[Vcftools-help] nucleotide divergence statistic (pi)

[Mohammed Al-A. <ab...@sq...>]

Dear vcftools team,

I would like to know what is the formula used in calculating the nucleotide divergence statistic.
I used the command "--window-pi" on SNPs called on a single individuals and I am getting results but I am not sure if one individual is good enough to call the results selection signatures. In one of the previous posts I saw that the nucleotide diversity is calculated within the individual (https://sourceforge.net/p/vcftools/mailman/message/29923488/). In another post it is mentioned that it is the estimate of the average number of differences between a pair of chromosomes (https://sourceforge.net/p/vcftools/bugs/42/). These two posts tell me that one individual is enough for the analysis but is this the same Nei's pi (Nei, M. (1987).Molecular Evolutionary Genetics.Columbia Univ. Press, New York.).
Is there possibly a formula that I can cite or look at to see how the command works?
I would really appreciate your kind help.