manhattan plots with nucleotide diversity and dxy estimates

Question

[truebeliever24]

Hi everyone,

Sorry for the ignorant question, but I want to create two separate manhattan plots for whole genome data (SNPs), one using dxy estimates and one using pi estimates across all of the chromosomes. I have these data in hand for each window, but I don't know how to calculate the p-values that I need for each manhattan plot. Where do they come from? I'm interested in using the manhattan plots to identify outlier SNPs for each analysis. Any help would be greatly appreciated. Thank you!