finding functional rare and synonymous alleles in a vcf file

Hello, I have to identify both rare synonymous and and functional variants in a humans exome for each gene region. I know there are some ready to use tools , bus also was suggested not to trust them very much. I think I will need to start to write my own script R, but have no idea, with what to start my code- like which libraries and functions to use. So, any suggestions will be appreciated.

HI @raven1960,
You have asked a very specific genetics question which is probably more suited to this different venue:

It seems unlikely that any R/BioConductor package already designed and distributed to solve this problem is not trustworthy - I'd start with the existing tools before trying to reinvent the wheel!

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