Mercurial > repos > artbio > lumpy_smoove
view test-data/test_vcf2hrdetect.vcf @ 9:7dcf61950215 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 5f62b58c65917afbb018296568c81ad132106012
| author | artbio |
|---|---|
| date | Wed, 05 Apr 2023 15:56:13 +0000 |
| parents | ad8853ee9909 |
| children |
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##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> ##fileDate=20201029 ##reference=reference.fa ##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"> ##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)"> ##contig=<ID=1,length=249250621> ##contig=<ID=2,length=243199373> ##contig=<ID=3,length=198022430> ##contig=<ID=4,length=191154276> ##contig=<ID=5,length=180915260> ##contig=<ID=6,length=171115067> ##contig=<ID=7,length=159138663> ##contig=<ID=8,length=146364022> ##contig=<ID=9,length=141213431> ##contig=<ID=10,length=135534747> ##contig=<ID=11,length=135006516> ##contig=<ID=12,length=133851895> 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##contig=<ID=GL000248.1,length=39786> ##contig=<ID=GL000244.1,length=39929> ##contig=<ID=GL000238.1,length=39939> ##contig=<ID=GL000202.1,length=40103> ##contig=<ID=GL000234.1,length=40531> ##contig=<ID=GL000232.1,length=40652> ##contig=<ID=GL000206.1,length=41001> ##contig=<ID=GL000240.1,length=41933> ##contig=<ID=GL000236.1,length=41934> ##contig=<ID=GL000241.1,length=42152> ##contig=<ID=GL000243.1,length=43341> ##contig=<ID=GL000242.1,length=43523> ##contig=<ID=GL000230.1,length=43691> ##contig=<ID=GL000237.1,length=45867> ##contig=<ID=GL000233.1,length=45941> ##contig=<ID=GL000204.1,length=81310> ##contig=<ID=GL000198.1,length=90085> ##contig=<ID=GL000208.1,length=92689> ##contig=<ID=GL000191.1,length=106433> ##contig=<ID=GL000227.1,length=128374> ##contig=<ID=GL000228.1,length=129120> ##contig=<ID=GL000214.1,length=137718> ##contig=<ID=GL000221.1,length=155397> ##contig=<ID=GL000209.1,length=159169> ##contig=<ID=GL000218.1,length=161147> ##contig=<ID=GL000220.1,length=161802> ##contig=<ID=GL000213.1,length=164239> ##contig=<ID=GL000211.1,length=166566> ##contig=<ID=GL000199.1,length=169874> ##contig=<ID=GL000217.1,length=172149> ##contig=<ID=GL000216.1,length=172294> ##contig=<ID=GL000215.1,length=172545> ##contig=<ID=GL000205.1,length=174588> ##contig=<ID=GL000219.1,length=179198> ##contig=<ID=GL000224.1,length=179693> ##contig=<ID=GL000223.1,length=180455> ##contig=<ID=GL000195.1,length=182896> ##contig=<ID=GL000212.1,length=186858> ##contig=<ID=GL000222.1,length=186861> ##contig=<ID=GL000200.1,length=187035> ##contig=<ID=GL000193.1,length=189789> ##contig=<ID=GL000194.1,length=191469> ##contig=<ID=GL000225.1,length=211173> ##contig=<ID=GL000192.1,length=547496> ##smoove_version=0.2.5 ##smoove_count_stats=TARGET-21-PAMXZY-15A-01D:0,646270,0,297568 ##smoove_count_stats=TARGET-21-PAMXZY-09A-03D:0,504761,0,141470 ##source=LUMPY ##bcftools_annotateVersion=1.10.2+htslib-1.10.2 ##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Thu Oct 29 18:30:42 2020 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##bcftools_viewVersion=1.10.2+htslib-1.10.2 ##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Thu