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Commit 58051aaf authored by van den Berg's avatar van den Berg
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1 merge request!2Add testing to vcf-to-varda
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.gitlab-ci.yml 0 → 100644
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variables:
GIT_SUBMODULE_STRATEGY: recursive
.before_script_anchor: &before_script_anchor
before_script:
- pip3 install pytest-workflow
.slurm_before_script_anchor: &slurm_before_script_anchor
before_script:
- export BASETEMP=$RUN_BASE_DIR/$CI_COMMIT_REF_NAME/$CI_JOB_ID
- source ${CONDA_SH}
- conda activate vcf-to-varda
- export PATH=${PATH}:${SINGULARITY_PATH}
- echo $BASETEMP
stages:
- sanity
- dry-run
- integration
test-sanity:
<<: *before_script_anchor
script:
- pytest --keep-workflow-wd-on-fail --tag sanity
image: lumc/singularity-snakemake:3.5.2-5.15.0
tags:
- docker
stage: sanity
test-dry-run:
<<: *before_script_anchor
script:
- pytest --keep-workflow-wd-on-fail --tag dry-run
image: lumc/singularity-snakemake:3.5.2-5.15.0
tags:
- docker
stage: dry-run
test-integration:
<<: *slurm_before_script_anchor
script:
- pytest --keep-workflow-wd-on-fail --basetemp ${BASETEMP} --tag integration
image: lumc/singularity-snakemake:3.5.2-5.15.0
tags:
- slurm
stage: integration
test/config/config-GIAB-chrM.json 0 → 100644
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{
"samples": {
"16699289": {
"disease_code": "TEST",
"gvcf": "test/data/16699289_chrM.g.vcf",
"vcf": "test/data/16699289_chrM.vcf"
}
}
}
test/data/16699289_chrM.g.vcf 0 → 100644
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View file @ 58051aaf
##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=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##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=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=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">
##contig=<ID=chrM,length=16571,assembly=hg19>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 16699289
chrM 1 . G <NON_REF> . . END=72 GT:DP:GQ:MIN_DP:PL 0/0:96:99:54:0,120,1800
chrM 73 . G A,<NON_REF> 4062.77 . DP=131;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=444604.00 GT:AD:DP:GQ:PL:SB 1/1:0,126,0:126:99:4091,378,0,4091,378,4091:0,0,66,60
chrM 74 . T <NON_REF> . . END=149 GT:DP:GQ:MIN_DP:PL 0/0:136:99:123:0,120,1800
chrM 150 . T C,<NON_REF> 5149.77 . DP=130;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=468000.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,117,0:117:99:0|1:150_T_C:5178,352,0,5178,352,5178:0,0,58,59
chrM 151 . C <NON_REF> . . END=151 GT:DP:GQ:MIN_DP:PL 0/0:122:99:122:0,120,1800
chrM 152 rs117135796 T C,<NON_REF> 5149.77 . DB;DP=126;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=453600.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,113,0:113:99:0|1:150_T_C:5178,352,0,5178,352,5178:0,0,57,56
