How to compare groups using WGS data?
I'm not familiar with the program, but apparently Hail is setting itself up as a swiss-army chainsaw project for doing downstream analysis on variant-called datasets.

An overview of Hail can be found here:

http://blog.cloudera.com/blog/2017/05/hail-scalable-genomics-analysis-with-spark/

A tutorial on association testing can be found here:

https://hail.is/hail/tutorial.html#Association-testing