Test MAC>=2 filtering before and after HiPhase

[hangsuUNC]

Will it change performance when doing MAC>=2 filtering before and after Hiphase? Doing filtering before Hiphase may reduce computational burden.

[hangsuUNC]

Here is the comparison based on main branch. The first panel of results is MAC filtering after hiphase, the second panel is MAC filtering before hiphase. You may notice SNP and indel recall drops but after shapeit, SV recall is improved.

[samuelklee]

What was the conclusion? Also, I’m not sure I understand the color coding above. Does [green, red] cover [0, 1] identically for each table? If so, this is a bit counterintuitive. I might instead suggest shading just the second table relative to the first, with green and red indicating increased and decreased performance, respectively.