number of individuals in each genotype group for a particular SNP

Question

[ATCG]

I have genotype plink files for 299 individuals and I'm interested in finding the number of individuals in each genotype group for a particular SNP. e.g: SNP1234--> GG n=?; GAn=?; AAn=?. Thanks!

[Kevin Blighe]

I am not sure that PLINK actually caters for this. Why not just do it manually by outputting your transposed dataset and then using a simple awk command to extract your genotype of interest?

[Ram]

I'd use bcftools query and then use awk. bcftools might even have a summary operation.