Mercurial > repos > iuc > delly_classify
view test-data/call_1.vcf.gz @ 0:d3bc6ec7881f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
| author | iuc |
|---|---|
| date | Fri, 22 Jan 2021 14:33:05 +0000 |
| parents | |
| children |
line wrap: on
line source
##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> ##fileDate=20200728 ##ALT=<ID=DEL,Description="Deletion"> ##ALT=<ID=DUP,Description="Duplication"> ##ALT=<ID=INV,Description="Inversion"> ##ALT=<ID=BND,Description="Translocation"> ##ALT=<ID=INS,Description="Insertion"> ##FILTER=<ID=LowQual,Description="Poor quality and insufficient number of PEs and SRs."> ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="PE confidence interval around END"> ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="PE confidence interval around POS"> ##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for POS2 coordinate in case of an inter-chromosomal translocation"> ##INFO=<ID=POS2,Number=1,Type=Integer,Description="Genomic position for CHR2 in case of an inter-chromosomal translocation"> ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant"> ##INFO=<ID=PE,Number=1,Type=Integer,Description="Paired-end support of the structural variant"> ##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends"> ##INFO=<ID=SRMAPQ,Number=1,Type=Integer,Description="Median mapping quality of split-reads"> ##INFO=<ID=SR,Number=1,Type=Integer,Description="Split-read support"> ##INFO=<ID=SRQ,Number=1,Type=Float,Description="Split-read consensus alignment quality"> ##INFO=<ID=CONSENSUS,Number=1,Type=String,Description="Split-read consensus sequence"> ##INFO=<ID=CE,Number=1,Type=Float,Description="Consensus sequence entropy"> ##INFO=<ID=CT,Number=1,Type=String,Description="Paired-end signature induced connection type"> ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Insertion length for SVTYPE=INS."> ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> ##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation"> ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> ##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV"> ##INFO=<ID=INSLEN,Number=1,Type=Integer,Description="Predicted length of the insertion"> ##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Predicted microhomology length using a max. edit distance of 2"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Log10-scaled genotype likelihoods for RR,RA,AA genotypes"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=FT,Number=1,Type=String,Description="Per-sample genotype filter"> ##FORMAT=<ID=RC,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the SV"> ##FORMAT=<ID=RCL,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the left control region"> ##FORMAT=<ID=RCR,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the right control region"> ##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Read-depth based copy-number estimate for autosomal sites"> ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference pairs"> ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant pairs"> ##FORMAT=<ID=RR,Number=1,Type=Integer,Description="# high-quality reference junction reads"> ##FORMAT=<ID=RV,Number=1,Type=Integer,Description="# high-quality variant junction reads"> ##reference=../data/v1/genome.fasta ##contig=<ID=chr10,length=135534747> ##contig=<ID=chr11,length=135006516> ##contig=<ID=chr11_gl000202_random,length=40103> ##contig=<ID=chr12,length=133851895> ##contig=<ID=chr13,length=115169878> ##contig=<ID=chr14,length=107349540> ##contig=<ID=chr15,length=102531392> ##contig=<ID=chr16,length=90354753> ##contig=<ID=chr17_ctg5_hap1,length=1680828> ##contig=<ID=chr17,length=81195210> ##contig=<ID=chr17_gl000203_random,length=37498> ##contig=<ID=chr17_gl000204_random,length=81310> ##contig=<ID=chr17_gl000205_random,length=174588> ##contig=<ID=chr17_gl000206_random,length=41001> ##contig=<ID=chr18,length=78077248> ##contig=<ID=chr18_gl000207_random,length=4262> ##contig=<ID=chr19,length=59128983> ##contig=<ID=chr19_gl000208_random,length=92689> ##contig=<ID=chr19_gl000209_random,length=159169> ##contig=<ID=chr1,length=249250621> ##contig=<ID=chr1_gl000191_random,length=106433> ##contig=<ID=chr1_gl000192_random,length=547496> ##contig=<ID=chr20,length=63025520> ##contig=<ID=chr21,length=48129895> ##contig=<ID=chr21_gl000210_random,length=27682> ##contig=<ID=chr22,length=51304566> ##contig=<ID=chr2,length=243199373> ##contig=<ID=chr3,length=198022430> ##contig=<ID=chr4_ctg9_hap1,length=590426> ##contig=<ID=chr4,length=191154276> ##contig=<ID=chr4_gl000193_random,length=189789> ##contig=<ID=chr4_gl000194_random,length=191469> ##contig=<ID=chr5,length=180915260> ##contig=<ID=chr6_apd_hap1,length=4622290> ##contig=<ID=chr6_cox_hap2,length=4795371> ##contig=<ID=chr6_dbb_hap3,length=4610396> ##contig=<ID=chr6,length=171115067> ##contig=<ID=chr6_mann_hap4,length=4683263> ##contig=<ID=chr6_mcf_hap5,length=4833398> ##contig=<ID=chr6_qbl_hap6,length=4611984> ##contig=<ID=chr6_ssto_hap7,length=4928567> ##contig=<ID=chr7,length=159138663> ##contig=<ID=chr7_gl000195_random,length=182896> ##contig=<ID=chr8,length=146364022> ##contig=<ID=chr8_gl000196_random,length=38914> ##contig=<ID=chr8_gl000197_random,length=37175> ##contig=<ID=chr9,length=141213431> ##contig=<ID=chr9_gl000198_random,length=90085> ##contig=<ID=chr9_gl000199_random,length=169874> ##contig=<ID=chr9_gl000200_random,length=187035> ##contig=<ID=chr9_gl000201_random,length=36148> ##contig=<ID=chrM,length=16571> ##contig=<ID=chrUn_gl000211,length=166566> ##contig=<ID=chrUn_gl000212,length=186858> ##contig=<ID=chrUn_gl000213,length=164239> ##contig=<ID=chrUn_gl000214,length=137718> ##contig=<ID=chrUn_gl000215,length=172545> ##contig=<ID=chrUn_gl000216,length=172294> ##contig=<ID=chrUn_gl000217,length=172149> ##contig=<ID=chrUn_gl000218,length=161147> ##contig=<ID=chrUn_gl000219,length=179198> ##contig=<ID=chrUn_gl000220,length=161802> ##contig=<ID=chrUn_gl000221,length=155397> ##contig=<ID=chrUn_gl000222,length=186861> ##contig=<ID=chrUn_gl000223,length=180455> ##contig=<ID=chrUn_gl000224,length=179693> ##contig=<ID=chrUn_gl000225,length=211173> ##contig=<ID=chrUn_gl000226,length=15008> ##contig=<ID=chrUn_gl000227,length=128374> ##contig=<ID=chrUn_gl000228,length=129120> ##contig=<ID=chrUn_gl000229,length=19913> ##contig=<ID=chrUn_gl000230,length=43691> ##contig=<ID=chrUn_gl000231,length=27386> ##contig=<ID=chrUn_gl000232,length=40652> ##contig=<ID=chrUn_gl000233,length=45941> ##contig=<ID=chrUn_gl000234,length=40531> ##contig=<ID=chrUn_gl000235,length=34474> ##contig=<ID=chrUn_gl000236,length=41934> ##contig=<ID=chrUn_gl000237,length=45867> ##contig=<ID=chrUn_gl000238,length=39939> ##contig=<ID=chrUn_gl000239,length=33824> ##contig=<ID=chrUn_gl000240,length=41933> ##contig=<ID=chrUn_gl000241,length=42152> ##contig=<ID=chrUn_gl000242,length=43523> ##contig=<ID=chrUn_gl000243,length=43341> ##contig=<ID=chrUn_gl000244,length=39929> ##contig=<ID=chrUn_gl000245,length=36651> ##contig=<ID=chrUn_gl000246,length=38154> ##contig=<ID=chrUn_gl000247,length=36422> ##contig=<ID=chrUn_gl000248,length=39786> ##contig=<ID=chrUn_gl000249,length=38502> ##contig=<ID=chrX,length=155270560> ##contig=<ID=chrY,length=59373566> ##bcftools_viewVersion=1.10.2+htslib-1.10.2 ##bcftools_viewCommand=view -Ov call_1.bcf.gz; Date=Sun Sep 27 02:27:42 2020 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR chr12 132969151 DEL00000000 G <DEL> 