annotate test-data/lumpy-test1.vcf @ 11:1adcc5678f70 draft default tip

planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 313a08616ebe4dea93d3e88d4e2a6f66ec920bf8

##fileformat=VCFv4.2
##source=LUMPY
##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">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants">
##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants">
##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants">
##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples">
##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend">
##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
##ALT=<ID=INS,Description="Insertion of novel sequence">
##ALT=<ID=CNV,Description="Copy number variable region">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	JSS-Vmut-01__Read	JSS-Vmut-12__Read	JSS-Vmut-14__Read
NC_009016.1	1417	1_1	N	[NC_009016.1:19752[N	.	.	SVTYPE=BND;STRANDS=--:5;EVENT=1;MATEID=1_2;CIPOS=-128,9;CIEND=-291,9;CIPOS95=-92,2;CIEND95=-121,2;IMPRECISE;SU=5;PE=5;SR=0	GT:SU:PE:SR	./.:1:1:0	./.:4:4:0	./.:0:0:0
NC_009016.1	19752	1_2	N	[NC_009016.1:1417[N	.	.	SVTYPE=BND;STRANDS=--:5;SECONDARY;EVENT=1;MATEID=1_1;CIPOS=-291,9;CIEND=-128,9;CIPOS95=-121,2;CIEND95=-92,2;IMPRECISE;SU=5;PE=5;SR=0	GT:SU:PE:SR	./.:1:1:0	./.:4:4:0	./.:0:0:0
NC_009016.1	10	2	N	<DUP>	.	.	SVTYPE=DUP;STRANDS=-+:350;SVLEN=38187;END=38197;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=350;PE=249;SR=101	GT:SU:PE:SR	./.:84:46:38	./.:162:123:39	./.:104:80:24