Mercurial > repos > artbio > lumpy_smoove

annotate test-data/result-6.vcf @ 8:b4dec06d8fc6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
author artbio
date Sun, 09 May 2021 17:09:33 +0000
parents bd4135caa3fa
children 7dcf61950215
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
1 ##fileformat=VCFv4.2
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
2 ##FILTER=<ID=PASS,Description="All filters passed">
8
b4dec06d8fc6 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
artbio
parents: 5
diff changeset
3 ##fileDate=20210508
5
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
4 ##reference=reference.fa
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
5 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
6 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
7 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
8 ##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
9 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
10 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
11 ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
12 ##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
13 ##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
14 ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
15 ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
16 ##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
17 ##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
18 ##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
19 ##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
20 ##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
21 ##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
22 ##ALT=<ID=DEL,Description="Deletion">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
23 ##ALT=<ID=DUP,Description="Duplication">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
24 ##ALT=<ID=INV,Description="Inversion">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
25 ##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
26 ##ALT=<ID=INS,Description="Insertion of novel sequence">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
27 ##ALT=<ID=CNV,Description="Copy number variable region">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
28 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
29 ##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
30 ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
31 ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
32 ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
33 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
34 ##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
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">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
36 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
37 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
38 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
39 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
40 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
41 ##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
42 ##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
43 ##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
44 ##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
45 ##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
46 ##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
47 ##contig=<ID=chrI,length=15072434>
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
48 ##smoove_version=0.2.5
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
49 ##smoove_count_stats=celegans-1:2869,2691,194,304
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
50 ##smoove_count_stats=celegans-2:2531,2421,134,276
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
51 ##source=LUMPY
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
52 ##bcftools_annotateVersion=1.10.2+htslib-1.10.2
8
b4dec06d8fc6 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
artbio
parents: 5
diff changeset
53 ##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Sat May 8 19:19:15 2021
5
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
54 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
55 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
56 ##bcftools_viewVersion=1.10.2+htslib-1.10.2
8
b4dec06d8fc6 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
artbio
parents: 5
diff changeset
57 ##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Sat May 8 19:19:15 2021
5
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
58 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT celegans-1 celegans-2
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents:
diff changeset
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