Compute P-Values for SNP Fst from Pairwise Fst Calculations (--weir-fst-pop)

Question

[Armin]

Hi Everyone,

I've calculated pairwise Fst values for two populations using PLINK's --weir-fst-pop option, and I now have Fst values for each SNP. How can I calculate p-values for these Fst values to determine which SNPs show statistically significant genetic differentiation? I know that I can plot the fst values directly but I need to have the p values to reduce the number of significant ones.

Thanks

Armin

Answer 1

[Jorge Amigo]

Why exactly you want to have p-values, since Fst is already enough to describe differentiation degree?

Have a look to this paper, which cites the original interpretation of F-statistics in a very succint way:

Fst values from 0.05 to 0.15 => moderate differentiation

Fst values from 0.15 to 0.25 => high differentiation

Fst values greater than 0.25 => very high differentiation

[Armin]

thanks for the reply Jorge. The problem is that the manhattan plot is too noisy although I made sure I picked only 1k high quality snps. So my interest in p value is to reduce the noise and possibly that noise see the hits.

[Jorge Amigo]

So what about plotting Fst > 0.25 values only? Or maybe the top Fst values ones only? That way you would be selecting and plotting statistically significant values, as you intented to do so with p values.