What's a good Variant effect predictor for draft genomes?

Question

[madkitty]

I'm working on an animal that has only a draft genome, no reference genome except for its mitochondrion. The mtDNA of this animal is well referenced, though I can't find it in the list of available genomes of the ensembl VEP. I obtained a list of SNPs from Samtools and now I need to annotate these variants and determine which one of these are non-synonymous. Anyone know a good tool for that?