chrM 153 . A <NON_REF> . . END=194 GT:DP:GQ:MIN_DP:PL 0/0:101:99:93:0,120,1800
chrM 195 . C T,<NON_REF> 2959.77 . DP=98;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=352800.00 GT:AD:DP:GQ:PL:SB 1/1:0,82,0:82:99:2988,246,0,2988,246,2988:0,0,36,46
chrM 196 . T <NON_REF> . . END=301 GT:DP:GQ:MIN_DP:PL 0/0:80:99:47:0,114,1401
chrM 302 . A <NON_REF> . . END=303 GT:DP:GQ:MIN_DP:PL 0/0:50:85:49:0,85,1355
chrM 304 . C <NON_REF> . . END=310 GT:DP:GQ:MIN_DP:PL 0/0:53:99:51:0,108,1620
chrM 311 . T <NON_REF> . . END=311 GT:DP:GQ:MIN_DP:PL 0/0:42:97:42:0,97,1515
chrM 312 . C <NON_REF> . . END=409 GT:DP:GQ:MIN_DP:PL 0/0:75:99:47:0,103,1765
chrM 410 . A T,<NON_REF> 3234.77 . DP=101;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=361330.00 GT:AD:DP:GQ:PL:SB 1/1:0,99,0:99:99:3263,296,0,3263,296,3263:0,0,43,56
chrM 411 . G <NON_REF> . . END=2260 GT:DP:GQ:MIN_DP:PL 0/0:117:99:57:0,120,1800
chrM 2261 . C T,<NON_REF> 2900.77 . DP=97;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=349200.00 GT:AD:DP:GQ:PL:SB 1/1:0,93,0:93:99:2929,276,0,2929,276,2929:0,0,52,41
chrM 2262 . A <NON_REF> . . END=2353 GT:DP:GQ:MIN_DP:PL 0/0:105:99:88:0,120,1800
chrM 2354 . C T,<NON_REF> 3755.77 . DP=117;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=421200.00 GT:AD:DP:GQ:PL:SB 1/1:0,114,0:114:99:3784,341,0,3784,341,3784:0,0,66,48
chrM 2355 . A <NON_REF> . . END=2484 GT:DP:GQ:MIN_DP:PL 0/0:117:99:104:0,120,1800
chrM 2485 . C T,<NON_REF> 4129.77 . DP=121;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=435600.00 GT:AD:DP:GQ:PL:SB 1/1:0,121,0:121:99:4158,362,0,4158,362,4158:0,0,68,53
chrM 2486 . C <NON_REF> . . END=2707 GT:DP:GQ:MIN_DP:PL 0/0:143:99:116:0,120,1800
chrM 2708 . G A,<NON_REF> 4474.77 . DP=127;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=454834.00 GT:AD:DP:GQ:PL:SB 1/1:0,127,0:127:99:4503,381,0,4503,381,4503:0,0,61,66
chrM 2709 . A <NON_REF> . . END=3578 GT:DP:GQ:MIN_DP:PL 0/0:120:99:82:0,120,1800
chrM 3579 . T <NON_REF> . . END=3579 GT:DP:GQ:MIN_DP:PL 0/0:104:0:104:0,0,2184
chrM 3580 . A <NON_REF> . . END=3590 GT:DP:GQ:MIN_DP:PL 0/0:140:99:130:0,120,1800
chrM 3591 . T <NON_REF> . . END=3591 GT:DP:GQ:MIN_DP:PL 0/0:97:84:97:0,84,2695
chrM 3592 . G <NON_REF> . . END=4745 GT:DP:GQ:MIN_DP:PL 0/0:109:99:57:0,120,1800
chrM 4746 . A G,<NON_REF> 2693.77 . DP=82;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=172445.00 GT:AD:DP:GQ:PL:SB 1/1:0,81,0:81:99:2722,242,0,2722,242,2722:0,0,40,41
chrM 4747 . T <NON_REF> . . END=5580 GT:DP:GQ:MIN_DP:PL 0/0:123:99:74:0,120,1800
chrM 5581 . C T,<NON_REF> 3091.77 . DP=96;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=213064.00 GT:AD:DP:GQ:PL:SB 1/1:0,95,0:95:99:3120,285,0,3120,285,3120:0,0,53,42
chrM 5582 . A <NON_REF> . . END=7028 GT:DP:GQ:MIN_DP:PL 0/0:144:99:64:0,104,1800
chrM 7029 . T C,<NON_REF> 3034.77 . DP=94;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=161816.00 GT:AD:DP:GQ:PL:SB 1/1:0,94,0:94:99:3063,282,0,3063,282,3063:0,0,47,47
