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.
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HGVS notation is an excellent way to describe variants in proteins, and VEP can interpret variants described this way to see if they are already known or if they affect other genomic features, so long as there is enough information to find a unique genomic location. If there isn’t, the Variant Recoder can help you to find the variant you need.
Interpreting a single variant can be a lot more involved than just finding out its consequence. Sometimes to understand a variant, you need to know exactly where it falls, which exon, which amino acid, sometimes even which base in the codon. The VEP gives you all of this by default.
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If you’re really delving into the role of a particular genetic variant, you might want to know about that base position in other species. VEP can get you ancestral alleles in human and conservation scores in many species for a variant position allowing you to assess if a position is evolutionarily important, or if an allele matches our primate ancestors.
If you’re trying to work out which variants are associated with a phenotype or disease, a major thing you might want to know is if someone else has already spotted it. And if not the variant, maybe the gene that it hits. You can get that through the VEP.
The number of genes and transcripts we have in Ensembl can make your VEP results very big. Filtering your results after running the VEP is the best way to make this more manageable, but you can also reduce the results in your run itself, to only get one result per variant or variant/gene combo.
Did you know you can upload your own data for display alongside the reference genomes in Ensembl? For some file types, and files larger than 20MB in size you will need to create a URL to attach the data, rather than uploading from your local directory. It’s not difficult to create these URLs, but there are quite a few steps, so read on to find out how!
The VEP can work as an offline or a web tool and it’s also available as REST service. Perfect for integrating into pipelines or displaying data on the web, the REST API VEP endpoints can take input as HGVS, genomic loci or variant identifiers and can interpret common forms of non-standard HGVS. They are all available using both GET and POST protocols, supporting queries on single or multiple variants respectively.
Ever come across a transcript that seems to span multiple genes? These are called ‘readthrough transcripts’, or sometimes ‘conjoined genes’, and they’re more common than you might think. Read on to find out about what they are and what they do, and how we annotate these at Ensembl.