Mercurial > repos > artbio > lumpy_smoove
diff test-data/result-5.vcf @ 10:8711df965d4b draft default tip
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 |
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--- a/test-data/result-5.vcf Wed Apr 05 15:56:13 2023 +0000 +++ b/test-data/result-5.vcf Wed Jan 24 19:26:57 2024 +0000 @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> -##fileDate=20210508 +##fileDate=20240124 ##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"> @@ -44,15 +44,15 @@ ##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=chrI,length=15072434> -##smoove_version=0.2.5 -##smoove_count_stats=celegans-1:2869,2691,202,330 +##contig=<ID=chrI_sub,length=100000> +##smoove_version=0.2.8 +##smoove_count_stats=RG1:0,638,0,598 ##source=LUMPY -##bcftools_annotateVersion=1.10.2+htslib-1.10.2 -##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Sat May 8 19:23:15 2021 +##bcftools_annotateVersion=1.17+htslib-1.17 +##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Jan 24 19:28:14 2024 ##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=Sat May 8 19:23:15 2021 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT celegans-1 -chrI 10416569 1 N <DUP> 130.28 . 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=2;AN=2 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 +##bcftools_viewVersion=1.17+htslib-1.17 +##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Jan 24 19:28:14 2024 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT RG1 +chrI_sub 50000 1 N <DUP> 71.54 . SVTYPE=DUP;SVLEN=981;END=50981;STRANDS=-+:4;IMPRECISE;CIPOS=-646,29;CIEND=-30,505;CIPOS95=-164,8;CIEND95=-9,133;SU=4;PE=4;SR=0;AC=2;AN=2 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:8:71.54:-8,-2,-1:9:3:5:3:5:0:0:0:3:5:0.62