ryanlayer
commented
5 years ago I am recommending that people use the new lumpy wrapper smoove
https://github.com/brentp/smoove
On Jun 6, 2019, at 2:31 AM, nelsonchanhk notifications@github.com wrote:
Hello, I'm new to lumpy. I've just tried lumpy express with multi-sample input. It generated a VCF with a sample column at the end. Yet, I cannot find any sample identifier in the column. Please kindly advise how I can refer the variant back to the sample. Thank you!
$ cat lumpy_express.sh
!/bin/bash
~/OPERATION/RedCellNGS/tools/lumpy-sv/bin/lumpyexpress -B 11H28680-2.bam,12H28270-5.bam,12H28309-8.bam,12H28470-7.bam,12H28618-7.bam,12H28723-6.bam,12H28754-2.bam,13H28294-9.bam,13H28372-0.bam,13H28504-5.bam,13H28587-0.bam,13H28619-4.bam,13H28944-1.bam,13H28944-1R.bam,14H0289496.bam,14H28307-4.bam,14H28348-3.bam,14H28384-7.bam,14H28448-4.bam,14H28534-4.bam,14H28539-9.bam,14H28622-8.bam,14H28625-9.bam,14H28626-6.bam,14H28698-1.bam,14H28699-8.bam,14H28844-0.bam,14H28947-2.bam,14H28999-1.bam,14H29009-2.bam,15H28027-7.bam,15H28179-7.bam,15H28244-4.bam,15H28299-4.bam,15H28324-9.bam,15H28349-0.bam,15H28381-6.bam,15H28452-5.bam,15H28458-7.bam,15H28547-8.bam,15H28548-5.bam,15H28571-5.bam,15H28577-7.bam,15H28691-2.bam,15H28714-0.bam,15H28715-7.bam,15H28823-7.bam,15H28908-7.bam,15H28910-4.bam,15H29145-7.bam,16H28053-8.bam,16H28186-9.bam,16H28202-8.bam,16H28241-3.bam,16H28242-0.bam,16H28304-3.bam,16H28327-0.bam,16H28379-9.bam,16H28380-9.bam,16H28411-6.bam,16H28412-3.bam,16H28462-8.bam,16H28464-2.bam,16H28488-6.bam,16H28517-9.bam,16H28540-9.bam,16H28622-8.bam,16H28647-9.bam,16H28652-7.bam,16H28656-5.bam,16H28677-8.bam,16H28706-1.bam,16H28732-2.bam,16H28786-5.bam,16H28787-2.bam,16H28818-9.bam,16H28820-6.bam,16H29092-0.bam,16H29122-0.bam,16H29190-7.bam,16H29240-3.bam,16H29325-3.bam,16H29327-7.bam,17H027436-0.bam,17H027437-7.bam,17H027439-1.bam,17H028279-8.bam,17H028305-0.bam,17H028363-4.bam,17H028450-1.bam,17H028452-5.bam,17H028465-9.bam,17H028514-8.bam,17H028529-6.bam,17H028531-3.bam,17H028589-4.bam,17H028623-5.bam,17H028626-6.bam,17H028669-9.bam,17H028707-8.bam,17H028708-5.bam,17H028710-2.bam,17H028733-9.bam,17H028736-0.bam,17H028737-7.bam,17H028763-8.bam,17H028769-0.bam,17H028776-2.bam,17H028827-5.bam,17H028832-3.bam,17H028861-5.bam,17H028883-5.bam,17H029017-1.bam,17H029119-6.bam,17H029120-6.bam,17H029144-0.bam,17H029179-4.bam,17H029267-8.bam,17H029322-2.bam,17H029354-5.bam,17H029403-4.bam,17H029472-8.bam,17H28050-7.bam,17H28052-1.bam,17H28102-7.bam,17H28120-9.bam,17H286651.bam,18H028007-1.bam,18H028197-9.bam,18H028461-1.bam,18H028488-6.bam,18H028593-5.bam,19H21103.bam,HA1.bam,HA10.bam,HA11.bam,HA12.bam,HA13.bam,HA14.bam,HA15.bam,HA16.bam,HA17.bam,HA18.bam,HA19.bam,HA2.bam,HA20.bam,HA21.bam,HA22.bam,HA23.bam,HA3.bam,HA4.bam,HA5.bam,HA6.bam,HA7.bam,HA8.bam,HA9.bam,HBD1.bam,HBD2.bam,HBD3.bam,HBD4.bam,HBD5.bam,HBD6.bam,HBD7.bam,HBD8.bam,Normal1.bam,Normal10.bam,Normal2.bam,Normal3.bam,Normal4.bam,Normal5.bam,Normal6.bam,Normal7.bam,Normal8.bam,Normal9.bam,RA35.bam,UW684347.bam -S 11H28680-2.splitters.bam,12H28270-5.splitters.bam,12H28309-8.splitters.bam,12H28470-7.splitters.bam,12H28618-7.splitters.bam,12H28723-6.splitters.bam,12H28754-2.splitters.bam,13H28294-9.splitters.bam,13H28372-0.splitters.bam,13H28504-5.splitters.bam,13H28587-0.splitters.bam,13H28619-4.splitters.bam,13H28944-1.splitters.bam,13H28944-1R.splitters.bam,14H0289496.splitters.bam,14H28307-4.splitters.bam,14H28348-3.splitters.bam,14H28384-7.splitters.bam,14H28448-4.splitters.bam,14H28534-4.splitters.bam,14H28539-9.splitters.bam,14H28622-8.splitters.bam,14H28625-9.splitters.bam,14H28626-6.splitters.bam,14H28698-1.splitters.bam,14H28699-8.splitters.bam,14H28844-0.splitters.bam,14H28947-2.splitters.bam,14H28999-1.splitters.bam,14H29009-2.splitters.bam,15H28027-7.splitters.bam,15H28179-7.splitters.bam,15H28244-4.