vcf
-
-diff testRun.info expected.testRun.info
-diff cleaned.testRun.dose.vcf cleaned.expected.testRun.dose.vcf
+d=m4_simple_test_output
+mkdir -p $d
+
+sampledata=ref_panel.vcf
+tarpanel=tar_panel.vcf
+ref_vcf=$d/$(basename $sampledata).gz
+ref_msav=$d/$(basename $sampledata .vcf).msav
+tar_vcf=$d/$(basename $tarpanel).gz
+imputed_vcf=$d/imputed.vcf.gz
+
+bcftools view $sampledata -Oz -o $ref_vcf
+bcftools index $ref_vcf
+bcftools view $tarpanel -Oz -o $tar_vcf
+bcftools index $tar_vcf
+minimac4 --compress-reference $ref_vcf > $ref_msav
+minimac4 $ref_msav $tar_vcf -f GT -O vcf.gz > $imputed_vcf
+
+gzip -cd $imputed_vcf | grep -v "^#" | cut -f9- > $d/imputed_gt_matrix.tsv
+gzip -cd $ref_vcf | grep -v "^#" | cut -f9- > $d/ref_gt_matrix.tsv
+diff $d/ref_gt_matrix.tsv $d/imputed_gt_matrix.tsv


=====================================
debian/upstream.docs/README deleted
=====================================
@@ -1,5 +0,0 @@
-# Download and extract example files from minimac3
-
-wget ftp://share.sph.umich.edu/minimac3/Minimac3.v2.0.1.tar.gz
-tar -xvzf Minimac3.v2.0.1.tar.gz Minimac3/test --strip-components=2
-gunzip -d *.gz -f


=====================================
debian/upstream.docs/refPanel.m3vcf deleted
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/upstream.docs/refPanel.vcf deleted
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/upstream.docs/refPanelChrX.Non.Auto.vcf deleted
=====================================
@@ -1,50 +0,0 @@
-##fileformat=VCFv4.1
-##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD">
-##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder">
-##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder">
-##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder">
-##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder">
-##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
-##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
-##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
-##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
-##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=AC,Number=.,Type=Integer,Description="Alternate Allele Count">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count">
-##ALT=<ID=DEL,Description="Deletion">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder">
-##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods">
-##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README">
-##INFO=<ID=AF,Number=1,Type=Float,Description="Global Allele Frequency based on AC/AN">
-##INFO=<ID=AMR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AMR based on AC/AN">
-##INFO=<ID=ASN_AF,Number=1,Type=Float,Description="Allele Frequency for samples from ASN based on AC/AN">
-##INFO=<ID=AFR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AFR based on AC/AN">
-##INFO=<ID=EUR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN">
-##INFO=<ID=VT,Number=1,Type=String,Description="indicates what type of variant the line represents">
-##INFO=<ID=SNPSOURCE,Number=.,Type=String,Description="indicates if a snp was called when analysing the low coverage or exome alignment data">
-##reference=GRCh37
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00096	HG00097	HG00099	HG00100	HG00101	HG00102	HG00103	HG00104	HG00106	HG00108	HG00109	HG00110	HG00111	HG00112	HG00113	HG00114	HG00116	HG00117	HG00118	HG00119	HG00120
-X	2699555	rs311165	C	A	100	PASS	.	GT	0	0|1	0|1	0|0	1	1|1	1	1|1	1|1	1	0	1|0	0|1	0	0	0	0	0	0|1	0	0|1
-X	2699559	rs186009975	A	G	100	PASS	.	GT	0	0|0	0|0	0|0	0	0|0	0	0|0	0|0	0	0	0|0	0|0	0	0	0	0	0	0|0	0	0|0
-X	2699625	rs6655038	A	G	100	PASS	.	GT	0	0|0	0|0	0|0	0	0|0	0	0|0	0|0	0	0	0|0	0|0	0	0	0	0	0	0|0	0	0|0
-X	2699645	rs28579419	G	T	100	PASS	.	GT	0	0|0	0|1	0|0	1	0|1	0	0|1	1|0	1	0	0|0	0|1	0	0	0	0	0	0|1	0	0|0
-X	2699676	rs60075487	G	A	100	PASS	.	GT	0	0|0	0|0	0|0	0	1|0	0	0|0	0|1	0	0	1|0	0|0	0	0	0	0	0	0|0	0	0|1
-X	2699683	rs148034730	G	A	100	PASS	.	GT	0	0|0	0|0	0|0	0	0|0	0	0|0	0|0	0	0	0|0	0|0	0	0	0	0	0	0|0	0	0|0
-X	2699739	rs190819059	G	C	100	PASS	.	GT	0	0|0	0|0	0|0	0	0|0	0	0|0	0|0	0	0	0|0	0|0	0	0	0	0	0	0|0	0	0|0
-X	2699898	.	C	CT	468	PASS	.	GT	0	0|0	0|0	0|0	0	1|0	0	0|0	0|1	0	0	1|0	0|0	0	0	0	0	0	0|0	0	0|1
-X	2699906	rs183147082	T	G	100	PASS	.	GT	0	0|0	0|0	0|0	0	0|0	0	0|0	0|0	0	0	0|0	0|0	0	0	0	0	0	0|0	0	0|0
-X	2699919	rs188840343	T	C	100	PASS	.	GT	0	0|0	0|0	0|0	0	0|0	0	0|0	0|0	0	0	0|0	0|0	0	0	0	0	0	0|0	0	0|0
-X	2699968	rs2306737	A	G	100	PASS	.	GT	1	0|1	1|0	1|1	0	0|0	1	1|0	0|0	0	1	0|1	1|0	1	0	0	1	0	1|0	1	1|0
-X	2700027	rs2306736	T	C	100	PASS	.	GT	1	0|1	1|0	1|1	0	0|0	1	1|0	0|0	0	1	0|1	1|0	1	0	0	1	0	1|0	1	1|0
-X	2700089	rs41297271	A	G	100	PASS	.	GT	0	0|0	0|0	0|0	0	0|0	0	0|0	0|0	0	0	0|0	0|0	0	0	0	0	0	0|0	0	0|0
-X	2700157	rs5939319	G	A	100	PASS	.	GT	0	1|0	0|1	0|0	1	0|1	0	0|1	1|0	1	0	0|0	0|1	0	0	0	0	0	0|1	0	0|0
-X	2700185	rs147531468	C	T	100	PASS	.	GT	0	0|0	0|0	0|0	0	0|0	0	0|0	0|0	0	0	0|0	0|0	0	0	0	0	0	0|0	0	0|0
-X	2700202	rs5939320	A	G	100	PASS	.	GT	0	1|0	0|1	0|0	1	1|1	0	0|1	1|1	1	0	1|0	0|1	0	0	0	0	0	0|1	0	0|1
-X	2700302	rs72619369	T	A	100	PASS	.	GT	0	0|0	0|0	0|0	0	1|0	0	0|0	0|1	0	0	1|0	0|0	0	0	0	0	0	0|0	0	0|1
-X	2700576	rs190878529	A	G	100	PASS	.	GT	0	0|0	0|0	0|0	0	1|0	0	0|0	0|0	0	0	0|0	0|0	0	0	0	0	0	0|0	0	0|0
-X	2700585	rs182591661	C	T	100	PASS	.	GT	0	0|0	0|0	0|0	0	0|0	0	0|0	0|0	0	0	0|0	0|0	0	0	0	0	0	0|0	0	0|0
-X	2700608	rs4892890	C	T	100	PASS	.	GT	1	1|1	1|1	1|1	1	0|1	0	1|1	1|0	1	1	0|1	1|1	1	0	0	1	0	1|1	1	1|0
-X	2700613	rs4892819	A	G	100	PASS	.	GT	1	0|1	1|0	1|0	0	1|0	1	1|0	0|0	1	1	0|1	1|0	1	0	0	1	0	1|0	1	1|0


