How to handle cases and controls in one Matrix Table or merge two table after their processing?

I want to process my samples as two separated groups.

  1. I already split my “big” Matrix Table into 2 separated Matrix Tables and process each of them. But I don’t know how to merge them correctly.
  2. I mean there is another one approach with marking samples by a list of indices inside one mt.
    How can I solve this?

I’m not sure exactly what you want to do yet. This cheat sheet has different ways to merge matrix tables on it:

Are you just looking for union_cols? Or are you doing something more complicated?