Entering edit mode
6.0 years ago
How to convert .tsv file to the VCF format correctly? Is it possible with bcftools --tsv2vcf or should I use CrossMap or whatever you can advise?
Here is a Linux Shell code with some error (produces empty VCF):
bcftools convert -s SampleName -f H37Rv_reference.fasta --tsv2vcf TuberculosisSampleDrugResistanceReport.tsv -o DrugResistanceReportVCF.vcf
Here is an input .tsv file (TuberculosisSampleDrugResistanceReport.tsv ):
AL123456 4246514 4249810 embB . -1 -1 . . . . . . . . 0
AL123456 1416181 1417347 embR . -1 -1 . . . . . . . . 0
AL123456 3489506 3490375 Rv3124 . -1 -1 . . . . . . . . 0
AL123456 3490476 3491651 Rv3125c . -1 -1 . . . . . . . . 0
AL123456 3491808 3492122 Rv3126 . -1 -1 . . . . . . . . 0
AL123456 408634 409173 Rv0340 AL123456 408722 408723 . 590 C T PASS DP=15;TD=19;BQ=39;MQ=53;QD=39;BC=0,0,0,15;QP=0,0,0,100;PC=57;IC=0;DC=0;XC=0;AC=2;AF=1.00 GT 1/1 1
AL123456 409362 410801 iniB . -1 -1 . . . . . . . . 0
AL123456 412757 414238 iniC . -1 -1 . . . . . . . . 0
AL123456 398658 399524 rmlA . -1 -1 . . . . . . . . 0
AL123456 3646895 3647809 rmlD . -1 -1 . . . . . . . . 0
AL123456 4326004 4327473 ethA . -1 -1 . . . . . . . . 0
AL123456 7302 9818 gyrA AL123456 7361 7362 . 742 G C PASS DP=21;TD=23;BQ=38;MQ=59;QD=35;BC=1,20,0,0;QP=2,98,0,0;PC=43;IC=0;DC=0;XC=2;AC=2;AF=0.98 GT 1/1 1
AL123456 7302 9818 gyrA AL123456 7584 7585 . 1042 G C PASS DP=27;TD=31;BQ=39;MQ=47;QD=38;BC=0,27,0,0;QP=0,100,0,0;PC=54;IC=0;DC=0;XC=2;AC=2;AF=1.00 GT 1/1 1
AL123456 7302 9818 gyrA AL123456 8039 8040 . 1018 G A PASS DP=29;TD=38;BQ=37;MQ=52;QD=35;BC=28,0,1,0;QP=99,0,1,0;PC=49;IC=0;DC=0;XC=1;AC=2;AF=0.99 GT 1/1 1
AL123456 7302 9818 gyrA AL123456 9303 9304 . 910 G A PASS DP=23;TD=26;BQ=40;MQ=56;QD=39;BC=23,0,0,0;QP=100,0,0,0;PC=51;IC=0;DC=0;XC=1;AC=2;AF=1.00 GT 1/1 1
AL123456 5123 7267 gyrB . -1 -1 . . . . . . . . 0
AL123456 1917940 1918746 tlyA AL123456 1917971 1917972 . 636 A G PASS DP=16;TD=20;BQ=40;MQ=56;QD=39;BC=0,0,16,0;QP=0,0,100,0;PC=111;IC=0;DC=0;XC=4;AC=2;AF=1.00 GT 1/1 1
AL123456 3073680 3074471 thyA AL123456 3073867 3073868 . 716 T C PASS DP=18;TD=27;BQ=40;MQ=52;QD=39;BC=0,18,0,0;QP=0,100,0,0;PC=137;IC=0;DC=0;XC=2;AC=2;AF=1.00 GT 1/1 1
AL123456 2518115 2519365 kasA AL123456 2518918 2518919 . 596 G A PASS DP=15;TD=19;BQ=40;MQ=57;QD=39;BC=15,0,0,0;QP=100,0,0,0;PC=102;IC=0;DC=0;XC=1;AC=2;AF=1.00 GT 1/1 1
AL123456 2101651 2103042 ndh . -1 -1 . . . . . . . . 0
AL123456 2725571 2726087 oxyR . -1 -1 . . . . . . . . 0
