HC pLoF filter for missense badness - Githubissues

broadinstitute / regional_missense_constraint

Code to calculate regional missense constraint

BSD 3-Clause "New" or "Revised" License

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HC pLoF filter for missense badness #284

Closed ch-kr closed 1 year ago

ch-kr commented 1 year ago

This PR adds a filter for high confidence predicted loss-of-function (pLoF) variants (as predicted by LOFTEE) prior to generating missense badness.

Minor changes:

Removed types from params in docstring
Removed outlier transcript filter (this was a duplicate filter; process_vep also removes outlier transcripts)

Major changes:

Added filter to remove pLoF that are predicted as OS or LC by LOFTEE; filter also removes variants that have LOFTEE flags (e.g., SINGLE_EXON)