107 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=132969179;PE=0;MAPQ=0;CT=3to5;CIPOS=-20,20;CIEND=-20,20;SRMAPQ=41;INSLEN=0;HOMLEN=19;SR=3;SRQ=1;CONSENSUS=CCCCACTCTCCCCCCGGACCCTCCGGCCACCCTGCTCTCCCCCGGGACCCTCCGACCACGTTGCTCTTCCCAGGGTTCTGGCAC;CE=1.70498 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 1/1:-10.3982,-0.901271,0:10:LowQual:28:44:28:2:0:0:0:3 0/1:-11.9941,0,-5.30498:53:PASS:92:160:127:1:0:0:2:4 chr17 40726730 DEL00000001 C <DEL> 133 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=40726765;PE=0;MAPQ=0;CT=3to5;CIPOS=-7,7;CIEND=-7,7;SRMAPQ=50;INSLEN=0;HOMLEN=9;SR=3;SRQ=1;CONSENSUS=CTCTCTCCCTCCTTCCTTCCTTCCTTTTTCCTCCCTCCCTCCCTCTTTCTCCCTCCCTTCCCTCTTTTCCTCTCTTTCTTTCTCTGT;CE=1.07866 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 1/1:-7.79989,-0.601951,0:7:LowQual:31:1:20:0:0:0:0:2 1/1:-6.29935,-0.601408,0:7:LowQual:66:5:34:0:0:0:0:2 chr17 74283142 DEL00000002 C <DEL> 145 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=74283171;PE=0;MAPQ=0;CT=3to5;CIPOS=-18,18;CIEND=-18,18;SRMAPQ=50;INSLEN=0;HOMLEN=18;SR=3;SRQ=1;CONSENSUS=CCCACCCCCTGCCCACACACCACATAACACACACACACACACACGATGGGAGGGACCTAGTTTTTGATGAGAGGTGGGAGGGCAGGGCCAAGCCAG;CE=1.91042 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 1/1:-6.99973,-0.601785,0:7:LowQual:28:89:217:1:0:0:0:2 1/1:-13.3977,-1.20187,0:12:LowQual:28:10:70:0:0:0:0:4 chr17 79612049 DEL00000003 A <DEL> 840 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=79612086;PE=0;MAPQ=0;CT=3to5;CIPOS=-5,5;CIEND=-5,5;SRMAPQ=50;INSLEN=0;HOMLEN=8;SR=17;SRQ=1;CONSENSUS=TTCCTCTTCCCTCTGCAGGAAACTGCAGGCCAGAAGCCCCTCTCTGTGCACAGGGAGGACCAGGCGGAGGCCTGGGGCTGCAGCTGCTGTCCCCCGGAGACCAAGCAC;CE=1.9233 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/1:-34.0593,0,-106.559:10000:PASS:844:1944:1927:1:0:0:30:12 0/1:-235.677,0,-181.078:10000:PASS:1973:3537:4588:1:0:0:54:68 chr5 13830007 DEL00000004 T <DEL> 135 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=13830038;PE=0;MAPQ=0;CT=3to5;CIPOS=-6,6;CIEND=-6,6;SRMAPQ=45;INSLEN=0;HOMLEN=5;SR=3;SRQ=0.987179;CONSENSUS=CTATTCATATGATCTTTGCTTAACACCAAAAGGTTTTCCATTCAAGAAAACAGATGACATATGACCAGGGAGATGCAT;CE=1.93383 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/1:-14.6949,0,-2.59501:26:PASS:67:26:69:0:0:0:1:4 0/1:-3.39797,0,-3.49798:31:PASS:30:37:47:1:0:0:1:1 chr5 74363006 DEL00000005 C <DEL> 350 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=74363047;PE=0;MAPQ=0;CT=3to5;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=50;INSLEN=0;HOMLEN=5;SR=7;SRQ=1;CONSENSUS=AAAGTGGTTTCTTGAGACAAAATCTACTCCTGGTGTGGTGATGTGAACACTTAGATGATAAAGCAGCAGCAGGGTGTAAGAGGATTGACTCCGATTTTCAA;CE=1.95354 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/1:-11.1851,0,-39.1848:112:PASS:382:637:460:2:0:0:11:4 0/1:-12.7889,0,-25.2888:128:PASS:279:415:490:1:0:0:7:4 chr5 75911568 DEL00000006 T <DEL> 745 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=75911598;PE=0;MAPQ=0;CT=3to5;CIPOS=-2,2;CIEND=-2,2;SRMAPQ=50;INSLEN=0;HOMLEN=1;SR=15;SRQ=1;CONSENSUS=TGTCTAATCACTAATGTCTTCCTTCCTGTCTAATCACTGAGTTAAGGGAAAAATAGTCATTTACTAATTCCATTTCCCCATTAAAAGCTATGTCTAAGAAAAAAAATAGTGGAGGCATTATTTAAAAC;CE=1.88992 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/1:-61.5633,0,-65.3615:10000:PASS:779:810:615:1:0:0:20:18 0/1:-39.5838,0,-14.884:149:PASS:357:220:320:1:0:0:5:11 chr5 79865393 DEL00000007 G <DEL> 150 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=79865420;PE=0;MAPQ=0;CT=3to5;CIPOS=-29,29;CIEND=-29,29;SRMAPQ=50;INSLEN=0;HOMLEN=31;SR=3;SRQ=1;CONSENSUS=CTCCTGCTGCCCAGCTGCCGAGGCACCTGCGGAGACGCGCCCAAGTCAGCCCCTCCGACCCGCGCGCTCTTGCGGCCCAGCGCGCGCCGCT;CE=1.74972 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV ./.:0,0,0:0:LowQual:12:0:0:0:0:0:0:0 0/1:-13.9933,0,-8.89295:89:PASS:117:172:133:1:0:0:3:4