I calculated Weir and Cockerham's Fst using VCF tools and want to use simulations to have a feeling whether my high Fst regions are likely under neutrality. The populations I am studying have been through severe bottlenecks and I want to see if these alone could explain the highest Fst regions. I think in this scenario recalculating Fst after permutations of individuals would not be sufficient but please correct me if that is not the case.
As far as I am aware Fst calculations require heterozygosity information, which does not seem to be possible with coalescent simulations. Is the only solution to do forward simulations of diploid individuals?
I noticed that some coalescent simulators (ie Mlcoalsim) appear to calculate Fst, but I am not sure how this is possible under the coalescent framework. If anyone has any experience with this or suggestions that would be greatly appreciated.
Thanks in advance!