view 2.4/src/temp/s_Test.vcf @ 13:e3609c8714fb draft

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date Fri, 30 May 2014 03:37:55 -0400
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##fileformat=VCFv4.1
##fileDate=2014-05-15 12:08:09
##source=SoftSearch.pl
##reference=chr1.small.fa
##Usage= SoftSearch.pl -l 5 -q 20 -r 5 -d 300 -m 5 -u 0 -s 6 -b Small_test.bam -f chr1.small.fa -o s_Test.vcf
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
##INFO=<ID=ISIZE,Number=.,Type=String,Description="Size of the SV">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##FORMAT=<ID=lSC,Number=1,Type=Integer,Description="Length of the longest soft clips supporting the BND">
##FORMAT=<ID=nSC,Number=1,Type=Integer,Description="Number of supporting soft-clips">
##FORMAT=<ID=uRP,Number=1,Type=Integer,Description="Number of unmated read pairs nearby Soft-Clips">
##FORMAT=<ID=levD_local,Number=1,Type=Float,Description="Levenstein distance between soft-clipped bases and the area around the original soft-clipped site">
##FORMAT=<ID=levD_distl,Number=1,Type=Float,Description="Levenstein distance between the soft-clipped bases and mate location">
##FORMAT=<ID=CTX,Number=1,Type=Integer,Description="Number of chromosomal translocations">
##FORMAT=<ID=DEL,Number=1,Type=Integer,Description="Number of reads supporting Large Deletions">
##FORMAT=<ID=INS,Number=1,Type=Integer,Description="Number of reads supporting Large insertions">
##FORMAT=<ID=NOV_INS,Number=1,Type=Integer,Description="Number of reads supporting novel sequence insertion">
##FORMAT=<ID=TDUP,Number=1,Type=Integer,Description="Number of reads supporting a tandem duplication">
##FORMAT=<ID=INV,Number=1,Type=Integer,Description="Number of reads supporting inversions">
##FORMAT=<ID=sDEL,Number=1,Type=Integer,Description="Number of reads supporting novel sequence insertion">
##INFO=<ID=NO_MATE_SC,Number=1,Type=Flag,Description="When there is no softclipping of the mate read location, an appromiate position is used">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Dummy value for maintaining VCF-Spec">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	s_Test
chr1	524004	BND_yyivkoxn	T	T[chr1:525966[	2.56	PASS	SVTYPE=BND;EVENT=DEL;END=525966;ISIZE=1962;MATEID=BND_xxqonpqo	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:2:16:0:0:0:0:0:0:0:0	
chr1	525966	BND_xxqonpqo	G	]chr1:524004]G	2.56	PASS	SVTYPE=BND;EVENT=DEL;END=524004;ISIZE=1962;MATEID=BND_yyivkoxn	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:2:16:0:0:0:0:31:7:0:0.39	
chr1	773527	BND_fhfdoayv	T	A[chr1:773527[	1000.00	PASS	SVTYPE=BND;EVENT=INV;END=781565;ISIZE=8038;MATEID=BND_wgzrxsyj	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:1:0:0:67:6:0:0:0:0:0	
chr1	773527	BND_ogxdwnot	T	T[chr1:773527[	1000.00	PASS	SVTYPE=BND;EVENT=INV;END=781624;ISIZE=8097;MATEID=BND_hrknrygd	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:1:0:0:60:4:0:0:0:0:0	
chr1	773904	BND_qtchcfsd	G	]chr1:773904]G	2.43	PASS	SVTYPE=BND;EVENT=INV;END=781564;ISIZE=7660;MATEID=BND_ilxfwbvc	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:19:0:0:76:6:0:32:11:6:0.41	
chr1	773907	BND_pudmiiuj	C	]chr1:773907]T	4.74	PASS	SVTYPE=BND;EVENT=INV;END=781107;ISIZE=7200;MATEID=BND_wvjtpogz	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:19:0:0:100:12:0:33:7:12:0.21	
chr1	773928	BND_tonkbaqx	C	A[chr1:773928[	16.39	PASS	SVTYPE=BND;EVENT=INV;END=781562;ISIZE=7634;MATEID=BND_nyshzixi	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:3:0:0:46:5:0:0:0:0:0	
