With all the fuss we make about our resources for human genomes, you might think the VEP was just for human; it’s not. We have really useful resources, like SIFT, phenotypes and caches for loads of other species in Ensembl.
All Ensembl vertebrate species have a cache available to use with the VEP, including all the gene data the VEP needs. If the species has known variation data, that will also be included in the cache. The best way to install the caches is as part of the install.pl script as then the VEP can find them easily, but you can also download them from our FTP site – just make sure you tell VEP where you’ve stored them. For mouse, there is also regulatory data in the cache, allowing you to return if a variant falls in a promoter, enhancer etc, and even filter by tissue.
Known phenotypes, indicating if a variant, gene or locus have been previously linked to a phenotype, are available for a number of species through the VEP. Many livestock species have QTLs from Animal QTLdb, many more species have gene/phenotype links from OMIA, plus we have species-specific data from sources like zFIN, IMPC and RGD.
For missense variants, SIFT scores have been pre-calculated to determine the likelihood that an amino acid change will affect a protein for farm animals and model organisms.