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view test-data/output_extended.vcf @ 5:6ae3a402b9af draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv commit e1bfc70a74f12ef8182d9afa0b3ab69d620fb3a8"
author artbio
date Sun, 24 May 2020 18:48:46 -0400
parents 796552c157de
children 48e97429a749
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line source

##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	sr_input_bam
	Evidence:	M00860:26:000000000-A6UGV:1:1101:22421:6659_2	hg38_gold_U07000.1	8	50	hg38_gold_U07000.1	1885	1932	0x17456f0	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:21503:6234_2	hg38_gold_U07000.1	13	52	hg38_gold_U07000.1	1885	1933	0x17451d0	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:14108:4338_2	hg38_gold_U07000.1	8	53	hg38_gold_U07000.1	1879	1932	0x1747410	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:22281:3587_2	hg38_gold_U07000.1	8	52	hg38_gold_U07000.1	1879	1944	0x174d920	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:9129:3504_2	hg38_gold_U07000.1	13	50	hg38_gold_U07000.1	1872	1932	0x1748e60	0	+	-	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:10154:5887_2	hg38_gold_U07000.1	10	41	hg38_gold_U07000.1	1872	1931	0x17499d0	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:9382:5932_2	hg38_gold_U07000.1	8	53	hg38_gold_U07000.1	1871	1921	0x174d580	0	+	-	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:22747:6442_2	hg38_gold_U07000.1	8	52	hg38_gold_U07000.1	1870	1933	0x1748cc0	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:6411:6050_2	hg38_gold_U07000.1	13	49	hg38_gold_U07000.1	1868	1932	0x17486a0	0	+	-	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:23865:5544_2	hg38_gold_U07000.1	13	56	hg38_gold_U07000.1	1868	1923	0x1748480	0	+	-	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:20349:5252_2	hg38_gold_U07000.1	13	51	hg38_gold_U07000.1	1868	1931	0x174ce80	0	+	-	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:22571:4203_2	hg38_gold_U07000.1	13	50	hg38_gold_U07000.1	1868	1926	0x1745050	0	+	-	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:16719:4051_2	hg38_gold_U07000.1	8	51	hg38_gold_U07000.1	1868	1932	0x1747b70	0	+	-	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:8961:3182_2	hg38_gold_U07000.1	15	51	hg38_gold_U07000.1	1868	1917	0x1744130	0	+	-	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:18427:2937_2	hg38_gold_U07000.1	8	41	hg38_gold_U07000.1	1868	1932	0x174b760	0	+	-	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:21139:5913_2	hg38_gold_U07000.1	12	50	hg38_gold_U07000.1	1868	1924	0x174d640	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:10523:5853_2	hg38_gold_U07000.1	8	50	hg38_gold_U07000.1	1868	1935	0x174de60	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:16433:5445_2	hg38_gold_U07000.1	13	51	hg38_gold_U07000.1	1868	1932	0x174d870	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:12490:4165_2	hg38_gold_U07000.1	13	58	hg38_gold_U07000.1	1868	1917	0x174d9f0	0	-	+	id:1	weight:1
hg38_gold_U07000.1	14	1_1	N	[hg38_gold_U07000.1:1876[N	.	.	SVTYPE=BND;STRANDS=--:19;EVENT=1;MATEID=1_2;CIPOS=0,0;CIEND=0,2;CIPOS95=0,0;CIEND95=0,0;SU=19;SR=19;PRPOS=1;PREND=0.99996,3.98091e-05,1.58483e-09	GT:SU:SR	./.:19:19
hg38_gold_U07000.1	1876	1_2	N	[hg38_gold_U07000.1:14[N	.	.	SVTYPE=BND;STRANDS=--:19;SECONDARY;EVENT=1;MATEID=1_1;CIPOS=0,2;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=19;SR=19;PRPOS=0.99996,3.98091e-05,1.58483e-09;PREND=1	GT:SU:SR	./.:19:19
