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How to convert .tsv file to the VCF format using bcftools --tsv2vcf correctly?

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
tsv2vcf conversion

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time. Formatting bar

It's like creating a cow from a steak. This 'tsv' file was most certainly a VCF file. How about getting this original VCF file ?

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