=====================================
debian/upstream.docs/sample.txt.filepart deleted
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/upstream.docs/targetStudy.vcf deleted
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/upstream.docs/targetStudyChrX.females.vcf deleted
=====================================
@@ -1,50 +0,0 @@
-##fileformat=VCFv4.1
-##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD">
-##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder">
-##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder">
-##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder">
-##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder">
-##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
-##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
-##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
-##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
-##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=AC,Number=.,Type=Integer,Description="Alternate Allele Count">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count">
-##ALT=<ID=DEL,Description="Deletion">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder">
-##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods">
-##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README">
-##INFO=<ID=AF,Number=1,Type=Float,Description="Global Allele Frequency based on AC/AN">
-##INFO=<ID=AMR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AMR based on AC/AN">
-##INFO=<ID=ASN_AF,Number=1,Type=Float,Description="Allele Frequency for samples from ASN based on AC/AN">
-##INFO=<ID=AFR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AFR based on AC/AN">
-##INFO=<ID=EUR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN">
-##INFO=<ID=VT,Number=1,Type=String,Description="indicates what type of variant the line represents">
-##INFO=<ID=SNPSOURCE,Number=.,Type=String,Description="indicates if a snp was called when analysing the low coverage or exome alignment data">
-##reference=GRCh37
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00097	HG00099	HG00100	HG00102	HG00104
-X	2699555	rs311165	C	A	100	PASS	.	GT	0|1	0|1	0|0	1|1	1|1
-X	2699559	rs186009975	A	G	100	PASS	.	GT	0|0	0|0	0|0	0|0	0|0
-X	2699625	rs6655038	A	G	100	PASS	.	GT	0|0	0|0	0|0	0|0	0|0
-X	2699645	rs28579419	G	T	100	PASS	.	GT	0|0	0|1	0|0	0|1	0|1
-X	2699676	rs60075487	G	A	100	PASS	.	GT	0|0	0|0	0|0	1|0	0|0
-X	2699683	rs148034730	G	A	100	PASS	.	GT	0|0	0|0	0|0	0|0	0|0
-X	2699739	rs190819059	G	C	100	PASS	.	GT	0|0	0|0	0|0	0|0	0|0
-X	2699898	.	C	CT	468	PASS	.	GT	0|0	0|0	0|0	1|0	0|0
-X	2699906	rs183147082	T	G	100	PASS	.	GT	0|0	0|0	0|0	0|0	0|0
-X	2699919	rs188840343	T	C	100	PASS	.	GT	0|0	0|0	0|0	0|0	0|0
-X	2699968	rs2306737	A	G	100	PASS	.	GT	0|1	1|0	1|1	0|0	1|0
-X	2700027	rs2306736	T	C	100	PASS	.	GT	0|1	1|0	1|1	0|0	1|0
-X	2700089	rs41297271	A	G	100	PASS	.	GT	0|0	0|0	0|0	0|0	0|0
-X	2700157	rs5939319	G	A	100	PASS	.	GT	1|0	0|1	0|0	0|1	0|1
-X	2700185	rs147531468	C	T	100	PASS	.	GT	0|0	0|0	0|0	0|0	0|0
-X	2700202	rs5939320	A	G	100	PASS	.	GT	1|0	0|1	0|0	1|1	0|1
-X	2700302	rs72619369	T	A	100	PASS	.	GT	0|0	0|0	0|0	1|0	0|0
-X	2700576	rs190878529	A	G	100	PASS	.	GT	0|0	0|0	0|0	1|0	0|0
-X	2700585	rs182591661	C	T	100	PASS	.	GT	0|0	0|0	0|0	0|0	0|0
-X	2700608	rs4892890	C	T	100	PASS	.	GT	1|1	1|1	1|1	0|1	1|1
-X	2700613	rs4892819	A	G	100	PASS	.	GT	0|1	1|0	1|0	1|0	1|0