chrM 7030 . C <NON_REF> . . END=7337 GT:DP:GQ:MIN_DP:PL 0/0:123:99:81:0,120,1800
chrM 7338 . G A,<NON_REF> 3647.77 . DP=111;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=282778.00 GT:AD:DP:GQ:PL:SB 1/1:0,111,0:111:99:3676,333,0,3676,333,3676:0,0,51,60
chrM 7339 . A <NON_REF> . . END=8701 GT:DP:GQ:MIN_DP:PL 0/0:150:99:83:0,120,1800
chrM 8702 . G A,<NON_REF> 55738.77 . BaseQRankSum=-2.533;ClippingRankSum=0.000;DP=1455;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=-0.857;RAW_MQ=4888503.00;ReadPosRankSum=-1.220 GT:AD:DP:GQ:PL:SB 1/1:3,1444,0:1447:99:55767,4213,0,55776,4330,55893:3,0,1352,92
chrM 8703 . C <NON_REF> . . END=9377 GT:DP:GQ:MIN_DP:PL 0/0:1504:99:438:0,120,1800
chrM 9378 . G A,<NON_REF> 15302.77 . BaseQRankSum=1.903;ClippingRankSum=0.000;DP=430;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=-1.678;RAW_MQ=1088513.00;ReadPosRankSum=-0.842 GT:AD:DP:GQ:PL:SB 1/1:2,425,0:427:99:15331,1231,0,15337,1275,15380:1,1,114,311
chrM 9379 . T <NON_REF> . . END=9540 GT:DP:GQ:MIN_DP:PL 0/0:319:99:256:0,120,1800
chrM 9541 . C T,<NON_REF> 7951.77 . BaseQRankSum=-1.006;ClippingRankSum=0.000;DP=242;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=0.000;RAW_MQ=869449.00;ReadPosRankSum=1.484 GT:AD:DP:GQ:PL:SB 1/1:1,238,0:239:99:7980,670,0,7983,708,8021:0,1,68,170
chrM 9542 . T <NON_REF> . . END=10398 GT:DP:GQ:MIN_DP:PL 0/0:121:99:81:0,120,1800
chrM 10399 . G A,<NON_REF> 2937.77 . DP=93;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=334800.00 GT:AD:DP:GQ:PL:SB 1/1:0,92,0:92:99:2966,275,0,2966,275,2966:0,0,51,41
chrM 10400 . C <NON_REF> . . END=10819 GT:DP:GQ:MIN_DP:PL 0/0:120:99:80:0,120,1800
chrM 10820 . G A,<NON_REF> 3446.77 . DP=114;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=401514.00 GT:AD:DP:GQ:PL:SB 1/1:0,111,0:111:99:3475,331,0,3475,331,3475:0,0,63,48
chrM 10821 . C <NON_REF> . . END=10873 GT:DP:GQ:MIN_DP:PL 0/0:110:99:99:0,120,1800
chrM 10874 . C T,<NON_REF> 3100.77 . DP=100;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=357320.00 GT:AD:DP:GQ:PL:SB 1/1:0,98,0:98:99:3129,292,0,3129,292,3129:0,0,48,50
chrM 10875 . C <NON_REF> . . END=11017 GT:DP:GQ:MIN_DP:PL 0/0:93:99:78:0,120,1800
chrM 11018 . C T,<NON_REF> 2952.77 . DP=90;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=316771.00 GT:AD:DP:GQ:PL:SB 1/1:0,89,0:89:99:2981,265,0,2981,265,2981:0,0,45,44
chrM 11019 . G <NON_REF> . . END=11719 GT:DP:GQ:MIN_DP:PL 0/0:142:99:91:0,120,1800
chrM 11720 . A G,<NON_REF> 5996.77 . DP=133;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=442009.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,133,0:133:99:0|1:11720_A_G:6025,412,0,6025,412,6025:0,0,68,65
chrM 11721 . C <NON_REF> . . END=11722 GT:DP:GQ:MIN_DP:PL 0/0:135:99:134:0,120,1800
chrM 11723 . C T,<NON_REF> 5947.77 . DP=132;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=438409.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,132,0:132:99:0|1:11720_A_G:5976,406,0,5976,406,5976:0,0,66,66