splitters.bam,15H28299-4.splitters.bam,15H28324-9.splitters.bam,15H28349-0.splitters.bam,15H28381-6.splitters.bam,15H28452-5.splitters.bam,15H28458-7.splitters.bam,15H28547-8.splitters.bam,15H28548-5.splitters.bam,15H28571-5.splitters.bam,15H28577-7.splitters.bam,15H28691-2.splitters.bam,15H28714-0.splitters.bam,15H28715-7.splitters.bam,15H28823-7.splitters.bam,15H28908-7.splitters.bam,15H28910-4.splitters.bam,15H29145-7.splitters.bam,16H28053-8.splitters.bam,16H28186-9.splitters.bam,16H28202-8.splitters.bam,16H28241-3.splitters.bam,16H28242-0.splitters.bam,16H28304-3.splitters.bam,16H28327-0.splitters.bam,16H28379-9.splitters.bam,16H28380-9.splitters.bam,16H28411-6.splitters.bam,16H28412-3.splitters.bam,16H28462-8.splitters.bam,16H28464-2.splitters.bam,16H28488-6.splitters.bam,16H28517-9.splitters.bam,16H28540-9.splitters.bam,16H28622-8.splitters.bam,16H28647-9.splitters.bam,16H28652-7.splitters.bam,16H28656-5.splitters.bam,16H28677-8.splitters.bam,16H28706-1.splitters.bam,16H28732-2.splitters.bam,16H28786-5.splitters.bam,16H28787-2.splitters.bam,16H28818-9.splitters.bam,16H28820-6.splitters.bam,16H29092-0.splitters.bam,16H29122-0.splitters.bam,16H29190-7.splitters.bam,16H29240-3.splitters.bam,16H29325-3.splitters.bam,16H29327-7.splitters.bam,17H027436-0.splitters.bam,17H027437-7.splitters.bam,17H027439-1.splitters.bam,17H028279-8.splitters.bam,17H028305-0.splitters.bam,17H028363-4.splitters.bam,17H028450-1.splitters.bam,17H028452-5.splitters.bam,17H028465-9.splitters.bam,17H028514-8.splitters.bam,17H028529-6.splitters.bam,17H028531-3.splitters.bam,17H028589-4.splitters.bam,17H028623-5.splitters.bam,17H028626-6.splitters.bam,17H028669-9.splitters.bam,17H028707-8.splitters.bam,17H028708-5.splitters.bam,17H028710-2.splitters.bam,17H028733-9.splitters.bam,17H028736-0.splitters.bam,17H028737-7.splitters.bam,17H028763-8.splitters.bam,17H028769-0.splitters.bam,17H028776-2.splitters.bam,17H028827-5.splitters.bam,17H028832-3.splitters.bam,17H028861-5.splitters.bam,17H028883-5.splitters.bam,17H029017-1.splitters.bam,17H029119-6.splitters.bam,17H029120-6.splitters.bam,17H029144-0.splitters.bam,17H029179-4.splitters.bam,17H029267-8.splitters.bam,17H029322-2.splitters.bam,17H029354-5.splitters.bam,17H029403-4.splitters.bam,17H029472-8.splitters.bam,17H28050-7.splitters.bam,17H28052-1.splitters.bam,17H28102-7.splitters.bam,17H28120-9.splitters.bam,17H286651.splitters.bam,18H028007-1.splitters.bam,18H028197-9.splitters.bam,18H028461-1.splitters.bam,18H028488-6.splitters.bam,18H028593-5.splitters.bam,19H21103.splitters.bam,HA1.splitters.bam,HA10.splitters.bam,HA11.splitters.bam,HA12.splitters.bam,HA13.splitters.bam,HA14.splitters.bam,HA15.splitters.bam,HA16.splitters.bam,HA17.splitters.bam,HA18.splitters.bam,HA19.splitters.bam,HA2.splitters.bam,HA20.splitters.bam,HA21.splitters.bam,HA22.splitters.bam,HA23.splitters.bam,HA3.splitters.bam,HA4.splitters.bam,HA5.splitters.bam,HA6.splitters.bam,HA7.splitters.bam,HA8.splitters.bam,HA9.splitters.bam,HBD1.splitters.bam,HBD2.splitters.bam,HBD3.splitters.bam,HBD4.splitters.bam,HBD5.splitters.bam,HBD6.splitters.bam,HBD7.splitters.bam,HBD8.splitters.bam,Normal1.splitters.bam,Normal10.splitters.bam,Normal2.splitters.bam,Normal3.splitters.bam,Normal4.splitters.bam,Normal5.splitters.bam,Normal6.splitters.bam,Normal7.splitters.bam,Normal8.splitters.bam,Normal9.splitters.bam,RA35.splitters.bam,UW684347.splitters.bam -D 