Functional annotation of VCF files

Question

[Sowmya Pulapet]

Hello everyone, I would like to know which tool or method to use to perform functional annotation of VCF files. My VCF files contain ensembl gene ids I need the gene ontology and other info for the same. Your suggestions would be really helpful.

Thanks in advance.

[iraun]

Hi! Are you familiar with the command line? If not, maybe a good starting point for functional annotation is VEP webinterface. If you are familiar with command line tools I'd recommend downloading VEP in your computer. Snpeff is also a nice alternative.