VCF coodinates to Genomic Features from GFF

[jgibbons1]

I think this is a relatively simple question but I haven't been able to figure out a solution yet.

Basically, I have a VCF file of variants and a GFF file of the genome with genomic features. I would like to extract the genomic features (introns, exons, etc.) of each of the variants in the VCF file.

Is there a simple way to glean this information?

[dpryan]

Have you tried using snpEff? I imagine that it can do most of what you want.

[jgibbons1]

Hmmm...have not seen snpEff before but it looks promising.

Thanks for the pointer. I will give this a try.

Any other solutions?