chr1	773963	BND_znjagoaw	T	]chr1:773963]G	2.77	PASS	SVTYPE=BND;EVENT=INV;END=781564;ISIZE=7601;MATEID=BND_bpepyyyk	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:19:0:0:76:6:0:36:10:6:0.36	
chr1	773967	BND_npgkjvzf	C	]chr1:773967]T	1000.00	PASS	SVTYPE=BND;EVENT=INV;END=781107;ISIZE=7140;MATEID=BND_vxbakedf	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:18:0:0:95:8:0:18:5:8:0.00	
chr1	781107	BND_vxbakedf	T	C[chr1:781107[	1000.00	PASS	SVTYPE=BND;EVENT=INV;END=773967;ISIZE=7140;MATEID=BND_npgkjvzf	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:18:0:0:95:8:0:0:0:0:0	
chr1	781107	BND_wvjtpogz	T	C[chr1:781107[	4.74	PASS	SVTYPE=BND;EVENT=INV;END=773907;ISIZE=7200;MATEID=BND_pudmiiuj	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:19:0:0:100:12:0:0:0:0:0	
chr1	781562	BND_nyshzixi	A	]chr1:781562]C	16.39	PASS	SVTYPE=BND;EVENT=INV;END=773928;ISIZE=7634;MATEID=BND_tonkbaqx	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:3:0:0:46:5:0:17:5:5:0.06	
chr1	781564	BND_bpepyyyk	G	T[chr1:781564[	2.77	PASS	SVTYPE=BND;EVENT=INV;END=773963;ISIZE=7601;MATEID=BND_znjagoaw	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:19:0:0:76:6:0:0:0:0:0	
chr1	781564	BND_ilxfwbvc	G	G[chr1:781564[	2.43	PASS	SVTYPE=BND;EVENT=INV;END=773904;ISIZE=7660;MATEID=BND_qtchcfsd	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:19:0:0:76:6:0:0:0:0:0	
chr1	781565	BND_wgzrxsyj	A	]chr1:781565]T	1000.00	PASS	SVTYPE=BND;EVENT=INV;END=773527;ISIZE=8038;MATEID=BND_fhfdoayv	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:1:0:0:67:6:0:34:12:6:0.00	
chr1	781624	BND_hrknrygd	T	]chr1:781624]T	1000.00	PASS	SVTYPE=BND;EVENT=INV;END=773527;ISIZE=8097;MATEID=BND_ogxdwnot	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:1:0:0:60:4:0:24:12:4:0.00	
chr1	813168	BND_qsyqdonc	G	G[chr1:813168[	1000.00	PASS	SVTYPE=BND;EVENT=INV;END=816792;ISIZE=3624;MATEID=BND_gicbelss	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:1:0:0:49:5:0:0:0:0:0	
chr1	813648	BND_jqgpjekt	G	G[chr1:813648[	2.49	PASS	SVTYPE=BND;EVENT=INV;END=816790;ISIZE=3142;MATEID=BND_mkjhthlc	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:0:0:56:7:0:0:0:0:0	
chr1	813648	BND_mqakrsii	G	]chr1:813648]T	1000.00	PASS	SVTYPE=BND;EVENT=INV;END=816343;ISIZE=2695;MATEID=BND_flkhmdiv	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:0:0:44:3:0:18:10:3:0.00	
chr1	816343	BND_flkhmdiv	T	G[chr1:816343[	1000.00	PASS	SVTYPE=BND;EVENT=INV;END=813648;ISIZE=2695;MATEID=BND_mqakrsii	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:0:0:44:3:0:0:0:0:0	
chr1	816790	BND_mkjhthlc	G	]chr1:816790]G	2.49	PASS	SVTYPE=BND;EVENT=INV;END=813648;ISIZE=3142;MATEID=BND_jqgpjekt	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:0:0:56:7:0:40:10:7:0.40	
chr1	816792	BND_gicbelss	G	]chr1:816792]G	1000.00	PASS	SVTYPE=BND;EVENT=INV;END=813168;ISIZE=3624;MATEID=BND_qsyqdonc	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:1:0:0:49:5:0:33:16:5:0.00	
chr1	854784	BND_pkqgmhxz	G	G[chr1:863640[	2.93	PASS	SVTYPE=BND;EVENT=DEL;END=863640;ISIZE=8856;MATEID=BND_eyaojldp	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:98:0:0:9:0:0:0:0:0	
chr1	854784	BND_vlxitdno	G	G[chr1:863642[	4.52	PASS	SVTYPE=BND;EVENT=DEL;END=863642;ISIZE=8858;MATEID=BND_bmvwcown	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:99:0:0:9:0:0:0:0:0	
