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arq5x / gemini

a lightweight db framework for exploring genetic variation.
http://gemini.readthedocs.org
MIT License
318 stars 120 forks source link

Update ClinVar VCF #641

Closed dgaston closed 8 years ago

dgaston commented 8 years ago

Looks like we should update the version of the ClinVar VCF being used for annotations. I noticed this because I am doing work on clinical specimens previously tested with other methods getting our clinical NGS pipeline operational and have come across variants annotated with a clinical significance of "other" in the 20150305 release that have been updated to pathogenic in newer versions. In this case the variant has always been pathogenic (since 2007 I believe) but ClinVar has had some issues with their VCFs and sorting things into the right categories.

arq5x commented 8 years ago

Awesome, Brent. Just a reminder to set the correct S3 permissions for the .gz and .gz.tbi file as I always forget to do so.

brentp commented 8 years ago

yep. doing a full install to check everything.