pixy

Unbiased estimation of nucleotide diversity and divergence in the presence of missing data. pixy is a command-line tool for painlessly and correctly estimating average nucleotide diversity within (π) and between (dxy) populations from a VCF. In particular, pixy facilitates the use of VCFs containing invariant (AKA monomorphic) sites, which are essential for the correct computation of π and dxy in the face of missing data (i.e. always). Unbiased estimation of nucleotide diversity within and between populations.