Mercurial > repos > artbio > lumpy_smoove

comparison test-data/result-2.vcf @ 10:8711df965d4b draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 355389e3d1b38d93b1bc1c683c25094d5c6f8223
author artbio
date Wed, 24 Jan 2024 19:26:57 +0000
parents 7dcf61950215
children
comparison
equal deleted inserted replaced
9:7dcf61950215 10:8711df965d4b
1 ##fileformat=VCFv4.2 1 ##fileformat=VCFv4.2
2 ##FILTER=<ID=PASS,Description="All filters passed"> 2 ##FILTER=<ID=PASS,Description="All filters passed">
3 ##fileDate=20230405 3 ##fileDate=20240124
4 ##reference=reference.fa 4 ##reference=reference.fa
5 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> 5 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
6 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> 6 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
7 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> 7 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
8 ##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"> 8 ##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
42 ##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally"> 42 ##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally">
43 ##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally"> 43 ##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally">
44 ##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally"> 44 ##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally">
45 ##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally"> 45 ##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
46 ##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)"> 46 ##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)">
47 ##contig=<ID=chrI,length=15072434> 47 ##contig=<ID=chrI_sub,length=100000>
48 ##smoove_version=0.2.8 48 ##smoove_version=0.2.8
49 ##smoove_count_stats=celegans-1:2869,2691,202,330 49 ##smoove_count_stats=RG1:0,638,0,598
50 ##smoove_count_stats=celegans-2:2531,2421,156,296 50 ##smoove_count_stats=RG2:0,466,0,448
51 ##source=LUMPY 51 ##source=LUMPY
52 ##bcftools_annotateVersion=1.16+htslib-1.17 52 ##bcftools_annotateVersion=1.17+htslib-1.17
53 ##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Apr 5 13:40:08 2023 53 ##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Jan 24 19:27:21 2024
54 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> 54 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
55 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> 55 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
56 ##bcftools_viewVersion=1.16+htslib-1.17 56 ##bcftools_viewVersion=1.17+htslib-1.17
57 ##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Apr 5 13:40:08 2023 57 ##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Jan 24 19:27:21 2024
58 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT celegans-1 celegans-2 58 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT RG1 RG2
59 chrI 10416569 1 N <DUP> 170.7 . SVTYPE=DUP;SVLEN=981;END=10417550;STRANDS=-+:4;IMPRECISE;CIPOS=-769,29;CIEND=-30,636;CIPOS95=-165,8;CIEND95=-9,128;SU=4;PE=4;SR=0;AC=4;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:16:130.28:-15,-4,-2:14:4:9:4:9:0:0:0:4:9:0.69 1/1:3:40.43:-4,-1,-1:7:4:3:4:3:0:0:0:4:3:0.43 59 chrI_sub 50007 1 N <DUP> 103.66 . SVTYPE=DUP;SVLEN=1148;END=51155;STRANDS=-+:5;IMPRECISE;CIPOS=0,22;CIEND=-30,331;CIPOS95=0,10;CIEND95=-10,82;SU=5;PE=5;SR=0;AC=4;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:10:74.81:-9,-3,-2:7:1:5:1:5:0:0:0:1:5:0.83 1/1:2:28.84:-3,-1,-1:5:2:2:2:2:0:0:0:2:2:0.5