I am trying to annotate few VCF files from VEP with Cosmic ID's and same VCF is being annotated using Cosmic VCF's. For some reasons I am getting I am more Cosmic hits from VEP annotation compare to the direct annotation from Cosmic VCF files.
If some one else has observed same trend ? How VEP is picking up cosmic annotations ? If sources are same then why I am getting different result from both.