gnomad_methods icon indicating copy to clipboard operation
gnomad_methods copied to clipboard

Update clinvar VCF to lateset release

Open mike-w-wilson opened this issue 4 years ago • 3 comments

ClinVar releases a new VCF every month. gnomAD v3.1 used the same VCF/HT as v3 which dates to Sept 2019. The new ClinVar resource should be added to the reference data module as a new version in the clinvar VersionedTableResource.

mike-w-wilson avatar Dec 11 '20 19:12 mike-w-wilson

Do we have a way to automatically update this each month, or do we only update when someone needs the newer version? We should also make sure this version is added to release HT global and the VCF header

jkgoodrich avatar Dec 11 '20 19:12 jkgoodrich

The release table isn't actually annotated with this ClinVar table, right? It looks like this ClinVar table is only used in variant QC. So maybe we only need to update before generating a callset vs every month?

nawatts avatar Dec 11 '20 19:12 nawatts

OK, that makes sense, then this doesn't impact v3.1 release at all really. I don't think those plots will change much and we used other metrics for evaluation as well.

jkgoodrich avatar Dec 11 '20 19:12 jkgoodrich

Closing, this is not relevant for the gnomAD releases

jkgoodrich avatar May 12 '23 18:05 jkgoodrich