Window-based Fst analysis

Question

[seta]

Hi all,

I used vcftools for Fst calculation of a set of snp (about 2000) with varying window size and step, like window and step size of 50bp-5bp, 500bp-50bp, 1000bp-100bp, and 100kbp-10kbp. Obviously, the calculated Fst is different among different parameters. But, I'm not sure how I should select the most appropriate window size and step. In this regard, I read in this forum that the variance inflation factor (VIF) and LD for each window should be calculated. However, I didn't see such the calculation along with Fst analysis in papers and also have no view how the right window size and step can be selected based on the VIF and LD. Could you please share your idea and any experience on this issue?

Thanks a lot

[Chenfei Zheng]

Hi, seta Have you found the way to choose the most appropriate window size for Fst caluculation?