Hi All,
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!
Hi Rubal,
It's so late; however, could you please tell me how you solve the problem?