Mercurial > repos > artbio > lumpy_smoove
diff test-data/result-1.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 | 7dcf61950215 |
| children |
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--- a/test-data/result-1.vcf Wed Apr 05 15:56:13 2023 +0000 +++ b/test-data/result-1.vcf Wed Jan 24 19:26:57 2024 +0000 @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> -##fileDate=20230405 +##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"> @@ -44,16 +44,16 @@ ##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> +##contig=<ID=chrI_sub,length=100000> ##smoove_version=0.2.8 -##smoove_count_stats=celegans-2:2531,2421,134,276 -##smoove_count_stats=celegans-1:2869,2691,194,304 +##smoove_count_stats=RG1:0,638,0,454 +##smoove_count_stats=RG2:0,466,0,362 ##source=LUMPY -##bcftools_annotateVersion=1.16+htslib-1.17 -##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Apr 5 16:07:34 2023 +##bcftools_annotateVersion=1.17+htslib-1.17 +##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Jan 24 19:27:03 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=1.16+htslib-1.17 -##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Apr 5 16:07:34 2023 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT celegans-1 celegans-2 -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 +##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 19:27:03 2024 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT RG1 RG2 +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