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?
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?