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##fileformat=VCFv4.1
##fileDate=2013-03-04 09:59:35
##source=SoftSearch.pl
##reference=chr1.small.fa
##Usage= SoftSearch.pl -l 5 -q 20 -r 5 -d 300 -m 5 -u 0 -s 4 -b Small_test.bam -f chr1.small.fa -o output.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=lSC,Number=1,Type=Integer,Description="Length of the longest soft clips supporting the BND">
##INFO=<ID=nSC,Number=1,Type=Integer,Description="Number of supporting soft-clips">
##INFO=<ID=nRP,Number=1,Type=Integer,Description="Number of read pairs overlapping Soft-Clips">
##INFO=<ID=uRP,Number=1,Type=Integer,Description="Number of unmated read pairs nearby Soft-Clips">
##INFO=<ID=Summary,Number=1,Type=String,Description="Number of each type of variation found">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
chr1	525967	.	BND_krm	]chr1:524013]T	.	PASS	SVTYPE=BND;EVENT=TDUP,15;ISIZE=1954;lSC=39;nSC=7;nRP=15;uRP=0;MATE_ID=BND_bzd;Summary=CTX,1:DEL,0:INS,0:INV,0:TDUP,15:NOV_INS,0	
chr1	524013	.	BND_bzd	T[chr1:525967[	.	PASS	SVTYPE=BND;EVENT=TDUP,15;ISIZE=1954;lSC=39;nSC=7;nRP=15;uRP=0;MATE_ID=BND_krm;Summary=CTX,1:DEL,0:INS,0:INV,0:TDUP,15:NOV_INS,0	
chr1	773905	.	BND_bxl	]chr1:773905]G	.	PASS	SVTYPE=BND;EVENT=INV,39;ISIZE=-7663;lSC=32;nSC=8;nRP=39;uRP=1;MATE_ID=BND_dek;Summary=CTX,10:DEL,0:INS,0:INV,39:TDUP,0:NOV_INS,0	
chr1	781568	.	BND_dek	C[chr1:781568[	.	PASS	SVTYPE=BND;EVENT=INV,39;ISIZE=-7663;lSC=32;nSC=8;nRP=39;uRP=1;MATE_ID=BND_bxl;Summary=CTX,10:DEL,0:INS,0:INV,39:TDUP,0:NOV_INS,0	
chr1	773905	.	BND_qok	]chr1:773905]G	.	PASS	r_SVTYPE=BND;EVENT=INV,93;ISIZE=7663;lSC=14;nSC=7;nRP=93;uRP=12;MATE_ID=BND_epk;Summary=CTX,16:DEL,0:INS,0:INV,93:TDUP,0:NOV_INS,0	
chr1	781568	.	BND_epk	C[chr1:781568[	.	PASS	r_SVTYPE=BND;EVENT=INV,93;ISIZE=7663;lSC=14;nSC=7;nRP=93;uRP=12;MATE_ID=BND_qok;Summary=CTX,16:DEL,0:INS,0:INV,93:TDUP,0:NOV_INS,0	
chr1	773966	.	BND_vej	]chr1:773966]G	.	PASS	SVTYPE=BND;EVENT=INV,39;ISIZE=-7602;lSC=37;nSC=12;nRP=39;uRP=1;MATE_ID=BND_yqd;Summary=CTX,10:DEL,0:INS,0:INV,39:TDUP,0:NOV_INS,0	
chr1	781568	.	BND_yqd	G[chr1:781568[	.	PASS	SVTYPE=BND;EVENT=INV,39;ISIZE=-7602;lSC=37;nSC=12;nRP=39;uRP=1;MATE_ID=BND_vej;Summary=CTX,10:DEL,0:INS,0:INV,39:TDUP,0:NOV_INS,0	
chr1	781562	.	BND_hoa	]chr1:781562]G	.	PASS	r_SVTYPE=BND;EVENT=INV,34;ISIZE=6;lSC=35;nSC=9;nRP=34;uRP=7;MATE_ID=BND_gtg;Summary=CTX,0:DEL,0:INS,0:INV,34:TDUP,0:NOV_INS,0	
chr1	781568	.	BND_gtg	A[chr1:781568[	.	PASS	r_SVTYPE=BND;EVENT=INV,34;ISIZE=6;lSC=35;nSC=9;nRP=34;uRP=7;MATE_ID=BND_hoa;Summary=CTX,0:DEL,0:INS,0:INV,34:TDUP,0:NOV_INS,0	