chrM 11724 . A <NON_REF> . . END=12705 GT:DP:GQ:MIN_DP:PL 0/0:111:99:73:0,120,1800
chrM 12706 . T C,<NON_REF> 3690.77 . DP=124;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=446400.00 GT:AD:DP:GQ:PL:SB 1/1:0,115,0:115:99:3719,343,0,3719,343,3719:0,0,62,53
chrM 12707 . T <NON_REF> . . END=12850 GT:DP:GQ:MIN_DP:PL 0/0:126:99:118:0,120,1800
chrM 12851 . G A,<NON_REF> 3972.77 . DP=128;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=460800.00 GT:AD:DP:GQ:PL:SB 1/1:0,128,0:128:99:4001,380,0,4001,380,4001:0,0,74,54
chrM 12852 . T <NON_REF> . . END=13326 GT:DP:GQ:MIN_DP:PL 0/0:148:99:120:0,120,1800
chrM 13327 . T C,<NON_REF> 5000.77 . DP=150;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=535069.00 GT:AD:DP:GQ:PL:SB 1/1:0,148,0:148:99:5029,445,0,5029,445,5029:0,0,66,82
chrM 13328 . A <NON_REF> . . END=13680 GT:DP:GQ:MIN_DP:PL 0/0:121:99:104:0,120,1800
chrM 13681 . C T,<NON_REF> 3752.77 . DP=123;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=442800.00 GT:AD:DP:GQ:PL:SB 1/1:0,121,0:121:99:3781,361,0,3781,361,3781:0,0,67,54
chrM 13682 . A <NON_REF> . . END=14212 GT:DP:GQ:MIN_DP:PL 0/0:100:99:75:0,120,1800
chrM 14213 . C T,<NON_REF> 2504.77 . DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=288097.00 GT:AD:DP:GQ:PL:SB 1/1:0,77,0:77:99:2533,231,0,2533,231,2533:0,0,39,38
chrM 14214 . A <NON_REF> . . END=14580 GT:DP:GQ:MIN_DP:PL 0/0:126:99:81:0,120,1800
chrM 14581 . G A,<NON_REF> 2819.77 . DP=90;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=323649.00 GT:AD:DP:GQ:PL:SB 1/1:0,88,0:88:99:2848,262,0,2848,262,2848:0,0,43,45
chrM 14582 . T <NON_REF> . . END=14766 GT:DP:GQ:MIN_DP:PL 0/0:77:99:66:0,120,1800
chrM 14767 . T C,<NON_REF> 2914.77 . DP=93;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=326448.00 GT:AD:DP:GQ:PL:SB 1/1:0,88,0:88:99:2943,264,0,2943,264,2943:0,0,54,34
chrM 14768 . T <NON_REF> . . END=14831 GT:DP:GQ:MIN_DP:PL 0/0:94:99:87:0,120,1800
chrM 14832 . G A,<NON_REF> 3447.77 . DP=111;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=397296.00 GT:AD:DP:GQ:PL:SB 1/1:0,108,0:108:99:3476,323,0,3476,323,3476:0,0,63,45
chrM 14833 . C <NON_REF> . . END=14872 GT:DP:GQ:MIN_DP:PL 0/0:119:99:113:0,120,1800
chrM 14873 . C T,<NON_REF> 3719.77 . DP=120;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=432000.00 GT:AD:DP:GQ:PL:SB 1/1:0,120,0:120:99:3748,358,0,3748,358,3748:0,0,64,56
chrM 14874 . C <NON_REF> . . END=14905 GT:DP:GQ:MIN_DP:PL 0/0:127:99:118:0,120,1800
chrM 14906 . A G,<NON_REF> 4327.77 . DP=127;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=452900.00 GT:AD:DP:GQ:PL:SB 1/1:0,127,0:127:99:4356,381,0,4356,381,4356:0,0,71,56
chrM 14907 . C <NON_REF> . . END=15301 GT:DP:GQ:MIN_DP:PL 0/0:113:99:90:0,120,1800
chrM 15302 . A G,<NON_REF> 3502.77 . DP=105;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=378000.00 GT:AD:DP:GQ:PL:SB 1/1:0,102,0:102:99:3531,306,0,3531,306,3531:0,0,48,54
