Question: how to compute Dxy using pool-seq frequency data.
gravatar for AGE
15 months ago by
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, 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 gives you the difference in allele frequency between two populations, not the actual frequency within each population.

snp R genome • 540 views
ADD COMMENTlink modified 8 months ago by samh0 • written 15 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 8 months ago by samh0
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