Best way to annotate a VCF file with a GFF File
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!
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Devon Ryan
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Daniel E Cook
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Daniel E Cook
1 answer
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.
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