chrM 15303 . C <NON_REF> . . END=15932 GT:DP:GQ:MIN_DP:PL 0/0:103:99:84:0,120,1800
chrM 15933 . C T,<NON_REF> 3115.77 . DP=97;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=349200.00 GT:AD:DP:GQ:PL:SB 1/1:0,94,0:94:99:3144,282,0,3144,282,3144:0,0,47,47
chrM 15934 . G <NON_REF> . . END=16023 GT:DP:GQ:MIN_DP:PL 0/0:100:99:94:0,120,1800
chrM 16024 . G A,<NON_REF> 1312.77 . BaseQRankSum=-2.823;ClippingRankSum=0.000;DP=111;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=399600.00;ReadPosRankSum=0.794 GT:AD:DP:GQ:PL:SB 0/1:55,53,0:108:99:1341,0,1621,1506,1779,3285:32,23,23,30
chrM 16025 . T <NON_REF> . . END=16161 GT:DP:GQ:MIN_DP:PL 0/0:100:99:92:0,102,1530
chrM 16162 . T <NON_REF> . . END=16162 GT:DP:GQ:MIN_DP:PL 0/0:109:87:109:0,87,1305
chrM 16163 . A <NON_REF> . . END=16165 GT:DP:GQ:MIN_DP:PL 0/0:111:75:111:0,75,1125
chrM 16166 . A <NON_REF> . . END=16167 GT:DP:GQ:MIN_DP:PL 0/0:111:69:111:0,69,1035
chrM 16168 . C <NON_REF> . . END=16169 GT:DP:GQ:MIN_DP:PL 0/0:112:51:111:0,51,765
chrM 16170 . C <NON_REF> . . END=16170 GT:DP:GQ:MIN_DP:PL 0/0:114:45:114:0,45,675
chrM 16171 . A <NON_REF> . . END=16172 GT:DP:GQ:MIN_DP:PL 0/0:115:42:114:0,42,630
chrM 16173 . C T,<NON_REF> 5037.77 . DP=116;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=415798.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,109,0:109:99:0|1:16173_C_T:5066,343,0,5066,343,5066:0,0,54,55
chrM 16174 . C <NON_REF> . . END=16174 GT:DP:GQ:MIN_DP:PL 0/0:119:42:119:0,42,630
chrM 16175 . C <NON_REF> . . END=16175 GT:DP:GQ:MIN_DP:PL 0/0:120:33:120:0,33,495
chrM 16176 . A <NON_REF> . . END=16178 GT:DP:GQ:MIN_DP:PL 0/0:119:27:114:0,27,405
chrM 16179 . T <NON_REF> . . END=16179 GT:DP:GQ:MIN_DP:PL 0/0:116:24:116:0,24,360
chrM 16180 . C <NON_REF> . . END=16180 GT:DP:GQ:MIN_DP:PL 0/0:119:15:119:0,15,225
chrM 16181 . A <NON_REF> . . END=16182 GT:DP:GQ:MIN_DP:PL 0/0:119:3:119:0,3,45
chrM 16183 . AC A,<NON_REF> 5020.73 . DP=120;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=430198.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,113,0:113:99:0|1:16173_C_T:5058,340,0,5058,340,5058:0,0,56,57
chrM 16185 . C A,<NON_REF> 5029.77 . DP=119;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=426598.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,112,0:112:99:0|1:16173_C_T:5058,340,0,5058,340,5058:0,0,56,56
chrM 16186 . C <NON_REF> . . END=16190 GT:DP:GQ:MIN_DP:PL 0/0:113:99:112:0,120,1800
chrM 16191 . C T,<NON_REF> 4831.77 . DP=115;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=412198.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,108,0:108:99:0|1:16173_C_T:4860,328,0,4860,328,4860:0,0,56,52
chrM 16192 . C <NON_REF> . . END=16224 GT:DP:GQ:MIN_DP:PL 0/0:116:99:110:0,120,1800
chrM 16225 . T C,<NON_REF> 3434.77 . DP=117;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=419398.00 GT:AD:DP:GQ:PL:SB 1/1:0,110,0:110:99:3463,329,0,3463,329,3463:0,0,58,52
chrM 16226 . T <NON_REF> . . END=16321 GT:DP:GQ:MIN_DP:PL 0/0:117:99:107:0,120,1800
