how to add a column summarizing in which samples the variant was identified

Question

[Adham]

Dear colleagues,

I need your help. I have a csv file (I also have the vcf files) containing the annotation results of the varians (SNV, InDels) of several samples combined. To facilitate prioritization I would like to add a column summarizing in which the variant was identified as homozygous and another column for the heterozygous variants (below an example for four samples).

Thanks in advance!!

CHROM   POS REF ALT Consequence sample1 sample2 sample3 sample4
chr1    17379   G   A   splice_polypyrimidine_tract_variant 0/1 0/0 0/0 0/0
chr1    1175818 A   G   missense_variant    0|1 0/1 0/0 0/1
chr1    1175880 G   A   missense_variant    1/1 1/1 1/1 1/1
chr1    6454481 C   T   synonymous_variant  0/0 0/1 0/1 0/0
chr1    44139023    G   GTCA    inframe_insertion   1|0 0/0 0/0 0/0
chr1    157124860   G   C   missense_variant    1/2 2/2 1/2 1/2
chr6    29944144    C   T   synonymous_variant  2/2 1|3 1/2 1/2
chr9    136011699   G   A   synonymous_variant  0/2 1/2 0/1 0/1
chr11   20508289    G   T   splice_polypyrimidine_tract_variant 1/3 1/2 2/3 1/2
chrX    136532301   G   T   splice_donor_5th_base_variant   0   0/0 0/1 0/1