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hammerlab / cohorts

Utilities for analyzing mutations and neoepitopes in patient cohorts
Apache License 2.0
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Fix effects filtering for splice sites #256

Closed tavinathanson closed 7 years ago

tavinathanson commented 7 years ago

Until varcode handles this better, I've just added some logic to filter_effects that handles splice sites with alternate effects that we don't want to filter out + relevant tests.

Fixes #255

coveralls commented 7 years ago

Coverage Status

Coverage increased (+0.2%) to 52.885% when pulling 645f9c1e8b7c54b88c54eab88e6a9b2b603cb2e4 on fix_effects_filtering into f9f4af2384760a656acadbfd74c5ccd8fade522a on master.

tavinathanson commented 7 years ago

Evaluated impact on lung data here (sorry for private repo link): https://github.com/hammerlab/msk-bms-lung/blob/master/analyses/notebooks/_exploratory_notebooks/Compare%20Cohorts%20Versions%20on%20mini_data.py%20vs.%20New%20Splice%20Filtering.ipynb