chrM 16322 . T C,<NON_REF> 3589.77 . DP=118;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=424800.00 GT:AD:DP:GQ:PL:SB 1/1:0,114,0:114:99:3618,340,0,3618,340,3618:0,0,56,58
chrM 16323 . C <NON_REF> . . END=16520 GT:DP:GQ:MIN_DP:PL 0/0:126:99:107:0,120,1800
chrM 16521 . C T,<NON_REF> 4251.77 . BaseQRankSum=1.212;ClippingRankSum=0.000;DP=149;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=0.000;RAW_MQ=536400.00;ReadPosRankSum=3.064 GT:AD:DP:GQ:PL:SB 1/1:2,138,0:140:99:4280,371,0,4286,414,4330:1,1,71,67
chrM 16522 . C <NON_REF> . . END=16561 GT:DP:GQ:MIN_DP:PL 0/0:134:99:108:0,120,1800
chrM 16562 . C <NON_REF> . . END=16571 GT:DP:GQ:MIN_DP:PL 0/0:101:0:97:0,0,0
test/data/16699289_chrM.vcf 0 → 100644
+ 78
− 0
View file @ 58051aaf
##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 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
chrM 410 . A T 3233.06 . AC=2;AF=1.00;AN=2;DP=101;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.81;QD=32.66;SOR=0.985 GT:AD:DP:GQ:PL 1/1:0,99:99:99:3263,296,0
chrM 2261 . C T 2900.77 . AC=2;AF=1.00;AN=2;DP=97;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.19;SOR=0.953 GT:AD:DP:GQ:PL 1/1:0,93:93:99:2929,276,0
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
chrM 2485 . C T 4129.77 . AC=2;AF=1.00;AN=2;DP=121;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.13;SOR=0.968 GT:AD:DP:GQ:PL 1/1:0,121:121:99:4158,362,0
chrM 2708 . G A 4474.77 . AC=2;AF=1.00;AN=2;DP=127;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.84;QD=32.93;SOR=0.774 GT:AD:DP:GQ:PL 1/1:0,127:127:99:4503,381,0
chrM 4746 . A G 2693.77 . AC=2;AF=1.00;AN=2;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.86;QD=33.26;SOR=0.718 GT:AD:DP:GQ:PL 1/1:0,81:81:99:2722,242,0
chrM 5581 . C T 3091.77 . AC=2;AF=1.00;AN=2;DP=96;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.11;QD=32.54;SOR=0.947 GT:AD:DP:GQ:PL 1/1:0,95:95:99:3120,285,0
chrM 7029 . T C 3034.77 . AC=2;AF=1.00;AN=2;DP=94;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.49;QD=32.28;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,94:94:99:3063,282,0
chrM 7338 . G A 3647.77 . AC=2;AF=1.00;AN=2;DP=111;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.47;QD=32.86;SOR=0.865 GT:AD:DP:GQ:PL 1/1:0,111:111:99:3676,333,0
chrM 8702 . G A 55738.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-2.533e+00;ClippingRankSum=0.00;DP=1455;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.96;MQRankSum=-8.570e-01;QD=30.83;ReadPosRankSum=-1.220e+00;SOR=2.655 GT:AD:DP:GQ:PL 1/1:3,1444:1447:99:55767,4213,0
chrM 9378 . G A 15302.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.90;ClippingRankSum=0.00;DP=430;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.31;MQRankSum=-1.678e+00;QD=29.67;ReadPosRankSum=-8.420e-01;SOR=2.124 GT:AD:DP:GQ:PL 1/1:2,425:427:99:15331,1231,0
