Predict the effect of SNPs in a VCF file generated using a Trinity assembly

Question

[TrentGenomics]

Is there software or script available to predict the effect of SNPs that have Trinity headers? Reference databases use different header formats than Trinity, so I can't use snpEff etc.

There must be a solution to this. Maybe not?

Answer 1

[Istvan Albert]

You can build custom annotations for SnpEff from a GFF file:

http://snpeff.sourceforge.net/SnpEff_manual.html#databases