I know that Nei's Pi (nucleotide diversity statistic) is calculated per site using sequences belonging to more than one individuals. However, in vcftools, it seems like they can be calculated on a per individual bases (https://sourceforge.net/p/vcftools/mailman/message/29923488/). In another post by vcftools, it was defined as "the average number of differences between a pair of chromosomes" (https://sourceforge.net/p/vcftools/bugs/42/) which means to me that only one individual is enough for its calculation. We plan to use this method in a paper we are about to write since we don't have more than one individual per breed. Does anyone know the formula used in vcftools or if it is at all valid to calculate Pi in this way?
I would really appreciate your kind advice on this.