I want to calculate markerwise Weir And Cockerham Fst for certain differentiating markers. I have my data in PLINK(bed/bim/fam) format. I have scourged the internet for packages to calculate the fst but very few seem to support native plink format directly as an input.
There exists snpstats(bioconductor R package) but the method of calculation seems to be a non standard one.
Can anyone suggest an R package/software that can calculate Fst(preferebly Weir And Cockerham) from PLINK format data as input?