New databases creation

[RP-Bioinfo]

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]

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 #202

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

[RP-Bioinfo]

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

[kmoad]

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]

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