Mercurial > repos > artbio > lumpy_smoove

comparison test-data/result-1.vcf @ 9:7dcf61950215 draft

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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 b4dec06d8fc6
children 8711df965d4b
comparison
equal deleted inserted replaced
8:b4dec06d8fc6 9:7dcf61950215
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=20210508 3 ##fileDate=20230405
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:++/--)">
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,length=15072434>
48 ##smoove_version=0.2.5 48 ##smoove_version=0.2.8
49 ##smoove_count_stats=celegans-2:2531,2421,134,276
49 ##smoove_count_stats=celegans-1:2869,2691,194,304 50 ##smoove_count_stats=celegans-1:2869,2691,194,304
50 ##smoove_count_stats=celegans-2:2531,2421,134,276
51 ##source=LUMPY 51 ##source=LUMPY
52 ##bcftools_annotateVersion=1.10.2+htslib-1.10.2 52 ##bcftools_annotateVersion=1.16+htslib-1.17
53 ##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Sat May 8 19:20:12 2021 53 ##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Apr 5 16:07:34 2023
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=1.10.2+htslib-1.10.2 56 ##bcftools_viewVersion=1.16+htslib-1.17
57 ##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Sat May 8 19:20:12 2021 57 ##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Apr 5 16:07:34 2023
58 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT celegans-1 celegans-2 58 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT celegans-1 celegans-2
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 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