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exomiser / Exomiser

A Tool to Annotate and Prioritize Exome Variants
https://exomiser.readthedocs.io
GNU Affero General Public License v3.0
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Use ClinVar variants for variant scoring #304

Closed julesjacobsen closed 5 years ago

julesjacobsen commented 5 years ago

I've put some changes in for this which is now a lot more consistent in reporting ClinVar variant data. Previously it would only report it for non-synonymous, coding region variants, but now they will be reported for all variants.

Secondly, variants with a ClinVar primary interpretation of Pathogenic, Pathogenic_or_likely_pathogenic and Likely_pathogenic , irrespective of their review status, are scored as maximally pathogenic.

Note that commit 7aa8485 doesn't override the frequency filtering for pathogenic ClinVar variants or implement a user-definable whitelist. Shall we wait for the performance testing/next release to re-visit those ideas?

Originally posted by @julesjacobsen in https://github.com/exomiser/Exomiser/issues/152#issuecomment-448565905

julesjacobsen commented 5 years ago

Just created this from #152 as we ended up talking about 2 related issues on that thread. This issue is to document adding an new feature to use ClinVar pathogenic variants in variant scoring. This has been implemented as a non user-definable feature.