Screening for high-impact mutations from WES-based variant calling and annotation

Question

[soniabedi.07]

I have performed WES with human sample followed by variant calling by Mutect2 and variant annotations. I am looking at few genes of interest, the problem is that even for those few genes I am getting a lot of variants. Is there any basis of shortlisting variants with probable deleterious impact?? Any suggestions??

[Pierre Lindenbaum]

search this site for VEP, snpEff, annovar....