How to set the size of window for calculating Fst?
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2.6 years ago
serpalma.v ▴ 70

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!

SNP Fst window • 1.4k views
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