chrM 9541 . C T 7951.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.006e+00;ClippingRankSum=0.00;DP=242;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.94;MQRankSum=0.00;QD=33.27;ReadPosRankSum=1.48;SOR=0.930 GT:AD:DP:GQ:PL 1/1:1,238:239:99:7980,670,0
chrM 10399 . G A 2937.77 . AC=2;AF=1.00;AN=2;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.93;SOR=0.929 GT:AD:DP:GQ:PL 1/1:0,92:92:99:2966,275,0
chrM 10820 . G A 3446.77 . AC=2;AF=1.00;AN=2;DP=114;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.35;QD=31.05;SOR=0.995 GT:AD:DP:GQ:PL 1/1:0,111:111:99:3475,331,0
chrM 10874 . C T 3100.77 . AC=2;AF=1.00;AN=2;DP=100;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.78;QD=31.64;SOR=0.734 GT:AD:DP:GQ:PL 1/1:0,98:98:99:3129,292,0
chrM 11018 . C T 2952.77 . AC=2;AF=1.00;AN=2;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.33;QD=33.18;SOR=0.715 GT:AD:DP:GQ:PL 1/1:0,89:89:99:2981,265,0
chrM 11720 . A G 5996.77 . AC=2;AF=1.00;AN=2;DP=133;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.65;QD=34.04;SOR=0.739 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,133:133:99:1|1:11720_A_G:6025,412,0
chrM 11723 . C T 5947.77 . AC=2;AF=1.00;AN=2;DP=132;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.63;QD=32.42;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,132:132:99:1|1:11720_A_G:5976,406,0
chrM 12706 . T C 3690.77 . AC=2;AF=1.00;AN=2;DP=124;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.09;SOR=0.859 GT:AD:DP:GQ:PL 1/1:0,115:115:99:3719,343,0
chrM 12851 . G A 3972.77 . AC=2;AF=1.00;AN=2;DP=128;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.04;SOR=1.051 GT:AD:DP:GQ:PL 1/1:0,128:128:99:4001,380,0
chrM 13327 . T C 5000.77 . AC=2;AF=1.00;AN=2;DP=150;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.73;QD=33.79;SOR=0.930 GT:AD:DP:GQ:PL 1/1:0,148:148:99:5029,445,0
chrM 13681 . C T 3752.77 . AC=2;AF=1.00;AN=2;DP=123;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.01;SOR=0.928 GT:AD:DP:GQ:PL 1/1:0,121:121:99:3781,361,0
chrM 14213 . C T 2504.77 . AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.64;QD=32.53;SOR=0.719 GT:AD:DP:GQ:PL 1/1:0,77:77:99:2533,231,0
chrM 14581 . G A 2819.77 . AC=2;AF=1.00;AN=2;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.97;QD=32.04;SOR=0.739 GT:AD:DP:GQ:PL 1/1:0,88:88:99:2848,262,0
chrM 14767 . T C 2914.77 . AC=2;AF=1.00;AN=2;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.25;QD=33.12;SOR=1.244 GT:AD:DP:GQ:PL 1/1:0,88:88:99:2943,264,0
chrM 14832 . G A 3447.77 . AC=2;AF=1.00;AN=2;DP=111;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.83;QD=31.92;SOR=1.077 GT:AD:DP:GQ:PL 1/1:0,108:108:99:3476,323,0
chrM 14873 . C T 3719.77 . AC=2;AF=1.00;AN=2;DP=120;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.00;SOR=0.833 GT:AD:DP:GQ:PL 1/1:0,120:120:99:3748,358,0
chrM 14906 . A G 4327.77 . AC=2;AF=1.00;AN=2;DP=127;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.72;QD=34.08;SOR=0.954 GT:AD:DP:GQ:PL 1/1:0,127:127:99:4356,381,0
