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KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
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New databases creation #211

Closed RP-Bioinfo closed 3 months ago

RP-Bioinfo commented 5 months ago

Hi, I would like to update Clinvar, Clinvar_ACMG and GnomAD to the latest releases. Do you have specific scripts for the creation of these databases starting from Clinvar XML full release and GnomAD raw files? Do you have already in program to update these databases shortly?

Best Regards,

Riccardo

kmoad commented 4 months ago

Clinvar, and Clinvar_ACMG are updated on the first of each month. You can get the updates with oc module update or in the store tab of the GUI. We are working on an updated GnomADv4 annotator https://github.com/KarchinLab/open-cravat/issues/202

I can share the clinvar build scripts if you'd like to modify them?

RP-Bioinfo commented 4 months ago

Ok thanks. It will be really appreciated if you share me clinvar build scripts!

kmoad commented 3 months ago

I've uploaded the autobuilder scripts here https://github.com/KarchinLab/open-cravat-extras/tree/main/module-builders/autobuilders

There is some internal stuff in there that is used to trigger automatic builds, but the files you want are clinvar/clinvar.py and clinvar_acmg/build.py. These should download clinvar data and build the OpenCRAVAT sqlite databases. You may have to make some minor edits to get it running on your machine.

RP-Bioinfo commented 3 months ago

Thanks for the scripts and for the fantastic work that you're doing on open-cravat!