I'm looking for a general variant annotator ... one that would call a variant as synonymous, non-synonymous, non-genic, UTR, frame-shift, truncation, etc. By general I mean that we should be able to supply a reference genome sequence (fasta), gene models (say, in GFF), and vcf-formatted SNPs or indels, and that's it.
Many or all of the tools I've looked at (Annovar, Ensembl's Variant Effect Predictor, etc.) depend on an external database (i.e. NCBI or EMBL) or requires you to build a local database, or only does SNPs, or ... you get the point. We need to look at the effect of both indels and SNPs, and we cannot use one of the publicly released builds for our organism. Any takers? (thanks in advance ...)