I am using the weir-fst in vcftools to calculate the pairwise fst. I have also written my own script using the Weir and Cockerham 1984.
The puzzling thing is that I get different estimates, the difference is between 0.004 to 0.01 but this is still puzzling to me, if both calculations are based on the same formula and considering the deterministic nature of weir-fst, I should get exactly the same estimates using exactly the same data.
I was wondering whether it is possible to get access to vcftools pairwise fst source code. I would also appreciate if you could share your ideas about this in case you have similar experience.