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simonhmartin / genomics_general

General tools for genomic analyses.
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Query Regarding Fst Calculation Method in popgenWindows.py #109

Open weirdfanny opened 9 months ago

weirdfanny commented 9 months ago

Hi Simon,

I have a quick question regarding the Fst value output from popgenWindows.py: What method did you use for the calculation of Fst? It seems like it is estimated using the method described in Weir and Cockerham’s 1984 paper, as some values appear to be negative. Could you please confirm if my assumption is correct?

Thank you for providing such a helpful tool for us!

Best regards, Guannan

simonhmartin commented 9 months ago

Hi Guannan, It uses the formula for "Kst", Equation 9 from:

Hudson, R. R., Boos, D. D., & Kaplan, N. L. (1992). A statistical test for detecting geographic subdivision. Molecular Biology and Evolution, 9(1), 138–151. https://doi.org/10.1093/oxfordjournals.molbev.a040703

This formulation suing pi allows inclusion of sites with partial missing data, and is not very sensitive to low sample sizes.