11H28680-2.discordants.bam,12H28270-5.discordants.bam,12H28309-8.discordants.bam,12H28470-7.discordants.bam,12H28618-7.discordants.bam,12H28723-6.discordants.bam,12H28754-2.discordants.bam,13H28294-9.discordants.bam,13H28372-0.discordants.bam,13H28504-5.discordants.bam,13H28587-0.discordants.bam,13H28619-4.discordants.bam,13H28944-1.discordants.bam,13H28944-1R.discordants.bam,14H0289496.discordants.bam,14H28307-4.discordants.bam,14H28348-3.discordants.bam,14H28384-7.discordants.bam,14H28448-4.discordants.bam,14H28534-4.discordants.bam,14H28539-9.discordants.bam,14H28622-8.discordants.bam,14H28625-9.discordants.bam,14H28626-6.discordants.bam,14H28698-1.discordants.bam,14H28699-8.discordants.bam,14H28844-0.discordants.bam,14H28947-2.discordants.bam,14H28999-1.discordants.bam,14H29009-2.discordants.bam,15H28027-7.discordants.bam,15H28179-7.discordants.bam,15H28244-4.discordants.bam,15H28299-4.discordants.bam,15H28324-9.discordants.bam,15H28349-0.discordants.bam,15H28381-6.discordants.bam,15H28452-5.discordants.bam,15H28458-7.discordants.bam,15H28547-8.discordants.bam,15H28548-5.discordants.bam,15H28571-5.discordants.bam,15H28577-7.discordants.bam,15H28691-2.discordants.bam,15H28714-0.discordants.bam,15H28715-7.discordants.bam,15H28823-7.discordants.bam,15H28908-7.discordants.bam,15H28910-4.discordants.bam,15H29145-7.discordants.bam,16H28053-8.discordants.bam,16H28186-9.discordants.bam,16H28202-8.discordants.bam,16H28241-3.discordants.bam,16H28242-0.discordants.bam,16H28304-3.discordants.bam,16H28327-0.discordants.bam,16H28379-9.discordants.bam,16H28380-9.discordants.bam,16H28411-6.discordants.bam,16H28412-3.discordants.bam,16H28462-8.discordants.bam,16H28464-2.discordants.bam,16H28488-6.discordants.bam,16H28517-9.discordants.bam,16H28540-9.discordants.bam,16H28622-8.discordants.bam,16H28647-9.discordants.bam,16H28652-7.discordants.bam,16H28656-5.discordants.bam,16H28677-8.discordants.bam,16H28706-1.discordants.bam,16H28732-2.discordants.bam,16H28786-5.discordants.bam,16H28787-2.discordants.bam,16H28818-9.discordants.bam,16H28820-6.discordants.bam,16H29092-0.discordants.bam,16H29122-0.discordants.bam,16H29190-7.discordants.bam,16H29240-3.discordants.bam,16H29325-3.discordants.bam,16H29327-7.discordants.bam,17H027436-0.discordants.bam,17H027437-7.discordants.bam,17H027439-1.discordants.bam,17H028279-8.discordants.bam,17H028305-0.discordants.bam,17H028363-4.discordants.bam,17H028450-1.discordants.bam,17H028452-5.discordants.bam,17H028465-9.discordants.bam,17H028514-8.discordants.bam,17H028529-6.discordants.bam,17H028531-3.discordants.bam,17H028589-4.discordants.bam,17H028623-5.discordants.bam,17H028626-6.discordants.bam,17H028669-9.discordants.bam,17H028707-8.discordants.bam,17H028708-5.discordants.bam,17H028710-2.discordants.bam,17H028733-9.discordants.bam,17H028736-0.discordants.bam,17H028737-7.discordants.bam,17H028763-8.discordants.bam,17H028769-0.discordants.bam,17H028776-2.discordants.bam,17H028827-5.discordants.bam,17H028832-3.discordants.bam,17H028861-5.discordants.bam,17H028883-5.discordants.bam,17H029017-1.discordants.bam,17H029119-6.discordants.bam,17H029120-6.discordants.bam,17H029144-0.discordants.bam,17H029179-4.discordants.bam,17H029267-8.discordants.bam,17H029322-2.discordants.bam,17H029354-5.discordants.bam,17H029403-4.discordants.bam,17H029472-8.discordants.bam,17H28050-7.discordants.bam,17H28052-1.discordants.bam,17H28102-7.discordants.bam,17H28120-9.discordants.bam,17H286651.discordants.bam,18H028007-1.discordants.bam,18H028197-9.discordants.bam,18H028461-1.discordants.bam,18H028488-6.discordants.bam,18H028593-5.discordants.bam,19H21103.discordants.bam,HA1.discordants.bam,HA10.discordants.bam,HA11.discordants.bam,HA12.discordants.bam,HA13.discordants.bam,HA14.discordants.bam,HA15.discordants.bam,HA16.discordants.bam,HA17.discordants.bam,HA18.discordants.bam,HA19.discordants.bam,HA2.discordants.bam,HA20.discordants.bam,HA21.discordants.bam,HA22.discordants.bam,HA23.discordants.bam,HA3.discordants.bam,HA4.discordants.bam,HA5.discordants.bam,HA6.discordants.bam,HA7.discordants.bam,HA8.discordants.bam,HA9.discordants.bam,HBD1.discordants.bam,HBD2.discordants.bam,HBD3.discordants.bam,HBD4.discordants.bam,HBD5.discordants.bam,HBD6.discordants.bam,HBD7.discordants.bam,HBD8.discordants.bam,Normal1.discordants.bam,Normal10.discordants.bam,Normal2.discordants.bam,Normal3.discordants.bam,Normal4.discordants.bam,Normal5.discordants.bam,Normal6.discordants.bam,Normal7.discordants.bam,Normal8.discordants.bam,Normal9.discordants.bam,RA35.discordants.bam,UW684347.discordants.bam -o RBC_lumpy_express.vcf
