[Vcftools-help] Information needed on nucleotide diversity calculation methodology

[Andre M. <av...@gm...>]

Hi everyone,

I've calculated nucleotide diversity with a sliding window using only 
one diploid genome, and the output look absolutely fine, but I'm not 
sure if the nucleotide diversity calculated was between the two 
haplotypes of my individual, or between my individual and the reference 
sequence. I'm asking because the first option would be useful to me, but 
not so much the second.

Thanks for any help,

Andre