Mercurial > repos > hepcat72 > vcfsamplecompare
view test-data/lest2.vcf @ 0:cdd7fecae37c draft
planemo upload commit c786cb50e512783d81d4a9ad57add9151ac5904f
| author | hepcat72 |
|---|---|
| date | Wed, 10 Oct 2018 18:53:14 -0400 |
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##fileformat=VCFv4.2 ##fileDate=20180104 ##reference= ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> ##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"> ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> ##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants"> ##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants"> ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends"> ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend"> ##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants"> ##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples"> ##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples"> ##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples"> ##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples"> ##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call"> ##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend"> ##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend"> ##ALT=<ID=DEL,Description="Deletion"> ##ALT=<ID=DUP,Description="Duplication"> ##ALT=<ID=INV,Description="Inversion"> ##ALT=<ID=DUP:TANDEM,Description="Tandem duplication"> ##ALT=<ID=INS,Description="Insertion of novel sequence"> ##ALT=<ID=CNV,Description="Copy number variable region"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant"> ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant"> ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant"> ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality"> ##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample"> ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations"> ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations"> ##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally"> ##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally"> ##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally"> ##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally"> ##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally"> ##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)"> ##source=LUMPY #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 195 213 chr1 668399 1_1 N N]chr1:674472] 86.29 . SVTYPE=BND;STRANDS=++:6;IMPRECISE;CIPOS=-6,571;CIEND=-10,562;CIPOS95=0,144;CIEND95=-2,133;MATEID=1_2;EVENT=1;SU=6;PE=6;SR=0 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:4:4:0:77:77.32:-23,-15,-76:105:91:13:91:13:91:13:0:0:0:0.12 0/1:2:2:0:8:8.97:-17,-16,-74:98:87:10:87:10:87:10:0:0:0:0.1 chr1 674472 1_2 N N]chr1:668399] 86.29 . SVTYPE=BND;STRANDS=++:6;IMPRECISE;CIPOS=-10,562;CIEND=-6,571;CIPOS95=-2,133;CIEND95=0,144;MATEID=1_1;EVENT=1;SECONDARY;SU=6;PE=6;SR=0 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:4:4:0:77:77.32:-23,-15,-76:105:91:13:91:13:91:13:0:0:0:0.12 0/1:2:2:0:8:8.97:-17,-16,-74:98:87:10:87:10:87:10:0:0:0:0.1 chr1 668400 2 N <DEL> 2055.89 . SVTYPE=DEL;SVLEN=-5997;END=674397;STRANDS=+-:85;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=85;PE=43;SR=42 