I have a big SNP whole-genome dataset (~ 6,000,000 SNPs, in total) from over 60 individuals of 6 different locations (~ 10 individuals in each population). I want to assess the (Weir & Cockerham) FST among populations in order to get a FST matrix. Anyone knows how to do this? I wanna know if any of my populations is extremely different from the rest. Thank you.
Hi Mendieta,
There is a plethora of software that compute Fst using high throughput SNP data (e.g., Popgene, FSTAT, Hierfstast, Pegas, diveRsity, BayeScan... ).
This question has already been answered on ResearchGate. Please, find below some links that might be helpful.
http://www.popgen.dk/angsd/index.php/Fst
https://www.researchgate.net/post/What_is_the_software_for_Fst_estimates_using_a_thousand_SNP
https://www.researchgate.net/post/Does_anyone_know_how_to_use_Fstat_software_to_calculate_the_Fst_Fis_and_Fit_for_different_populations
VCFTools (Danecek et al., 2011) can be used for Fst calculation. For more details you can also refer to the article "Identifying signatures of positive selection in pigmentation genes in two South Asian populations" DOI: 10.1002/ajhb.23012
http://onlinelibrary.wiley.com/doi/10.1002/ajhb.23012/abstract;jsessionid=33554013F60AEDB73B4AE0816C91BDBA.f03t01
The package SNPRelate is extremely fast for calculating the Fst values with a large number of SNPs.
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