I have a VCF with ~6000 variants. The build is GRCh37.
I want to annotate each variant with its type (substitution, deletion, inversion) and its effect (missense, silent, intergenic). If there are competing or multiple effects, I want to know which one is the most deleterious.
What tool is the best way to do this, and what database?
Currently, I used ANNOVAR, but I am getting many missing fields. For some of the variants, it will label the type (eg nonsynonymous SNV) and for others it will label the effect (e.g. nonframeshift deletion) but not both and not for all fields.