I have a VCF file having multiple population samples. Is there any way to calculate the observed counts of genotypes called and observed genotype frequency of a subset of individuals from a given population within VCF file?
For example (genotype freq) : 0|0 : 0.2, 0|1: 0.5, 1|1: 0.3
just an analogous to --freq option in VCFtools field that calculates the allele frequency of REF and ALT allelic forms at given site.
Thanks a lot!