I am very new to WGS analysis. I have a multisample VCF file that I have annotated using snpEFF.
I wanted to see if I can find what alternate alleles are conserved between samples for each genomic location.
For eg: Chr1 pos: 1001, has a reference A and the alternate allele seen are T, AAT, TTT, AA and there are 10 samples.
I want to count what samples have TTT, AA and so on. This way I can understand what allele is dominant across samples for each position.
All help is appreciated