Mercurial > repos > iuc > strelka_germline
comparison test-data/variants_test2.vcf @ 0:1fbe84e8a740 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
| author | iuc |
|---|---|
| date | Wed, 27 Jan 2021 14:48:23 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:1fbe84e8a740 |
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| 1 ##fileformat=VCFv4.1 | |
| 2 ##fileDate=. | |
| 3 ##source=strelka | |
| 4 ##source_version=2.9.10 | |
| 5 ##startTime=. | |
| 6 ##cmdline=./configureStrelkaGermlineWorkflow.py --bam input_sample_0.cram --bam input_sample_1.cram --disableSequenceErrorEstimation --config=/tmp/tmpmxn8erma/job_working_directory/000/4/configs/tmpx1j1a_0u --referenceFasta input_ref.fasta --runDir results | |
| 7 ##reference=file:///tmp/tmpmxn8erma/job_working_directory/000/4/working/input_ref.fasta | |
| 8 ##contig=<ID=demo20,length=5000> | |
| 9 ##content=strelka germline small-variant calls | |
| 10 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the region described in this record"> | |
| 11 ##INFO=<ID=BLOCKAVG_min30p3a,Number=0,Type=Flag,Description="Non-variant multi-site block. Non-variant blocks are defined independently for each sample. All sites in such a block are constrained to be non-variant, have the same filter value, and have sample values {GQX,DP,DPF} in range [x,y], y <= max(x+3,(x*1.3))."> | |
| 12 ##INFO=<ID=SNVHPOL,Number=1,Type=Integer,Description="SNV contextual homopolymer length"> | |
| 13 ##INFO=<ID=CIGAR,Number=A,Type=String,Description="CIGAR alignment for each alternate indel allele"> | |
| 14 ##INFO=<ID=RU,Number=A,Type=String,Description="Smallest repeating sequence unit extended or contracted in the indel allele relative to the reference. RUs are not reported if longer than 20 bases"> | |
| 15 ##INFO=<ID=REFREP,Number=A,Type=Integer,Description="Number of times RU is repeated in reference"> | |
| 16 ##INFO=<ID=IDREP,Number=A,Type=Integer,Description="Number of times RU is repeated in indel allele"> | |
| 17 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="RMS of mapping quality"> | |
| 18 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| 19 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | |
| 20 ##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Empirically calibrated genotype quality score for variant sites, otherwise minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}"> | |
| 21 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Filtered basecall depth used for site genotyping. In a non-variant multi-site block this value represents the average of all sites in the block."> | |
| 22 ##FORMAT=<ID=DPF,Number=1,Type=Integer,Description="Basecalls filtered from input prior to site genotyping. In a non-variant multi-site block this value represents the average of all sites in the block."> | |
| 23 ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum filtered basecall depth used for site genotyping within a non-variant multi-site block"> | |
| 24 ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed. For indels this value only includes reads which confidently support each allele (posterior prob 0.51 or higher that read contains indicated allele vs all other intersecting indel alleles)"> | |
| 25 ##FORMAT=<ID=ADF,Number=.,Type=Integer,Description="Allelic depths on the forward strand"> | |
| 26 ##FORMAT=<ID=ADR,Number=.,Type=Integer,Description="Allelic depths on the reverse strand"> | |
| 27 ##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample filter, 'PASS' indicates that all filters have passed for this sample"> | |
| 28 ##FORMAT=<ID=DPI,Number=1,Type=Integer,Description="Read depth associated with indel, taken from the site preceding the indel"> | |
| 29 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> | |
| 30 ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phase set identifier"> | |
| 31 ##FORMAT=<ID=SB,Number=1,Type=Float,Description="Sample site strand bias"> | |
| 32 ##FILTER=<ID=IndelConflict,Description="Indel genotypes from two or more loci conflict in at least one sample"> | |
| 33 ##FILTER=<ID=SiteConflict,Description="Site is filtered due to an overlapping indel call filter"> | |
| 34 ##FILTER=<ID=LowGQX,Description="Locus GQX is below threshold or not present"> | |
| 35 ##FILTER=<ID=HighDPFRatio,Description="The fraction of basecalls filtered out at a site is greater than 0.4"> | |
| 36 ##FILTER=<ID=HighSNVSB,Description="Sample SNV strand bias value (SB) exceeds 10"> | |
