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?

Geneland seems to calculates Weir And Cockerham Fstat. Though you will have to convert plink files into matrix: "Diploid codominant genotype data. A matrix with one line per individual and 2 columns per locus"

Thanks for the reply. Geneland seems to be useful and i will try to give a shot to coverting the data into required format. Though it will be preferrable to have a tool which directly uses PLINK files since it seems to be pretty prevalent standard. I am pretty surprised by the scarcity of such tools.