nelson@Ubuntu-testing ~/OPERATION/RedCellNGS/Processed_bam_vcf/lumpy $ head -n 50 RBC_lumpy_express.vcf
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CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
chr1 1212070 1_1 N N]chr1:1212187] . . SVTYPE=BND;STRANDS=++:5;EVENT=1;MATEID=1_2;CIPOS=-10,2;CIEND=-10,5;CIPOS95=-3,1;CIEND95=-3,1;IMPRECISE;SU=5;PE=2;SR=3 GT:SU:PE:SR ./.:5:2:3 chr1 1212187 1_2 N N]chr1:1212070] . . SVTYPE=BND;STRANDS=++:5;SECONDARY;EVENT=1;MATEID=1_1;CIPOS=-10,5;CIEND=-10,2;CIPOS95=-3,1;CIEND95=-3,1;IMPRECISE;SU=5;PE=2;SR=3 GT:SU:PE:SR ./.:5:2:3 chr1 1028530 2 N . . SVTYPE=DEL;STRANDS=+-:6;SVLEN=-510;END=1029040;CIPOS=-10,355;CIEND=-396,9;CIPOS95=-2,60;CIEND95=-71,3;IMPRECISE;SU=6;PE=6;SR=0 GT:SU:PE:SR ./.:6:6:0 chr1 1211059 3 N . . SVTYPE=DEL;STRANDS=+-:5;SVLEN=-197;END=1211256;CIPOS=-3,9;CIEND=-8,6;CIPOS95=0,1;CIEND95=-1,0;IMPRECISE;SU=5;PE=0;SR=5 GT:SU:PE:SR ./.:5:0:5 chr1 1211201 4 N . . SVTYPE=INV;STRANDS=++:1,--:8;SVLEN=240;END=1211441;CIPOS=-449,9;CIEND=-19,9;CIPOS95=-85,2;CIEND95=-19,0;IMPRECISE;SU=9;PE=9;SR=0 GT:SU:PE:SR ./.:9:9:0 chr1 1211472 5 N . . SVTYPE=INV;STRANDS=++:1,--:4;SVLEN=91;END=1211563;CIPOS=-1,9;CIEND=-10,1;CIPOS95=0,1;CIEND95=-1,0;IMPRECISE;SU=5;PE=0;SR=5 GT:SU:PE:SR ./.:5:0:5 chr1 1211452 6 N . . SVTYPE=INV;STRANDS=++:1,--:3;SVLEN=137;END=1211589;CIPOS=-4,9;CIEND=-4,9;CIPOS95=0,1;CIEND95=0,1;IMPRECISE;SU=4;PE=0;SR=4 GT:SU:PE:SR ./.:4:0:4 chr1 1211411 7 N . . SVTYPE=INV;STRANDS=++:9,--:5;SVLEN=204;END=1211615;CIPOS=-10,3;CIEND=-10,9;CIPOS95=-1,0;CIEND95=-1,1;IMPRECISE;SU=14;PE=11;SR=3 GT:SU:PE:SR ./.:14:11:3 chr1 1211641 8_1 N N]chr1:1211906] . . SVTYPE=BND;STRANDS=++:10;EVENT=8;MATEID=8_2;CIPOS=-10,24;CIEND=-10,316;CIPOS95=0,23;CIEND95=-3,51;IMPRECISE;SU=10;PE=10;SR=0 GT:SU:PE:SR ./.:10:10:0 chr1 1211906 8_2 N N]chr1:1211641] . . SVTYPE=BND;STRANDS=++:10;SECONDARY;EVENT=8;MATEID=8_1;CIPOS=-10,316;CIEND=-10,24;CIPOS95=-3,51;CIEND95=0,23;IMPRECISE;SU=10;PE=10;SR=0 GT:SU:PE:SR ./.:10:10:0 chr1 1211785 9_1 N N]chr1:1211854] . . SVTYPE=BND;STRANDS=++:4;EVENT=9;MATEID=9_2;CIPOS=-7,0;CIEND=-5,9;CIPOS95=-7,0;CIEND95=0,1;IMPRECISE;SU=4;PE=0;SR=4 GT:SU:PE:SR ./.:4:0:4 chr1 1211854 9_2 N N]chr1:1211785] . . SVTYPE=BND;STRANDS=++:4;SECONDARY;EVENT=9;MATEID=9_1;CIPOS=-5,9;CIEND=-7,0;CIPOS95=0,1;CIEND95=-7,0;IMPRECISE;SU=4;PE=0;SR=4 GT:SU:PE:SR ./.:4:0:4 chr1 1211196 10 N . . SVTYPE=DUP;STRANDS=-+:6;SVLEN=457;END=1211653;CIPOS=-286,9;CIEND=-10,282;CIPOS95=-72,1;CIEND95=-3,72;IMPRECISE;SU=6;PE=6;SR=0 GT:SU:PE:SR ./.:6:6:0 chr1 1211930 11 N . . SVTYPE=INV;STRANDS=++:2,--:2;SVLEN=61;END=1211991;CIPOS=-3,5;CIEND=0,7;CIPOS95=-1,2;CIEND95=0,2;IMPRECISE;SU=4;PE=0;SR=4 GT:SU:PE:SR ./.:4:0:4 chr1 1211877 12 N . . SVTYPE=INV;STRANDS=++:8,--:2;SVLEN=159;END=1212036;CIPOS=-10,2;CIEND=-10,1;CIPOS95=-3,1;CIEND95=-1,1;IMPRECISE;SU=10;PE=5;SR=5 GT:SU:PE:SR ./.:10:5:5 chr1 1211794 13 N . . SVTYPE=INV;STRANDS=++:8,--:7;SVLEN=128;END=1211922;CIPOS=-5,8;CIEND=-6,9;CIPOS95=-2,6;CIEND95=-1,1;IMPRECISE;SU=15;PE=6;SR=9 GT:SU:PE:SR ./.:15:6:9 chr1 1212302 14 N . . SVTYPE=DEL;STRANDS=+-:17;SVLEN=-31;END=1212333;CIPOS=-2,1;CIEND=-6,0;CIPOS95=0,0;CIEND95=0,0;SU=17;PE=0;SR=17 GT:SU:PE:SR ./.:17:0:17
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Hello, I'm new to lumpy. I've just tried lumpy express with multi-sample input. It generated a VCF with a sample column at the end. Yet, I cannot find any sample identifier in the column. Please kindly advise how I can refer the variant back to the sample. Thank you!