Oct 29 18:30:42 2020 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TARGET-21-PAMXZY-15A-01D TARGET-21-PAMXZY-09A-03D 1 14436660 4 N <DUP> 40.38 . SVTYPE=DUP;SVLEN=1903;END=14438563;STRANDS=-+:11;IMPRECISE;CIPOS=-219,29;CIEND=-30,224;CIPOS95=-93,4;CIEND95=-4,95;SU=11;PE=11;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:19:0.05:-0,-2,-4:21:21:0:21:0:21:0:0:0:0:0 0/1:40:40.33:-7,-3,-8:110:98:11:97:10:44:0:0:53:10:0.093 1 28515659 1971_1 N N]19:24027918] 194.49 . SVTYPE=BND;STRANDS=++:12;IMPRECISE;CIPOS=-24,212;CIEND=-30,228;CIPOS95=-4,93;CIEND95=-4,73;MATEID=1971_2;EVENT=1971;SU=12;PE=12;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:162:0:-0,-16,-54:56:55:0:54:0:23:0:0:31:0:0 0/1:194:194.49:-27,-8,-47:76:61:14:61:14:0:0:0:61:14:0.19 1 42552553 1942_1 N N[4:44842163[ 59.54 . SVTYPE=BND;STRANDS=+-:7;IMPRECISE;CIPOS=-15,285;CIEND=-238,29;CIPOS95=-1,137;CIEND95=-86,5;MATEID=1942_2;EVENT=1942;SU=7;PE=7;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:57:0:-3,-9,-34:40:37:2:37:2:0:0:0:37:2:0.051 0/1:59:59.54:-16,-10,-51:71:61:9:61:9:0:0:0:61:9:0.13 1 43694066 15 N <DEL> 353.17 . SVTYPE=DEL;SVLEN=-1472;END=43695538;STRANDS=+-:26;IMPRECISE;CIPOS=-30,203;CIEND=-202,29;CIPOS95=-7,39;CIEND95=-55,4;SU=26;PE=26;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:60:0:-5,-11,-43:52:48:4:47:3:23:0:1:24:2:0.06 0/1:200:353.17:-47,-11,-74:124:99:24:98:24:47:0:2:51:22:0.2 1 44059282 17_1 N N]1:44059890] 50.66 . SVTYPE=BND;STRANDS=++:11;IMPRECISE;CIPOS=-30,193;CIEND=-30,225;CIPOS95=-7,65;CIEND95=-4,94;MATEID=17_2;EVENT=17;SU=11;PE=11;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:36:0:-3,-7,-27:33:30:2:30:2:0:0:0:30:2:0.062 0/1:50:50.65:-13,-8,-38:54:46:7:46:7:0:0:0:46:7:0.13 1 44059890 17_2 N N]1:44059282] 50.66 . SVTYPE=BND;STRANDS=++:11;IMPRECISE;CIPOS=-30,225;CIEND=-30,193;CIPOS95=-4,94;CIEND95=-7,65;MATEID=17_1;EVENT=17;SECONDARY;SU=11;PE=11;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:36:0:-3,-7,-27:33:30:2:30:2:0:0:0:30:2:0.062 0/1:50:50.65:-13,-8,-38:54:46:7:46:7:0:0:0:46:7:0.13 1 64897140 1952_1 N [6:159204434[N 35.75 . SVTYPE=BND;STRANDS=--:6;IMPRECISE;CIPOS=-289,21;CIEND=-250,29;CIPOS95=-137,3;CIEND95=-106,5;MATEID=1952_2;EVENT=1952;SU=6;PE=6;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:75:0:-0,-8,-25:27:26:0:25:0:9:0:0:16:0:0 0/1:35:35.75:-9,-6,-28:39:33:5:33:5:0:0:0:33:5:0.13 1 66804423 1961_1 N [13:59377693[N 23.75 . SVTYPE=BND;STRANDS=--:6;IMPRECISE;CIPOS=-294,16;CIEND=-240,29;CIPOS95=-142,1;CIEND95=-83,5;MATEID=1961_2;EVENT=1961;SU=6;PE=6;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:12:0.25:-5,-6,-27:35:31:3:31:3:0:0:0:31:3:0.088 0/1:23:23.49:-16,-13,-62:83:73:9:73:9:0:0:0:73:9:0.11 1 80221789 47 N <DEL> 116.67 . SVTYPE=DEL;SVLEN=-1243;END=80223032;STRANDS=+-:12;IMPRECISE;CIPOS=-30,178;CIEND=-194,29;CIPOS95=-5,42;CIEND95=-47,8;SU=12;PE=12;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:24:0.02:-5,-8,-31:40:36:4:35:3:13:0:0:22:3:0.079 0/1:116:116.66:-18,-6,-33:52:42:9:42:9:0:0:0:42:9:0.18 1 80794627 48_1 N [1:80795137[N 41.32 . SVTYPE=BND;STRANDS=--:17;IMPRECISE;CIPOS=-193,21;CIEND=-179,21;CIPOS95=-79,2;CIEND95=-65,2;MATEID=48_2;EVENT=48;SU=17;PE=17;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:45:0:-5,-9,-38:46:42:3:42:3:0:0:0:42:3:0.067 0/1:41:41.32:-21,-17,-79:107:94:12:94:12:0:0:0:94:12:0.11 1 80795137 48_2 N [1:80794627[N 41.32 . SVTYPE=BND;STRANDS=--:17;IMPRECISE;CIPOS=-179,21;CIEND=-193,21;CIPOS95=-65,2;CIEND95=-79,2;MATEID=48_1;EVENT=48;SECONDARY;SU=17;PE=17;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:45:0:-5,-9,-38:46:42:3:42:3:0:0:0:42:3:0.067 0/1:41:41.32:-21,-17,-79:107:94:12:94:12:0:0:0:94:12:0.11 1 91151631 1956_1 N N[8:85437297[ 53.53 . SVTYPE=BND;STRANDS=+-:10;IMPRECISE;CIPOS=-25,239;CIEND=-237,25;CIPOS95=-3,111;CIEND95=-101,2;MATEID=1956_2;EVENT=1956;SU=10;PE=10;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:171:0:-0,-17,-57:59:58:0:57:0:30:0:0:27:0:0 0/1:53:53.53:-16,-11,-52:73:63:9:63:9:0:0:0:63:9:0.12 1 92232065 60 N <DEL> 35.11 . SVTYPE=DEL;SVLEN=-1297;END=92233362;STRANDS=+-:17;IMPRECISE;CIPOS=-30,298;CIEND=-197,15;CIPOS95=-4,80;CIEND95=-82,4;SU=17;PE=17;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:69:0:-5,-12,-46:55:51:3:50:3:24:0:1:26:2:0.057 0/1:35:35.11:-25,-22,-104:140:124:15:123:15:66:0:2:57:13:0.11 1 105428633 1954_1 N N[7:93357413[ 104.7 . SVTYPE=BND;STRANDS=+-:9;IMPRECISE;CIPOS=-21,258;CIEND=-225,29;CIPOS95=-2,129;CIEND95=-93,4;MATEID=1954_2;EVENT=1954;SU=9;PE=9;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:102:0:-0,-10,-34:36:35:0:34:0:16:0:0:18:0:0 0/1:104:104.7:-16,-5,-29:46:37:8:37:8:0:0:0:37:8:0.18 1 119401195 1963_1 N N[15:51189306[ 41.32 . SVTYPE=BND;STRANDS=+-:14;IMPRECISE;CIPOS=-30,271;CIEND=-192,29;CIPOS95=-3,87;CIEND95=-71,6;MATEID=1963_2;EVENT=1963;SU=14;PE=14;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:60:0:-5,-11,-43:51:47:3:47:3:0:0:0:47:3:0.06 0/1:41:41.32:-21,-17,-79:107:94:12:94:12:0:0:0:94:12:0.11 1 168024578 1972_1 N ]19:24033135]N 4.57 . SVTYPE=BND;STRANDS=-+:8;IMPRECISE;CIPOS=-274,18;CIEND=-30,210;CIPOS95=-129,2;CIEND95=-6,75;MATEID=1972_2;EVENT=1972;SU=8;PE=8;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:27:0.01:-2,-4,-17:20:18:1:18:1:0:0:0:18:1:0.053 0/1:2:4.56:-9,-8,-38:50:44:5:44:5:0:0:0:44:5:0.1 1 221827800 1962_1 N N[13:61315891[ 53.72 . SVTYPE=BND;STRANDS=+-:6;IMPRECISE;CIPOS=-30,271;CIEND=-349,29;CIPOS95=-3,117;CIEND95=-139,3;MATEID=1962_2;EVENT=1962;SU=6;PE=6;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:81:0:-0,-8,-27:28:28:0:27:0:14:0:0:13:0:0 0/1:53:53.72:-11,-6,-30:43:36:6:36:6:0:0:0:36:6:0.14 1 234805693 1969_1 N N[16:59323740[ 20.7 . SVTYPE=BND;STRANDS=+-:7;IMPRECISE;CIPOS=-30,282;CIEND=-347,29;CIPOS95=-4,98;CIEND95=-138,1;MATEID=1969_2;EVENT=1969;SU=7;PE=7;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:138:0:-0,-14,-46:47:47:0:46:0:24:0:0:22:0:0 0/1:20:20.7:-11,-9,-40:54:47:6:47:6:0:0:0:47:6:0.11 2 12019022 1982_1 N N]7:52399206] 14.67 . SVTYPE=BND;STRANDS=++:9;IMPRECISE;CIPOS=-30,221;CIEND=-19,261;CIPOS95=-2,91;CIEND95=-2,131;MATEID=1982_2;EVENT=1982;SU=9;PE=9;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:200:0:-0,-24,-80:81:81:0:80:0:41:0:0:39:0:0 0/1:14:14.67:-14,-12,-57:76:67:8:67:8:0:0:0:67:8:0.11 2 18118870 172 N <DEL> 233.63 . 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