chr1	781620	.	BND_rbh	]chr1:781620]A	.	PASS	SVTYPE=BND;EVENT=INV,11;ISIZE=7696;lSC=37;nSC=5;nRP=11;uRP=9;MATE_ID=BND_hwz;Summary=CTX,0:DEL,0:INS,0:INV,11:TDUP,0:NOV_INS,0	
chr1	773924	.	BND_hwz	A[chr1:773924[	.	PASS	SVTYPE=BND;EVENT=INV,11;ISIZE=7696;lSC=37;nSC=5;nRP=11;uRP=9;MATE_ID=BND_rbh;Summary=CTX,0:DEL,0:INS,0:INV,11:TDUP,0:NOV_INS,0	
chr1	781620	.	BND_pff	]chr1:781620]A	.	PASS	r_SVTYPE=BND;EVENT=INV,27;ISIZE=-7696;lSC=37;nSC=12;nRP=27;uRP=2;MATE_ID=BND_axj;Summary=CTX,0:DEL,0:INS,0:INV,27:TDUP,0:NOV_INS,0	
chr1	773924	.	BND_axj	A[chr1:773924[	.	PASS	r_SVTYPE=BND;EVENT=INV,27;ISIZE=-7696;lSC=37;nSC=12;nRP=27;uRP=2;MATE_ID=BND_pff;Summary=CTX,0:DEL,0:INS,0:INV,27:TDUP,0:NOV_INS,0	
chr1	813647	.	BND_qzw	]chr1:813647]G	.	PASS	SVTYPE=BND;EVENT=INV,51;ISIZE=-3145;lSC=22;nSC=5;nRP=51;uRP=7;MATE_ID=BND_zle;Summary=CTX,0:DEL,0:INS,0:INV,51:TDUP,0:NOV_INS,0	
chr1	816792	.	BND_zle	T[chr1:816792[	.	PASS	SVTYPE=BND;EVENT=INV,51;ISIZE=-3145;lSC=22;nSC=5;nRP=51;uRP=7;MATE_ID=BND_qzw;Summary=CTX,0:DEL,0:INS,0:INV,51:TDUP,0:NOV_INS,0	
chr1	813647	.	BND_ngc	]chr1:813647]G	.	PASS	r_SVTYPE=BND;EVENT=INV,31;ISIZE=3145;lSC=18;nSC=10;nRP=31;uRP=3;MATE_ID=BND_are;Summary=CTX,0:DEL,0:INS,0:INV,31:TDUP,0:NOV_INS,0	
chr1	816792	.	BND_are	T[chr1:816792[	.	PASS	r_SVTYPE=BND;EVENT=INV,31;ISIZE=3145;lSC=18;nSC=10;nRP=31;uRP=3;MATE_ID=BND_ngc;Summary=CTX,0:DEL,0:INS,0:INV,31:TDUP,0:NOV_INS,0	
chr1	816790	.	BND_fca	]chr1:816790]G	.	PASS	SVTYPE=BND;EVENT=INV,56;ISIZE=3142;lSC=29;nSC=12;nRP=56;uRP=10;MATE_ID=BND_efc;Summary=CTX,0:DEL,0:INS,0:INV,56:TDUP,0:NOV_INS,0	
chr1	813648	.	BND_efc	G[chr1:813648[	.	PASS	SVTYPE=BND;EVENT=INV,56;ISIZE=3142;lSC=29;nSC=12;nRP=56;uRP=10;MATE_ID=BND_fca;Summary=CTX,0:DEL,0:INS,0:INV,56:TDUP,0:NOV_INS,0	
chr1	816790	.	BND_pes	]chr1:816790]G	.	PASS	r_SVTYPE=BND;EVENT=INV,49;ISIZE=-3142;lSC=34;nSC=14;nRP=49;uRP=8;MATE_ID=BND_yag;Summary=CTX,1:DEL,0:INS,0:INV,49:TDUP,0:NOV_INS,0	
chr1	813648	.	BND_yag	G[chr1:813648[	.	PASS	r_SVTYPE=BND;EVENT=INV,49;ISIZE=-3142;lSC=34;nSC=14;nRP=49;uRP=8;MATE_ID=BND_pes;Summary=CTX,1:DEL,0:INS,0:INV,49:TDUP,0:NOV_INS,0	
chr1	855226	.	BND_rki	]chr1:813648]T	.	PASS	r_SVTYPE=BND;EVENT=DEL,104;ISIZE=-41578;lSC=35;nSC=18;nRP=104;uRP=11;MATE_ID=BND_mln;Summary=CTX,0:DEL,104:INS,0:INV,0:TDUP,0:NOV_INS,0	
chr1	813648	.	BND_mln	G[chr1:855226[	.	PASS	r_SVTYPE=BND;EVENT=DEL,104;ISIZE=-41578;lSC=35;nSC=18;nRP=104;uRP=11;MATE_ID=BND_rki;Summary=CTX,0:DEL,104:INS,0:INV,0:TDUP,0:NOV_INS,0	
chr1	863643	.	BND_ldx	]chr1:854833]G	.	PASS	SVTYPE=BND;EVENT=TDUP,97;ISIZE=8810;lSC=39;nSC=14;nRP=97;uRP=10;MATE_ID=BND_trp;Summary=CTX,0:DEL,0:INS,0:INV,0:TDUP,97:NOV_INS,0	