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:49:26:23:149:1276.83:-131,-3,-56:157:97:59:96:58:42:22:5:54:30:0.38 0/1:36:17:19:146:779.06:-84,-6,-59:133:92:40:91:39:43:18:2:48:18:0.3 chr1 67654 3 N <DUP> 0.00 . SVTYPE=DUP;SVLEN=942067;END=1009721;STRANDS=-+:4;IMPRECISE;CIPOS=-10,8;CIEND=-10,9;CIPOS95=-1,0;CIEND95=-1,1;SU=4;PE=2;SR=2 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:0:0:0:94:0.00:-0,-10,-18:66:64:1:64:1:64:0:1:0:0:0.015 0/0:4:2:2:200:0.00:-1,-26,-46:169:165:3:164:2:78:1:0:86:1:0.012 chr1 1661491 4 N <DEL> 0.00 . SVTYPE=DEL;SVLEN=-1223;END=1662714;STRANDS=+-:4;IMPRECISE;CIPOS=-10,142;CIEND=-675,9;CIPOS95=-2,101;CIEND95=-232,2;SU=4;PE=4;SR=0 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:4:4:0:152:0.00:-1,-365,-1230:1243:1239:4:1238:3:607:0:1:631:1:0.0024 0/0:0:0:0:200:0.00:-0,-34,-114:115:115:0:114:0:58:0:0:56:0:0 chr1 1664595 5 N <INV> 0.00 . SVTYPE=INV;SVLEN=182;END=1664777;STRANDS=++:4,--:1;IMPRECISE;CIPOS=-10,33;CIEND=0,20;CIPOS95=0,33;CIEND95=0,12;SU=5;PE=5;SR=0 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:5:5:0:153:0.00:-2,-368,-1244:1262:1256:5:1255:4:759:0:0:496:4:0.0032 0/0:0:0:0:200:0.00:-0,-30,-100:101:101:0:100:0:59:0:0:41:0:0 chr1 1659220 6 N <DUP> 13154.05 . SVTYPE=DUP;SVLEN=6530;END=1665750;STRANDS=-+:627;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=627;PE=482;SR=145 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:627:482:145:200:13154.05:-1452,-264,-136:890:97:792:96:791:43:144:129:53:517:0.89 0/0:0:0:0:151:0.00:-0,-16,-27:90:90:0:89:0:42:0:0:47:0:0 chr1 1731911 7 N <DUP> 660.53 . SVTYPE=DUP;SVLEN=406;END=1732317;STRANDS=-+:18;IMPRECISE;CIPOS=-240,9;CIEND=-10,253;CIPOS95=-37,3;CIEND95=-1,57;SU=18;PE=18;SR=0 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:7:7:0:101:168.01:-22,-5,-15:141:116:25:115:24:43:0:0:72:24:0.17 0/1:11:11:0:14:492.53:-50,-1,-3:108:68:40:68:40:0:0:0:68:40:0.37 chr1 1733864 8 N <DUP> 783.87 . SVTYPE=DUP;SVLEN=298;END=1734162;STRANDS=-+:38;IMPRECISE;CIPOS=-240,9;CIEND=-6,251;CIPOS95=-52,1;CIEND95=-2,64;SU=38;PE=38;SR=0 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:16:16:0:122:267.06:-32,-5,-17:182:147:35:146:34:63:0:3:83:31:0.19 0/1:22:22:0:146:516.81:-58,-7,-26:302:241:61:240:61:112:0:9:128:52:0.2 chr1 2206996 9 N <DEL> 502.28 . SVTYPE=DEL;SVLEN=-26;END=2207022;STRANDS=+-:18;CIPOS=-2,1;CIEND=-6,9;CIPOS95=0,0;CIEND95=0,0;SU=18;PE=0;SR=18 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:9:0:9:22:265.90:-27,-3,-0:9:0:9:0:9:0:0:9:0:0:1 1/1:9:0:9:20:236.38:-24,-2,-0:8:0:8:0:8:0:0:8:0:0:1 chr1 431018 10 N <DUP> 0.00 . SVTYPE=DUP;SVLEN=1900013;END=2331031;STRANDS=-+:4;IMPRECISE;CIPOS=-10,8;CIEND=-10,9;CIPOS95=-1,0;CIEND95=-1,1;SU=4;PE=2;SR=2 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:0:0:0:156:0.00:-1,-32,-55:184:184:0:183:0:85:0:0:98:0:0 0/0:4:2:2:156:0.00:-1,-25,-44:162:158:3:157:2:81:1:0:76:1:0.013 chr1 2687759 11 N <DEL> 1942.68 . SVTYPE=DEL;SVLEN=-215;END=2687974;STRANDS=+-:68;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=68;PE=0;SR=68 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:38:0:38:200:1025.29:-104,-1,-22:89:45:43:45:43:45:37:5:0:0:0.49 0/1:30:0:30:153:917.39:-93,-1,-17:75:36:38:36:38:36:29:8:0:0:0.51 chr1 2687860 12 N <DUP> 1665.77 . SVTYPE=DUP;SVLEN=210;END=2688070;STRANDS=-+:8;IMPRECISE;CIPOS=-546,6;CIEND=-6,532;CIPOS95=-130,0;CIEND95=0,134;SU=8;PE=8;SR=0 