Mercurial > repos > artbio > lumpy_smoove

comparison test-data/result-1.vcf @ 3:65b400409455 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
author artbio
date Wed, 26 Aug 2020 12:24:07 -0400
parents ee8fc44b1655
children b4dec06d8fc6
comparison
equal deleted inserted replaced
2:49a8a327cc72 3:65b400409455
1 ##fileformat=VCFv4.2 1 ##fileformat=VCFv4.2
2 ##contig=<ID=chrI,length=15072434> 2 ##FILTER=<ID=PASS,Description="All filters passed">
3 ##smoove_version=0.2.5 3 ##fileDate=20200826
4 ##reference=reference.fa 4 ##reference=reference.fa
5 ##smoove_count_stats=tumor:2531,2421,134,276
6 ##smoove_count_stats=normal:2869,2691,194,304
7 ##source=LUMPY
8 ##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">
9 ##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">
10 ##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">
11 ##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:++/--)">
12 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> 9 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
20 ##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples"> 17 ##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
21 ##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples"> 18 ##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
22 ##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples"> 19 ##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
23 ##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples"> 20 ##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples">
24 ##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call"> 21 ##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
25 ##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend">
26 ##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend">
27 ##ALT=<ID=DEL,Description="Deletion"> 22 ##ALT=<ID=DEL,Description="Deletion">
28 ##ALT=<ID=DUP,Description="Duplication"> 23 ##ALT=<ID=DUP,Description="Duplication">
29 ##ALT=<ID=INV,Description="Inversion"> 24 ##ALT=<ID=INV,Description="Inversion">
30 ##ALT=<ID=DUP:TANDEM,Description="Tandem duplication"> 25 ##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
31 ##ALT=<ID=INS,Description="Insertion of novel sequence"> 26 ##ALT=<ID=INS,Description="Insertion of novel sequence">
33 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 28 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
34 ##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant"> 29 ##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
35 ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant"> 30 ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
36 ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant"> 31 ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
37 ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant"> 32 ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant">
38 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal tumor 33 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
39 chrI 10416569 1 N <DUP> . . SVTYPE=DUP;STRANDS=-+:4;SVLEN=981;END=10417550;CIPOS=-769,29;CIEND=-30,636;CIPOS95=-165,8;CIEND95=-9,128;IMPRECISE;SU=4;PE=4;SR=0 GT:SU:PE:SR ./.:4:4:0 ./.:0:0:0 34 ##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample">
35 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
36 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
37 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
38 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
39 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations">
40 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations">
41 ##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference 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">
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">
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>
48 ##smoove_version=0.2.5
49 ##smoove_count_stats=celegans-2:2531,2421,134,276
50 ##smoove_count_stats=celegans-1:2869,2691,194,304
51 ##source=LUMPY
52 ##bcftools_annotateVersion=1.10.2+htslib-1.10.2
53 ##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Aug 26 16:53:42 2020
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">
56 ##bcftools_viewVersion=1.10.2+htslib-1.10.2
57 ##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Aug 26 16:53:42 2020
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