What's the difference between weighted Fst and mean Fst from VCFtools?

Question

[coly_fu]

Hi, there,

I have got two Fst estimators from VCFtools, the mean and weighted. Since there's a big difference between them, I can't decide to use which one in my study. I have spent hours to Google, but still have no idea yet.

I need your help, thank you.

Answer 1

[coly_fu]

Maybe I have found the answer. The weighted Fst was just calculated in a window mode. So weighted Fst = sum(numerators) / sum(denominator) when mean Fst = average per site Fst.

So weighted Fst has more weight on sites have a bigger between population variance.

Is it?