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:5:5:0:17:642.58:-66,-1,-3:141:88:53:87:52:27:11:24:60:16:0.37 1/1:3:3:0:5:1023.19:-104,-3,-2:190:109:80:108:79:44:24:28:64:26:0.42 chr1 2687860 13 N <DUP> 1668.43 . SVTYPE=DUP;SVLEN=211;END=2688071;STRANDS=-+:37;CIPOS=-1,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=37;PE=0;SR=37 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:12:0:12:17:642.58:-66,-1,-3:142:88:53:87:52:27:11:24:60:16:0.37 1/1:25:0:25:6:1025.85:-105,-3,-2:188:108:80:107:79:43:24:29:64:25:0.42 chr1 907970 14 N <DUP> 0.00 . SVTYPE=DUP;SVLEN=1931107;END=2839077;STRANDS=-+:4;IMPRECISE;CIPOS=-10,8;CIEND=-10,9;CIPOS95=-1,0;CIEND95=-1,1;SU=4;PE=2;SR=2 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:4:2:2:156:0.00:-1,-25,-45:166:162:3:161:2:72:1:0:89:1:0.012 0/0:0:0:0:200:0.00:-1,-29,-49:163:163:0:162:0:75:0:0:87:0:0 chr1 10 15 N <DUP> 3194.06 . SVTYPE=DUP;SVLEN=3288548;END=3288558;STRANDS=-+:212;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=212;PE=88;SR=124 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:122:55:67:200:1817.90:-214,-51,-32:108:0:108:0:107:0:32:11:0:63:1 1/1:90:33:57:140:1376.17:-162,-39,-24:82:0:82:0:81:0:28:11:0:42:1 chr2 786218 16 N <DUP> 0.00 . SVTYPE=DUP;SVLEN=413;END=786631;STRANDS=-+:4;IMPRECISE;CIPOS=-10,8;CIEND=-10,9;CIPOS95=-1,0;CIEND95=-1,1;SU=4;PE=2;SR=2 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:0:0:0:156:0.00:-1,-32,-54:181:181:0:180:0:94:0:0:86:0:0 0/0:4:2:2:200:0.00:-1,-33,-61:232:226:5:225:4:129:1:0:96:3:0.017 chr2 1636681 17 N <DUP> 0.00 . SVTYPE=DUP;SVLEN=30926;END=1667607;STRANDS=-+:4;IMPRECISE;CIPOS=-10,8;CIEND=-10,9;CIPOS95=-1,0;CIEND95=-1,1;SU=4;PE=2;SR=2 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:4:2:2:156:0.00:-1,-40,-72:264:259:4:258:3:128:1:0:130:1:0.011 0/0:0:0:0:151:0.00:-1,-48,-82:272:272:0:271:0:130:0:0:141:0:0 chr2 1846648 18_1 N N]chr2:1847584] 910.74 . SVTYPE=BND;STRANDS=++:24;IMPRECISE;CIPOS=-2,249;CIEND=-10,618;CIPOS95=0,69;CIEND95=-1,60;MATEID=18_2;EVENT=18;SU=24;PE=24;SR=0 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:7:7:0:200:362.51:-40,-4,-34:70:50:19:50:19:50:19:0:0:0:0.28 0/1:17:17:0:146:548.24:-61,-6,-53:108:78:29:78:29:78:29:0:0:0:0.27 chr2 1847584 18_2 N N]chr2:1846648] 910.74 . SVTYPE=BND;STRANDS=++:24;IMPRECISE;CIPOS=-10,618;CIEND=-2,249;CIPOS95=-1,60;CIEND95=0,69;MATEID=18_1;EVENT=18;SECONDARY;SU=24;PE=24;SR=0 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:7:7:0:200:362.51:-40,-4,-34:70:50:19:50:19:50:19:0:0:0:0.28 0/1:17:17:0:146:548.24:-61,-6,-53:108:78:29:78:29:78:29:0:0:0:0.27 chr2 1846649 19 N <DEL> 8567.30 . SVTYPE=DEL;SVLEN=-882;END=1847531;STRANDS=+-:193;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=193;PE=109;SR=84 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:84:51:33:146:3574.63:-363,-36,-6:122:0:122:0:121:0:32:17:0:71:1 1/1:109:58:51:200:4992.67:-507,-51,-8:170:0:170:0:169:0:50:20:0:98:1 chr2 10 20 N <DUP> 4604.21 . SVTYPE=DUP;SVLEN=1877202;END=1877212;STRANDS=-+:241;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=241;PE=188;SR=53 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:146:119:27:200:2769.32:-326,-78,-49:164:0:164:0:163:0:13:12:0:137:1 1/1:95:69:26:200:1834.89:-216,-52,-33:109:0:109:0:108:0:12:11:0:84:1