I have a large WGS dataset composed of ~350 individuals from 6 different populations and I want to figure out the fixed differences between each population (and the rest) for the sake of calculating the direction of selection: DoS = Dn/(Dn + Ds) - Pn/(Pn + Ps).

I can easily calculate the within-population polymorphic differences (Pn/Ps) by splitting the VCF based on population and running each through SnpEff separately, but it is the Dn/Ds ration I'm having trouble figuring out (fixed differences between a given population and the rest). Any ideas?
`bcftools` will do this with `--private`. See [here][1]. You'll need to specify the samples belonging to the population of interest.


  [1]: https://samtools.github.io/bcftools/bcftools.html