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?
How are your subpopulations defined? (I may just go ahead and add this to PLINK, but I first want to make sure that your subpopulations are defined in a PLINK-friendly manner.)