	Evidence:	M00860:26:000000000-A6UGV:1:1101:7043:5583_2	hg38_gold_U07000.1	13	56	hg38_gold_U07000.1	1899	1935	0x1742010	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:19472:2185_2	hg38_gold_U07000.1	0	56	hg38_gold_U07000.1	1898	1945	0x1744270	0	+	-	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:9324:6462_2	hg38_gold_U07000.1	0	51	hg38_gold_U07000.1	1898	1933	0x1748fd0	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:23764:6273_2	hg38_gold_U07000.1	13	48	hg38_gold_U07000.1	1898	1945	0x17490a0	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:7772:5906_2	hg38_gold_U07000.1	0	54	hg38_gold_U07000.1	1898	1942	0x1747240	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:6971:4906_2	hg38_gold_U07000.1	13	51	hg38_gold_U07000.1	1898	1935	0x1746170	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:10511:4776_2	hg38_gold_U07000.1	8	50	hg38_gold_U07000.1	1898	1934	0x174a840	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:19677:3538_2	hg38_gold_U07000.1	13	51	hg38_gold_U07000.1	1898	1940	0x174c190	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:22109:4922_2	hg38_gold_U07000.1	13	53	hg38_gold_U07000.1	1897	1933	0x1743ac0	0	+	-	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:14027:4470_2	hg38_gold_U07000.1	0	51	hg38_gold_U07000.1	1896	1933	0x174b500	0	+	-	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:22736:5607_2	hg38_gold_U07000.1	13	57	hg38_gold_U07000.1	1893	1945	0x174cf30	0	+	-	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:10768:5508_2	hg38_gold_U07000.1	13	56	hg38_gold_U07000.1	1893	1935	0x17480b0	0	+	-	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:14449:3437_2	hg38_gold_U07000.1	13	48	hg38_gold_U07000.1	1893	1933	0x174b150	0	+	-	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:18009:3360_2	hg38_gold_U07000.1	13	47	hg38_gold_U07000.1	1893	1925	0x1749390	0	+	-	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:16615:6513_2	hg38_gold_U07000.1	13	51	hg38_gold_U07000.1	1893	1931	0x174b860	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:19235:5076_2	hg38_gold_U07000.1	13	45	hg38_gold_U07000.1	1893	1932	0x174a790	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:14629:4828_2	hg38_gold_U07000.1	8	50	hg38_gold_U07000.1	1893	1932	0x174b360	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:22780:4994_2	hg38_gold_U07000.1	13	50	hg38_gold_U07000.1	1892	1924	0x174aaf0	0	-	+	id:1	weight:1
	Evidence:	M00860:26:000000000-A6UGV:1:1101:12387:3929_2	hg38_gold_U07000.1	13	51	hg38_gold_U07000.1	1892	1931	0x174c000	0	-	+	id:1	weight:1
hg38_gold_U07000.1	10	2_1	N	[hg38_gold_U07000.1:1897[N	.	.	SVTYPE=BND;STRANDS=--:19;EVENT=2;MATEID=2_2;CIPOS=-1,0;CIEND=-7,5;CIPOS95=0,1;CIEND95=-2,1;IMPRECISE;SU=19;SR=19;PRPOS=9.99999e-13,9.99999e-07;PREND=4.89496e-31,1.94872e-23,7.75799e-16,3.08851e-08,0.0308851,0.0775799,0.194872,0.489496,0.194872,0.0122956,1.94872e-09,4.89496e-17,1.22956e-24	GT:SU:SR	./.:19:19
hg38_gold_U07000.1	1897	2_2	N	[hg38_gold_U07000.1:10[N	.	.	SVTYPE=BND;STRANDS=--:19;SECONDARY;EVENT=2;MATEID=2_1;CIPOS=-7,5;CIEND=-1,0;CIPOS95=-2,1;CIEND95=0,1;IMPRECISE;SU=19;SR=19;PRPOS=4.89496e-31,1.94872e-23,7.75799e-16,3.08851e-08,0.0308851,0.0775799,0.194872,0.489496,0.194872,0.0122956,1.94872e-09,4.89496e-17,1.22956e-24;PREND=9.99999e-13,9.99999e-07	GT:SU:SR	./.:19:19