Mercurial > repos > plus > ss_tool
diff test-data/test.out.vcf @ 0:367704fcdabe draft
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| author | plus |
|---|---|
| date | Mon, 02 Jun 2014 11:32:21 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.out.vcf Mon Jun 02 11:32:21 2014 -0400 @@ -0,0 +1,53 @@ +##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