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.
Is it true?
I think I will need to start to write my own script, but have no idea, with what to start my code.
So, any suggestions will be appreciated.