I think unfortunately there is no correct way to calculate nucleotide diversity from the HapMap3 data, as you need to know the denominator which should be the number of sequenced bp (not the window size nor the number of SNPs). See this paper for reference on why: https://doi.org/10.1111/1755-0998.13326
I think unfortunately there is no correct way to calculate nucleotide diversity from the HapMap3 data, as you need to know the denominator which should be the number of sequenced bp (not the window size nor the number of SNPs). See this paper for reference on why: https://doi.org/10.1111/1755-0998.13326