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broadinstitute / genetic-prevalence-estimator

https://genie.broadinstitute.org/
BSD 3-Clause "New" or "Revised" License
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"Included from" column blank #85

Closed sambaxter closed 2 years ago

sambaxter commented 2 years ago

There are some variants coming into the recommended list where the included from column is blank (see example: https://website-sauthoia2q-uc.a.run.app/variant-lists/d02e0854-2c1d-47cf-a245-2ffe8681e19e/) Interestingly many of these have clinvar listings so I think there is a bug in the logic

nawatts commented 2 years ago

It looks like the issue is that clinical significance is formatted in the import pipeline to replace underscores with spaces and the frontend code is comparing those to the versions with underscores to determine determine the category.

https://github.com/broadinstitute/aggregate-frequency-calculator/blob/fa55b0beda132977eba115e80bf907fdecd465a5/data-pipelines/import_clinvar.py#L166-L171

https://github.com/broadinstitute/aggregate-frequency-calculator/blob/fa55b0beda132977eba115e80bf907fdecd465a5/frontend/src/constants/clinvar.ts#L3-L36