You can directly use the contig as input in Mutation Taster Translate the contig and align with protein sequence, will help u to find the amino acid position in the protein.

For Translating

For functional analysis of nsSNP

a) HANSA (From our lab),

b) PolyPhen

c) Mutation Taster

d) Condel

e) Panther

Hope this helps

If you need to extract the protein coordinates for your mutations, Oncotator tool might be helpful -- it will also provide you some extra annotation.

For testing functional impact, there is also Mutation Assessor.

Use snpEff to annotate your VCF file. In case of nonsynonymous mutation, it gives you the position of amino acid that has changed along with the before-after amino acids. I think that information can be fed into Polyphen2.