AL123456 2726193 2726780 ahpC . -1 -1 . . . . . . . . 0
AL123456 1673440 1674183 mabA . -1 -1 . . . . . . . . 0
AL123456 1674202 1675011 inhA . -1 -1 . . . . . . . . 0
AL123456 408634 409173 furA AL123456 408722 408723 . 590 C T PASS DP=15;TD=19;BQ=39;MQ=53;QD=39;BC=0,0,0,15;QP=0,0,0,100;PC=57;IC=0;DC=0;XC=0;AC=2;AF=1.00 GT 1/1 1
AL123456 408634 409173 Rv0340 AL123456 408722 408723 . 590 C T PASS DP=15;TD=19;BQ=39;MQ=53;QD=39;BC=0,0,0,15;QP=0,0,0,100;PC=57;IC=0;DC=0;XC=0;AC=2;AF=1.00 GT 1/1 1
AL123456 1792400 1793740 Rv1592c . -1 -1 . . . . . . . . 0
AL123456 2006636 2006947 Rv1772 . -1 -1 . . . . . . . . 0
AL123456 2516787 2517695 fabD . -1 -1 . . . . . . . . 0
AL123456 2520743 2522164 accD6 AL123456 2521341 2521342 . 755 T C PASS DP=19;TD=20;BQ=40;MQ=52;QD=39;BC=0,19,0,0;QP=0,100,0,0;PC=104;IC=0;DC=0;XC=0;AC=2;AF=1.00 GT 1/1 1
AL123456 156578 157600 fbpC AL123456 157291 157292 . 1608 C T PASS DP=41;TD=47;BQ=39;MQ=49;QD=39;BC=0,0,0,41;QP=0,0,0,100;PC=59;IC=0;DC=0;XC=0;AC=2;AF=1.00 GT 1/1 1
AL123456 3505363 3506769 fadE24 . -1 -1 . . . . . . . . 0
AL123456 3153039 3154631 efpA . -1 -1 . . . . . . . . 0
AL123456 4007331 4008182 nhoA . -1 -1 . . . . . . . . 0
AL123456 4407528 4408202 gid AL123456 4407719 4407720 . 612 G C PASS DP=16;TD=17;BQ=38;MQ=58;QD=38;BC=0,16,0,0;QP=0,100,0,0;PC=38;IC=0;DC=0;XC=1;AC=2;AF=1.00 GT 1/1 1
AL123456 4407528 4408202 gid AL123456 4408155 4408156 . 848 A C PASS DP=22;TD=27;BQ=39;MQ=58;QD=38;BC=0,22,0,0;QP=0,100,0,0;PC=43;IC=0;DC=0;XC=1;AC=2;AF=1.00 GT 1/1 1
AL123456 781560 781934 rpsL AL123456 781686 781687 . 1353 A G PASS DP=34;TD=38;BQ=40;MQ=54;QD=39;BC=0,0,34,0;QP=0,0,100,0;PC=125;IC=0;DC=0;XC=0;AC=2;AF=1.00 GT 1/1 1
AL123456 2288681 2289241 pncA . -1 -1 . . . . . . . . 0
AL123456 4239863 4243147 embC AL123456 4242642 4242643 . 841 C T PASS DP=25;TD=28;BQ=40;MQ=55;QD=33;BC=0,1,0,24;QP=0,4,0,96;PC=52;IC=0;DC=0;XC=1;AC=2;AF=0.96 GT 1/1 1
AL123456 4246514 4249810 embB AL123456 4247430 4247431 . 1329 G C PASS DP=35;TD=47;BQ=38;MQ=57;QD=37;BC=0,35,0,0;QP=0,100,0,0;PC=63;IC=0;DC=0;XC=0;AC=2;AF=1.00 GT 1/1 1
AL123456 4243233 4246517 embA . -1 -1 . . . . . . . . 0
AL123456 759807 763325 rpoB AL123456 761154 761155 . 712 C T PASS DP=18;TD=23;BQ=40;MQ=59;QD=39;BC=0,0,0,18;QP=0,0,0,100;PC=110;IC=0;DC=0;XC=1;AC=2;AF=1.00 GT 1/1 1
AL123456 2153889 2156111 katG AL123456 2155167 2155168 . 550 C G PASS DP=14;TD=21;BQ=39;MQ=60;QD=39;BC=0,0,14,0;QP=0,0,100,0;PC=107;IC=0;DC=0;XC=1;AC=2;AF=1.00 GT 1/1 1
