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Old 03-10-2020, 12:40 AM   #1
pitch_
Junior Member
 
Location: Singapore

Join Date: Mar 2019
Posts: 5
Default Calculating per site Dxy

Hi everyone,

I am trying to calculate Dxy per site between two populations from ANGSD output. I am using the CalcDxy.R script from NGSpopgen for this purpose. I seem to be getting really high Dxy estimates for all my SNP sites, these are very different from the Fst estimates of the same comparison. I have attached a manhattan plot to illustrate this.

Other than quality filters, I have used SNP_pval 1e-6 and skipTriallelic 1 during SNP calling.

Does anyone have any idea as to why I am getting numbers like this?
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