Hello Biostars,
I have done targeted NGS in to discover novel variants associated with a trait of interest. I am currently trying to prioritize those variants from my created .vcf to then genotype them in a larger population. Part of our variant prioritization is determining how many of the subjects, out of the 183 total, have the variant of interest. I am wondering if anyone would know how to go about this, without having to hand count each GT field, or had any suggestions.
Thank you!
Does it matter if the genotype is homozygous or heterozygous? Or is the question just "how many sample have at least one allele with this variant"?
It is how many samples have at least one allele with an individual variant, and I have 7,531 variants I need to determine this for.
for a start: