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broadinstitute / gnomad_qc

BSD 3-Clause "New" or "Revised" License
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Assess how much sample QC metric distributions change when underlying set of variants being assessed changes #176

Open gtiao opened 3 years ago

gtiao commented 3 years ago

Will we need to update underlying set of QC variants for sample QC as more diverse samples get added to gnomAD?

gtiao commented 3 years ago

Pipeline (v3) currently uses v2.1 sample QC variants+purcell 5K to assess sample QC outlier metrics. We will need to run the entire sample QC process on v4 with both picking the new v4 sites and using the v2.1 + purcell 5K sites.

jkgoodrich commented 3 years ago

-Look at comparison of sample QC metrics using v2 sites compared to using newly picked sites. -Also look at the actual sample QC status with each