Mercurial > repos > artbio > lumpy_smoove

comparison test-data/result-4.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 b4dec06d8fc6
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=20210508 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:++/--)">
44 ##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally"> 44 ##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally">
45 ##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally"> 45 ##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally">
46 ##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally"> 46 ##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally">
47 ##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally"> 47 ##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
48 ##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)"> 48 ##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)">
49 ##contig=<ID=chrI,length=15072434> 49 ##contig=<ID=chrI_sub,length=100000>
50 ##smoove_version=0.2.5 50 ##smoove_version=0.2.8
51 ##smoove_count_stats=celegans-2:2531,2421,156,296 51 ##smoove_count_stats=RG1:0,638,0,598
52 ##smoove_count_stats=celegans-1:2869,2691,202,330 52 ##smoove_count_stats=RG2:0,466,0,448
53 ##source=LUMPY 53 ##source=LUMPY
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=1.17+htslib-1.17
57 ##bcftools_viewCommand=view -O z -c 1 -o output-smoove.genotyped.vcf.gz; Date=Sat May 8 19:22:36 2021 57 ##bcftools_viewCommand=view -O z -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Jan 24 19:27:57 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 . 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