| 37 ##FILTER=<ID=HighDepth,Description="Locus depth is greater than 3x the mean chromosome depth"> | |
| 38 ##Depth_demo20=53.00 | |
| 39 ##FILTER=<ID=LowDepth,Description="Locus depth is below 3"> | |
| 40 ##FILTER=<ID=NotGenotyped,Description="Locus contains forcedGT input alleles which could not be genotyped"> | |
| 41 ##FILTER=<ID=PloidyConflict,Description="Genotype call from variant caller not consistent with chromosome ploidy"> | |
| 42 ##FILTER=<ID=NoPassedVariantGTs,Description="No samples at this locus pass all sample filters and have a variant genotype"> | |
| 43 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12891 NA12892 | |
| 44 demo20 991 . C G 38 PASS SNVHPOL=2;MQ=59 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 0/1:71:9:9:1:5,4:1,4:4,0:2.8:PASS:72,0,123 0/0:33:33:12:0:12,0:9,0:3,0:0.0:PASS:0,36,258 | |
| 45 demo20 1148 . C CTAT 72 PASS CIGAR=1M3I;RU=TAT;REFREP=1;IDREP=2;MQ=60 GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL 0/1:114:27:20:11,8:5,3:6,5:PASS:111,0,147 0/0:69:69:28:24,0:12,0:12,0:PASS:0,72,443 | |
| 46 demo20 1271 . A G 134 PASS SNVHPOL=4;MQ=60 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 0/1:126:30:18:0:8,10:7,6:1,4:-18.6:PASS:169,0,123 0/0:75:75:26:0:26,0:18,0:8,0:0.0:PASS:0,78,370 | |
| 47 demo20 1508 . A G 156 PASS SNVHPOL=3;MQ=60 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 0/1:172:30:22:1:10,12:4,6:6,6:-21.5:PASS:191,0,169 0/0:108:108:37:2:37,0:19,0:18,0:0.0:PASS:0,111,370 | |
| 48 demo20 1706 . C T 304 PASS SNVHPOL=2;MQ=59 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 1/1:54:30:19:0:0,19:0,8:0,11:-35.5:PASS:342,57,0 0/0:90:90:31:2:31,0:7,0:24,0:0.0:PASS:0,93,370 | |
| 49 demo20 1744 . C T 156 PASS SNVHPOL=3;MQ=59 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 0/1:159:30:21:0:9,12:5,6:4,6:-20.7:PASS:191,0,156 0/0:78:78:27:0:27,0:6,0:21,0:0.0:PASS:0,81,370 | |
| 50 demo20 1846 . C T 83 PASS SNVHPOL=3;MQ=60 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 0/1:116:30:24:1:16,8:13,5:3,3:-12.4:PASS:117,0,224 0/0:60:60:21:0:21,0:14,0:7,0:0.0:PASS:0,63,370 | |
| 51 demo20 1873 . C T 122 PASS SNVHPOL=3;MQ=60 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 0/0:60:60:21:0:21,0:15,0:6,0:0.0:PASS:0,63,360 0/1:155:30:23:0:13,10:8,7:5,3:-14.9:PASS:157,0,195 | |
| 52 demo20 2074 . T C 123 PASS SNVHPOL=2;MQ=60 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 0/1:156:30:24:1:13,11:4,8:9,3:-9.7:PASS:158,0,191 0/0:75:75:26:0:26,0:14,0:12,0:0.0:PASS:0,78,370 | |
| 53 demo20 2199 . G A 149 PASS SNVHPOL=3;MQ=60 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 0/1:181:30:28:1:14,14:12,5:2,9:-14.3:PASS:183,0,189 0/0:96:96:33:0:33,0:17,0:16,0:0.0:PASS:0,99,370 | |
| 54 demo20 2301 . G T 184 PASS SNVHPOL=2;MQ=59 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 0/1:161:22:29:1:12,17:6,11:6,6:-21.0:PASS:219,0,158 0/0:75:75:26:1:26,0:15,0:11,0:0.0:PASS:0,78,370 | |
| 55 demo20 2455 . T C 445 PASS SNVHPOL=2;MQ=60 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 1/1:90:30:31:2:0,31:0,14:0,17:-51.4:PASS:370,93,0 0/0:78:78:27:1:27,0:11,0:16,0:0.0:PASS:0,81,370 | |
| 56 demo20 2512 . A G 266 PASS SNVHPOL=2;MQ=59 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 0/1:151:22:39:1:13,26:9,11:4,15:-28.4:PASS:300,0,148 0/0:69:69:24:2:24,0:8,0:16,0:0.0:PASS:0,72,370 | |
| 57 demo20 2640 . C T 375 PASS SNVHPOL=3;MQ=60 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 1/1:81:30:28:0:0,28:0,14:0,14:-47.3:PASS:370,84,0 0/0:102:102:35:0:35,0:17,0:18,0:0.0:PASS:0,105,370 | |
| 58 demo20 2660 . G T 283 PASS SNVHPOL=3;MQ=60 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 1/1:60:30:21:1:0,21:0,11:0,10:-36.2:PASS:321,63,0 0/0:87:87:30:0:30,0:15,0:15,0:0.0:PASS:0,90,370 | |
| 59 demo20 3054 . G C 107 PASS SNVHPOL=2;MQ=58 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 0/1:140:22:20:0:10,10:6,6:4,4:-12.8:PASS:142,0,153 0/0:24:24:9:2:9,0:4,0:5,0:0.0:PASS:0,27,201 | |
| 60 demo20 3366 . G T 377 PASS SNVHPOL=4;MQ=60 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 1/1:75:30:26:0:0,26:0,15:0,11:-42.1:PASS:370,78,0 0/0:75:75:26:0:26,0:13,0:13,0:0.0:PASS:0,78,370 | |
| 61 demo20 3537 . C T 95 PASS SNVHPOL=2;MQ=59 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 0/1:128:22:31:1:21,10:8,6:13,4:-11.3:PASS:130,0,256 0/0:84:84:29:1:29,0:10,0:19,0:0.0:PASS:0,87,370 | |
| 62 demo20 3664 . TC T 286 PASS CIGAR=1M1D;RU=C;REFREP=4;IDREP=3;MQ=59 GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL 0/1:249:27:41:18,20:10,10:8,10:PASS:322,0,246 0/0:70:70:25:25,0:10,0:15,0:PASS:0,73,493 |