I would like to determine allele frequency difference of a set of SNPs (say 2500 SNPs) between various populations as my first experience in this regard. I think of using the statistical test (Fisher’exact or chi-square test) with the allele count for it. However, I see the estimating Fst value mostly used. Could you please let me know which method is more appropriate for finding varying SNPs among the populations and why?
Also, please kindly tell me what is the suitable tool for calculating Fst, there lots of tools, which one do you suggest? and what’s your advice for finding statistically significant outlier Fst?
Thanks in advance