Question: Calculating Tajima's D from SNP frequency data
gravatar for mphillips6789
5.2 years ago by
United States
mphillips678910 wrote:

I have recently run some forward simulations that produce a table with with the major allele frequency for every SNP along single chromosome in my simulations populations. The table looks something like:


chr	pos	ref	pop1	pop2	pop3
3R	56	A	0.833	0.902	0.523
3R	89	C	0.711	0.622	0.623

I was primarily interested in doing some heterzygosity calculations and Fst estimations to compare to results from my real data set, which was straight forward enough. However, if possible, I would also like to do Tajima's D calculations across 50kb windows from this simulated data set. Apologize if this is actually something really simple, but not quite sure how to do this with just SNP frequencies based on what I have read on how to do this calculation.

snp R • 3.1k views
ADD COMMENTlink written 5.2 years ago by mphillips678910

Did you ever find a way to do this?

ADD REPLYlink written 15 months ago by Kevin Blighe55k
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