Is it possible to use vcftools weir-fst-pop on haploid genomes? I do not seem to be able to find any option to specify the ploidy of my samples.
Thank you in advance.
Have you actually found a solution? (I have the question)
Fst involves measuring expected heterozygosity. Given that, it is impossible to calculate Fst for haploid organisms.
Technically you can calculate Fst for haploids using haplotype diversity instead of heterozigosity, but I guess vcftools does not take that into consideration. Thank you for your reply.
Does anyone would know a tool that computes FST on haploid populations thanks to SNPs data?
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