$ cat lumpy_express.sh
!/bin/bash
~/OPERATION/RedCellNGS/tools/lumpy-sv/bin/lumpyexpress \ -B 11H28680-2.bam,12H28270-5.bam,12H28309-8.bam,12H28470-7.bam,12H28618-7.bam,12H28723-6.bam,12H28754-2.bam,13H28294-9.bam,13H28372-0.bam,13H28504-5.bam,13H28587-0.bam,13H28619-4.bam,13H28944-1.bam,13H28944-1R.bam,14H0289496.bam,14H28307-4.bam,14H28348-3.bam,14H28384-7.bam,14H28448-4.bam,14H28534-4.bam,14H28539-9.bam,14H28622-8.bam,14H28625-9.bam,14H28626-6.bam,14H28698-1.bam,14H28699-8.bam,14H28844-0.bam,14H28947-2.bam,14H28999-1.bam,14H29009-2.bam,15H28027-7.bam,15H28179-7.bam,15H28244-4.bam,15H28299-4.bam,15H28324-9.bam,15H28349-0.bam,15H28381-6.bam,15H28452-5.bam,15H28458-7.bam,15H28547-8.bam,15H28548-5.bam,15H28571-5.bam,15H28577-7.bam,15H28691-2.bam,15H28714-0.bam,15H28715-7.bam,15H28823-7.bam,15H28908-7.bam,15H28910-4.bam,15H29145-7.bam,16H28053-8.bam,16H28186-9.bam,16H28202-8.bam,16H28241-3.bam,16H28242-0.bam,16H28304-3.bam,16H28327-0.bam,16H28379-9.bam,16H28380-9.bam,16H28411-6.bam,16H28412-3.bam,16H28462-8.bam,16H28464-2.bam,16H28488-6.bam,16H28517-9.bam,16H28540-9.bam,16H28622-8.bam,16H28647-9.bam,16H28652-7.bam,16H28656-5.bam,16H28677-8.bam,16H28706-1.bam,16H28732-2.bam,16H28786-5.bam,16H28787-2.bam,16H28818-9.bam,16H28820-6.bam,16H29092-0.bam,16H29122-0.bam,16H29190-7.bam,16H29240-3.bam,16H29325-3.bam,16H29327-7.bam,17H027436-0.bam,17H027437-7.bam,17H027439-1.bam,17H028279-8.bam,17H028305-0.bam,17H028363-4.bam,17H028450-1.bam,17H028452-5.bam,17H028465-9.bam,17H028514-8.bam,17H028529-6.bam,17H028531-3.bam,17H028589-4.bam,17H028623-5.bam,17H028626-6.bam,17H028669-9.bam,17H028707-8.bam,17H028708-5.bam,17H028710-2.bam,17H028733-9.bam,17H028736-0.bam,17H028737-7.bam,17H028763-8.bam,17H028769-0.bam,17H028776-2.bam,17H028827-5.bam,17H028832-3.bam,17H028861-5.bam,17H028883-5.bam,17H029017-1.bam,17H029119-6.bam,17H029120-6.bam,17H029144-0.bam,17H029179-4.bam,17H029267-8.bam,17H029322-2.bam,17H029354-5.bam,17H029403-4.bam,17H029472-8.bam,17H28050-7.bam,17H28052-1.bam,17H28102-7.bam,17H28120-9.bam,17H286651.bam,18H028007-1.bam,18H028197-9.bam,18H028461-1.bam,18H028488-6.bam,18H028593-5.bam,19H21103.bam,HA1.bam,HA10.bam,HA11.bam,HA12.bam,HA13.bam,HA14.bam,HA15.bam,HA16.bam,HA17.bam,HA18.bam,HA19.bam,HA2.bam,HA20.bam,HA21.bam,HA22.bam,HA23.bam,HA3.bam,HA4.bam,HA5.bam,HA6.bam,HA7.bam,HA8.bam,HA9.bam,HBD1.bam,HBD2.bam,HBD3.bam,HBD4.bam,HBD5.bam,HBD6.bam,HBD7.bam,HBD8.bam,Normal1.bam,Normal10.bam,Normal2.bam,Normal3.bam,Normal4.bam,Normal5.bam,Normal6.bam,Normal7.bam,Normal8.bam,Normal9.bam,RA35.bam,UW684347.bam \ -S 11H28680-2.splitters.bam,12H28270-5.splitters.bam,12H28309-8.splitters.bam,12H28470-7.splitters.bam,12H28618-7.splitters.bam,12H28723-6.splitters.bam,12H28754-2.splitters.bam,13H28294-9.splitters.bam,13H28372-0.splitters.bam,13H28504-5.splitters.bam,13H28587-0.splitters.bam,13H28619-4.splitters.bam,13H28944-1.splitters.bam,13H28944-1R.splitters.bam,14H0289496.splitters.bam,14H28307-4.splitters.bam,14H28348-3.splitters.bam,14H28384-7.splitters.bam,14H28448-4.splitters.bam,14H28534-4.splitters.bam,14H28539-9.splitters.bam,14H28622-8.splitters.bam,14H28625-9.splitters.bam,14H28626-6.splitters.bam,14H28698-1.splitters.bam,14H28699-8.splitters.bam,14H28844-0.splitters.bam,14H28947-2.splitters.bam,14H28999-1.splitters.bam,14H29009-2.splitters.bam,15H28027-7.splitters.bam,15H28179-7.splitters.bam,15H28244-4.splitters.bam,15H28299-4.splitters.bam,15H28324-9.splitters.bam,15H28349-0.splitters.bam,15H28381-6.splitters.bam,15H28452-5.splitters.bam,15H28458-7.splitters.bam,15H28547-8.splitters.bam,15H28548-5.splitters.bam,15H28571-5.splitters.bam,15H28577-7.splitters.bam,15H28