=====================================
debian/upstream.docs/targetStudyChrX.males.vcf deleted
=====================================
@@ -1,50 +0,0 @@
-##fileformat=VCFv4.1
-##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD">
-##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder">
-##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder">
-##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder">
-##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder">
-##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
-##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
-##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
-##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
-##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=AC,Number=.,Type=Integer,Description="Alternate Allele Count">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count">
-##ALT=<ID=DEL,Description="Deletion">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder">
-##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods">
-##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README">
-##INFO=<ID=AF,Number=1,Type=Float,Description="Global Allele Frequency based on AC/AN">
-##INFO=<ID=AMR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AMR based on AC/AN">
-##INFO=<ID=ASN_AF,Number=1,Type=Float,Description="Allele Frequency for samples from ASN based on AC/AN">
-##INFO=<ID=AFR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AFR based on AC/AN">
-##INFO=<ID=EUR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN">
-##INFO=<ID=VT,Number=1,Type=String,Description="indicates what type of variant the line represents">
-##INFO=<ID=SNPSOURCE,Number=.,Type=String,Description="indicates if a snp was called when analysing the low coverage or exome alignment data">
-##reference=GRCh37
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00096	HG00101	HG00103	HG00108	HG00109
-X	2699555	rs311165	C	A	100	PASS	.	GT	0	1	1	1	0
-X	2699559	rs186009975	A	G	100	PASS	.	GT	0	0	0	0	0
-X	2699625	rs6655038	A	G	100	PASS	.	GT	0	0	0	0	0
-X	2699645	rs28579419	G	T	100	PASS	.	GT	0	1	0	1	0
-X	2699676	rs60075487	G	A	100	PASS	.	GT	0	0	0	0	0
-X	2699683	rs148034730	G	A	100	PASS	.	GT	0	0	0	0	0
-X	2699739	rs190819059	G	C	100	PASS	.	GT	0	0	0	0	0
-X	2699898	.	C	CT	468	PASS	.	GT	0	0	0	0	0
-X	2699906	rs183147082	T	G	100	PASS	.	GT	0	0	0	0	0
-X	2699919	rs188840343	T	C	100	PASS	.	GT	0	0	0	0	0
-X	2699968	rs2306737	A	G	100	PASS	.	GT	1	0	1	0	1
-X	2700027	rs2306736	T	C	100	PASS	.	GT	1	0	1	0	1
-X	2700089	rs41297271	A	G	100	PASS	.	GT	0	0	0	0	0
-X	2700157	rs5939319	G	A	100	PASS	.	GT	0	1	0	1	0
-X	2700185	rs147531468	C	T	100	PASS	.	GT	0	0	0	0	0
-X	2700202	rs5939320	A	G	100	PASS	.	GT	0	1	0	1	0
-X	2700302	rs72619369	T	A	100	PASS	.	GT	0	0	0	0	0
-X	2700576	rs190878529	A	G	100	PASS	.	GT	0	0	0	0	0
-X	2700585	rs182591661	C	T	100	PASS	.	GT	0	0	0	0	0
-X	2700608	rs4892890	C	T	100	PASS	.	GT	1	1	0	1	1
-X	2700613	rs4892819	A	G	100	PASS	.	GT	1	0	1	1	1



View it on GitLab: https://salsa.debian.org/med-team/minimac4/-/commit/73be6ef522ebe2901f294f8a5453ddad94d4273b

-- 
View it on GitLab: https://salsa.debian.org/med-team/minimac4/-/commit/73be6ef522ebe2901f294f8a5453ddad94d4273b
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