Mercurial > repos > iuc > strelka_germline
comparison test-data/genome_test1.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 |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:1fbe84e8a740 |
|---|---|
| 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.bam --bam input_sample_1.bam --bam input_sample_2.bam --disableSequenceErrorEstimation --config=/tmp/tmpmywmzdlj/job_working_directory/000/7/configs/tmpzw3187cr --referenceFasta input_ref.fasta --runDir results | |
| 7 ##reference=file:///tmp/tmpmywmzdlj/job_working_directory/000/7/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=79.00 | |
| 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 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12891 | |
| 43 demo20 1 . T . . LowGQX END=899;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP .:.:0:0:0 | |
| 44 demo20 900 . G . . LowGQX;LowDepth END=906;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:5:2:0:2 | |
| 45 demo20 907 . T . . LowGQX END=931;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:7:4:0:3 | |
| 46 demo20 932 . G . . PASS END=990;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:15:8:0:6 | |
| 47 demo20 991 . C G 75 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 | |
| 48 demo20 992 . C . . PASS END=1084;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:24:14:0:9 | |
| 49 demo20 1085 . T . . PASS . GT:GQX:DP:DPF:MIN_DP 0/0:22:21:1:21 | |
| 50 demo20 1086 . G . . PASS END=1148;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:54:22:1:19 | |
| 51 demo20 1148 . C CTAT 144 PASS CIGAR=1M3I;RU=TAT;REFREP=1;IDREP=2;MQ=59 GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL 0/1:114:27:20:11,8:5,3:6,5:PASS:111,0,147 | |
| 52 demo20 1149 . T . . PASS END=1270;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:39:19:0:14 | |
| 53 demo20 1271 . A G 268 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 | |
| 54 demo20 1272 . G . . PASS END=1507;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:39:20:1:14 | |
| 55 demo20 1508 . A G 312 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 | |
| 56 demo20 1509 . G . . PASS END=1582;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:27:17:0:10 | |
| 57 demo20 1583 . A . . PASS END=1669;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:21:15:0:8 | |
| 58 demo20 1670 . C . . PASS END=1705;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:45:19:0:16 | |
| 59 demo20 1706 . C T 608 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 | |
| 60 demo20 1707 . G . . PASS END=1743;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:54:21:0:19 | |
| 61 demo20 1744 . C T 312 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 | |
| 62 demo20 1745 . G . . PASS END=1845;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:40:21:1:16 | |
| 63 demo20 1846 . C T 165 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 | |
| 64 demo20 1847 . G . . PASS END=1872;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:60:23:1:21 | |
| 65 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 | |
| 66 demo20 1874 . C . . PASS END=2073;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:45:21:0:16 | |
| 67 demo20 2074 . T C 246 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 | |
| 68 demo20 2075 . A . . PASS END=2198;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:63:31:1:22 | |
| 69 demo20 2199 . G A 297 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 | |
| 70 demo20 2200 . C . . PASS END=2300;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:60:30:1:26 | |
| 71 demo20 2301 . G T 369 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 | |
| 72 demo20 2302 . T . . PASS END=2454;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:72:30:0:25 | |
| 73 demo20 2455 . T C 889 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 | |
| 74 demo20 2456 . G . . PASS END=2511;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:87:36:2:30 | |
| 75 demo20 2512 . A G 531 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 | |
| 76 demo20 2513 . T . . PASS END=2639;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:81:37:1:28 | |
| 77 demo20 2640 . C T 751 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 | |
| 78 demo20 2641 . T . . PASS END=2659;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:60:23:0:21 | |
| 79 demo20 2660 . G T 567 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 | |
| 80 demo20 2661 . G . . PASS END=3037;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:41:27:1:18 | |
| 81 demo20 3038 . C . . PASS END=3053;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:27:20:1:17 | |
| 82 demo20 3054 . G C 214 PASS SNVHPOL=2;MQ=59 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 | |
| 83 demo20 3055 . C . . PASS END=3365;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:51:25:1:18 | |
| 84 demo20 3366 . G T 753 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 | |
| 85 demo20 3367 . G . . PASS END=3536;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:60:28:0:21 | |
| 86 demo20 3537 . C T 191 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 | |
| 87 demo20 3538 . T . . PASS END=3664;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:54:29:1:19 | |
| 88 demo20 3664 . TC T 572 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 | |
| 89 demo20 3665 . C . . PASS . GT:GQX:DP:DPF:MIN_DP 0:249:19:0:19 | |
| 90 demo20 3666 . C . . PASS END=4019;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:48:32:1:17 | |
| 91 demo20 4020 . C . . PASS END=4059;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:24:12:1:9 | |
| 92 demo20 4060 . C . . PASS END=4072;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:15:6:0:6 | |
| 93 demo20 4073 . C . . LowGQX END=4091;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:7:4:0:3 | |
| 94 demo20 4092 . T . . LowGQX;LowDepth END=4100;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:3:1:0:1 | |
| 95 demo20 4101 . T . . LowGQX END=5000;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP .:.:0:0:0 |