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broadinstitute / lrma-aou1-panel-creation

Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 1 long-reads callset.
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Test MAC>=2 filtering before and after HiPhase #40

Open hangsuUNC opened 1 month ago

hangsuUNC commented 1 month ago

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

hangsuUNC commented 1 month ago

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.

image
samuelklee commented 1 month ago

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.