chrM 15302 . A G 3502.77 . AC=2;AF=1.00;AN=2;DP=105;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.34;SOR=0.815 GT:AD:DP:GQ:PL 1/1:0,102:102:99:3531,306,0
chrM 15933 . C T 3115.77 . AC=2;AF=1.00;AN=2;DP=97;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.15;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,94:94:99:3144,282,0
chrM 16024 . G A 1312.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.823e+00;ClippingRankSum=0.00;DP=111;ExcessHet=3.0103;FS=7.507;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=12.16;ReadPosRankSum=0.794;SOR=0.787 GT:AD:DP:GQ:PL 0/1:55,53:108:99:1341,0,1621
chrM 16173 . C T 5037.77 . AC=2;AF=1.00;AN=2;DP=116;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.87;QD=37.76;SOR=0.711 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,109:109:99:1|1:16173_C_T:5066,343,0
chrM 16183 . AC A 5020.73 . AC=2;AF=1.00;AN=2;DP=120;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.87;QD=27.64;SOR=0.711 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,113:113:99:1|1:16173_C_T:5058,340,0
chrM 16185 . C A 5029.77 . AC=2;AF=1.00;AN=2;DP=119;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.87;QD=29.43;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,112:112:99:1|1:16173_C_T:5058,340,0
chrM 16191 . C T 4831.77 . AC=2;AF=1.00;AN=2;DP=115;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.87;QD=30.09;SOR=0.769 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,108:108:99:1|1:16173_C_T:4860,328,0
chrM 16225 . T C 3434.77 . AC=2;AF=1.00;AN=2;DP=117;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.87;QD=31.23;SOR=0.806 GT:AD:DP:GQ:PL 1/1:0,110:110:99:3463,329,0
chrM 16322 . T C 3589.77 . AC=2;AF=1.00;AN=2;DP=118;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.49;SOR=0.728 GT:AD:DP:GQ:PL 1/1:0,114:114:99:3618,340,0
chrM 16521 . C T 4251.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.21;ClippingRankSum=0.00;DP=149;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.00;QD=30.37;ReadPosRankSum=3.06;SOR=0.752 GT:AD:DP:GQ:PL 1/1:2,138:140:99:4280,371,0
test/test-dry-run.yml 0 → 100644
+ 11
− 0
View file @ 58051aaf
- name: test-dry-run-GIAB-chrM
tags:
- dry-run
command: >
snakemake -n
--configfile test/config/config-GIAB-chrM.json
--use-singularity
stdout:
contains:
- "Job counts:"
test/test-integration.yml 0 → 100644
+ 14
− 0
View file @ 58051aaf
- name: test-integration-GIAB-chrM
tags:
- integration
command: >
snakemake
--configfile test/config/config-GIAB-chrM.json
--use-singularity
--singularity-args ' --containall --bind /tmp'
--cores 1
16699289_coverage.varda 16699289_variants.varda
files:
- path: 16699289_coverage.varda
- path: 16699289_variants.varda
test/test-sanity.yml 0 → 100644
+ 14
− 0
View file @ 58051aaf
- name: test-sanity-singularity
tags:
- sanity
command: >
singularity --version
stdout:
contains:
- "singularity version 3"
- name: test-sanity-snakemake
tags:
- sanity
command: >
snakemake --version
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