Best way to annotate a VCF file with a GFF File

Question

[Daniel E Cook]

Does anyone know of a good way to annotate a VCF File with a GFF File? We would like to be able to do this in order to examine variants within associated regions using genome wide association.

I was thinking of writing a tool for doing something along these lines, but wanted to ask if anyone knew of a good tool. Ideally, annotations would be placed into the INFO line of a VCF...

Thanks!

Answer 1

[Devon Ryan]

Just use the VariantAnnotation package from Bioconductor. So, for example, section 3 in the vignette.

Edit: BTW, if your genome is supported by Ensembl then you can probably also just use VEP.