Hi Chris, looking good.

A few small suggestions in the implementation.

On the testing side, re when to use pytest.parametrize the key question is whether it means you can avoid duplicating testing code. I.e., you should be able to run at least some code under all values of the variables you are parametrizing, other there is no point and witchery is right you're better off to break up into separate functions. I think this applies to the test_snp_allele_frequencies() function.

Re test_gene_cnv_frequencies() there's a couple of things could be tightened up. More than happy to discuss or do paired if not immediately obvious.

Awesome 💐