NCBI has announced big changes to how dbSNP manages human variation data, which will be reflected in Ensembl. These changes include a new allele normalisation approach and the removal of some older population genetics data.
Author: Emily (Outreach)
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.
Ensembl 98 (and Ensembl Genomes 45) are due out next month, so it’s time to pig-out on the tasty morsels we have to offer. As with all releases, we cannot guarantee that anything listed here will make it into the final release.
The archive website for Ensembl 76 will be retired with the release of Ensembl 98 in the Autumn. This is inline with our rolling retirement policy, where archives are retired after five years, unless they contain the last instance of an important dataset for a key species.
The database will still be available for direct queries and on our FTP site.
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.
Work continues on our exciting new website, which is available as a pre-alpha release. We’ve been consulting with some of you in various ways, such as interviews and meetings, because we want to make sure that the new Ensembl serves your needs. We’re now asking for your help with a short survey, which will just take a couple of minutes to fill in. Plus, you can enter into a draw to win an EMBL-EBI t-shirt.
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.