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  • pitch_
    Junior Member
    • Mar 2019
    • 8
    #1

    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?
    Attached Files
    Tags: angsd, dxy, ngspopgen
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