691-2.splitters.bam,15H28714-0.splitters.bam,15H28715-7.splitters.bam,15H28823-7.splitters.bam,15H28908-7.splitters.bam,15H28910-4.splitters.bam,15H29145-7.splitters.bam,16H28053-8.splitters.bam,16H28186-9.splitters.bam,16H28202-8.splitters.bam,16H28241-3.splitters.bam,16H28242-0.splitters.bam,16H28304-3.splitters.bam,16H28327-0.splitters.bam,16H28379-9.splitters.bam,16H28380-9.splitters.bam,16H28411-6.splitters.bam,16H28412-3.splitters.bam,16H28462-8.splitters.bam,16H28464-2.splitters.bam,16H28488-6.splitters.bam,16H28517-9.splitters.bam,16H28540-9.splitters.bam,16H28622-8.splitters.bam,16H28647-9.splitters.bam,16H28652-7.splitters.bam,16H28656-5.splitters.bam,16H28677-8.splitters.bam,16H28706-1.splitters.bam,16H28732-2.splitters.bam,16H28786-5.splitters.bam,16H28787-2.splitters.bam,16H28818-9.splitters.bam,16H28820-6.splitters.bam,16H29092-0.splitters.bam,16H29122-0.splitters.bam,16H29190-7.splitters.bam,16H29240-3.splitters.bam,16H29325-3.splitters.bam,16H29327-7.splitters.bam,17H027436-0.splitters.bam,17H027437-7.splitters.bam,17H027439-1.splitters.bam,17H028279-8.splitters.bam,17H028305-0.splitters.bam,17H028363-4.splitters.bam,17H028450-1.splitters.bam,17H028452-5.splitters.bam,17H028465-9.splitters.bam,17H028514-8.splitters.bam,17H028529-6.splitters.bam,17H028531-3.splitters.bam,17H028589-4.splitters.bam,17H028623-5.splitters.bam,17H028626-6.splitters.bam,17H028669-9.splitters.bam,17H028707-8.splitters.bam,17H028708-5.splitters.bam,17H028710-2.splitters.bam,17H028733-9.splitters.bam,17H028736-0.splitters.bam,17H028737-7.splitters.bam,17H028763-8.splitters.bam,17H028769-0.splitters.bam,17H028776-2.splitters.bam,17H028827-5.splitters.bam,17H028832-3.splitters.bam,17H028861-5.splitters.bam,17H028883-5.splitters.bam,17H029017-1.splitters.bam,17H029119-6.splitters.bam,17H029120-6.splitters.bam,17H029144-0.splitters.bam,17H029179-4.splitters.bam,17H029267-8.splitters.bam,17H029322-2.splitters.bam,17H029354-5.splitters.bam,17H029403-4.splitters.bam,17H029472-8.splitters.bam,17H28050-7.splitters.bam,17H28052-1.splitters.bam,17H28102-7.splitters.bam,17H28120-9.splitters.bam,17H286651.splitters.bam,18H028007-1.splitters.bam,18H028197-9.splitters.bam,18H028461-1.splitters.bam,18H028488-6.splitters.bam,18H028593-5.splitters.bam,19H21103.splitters.bam,HA1.splitters.bam,HA10.splitters.bam,HA11.splitters.bam,HA12.splitters.bam,HA13.splitters.bam,HA14.splitters.bam,HA15.splitters.bam,HA16.splitters.bam,HA17.splitters.bam,HA18.splitters.bam,HA19.splitters.bam,HA2.splitters.bam,HA20.splitters.bam,HA21.splitters.bam,HA22.splitters.bam,HA23.splitters.bam,HA3.splitters.bam,HA4.splitters.bam,HA5.splitters.bam,HA6.splitters.bam,HA7.splitters.bam,HA8.splitters.bam,HA9.splitters.bam,HBD1.splitters.bam,HBD2.splitters.bam,HBD3.splitters.bam,HBD4.splitters.bam,HBD5.splitters.bam,HBD6.splitters.bam,HBD7.splitters.bam,HBD8.splitters.bam,Normal1.splitters.bam,Normal10.splitters.bam,Normal2.splitters.bam,Normal3.splitters.bam,Normal4.splitters.bam,Normal5.splitters.bam,Normal6.splitters.bam,Normal7.splitters.bam,Normal8.splitters.bam,Normal9.splitters.bam,RA35.splitters.bam,UW684347.splitters.bam \ -D 