Clinvar using CAVA?

[Sally Guthrie]

I would be interested in applying ClinVar annotations using CAVA, but I can't seem to find a good way to integrate the two. Are there any recommended methods for syncing ClinVar annotations of interest and CAVA?

Thanks!
Sally

[Elise Ruark]

Taking a quick look at the available formats for ClinVar annotations, I would recommend annotating their VCF with CAVA to ensure indel compatibility. Then use of the Gene and CSN fields will allow direct matching between the ClinVar file and your file of interest, irrespective of representation in the chromosome/position/reference/alternate allele columns.
CAVA does not currently support integration of external annotations beyond dbSNP, but we are also working on this functionality.
Best wishes,
Elise