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Commit d3f4c595 authored by van den Berg's avatar van den Berg
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Merge branch 'gitlab-ci' into devel

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1 merge request!2Add testing to vcf-to-varda
Pipeline #3738 passed
Stage: sanity
Stage: dry-run
Stage: integration
This commit is part of merge request !2. Comments created here will be created in the context of that merge request.
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test/config/config-multiallelic.json 0 → 100644
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{
"samples": {
"16699289": {
"disease_code": "TEST",
"gvcf": "test/data/16699289_chrM.g.vcf",
"vcf": "test/data/fake_chrM_multiallelic.vcf"
}
}
}
test/config/config-noalt-uncalled.json 0 → 100644
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View file @ d3f4c595
{
"samples": {
"16699289": {
"disease_code": "TEST",
"gvcf": "test/data/16699289_chrM.g.vcf",
"vcf": "test/data/16699289_chrM_noalt_uncalled.vcf"
}
}
}
test/data/16699289_chrM_noalt_uncalled.vcf 0 → 100644
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View file @ d3f4c595
##fileformat=VCFv4.2
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##FILTER=<ID=LowQual,Description="Low quality">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##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=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##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=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
##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">
##contig=<ID=chrM,length=16571,assembly=hg19>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 16699289
chrM 73 . G A 4062.77 . AC=2;AF=1.00;AN=2;DP=131;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.26;QD=32.24;SOR=0.791 GT:AD:DP:GQ:PL 1/1:0,126:126:99:4091,378,0
chrM 150 . T C 5149.77 . AC=2;AF=1.00;AN=2;DP=130;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.24;SOR=0.710 GT:AD:DP:GQ:PGT:PID:PL 0/0:0,117:117:99:1|1:150_T_C:5178,352,0
chrM 152 . T C 5149.77 . AC=2;AF=1.00;AN=2;DP=126;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.63;SOR=0.711 GT:AD:DP:GQ:PGT:PID:PL ./.:0,113:113:99:1|1:150_T_C:5178,352,0
chrM 195 . C T 2959.77 . AC=2;AF=1.00;AN=2;DP=98;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.09;SOR=0.961 GT:AD:DP:GQ:PL 1/1:0,82:82:99:2988,246,0
test/data/fake_chrM_multiallelic.vcf 0 → 100644
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− 0
View file @ d3f4c595
##fileformat=VCFv4.2
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##FILTER=<ID=LowQual,Description="Low quality">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##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=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##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=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
##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">
##contig=<ID=chrM,length=16571,assembly=hg19>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 16699289
chrM 73 . G A 4062.77 . AC=2;AF=1.00;AN=2;DP=131;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.26;QD=32.24;SOR=0.791 GT:AD:DP:GQ:PL 1/1:0,126:126:99:4091,378,0
chrM 150 . T C 5149.77 . AC=2;AF=1.00;AN=2;DP=130;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.24;SOR=0.710 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,117:117:99:1|1:150_T_C:5178,352,0
chrM 152 . T C 5149.77 . AC=2;AF=1.00;AN=2;DP=126;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.63;SOR=0.711 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,113:113:99:1|1:150_T_C:5178,352,0
chrM 195 . C T,* 690.21 . AC=0,1;AF=0.00,0.500;AN=2;BaseQRankSum=-1.150e+00;ClippingRankSum=0.00;DP=17;ExcessHet=3.9794;FS=8.872;MQ=39.83;MQRankSum=-9.210e-01;QD=21.57;ReadPosRankSum=-4.390e-01;SOR=2.038 GT:AD:DP:GQ:PL 0/2:9,0,8:17:99:303,330,1227,0,897,873
chrM 410 . A C,G 4849.13 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.910;ClippingRankSum=0.00;DP=76;ExcessHet=3.0103;FS=6.027;MQ=52.15;MQRankSum=-4.344e+00;QD=22.98;ReadPosRankSum=0.687;SOR=1.420 GT:AD:DP:GQ:PL 0/1:33,35,8:76:99:836,0,820,685,673,1584
chrM 2261 . C T,CATTTT 4096.90 . AC=2,0;AF=1.00,0.00;AN=2;DP=37;ExcessHet=3.0103;FS=0.000;MQ=60.00;QD=29.45;SOR=4.768 GT:AD:DP:GQ:PL 1/1:0,37,0:37:99:1248,110,0,1248,110,1248
chrM 2354 . C T 3755.77 . AC=2;AF=1.00;AN=2;DP=117;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.95;SOR=1.054 GT:AD:DP:GQ:PL 1/1:0,114:114:99:3784,341,0
test/test-integration.yml
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......@@ -6,9 +6,54 @@
--configfile test/config/config-GIAB-chrM.json
--use-singularity
--singularity-args ' --containall --bind /tmp'
--notemp
--cores 1
16699289_coverage.varda 16699289_variants.varda
files:
- path: 16699289_coverage.varda
- path: 16699289_variants.varda
- name: test-trim-alt-exclude-uncalled
tags:
- integration
command: >
snakemake
--configfile test/config/config-noalt-uncalled.json
--use-singularity
--singularity-args ' --containall --bind /tmp'
--notemp
--cores 1
16699289_trimmed.vcf
files:
- path: 16699289_trimmed.vcf
must_not_contain:
- "chrM\t150\t.\tT\tC"
- "chrM\t152\t.\tT\tC"
contains:
- "chrM\t73\t.\tG\tA"
- "chrM\t150\t.\tT\t."
- "chrM\t152\t.\tT\t."
- "chrM\t195\t.\tC\tT"
- name: test-multiallelic
tags:
- integration
- new
command: >
snakemake
--configfile test/config/config-multiallelic.json
--use-singularity
--singularity-args ' --containall --bind /tmp'
--notemp
--cores 1
16699289_trimmed.vcf
files:
- path: 16699289_trimmed.vcf
must_not_contain:
- "chrM\t195\t.\tC\tT,*"
- "chrM\t410\t.\tA\tC,G"
- "chrM\t2261\t.\tC\tT,CATTTT"
contains:
- "chrM\t195\t.\tC\t*"
- "chrM\t410\t.\tA\tC"
- "chrM\t2261\t.\tC\tT"
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