People routinely ask me about a place to find pairwise Fst values. I have a dataset with 250,000 SNPs and 200 populations, and a script using plink that generates pairwise differences crosses populations. Here are two files with the results:
A file with the Fst values between populations in rows
A file with the Fst values between populations as a matrix
Looks like a good reference for a set of populations that aren’t covered so well by the Human Origins Fst panel. Makes a nice dendrogram when I try it : https://imgur.com/a/Vl6cfRR . You can see some intense branches on some populations there (strong founder effects I think?).
Unless I’ve done something wrong when downloading the file, only thing that looked very odd to me that popped out was that some of the Fst between some Siberian populations and Europeans looked way too low to be similar to what is the case in Global 25, Human Origins etc. E.g. See here – https://imgur.com/a/T0pIbQR
(Also on a lesser note some Fst to far populations seem odd – the Fst for Surui to British and Surui to Poles or Mbuti to British and Mbuti to Poles looks very different, which is not normally how it turns out for closely related populations. But the fine scale all looks like the standard thing to me!).
(Another Fst table for modern people calculated on the Human Origins with the ADMIXTOOLS function, can’t remember how many SNPs but think it got most of the 597573 – https://pastebin.com/8gHgy5Kj).
Is there any way to make the word identifications on the image readable? I tried opening it as a separate image and magnifying it, but the words overlap each other so much I can only read a few of them.