chr1	855228	BND_qjfgagwf	C	]chr1:863644]C	2.49	PASS	SVTYPE=BND;EVENT=DEL;END=863644;ISIZE=8416;MATEID=BND_zjggijxo	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:104:0:0:8:0:30:18:8:0.40	
chr1	863640	BND_eyaojldp	C	]chr1:854784]C	2.93	PASS	SVTYPE=BND;EVENT=DEL;END=854784;ISIZE=8856;MATEID=BND_pkqgmhxz	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:98:0:0:9:0:35:10:9:0.34	
chr1	863642	BND_bmvwcown	G	]chr1:854784]G	4.52	PASS	SVTYPE=BND;EVENT=DEL;END=854784;ISIZE=8858;MATEID=BND_vlxitdno	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:99:0:0:9:0:18:6:9:0.22	
chr1	863644	BND_zjggijxo	T	T[chr1:855228[	2.49	PASS	SVTYPE=BND;EVENT=DEL;END=855228;ISIZE=8416;MATEID=BND_qjfgagwf	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:104:0:0:8:0:0:0:0:0	
chr1	903148	BND_jqxbndcc	G	C[chr1:903148[	1000.00	PASS	SVTYPE=BND;EVENT=INV;END=915991;ISIZE=12843;MATEID=BND_aveewewc	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:0:0:64:3:0:0:0:0:0	
chr1	903615	BND_fsafnyyz	T	]chr1:903615]C	3.12	PASS	SVTYPE=BND;EVENT=INV;END=915991;ISIZE=12376;MATEID=BND_uuhsrkwh	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:0:0:60:11:0:19:7:11:0.32	
chr1	903617	BND_peaqkjha	C	]chr1:903617]C	1000.00	PASS	SVTYPE=BND;EVENT=INV;END=915564;ISIZE=11947;MATEID=BND_dxtofeax	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:0:0:64:4:0:29:14:4:0.00	
chr1	903617	BND_veysrihm	C	G[chr1:903617[	3.83	PASS	SVTYPE=BND;EVENT=INV;END=915989;ISIZE=12372;MATEID=BND_yvvvrmzs	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:0:0:61:7:0:0:0:0:0	
chr1	915564	BND_dxtofeax	C	C[chr1:915564[	1000.00	PASS	SVTYPE=BND;EVENT=INV;END=903617;ISIZE=11947;MATEID=BND_peaqkjha	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:0:0:64:4:0:0:0:0:0	
chr1	915989	BND_yvvvrmzs	G	]chr1:915989]C	3.83	PASS	SVTYPE=BND;EVENT=INV;END=903617;ISIZE=12372;MATEID=BND_veysrihm	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:0:0:61:7:0:23:7:7:0.26	
chr1	915991	BND_aveewewc	C	]chr1:915991]G	1000.00	PASS	SVTYPE=BND;EVENT=INV;END=903148;ISIZE=12843;MATEID=BND_jqxbndcc	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:0:0:64:3:0:42:14:3:0.00	
chr1	915991	BND_uuhsrkwh	C	T[chr1:915991[	3.12	PASS	SVTYPE=BND;EVENT=INV;END=903615;ISIZE=12376;MATEID=BND_fsafnyyz	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:0:0:60:11:0:0:0:0:0	
chr1	937624	BND_ihjevxqn	A	T[chr1:937624[	1000.00	PASS	SVTYPE=BND;EVENT=INV;END=958311;ISIZE=20687;MATEID=BND_mkxueciv	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:0:0:52:3:0:0:0:0:0	
chr1	938004	BND_jritmtfi	T	]chr1:938004]A	4.98	PASS	SVTYPE=BND;EVENT=INV;END=958308;ISIZE=20304;MATEID=BND_ytttwmfe	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:0:0:59:7:0:10:5:7:0.20	
chr1	938006	BND_ipkrlpfe	A	G[chr1:938006[	3.98	PASS	SVTYPE=BND;EVENT=INV;END=958306;ISIZE=20300;MATEID=BND_khfaewsn	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:0:0:59:4:0:0:0:0:0	
chr1	958306	BND_khfaewsn	G	]chr1:958306]A	3.98	PASS	SVTYPE=BND;EVENT=INV;END=938006;ISIZE=20300;MATEID=BND_ipkrlpfe	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:0:0:59:4:0:40:10:4:0.25	
chr1	958308	BND_ytttwmfe	A	T[chr1:958308[	4.98	PASS	SVTYPE=BND;EVENT=INV;END=938004;ISIZE=20304;MATEID=BND_jritmtfi	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:0:0:59:7:0:0:0:0:0	
chr1	958311	BND_mkxueciv	T	]chr1:958311]A	1000.00	PASS	SVTYPE=BND;EVENT=INV;END=937624;ISIZE=20687;MATEID=BND_ihjevxqn	GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD	0/1:0:0:0:52:3:0:35:11:3:0.00