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genome / docker-basespace_chromoseq

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Fix VEP filter #31

Closed dhspence closed 5 years ago

dhspence commented 5 years ago

We're missing some gene variants in TP53 because they apparently have population AF >= 0.001. We should switch the VEP filter string to:

--filter "(MAX_AF < 0.001 or not MAX_AF) or (SOMATIC and (CLIN_SIG is pathogenic or CLIN_SIG is likely_pathogenic))"

I tested this and it works.

johnegarza commented 5 years ago

Fixed in dbd9d47 and added to the v12 repo tag/docker image