I am trying to figure out which tool VEP or Annovar, is most accurate in terms of SIFT and Polyphen annotation. I annotated my file with both Annovar and VEP. I got about 2386 SIFT deleterious variants and 1547 Polyphen deletrious from annovar. And from VEP I got 37323 SIFT deleterious and 26530 polyphen deleterious. But problem with VEP is that, it annotate different transcripts of a single genes, so there are many records for single snp.
So I am confused as to what tool I should use to find out deleterious variants.