11H28680-2.discordants.bam,12H28270-5.discordants.bam,12H28309-8.discordants.bam,12H28470-7.discordants.bam,12H28618-7.discordants.bam,12H28723-6.discordants.bam,12H28754-2.discordants.bam,13H28294-9.discordants.bam,13H28372-0.discordants.bam,13H28504-5.discordants.bam,13H28587-0.discordants.bam,13H28619-4.discordants.bam,13H28944-1.discordants.bam,13H28944-1R.discordants.bam,14H0289496.discordants.bam,14H28307-4.discordants.bam,14H28348-3.discordants.bam,14H28384-7.discordants.bam,14H28448-4.discordants.bam,14H28534-4.discordants.bam,14H28539-9.discordants.bam,14H28622-8.discordants.bam,14H28625-9.discordants.bam,14H28626-6.discordants.bam,14H28698-1.discordants.bam,14H28699-8.discordants.bam,14H28844-0.discordants.bam,14H28947-2.discordants.bam,14H28999-1.discordants.bam,14H29009-2.discordants.bam,15H28027-7.discordants.bam,15H28179-7.discordants.bam,15H28244-4.discordants.bam,15H28299-4.discordants.bam,15H28324-9.discordants.bam,15H28349-0.discordants.bam,15H28381-6.discordants.bam,15H28452-5.discordants.bam,15H28458-7.discordants.bam,15H28547-8.discordants.bam,15H28548-5.discordants.bam,15H28571-5.discordants.bam,15H28577-7.discordants.bam,15H28691-2.discordants.bam,15H28714-0.discordants.bam,15H28715-7.discordants.bam,15H28823-7.discordants.bam,15H28908-7.discordants.bam,15H28910-4.discordants.bam,15H29145-7.discordants.bam,16H28053-8.discordants.bam,16H28186-9.discordants.bam,16H28202-8.discordants.bam,16H28241-3.discordants.bam,16H28242-0.discordants.bam,16H28304-3.discordants.bam,16H28327-0.discordants.bam,16H28379-9.discordants.bam,16H28380-9.discordants.bam,16H28411-6.discordants.bam,16H28412-3.discordants.bam,16H28462-8.discordants.bam,16H28464-2.discordants.bam,16H28488-6.discordants.bam,16H28517-9.discordants.bam,16H28540-9.discordants.bam,16H28622-8.discordants.bam,16H28647-9.discordants.bam,16H28652-7.discordants.bam,16H28656-5.discordants.bam,16H28677-8.discordants.bam,16H28706-1.discordants.bam,16H28732-2.discordants.bam,16H28786-5.discordants.bam,16H28787-2.discordants.bam,16H28818-9.discordants.bam,16H28820-6.discordants.bam,16H29092-0.discordants.bam,16H29122-0.discordants.bam,16H29190-7.discordants.bam,16H29240-3.discordants.bam,16H29325-3.discordants.bam,16H29327-7.discordants.bam,17H027436-0.discordants.bam,17H027437-7.discordants.bam,17H027439-1.discordants.bam,17H028279-8.discordants.bam,17H028305-0.discordants.bam,17H028363-4.discordants.bam,17H028450-1.discordants.bam,17H028452-5.discordants.bam,17H028465-9.discordants.bam,17H028514-8.discordants.bam,17H028529-6.discordants.bam,17H028531-3.discordants.bam,17H028589-4.discordants.bam,17H028623-5.discordants.bam,17H028626-6.discordants.bam,17H028669-9.discordants.bam,17H028707-8.discordants.bam,17H028708-5.discordants.bam,17H028710-2.discordants.bam,17H028733-9.discordants.bam,17H028736-0.discordants.bam,17H028737-7.discordants.bam,17H028763-8.discordants.bam,17H028769-0.discordants.bam,17H028776-2.discordants.bam,17H028827-5.discordants.bam,17H028832-3.discordants.bam,17H028861-5.discordants.bam,17H028883-5.discordants.bam,17H029017-1.discordants.bam,17H029119-6.discordants.bam,17H029120-6.discordants.bam,17H029144-0.discordants.bam,17H029179-4.discordants.bam,17H029267-8.discordants.bam,17H029322-2.discordants.bam,17H029354-5.discordants.bam,17H029403-4.discordants.bam,17H029472-8.discordants.bam,17H28050-7.discordants.bam,17H28052-1.discordants.bam,17H28102-7.discordants.bam,17H28120-9.discordants.bam,17H286651.discordants.bam,18H028007-1.discordants.bam,18H028197-9.discordants.bam,18H028461-1.discordants.bam,18H028488-6.discordants.bam,18H028593-5.discordants.bam,19H21103.discordants.bam,HA1.discordants.bam,HA10.discordants.bam,HA11.discordants.bam,HA12.discordants.bam,HA13.discordants.bam,HA14.discordants.bam,HA15.discordants.bam,HA16.discordants.bam,HA17.discordants.bam,HA18.discordants.bam,HA19.discordants.bam,HA2.discordants.bam,HA20.discordants.bam,HA21.discordants.bam,HA22.discordants.bam,HA23.discordants.bam,HA3.discordants.bam,HA4.discordants.bam,HA5.discordants.bam,HA6.discordants.bam,HA7.discordants.bam,HA8.discordants.bam,HA9.discordants.bam,HBD1.discordants.bam,HBD2.discordants.bam,HBD3.discordants.bam,HBD4.discordants.bam,HBD5.discordants.bam,HBD6.discordants.bam,HBD7.discordants.bam,HBD8.discordants.bam,Normal1.discordants.bam,Normal10.discordants.bam,Normal2.discordants.bam,Normal3.discordants.bam,Normal4.discordants.bam,Normal5.discordants.bam,Normal6.discordants.bam,Normal7.discordants.bam,Normal8.discordants.bam,Normal9.discordants.bam,RA35.discordants.bam,UW684347.discordants.bam \ -o RBC_lumpy_express.vcf
