Question: how to compute Dxy using pool-seq frequency data.
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gravatar for AGE
9 months ago by
AGE20
AGE20 wrote:

I'm wondering how Dxy is computed using allele frequency data from pool-seq.

For example here:

"Allele frequencies based on SNPs were estimated with snp-frequency-diff.pl, filtering with the same thresholds a described for FST estimates. We computed the measure of divergence DXY for bi-allelic loci (~99.2% of the total allele estimates) as the average number of nucleotide differences for each gene based on the formula using allele frequencies from Smith and Kronforst (2013) defined as Dxy = 1/n Σ pix(1-piy) - piy(1-pix)." (Schirrmann et al.,2018).

The snp-frequency-diff.pl gives you the difference in allele frequency between two populations, not the actual frequency within each population.

snp R genome • 346 views
ADD COMMENTlink modified 10 weeks ago by samh0 • written 9 months ago by AGE20

hi, have you found a solution for this ? I have used Popoolation and created the sync file. Now I want to calculate dXY but I'm still struggling. thanks

ADD REPLYlink written 10 weeks ago by samh0
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