chr1	854833	.	BND_trp	A[chr1:863643[	.	PASS	SVTYPE=BND;EVENT=TDUP,97;ISIZE=8810;lSC=39;nSC=14;nRP=97;uRP=10;MATE_ID=BND_ldx;Summary=CTX,0:DEL,0:INS,0:INV,0:TDUP,97:NOV_INS,0	
chr1	903616	.	BND_enp	]chr1:903616]C	.	PASS	SVTYPE=BND;EVENT=INV,60;ISIZE=-12375;lSC=19;nSC=10;nRP=60;uRP=14;MATE_ID=BND_kju;Summary=CTX,0:DEL,0:INS,0:INV,60:TDUP,0:NOV_INS,0	
chr1	915991	.	BND_kju	T[chr1:915991[	.	PASS	SVTYPE=BND;EVENT=INV,60;ISIZE=-12375;lSC=19;nSC=10;nRP=60;uRP=14;MATE_ID=BND_enp;Summary=CTX,0:DEL,0:INS,0:INV,60:TDUP,0:NOV_INS,0	
chr1	903616	.	BND_gxr	]chr1:903616]C	.	PASS	r_SVTYPE=BND;EVENT=INV,64;ISIZE=12375;lSC=19;nSC=13;nRP=64;uRP=6;MATE_ID=BND_aad;Summary=CTX,0:DEL,0:INS,0:INV,64:TDUP,0:NOV_INS,0	
chr1	915991	.	BND_aad	T[chr1:915991[	.	PASS	r_SVTYPE=BND;EVENT=INV,64;ISIZE=12375;lSC=19;nSC=13;nRP=64;uRP=6;MATE_ID=BND_gxr;Summary=CTX,0:DEL,0:INS,0:INV,64:TDUP,0:NOV_INS,0	
chr1	915990	.	BND_yjv	]chr1:915990]C	.	PASS	SVTYPE=BND;EVENT=INV,61;ISIZE=12373;lSC=23;nSC=11;nRP=61;uRP=9;MATE_ID=BND_oqn;Summary=CTX,0:DEL,0:INS,0:INV,61:TDUP,0:NOV_INS,0	
chr1	903617	.	BND_oqn	C[chr1:903617[	.	PASS	SVTYPE=BND;EVENT=INV,61;ISIZE=12373;lSC=23;nSC=11;nRP=61;uRP=9;MATE_ID=BND_yjv;Summary=CTX,0:DEL,0:INS,0:INV,61:TDUP,0:NOV_INS,0	
chr1	915990	.	BND_gqz	]chr1:915990]C	.	PASS	r_SVTYPE=BND;EVENT=INV,64;ISIZE=-12373;lSC=38;nSC=12;nRP=64;uRP=5;MATE_ID=BND_taa;Summary=CTX,0:DEL,0:INS,0:INV,64:TDUP,0:NOV_INS,0	
chr1	903617	.	BND_taa	C[chr1:903617[	.	PASS	r_SVTYPE=BND;EVENT=INV,64;ISIZE=-12373;lSC=38;nSC=12;nRP=64;uRP=5;MATE_ID=BND_gqz;Summary=CTX,0:DEL,0:INS,0:INV,64:TDUP,0:NOV_INS,0	
chr1	938005	.	BND_qky	]chr1:938005]A	.	PASS	SVTYPE=BND;EVENT=INV,60;ISIZE=-20303;lSC=32;nSC=6;nRP=60;uRP=13;MATE_ID=BND_abd;Summary=CTX,0:DEL,0:INS,0:INV,60:TDUP,0:NOV_INS,0	
chr1	958308	.	BND_abd	T[chr1:958308[	.	PASS	SVTYPE=BND;EVENT=INV,60;ISIZE=-20303;lSC=32;nSC=6;nRP=60;uRP=13;MATE_ID=BND_qky;Summary=CTX,0:DEL,0:INS,0:INV,60:TDUP,0:NOV_INS,0	
chr1	958307	.	BND_gju	]chr1:958307]A	.	PASS	SVTYPE=BND;EVENT=INV,59;ISIZE=20301;lSC=15;nSC=10;nRP=59;uRP=6;MATE_ID=BND_cwc;Summary=CTX,0:DEL,0:INS,0:INV,59:TDUP,0:NOV_INS,0	
chr1	938006	.	BND_cwc	C[chr1:938006[	.	PASS	SVTYPE=BND;EVENT=INV,59;ISIZE=20301;lSC=15;nSC=10;nRP=59;uRP=6;MATE_ID=BND_gju;Summary=CTX,0:DEL,0:INS,0:INV,59:TDUP,0:NOV_INS,0	
chr1	958310	.	BND_rsp	]chr1:958310]A	.	PASS	r_SVTYPE=BND;EVENT=INV,52;ISIZE=-20304;lSC=18;nSC=11;nRP=52;uRP=7;MATE_ID=BND_xxl;Summary=CTX,0:DEL,0:INS,0:INV,52:TDUP,0:NOV_INS,0	
chr1	938006	.	BND_xxl	T[chr1:938006[	.	PASS	r_SVTYPE=BND;EVENT=INV,52;ISIZE=-20304;lSC=18;nSC=11;nRP=52;uRP=7;MATE_ID=BND_rsp;Summary=CTX,0:DEL,0:INS,0:INV,52:TDUP,0:NOV_INS,0