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I have a VCF file and wish to calculate a few indices of population divergence over a sliding window.

I consider using pypgen but the documentation is currently very limited. Can you please give me an example (for Jost'D for example) of a code that would work?

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  • $\begingroup$ vcftools can compute a few things in sliding windows (Tajima's D, Pi, Fst, LD at least), but that's probably not enough, is it? $\endgroup$ – AlexDeLarge Mar 15 '17 at 19:30
  • $\begingroup$ Nope it is not indeed. It cannot calculate Jost's D or Dxy for example. There is also EggLib (for which I am currently reading the documentation). $\endgroup$ – Remi.b Mar 15 '17 at 19:33

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