Have you checked out scikit-allel? It is fairly comprehensive in terms of calculating basic population stats, and the developer is highly active.

scikit-allel: http://scikit-allel.readthedocs.io/en/latest/index.html

scikit-allel example: http://alimanfoo.github.io/2015/09/21/estimating-fst.html

zarr: https://github.com/zarr-developers/zarr