nelson@Ubuntu-testing ~/OPERATION/RedCellNGS/Processed_bam_vcf/lumpy $ head -n 50 RBC_lumpy_express.vcf
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CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
chr1 1212070 1_1 N N]chr1:1212187] . . SVTYPE=BND;STRANDS=++:5;EVENT=1;MATEID=1_2;CIPOS=-10,2;CIEND=-10,5;CIPOS95=-3,1;CIEND95=-3,1;IMPRECISE;SU=5;PE=2;SR=3 GT:SU:PE:SR ./.:5:2:3 chr1 1212187 1_2 N N]chr1:1212070] . . SVTYPE=BND;STRANDS=++:5;SECONDARY;EVENT=1;MATEID=1_1;CIPOS=-10,5;CIEND=-10,2;CIPOS95=-3,1;CIEND95=-3,1;IMPRECISE;SU=5;PE=2;SR=3 GT:SU:PE:SR ./.:5:2:3 chr1 1028530 2 N
. . SVTYPE=DEL;STRANDS=+-:6;SVLEN=-510;END=1029040;CIPOS=-10,355;CIEND=-396,9;CIPOS95=-2,60;CIEND95=-71,3;IMPRECISE;SU=6;PE=6;SR=0 GT:SU:PE:SR ./.:6:6:0 chr1 1211059 3 N. . SVTYPE=DEL;STRANDS=+-:5;SVLEN=-197;END=1211256;CIPOS=-3,9;CIEND=-8,6;CIPOS95=0,1;CIEND95=-1,0;IMPRECISE;SU=5;PE=0;SR=5 GT:SU:PE:SR ./.:5:0:5 chr1 1211201 4 N . . SVTYPE=INV;STRANDS=++:1,--:8;SVLEN=240;END=1211441;CIPOS=-449,9;CIEND=-19,9;CIPOS95=-85,2;CIEND95=-19,0;IMPRECISE;SU=9;PE=9;SR=0 GT:SU:PE:SR ./.:9:9:0
chr1 1211472 5 N . . SVTYPE=INV;STRANDS=++:1,--:4;SVLEN=91;END=1211563;CIPOS=-1,9;CIEND=-10,1;CIPOS95=0,1;CIEND95=-1,0;IMPRECISE;SU=5;PE=0;SR=5 GT:SU:PE:SR ./.:5:0:5
chr1 1211452 6 N . . SVTYPE=INV;STRANDS=++:1,--:3;SVLEN=137;END=1211589;CIPOS=-4,9;CIEND=-4,9;CIPOS95=0,1;CIEND95=0,1;IMPRECISE;SU=4;PE=0;SR=4 GT:SU:PE:SR ./.:4:0:4
chr1 1211411 7 N . . SVTYPE=INV;STRANDS=++:9,--:5;SVLEN=204;END=1211615;CIPOS=-10,3;CIEND=-10,9;CIPOS95=-1,0;CIEND95=-1,1;IMPRECISE;SU=14;PE=11;SR=3 GT:SU:PE:SR ./.:14:11:3
chr1 1211641 8_1 N N]chr1:1211906] . . SVTYPE=BND;STRANDS=++:10;EVENT=8;MATEID=8_2;CIPOS=-10,24;CIEND=-10,316;CIPOS95=0,23;CIEND95=-3,51;IMPRECISE;SU=10;PE=10;SR=0 GT:SU:PE:SR ./.:10:10:0
chr1 1211906 8_2 N N]chr1:1211641] . . SVTYPE=BND;STRANDS=++:10;SECONDARY;EVENT=8;MATEID=8_1;CIPOS=-10,316;CIEND=-10,24;CIPOS95=-3,51;CIEND95=0,23;IMPRECISE;SU=10;PE=10;SR=0 GT:SU:PE:SR ./.:10:10:0
chr1 1211785 9_1 N N]chr1:1211854] . . SVTYPE=BND;STRANDS=++:4;EVENT=9;MATEID=9_2;CIPOS=-7,0;CIEND=-5,9;CIPOS95=-7,0;CIEND95=0,1;IMPRECISE;SU=4;PE=0;SR=4 GT:SU:PE:SR ./.:4:0:4
chr1 1211854 9_2 N N]chr1:1211785] . . SVTYPE=BND;STRANDS=++:4;SECONDARY;EVENT=9;MATEID=9_1;CIPOS=-5,9;CIEND=-7,0;CIPOS95=0,1;CIEND95=-7,0;IMPRECISE;SU=4;PE=0;SR=4 GT:SU:PE:SR ./.:4:0:4
chr1 1211196 10 N . . SVTYPE=DUP;STRANDS=-+:6;SVLEN=457;END=1211653;CIPOS=-286,9;CIEND=-10,282;CIPOS95=-72,1;CIEND95=-3,72;IMPRECISE;SU=6;PE=6;SR=0 GT:SU:PE:SR ./.:6:6:0
chr1 1211930 11 N . . SVTYPE=INV;STRANDS=++:2,--:2;SVLEN=61;END=1211991;CIPOS=-3,5;CIEND=0,7;CIPOS95=-1,2;CIEND95=0,2;IMPRECISE;SU=4;PE=0;SR=4 GT:SU:PE:SR ./.:4:0:4
chr1 1211877 12 N . . SVTYPE=INV;STRANDS=++:8,--:2;SVLEN=159;END=1212036;CIPOS=-10,2;CIEND=-10,1;CIPOS95=-3,1;CIEND95=-1,1;IMPRECISE;SU=10;PE=5;SR=5 GT:SU:PE:SR ./.:10:5:5
chr1 1211794 13 N . . SVTYPE=INV;STRANDS=++:8,--:7;SVLEN=128;END=1211922;CIPOS=-5,8;CIEND=-6,9;CIPOS95=-2,6;CIEND95=-1,1;IMPRECISE;SU=15;PE=6;SR=9 GT:SU:PE:SR ./.:15:6:9
chr1 1212302 14 N . . SVTYPE=DEL;STRANDS=+-:17;SVLEN=-31;END=1212333;CIPOS=-2,1;CIEND=-6,0;CIPOS95=0,0;CIEND95=0,0;SU=17;PE=0;SR=17 GT:SU:PE:SR ./.:17:0:17