VCFTools weir-fst-pop on haploid organisms

Question

[kawaiilain]

Hello,

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.

[guillaume.rbt]

Hi, Have you actually found a solution? (I have the question)

Answer 1

[Adrian Pelin]

Fst involves measuring expected heterozygosity. Given that, it is impossible to calculate Fst for haploid organisms.

[kawaiilain]

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.

Answer 2

[guillaume.rbt]

update : Does anyone would know a tool that computes FST on haploid populations thanks to SNPs data? Thanks