I have a vcf file with 3 different samples that are compared to the reference genome. I am looking for a way to count the ALT genotypes that appear for each sample. But I would like to take this a step further by using some code to look into the accumulating variants. Thus, I would like to view counts of ALTs genotypes appearing in sample 1 + 2, and sample 1+2+3. I am currently looking into methods using the following: vcftools, bcftools, vcfR, java, and perl. Any help would be greatly appreciated! Thank you.