I have list of snps and trying to annotate them using Annovar. How can I use Annovar for classifying SNPs into Missense, Silent and Others using Annovar tool? Can we calculate hom/het ratio also using Annovar?
They have a detail tutorial section where you can just follow to get the Snps to be annotated. For the hom/het ratio, I am not sure if annovar can do it for you or not. But it is very easy for you to calculate based on the Annovar output (or even, the original vcf)