This is a test version of Biostars. For the public version, visit https://www.biostars.org.
What's the difference between weighted Fst and mean Fst from VCFtools?

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.

vcftools weighted fst mean fst
• 10,971 views • link
written by coly_fu • coly_fu

1 answer

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?

• 0 views • link
written by coly_fu • coly_fu

Log in to answer this question.

More posts like this