Hello, I am trying to determine the window size to calculate Fst between two populations at each SNP within, then get the average of those Fst's. Do this in a sliding window approach.
I've seen a study stating that the size of the window was determined by estimating the length of linkage disequilibrium.
This thread ask almost the same quistion I am asking. But I do not know how to generalize from there.
Could someone give some tips on how to go about this?
I imagine it would be something like calculating the mean r2 over different window sizes, and then see at which size there is a dramatic drop in r2.
Thanks in advance!