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comparison test-data/sample.vcf @ 0:477a07f387e0 draft

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"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
author iuc
date Thu, 12 Nov 2020 16:48:15 +0000
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-1:000000000000 0:477a07f387e0
1 ##fileformat=VCFv4.2
2 ##source=LUMPY
3 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
4 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
5 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
6 ##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
7 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
8 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
9 ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
10 ##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants">
11 ##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants">
12 ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
13 ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
14 ##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants">
15 ##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
16 ##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
17 ##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
18 ##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples">
19 ##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
20 ##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend">
21 ##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend">
22 ##ALT=<ID=DEL,Description="Deletion">
23 ##ALT=<ID=DUP,Description="Duplication">
24 ##ALT=<ID=INV,Description="Inversion">
25 ##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
26 ##ALT=<ID=INS,Description="Insertion of novel sequence">
27 ##ALT=<ID=CNV,Description="Copy number variable region">
28 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
29 ##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
30 ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
31 ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
32 ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant">
33 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1
34 chr8 245202 1 N <DEL> . . SVTYPE=DEL;STRANDS=+-:3;SVLEN=-229;END=245431;CIPOS=-10,64;CIEND=-51,9;CIPOS95=-1,33;CIEND95=-22,3;IMPRECISE;SU=3;PE=3 GT:SU:PE ./.:3:3
35 chr8 246846 2 N <DEL> . . SVTYPE=DEL;STRANDS=+-:2;SVLEN=-176;END=247022;CIPOS=-10,186;CIEND=-159,21;CIPOS95=0,137;CIEND95=-95,13;IMPRECISE;SU=2;PE=2 GT:SU:PE ./.:2:2