Hi everyone,

I have this vcf file which I want to filter and generate a second vcf file. I want to filter based on the genotype of fist two samples.

I am looking for variant where sample1 is 0/0 when sample2 is 1/1 and sample1 is 1/1 when sample2 is 0/0.

Following is how the rows of the vcf file looks like. Both sample1 and sample2 are 0/0 in the first example variant.

chr1    376878  .       A       C       17830.7 .       .       GT:AD:DP:GQ:PGT:PID:PL:PS       0/0:16,0:16:45:.:.:0,45,675:.   0/0:13,0:13:39:.:.:0,3
9,504:. 1/1:0,46:46:99:.:.:1855,138,0:. 1/1:0,46:46:99:.:.:1785,138,0:. 1/1:0,63:63:99:.:.:1876,189,0:. 1|1:0,61:61:99:1|1:376878_A_C:2423,183,0:37687
8       1|1:0,19:19:66:1|1:376878_A_C:914,66,0:376878   1/1:0,9:9:27:.:.:335,27,0:.     1/1:0,26:26:78:.:.:801,78,0:.   1/1:0,61:61:99:.:.:2812,202,0:
.       1|1:0,24:24:72:1|1:376878_A_C:1052,72,0:376878
chr1    376881  .       T       C       6133.93 .       .       GT:AD:DP:GQ:PGT:PID:PL:PS       0/0:16,0:16:45:.:.:0,45,675:.   0/0:14,0:14:42:.:.:0,4
2,538:. 0/0:36,0:36:99:.:.:0,99,1453:.  0/0:39,0:39:99:.:.:0,108,1620:. 0/0:53,0:53:99:.:.:0,105,1575:. 1|1:0,47:47:99:1|1:376878_A_C:2314,171,0:37687
8       1|1:0,22:22:69:1|1:376878_A_C:951,69,0:376878   0/0:9,0:9:24:.:.:0,24,360:.     0/0:25,0:25:66:.:.:0,66,990:.   1/1:0,67:67:99:.:.:1941,204,0:
.       1|1:0,22:22:66:1|1:376878_A_C:990,66,0:376878

Please tell me if anyone knows how to do this.
Thank you



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