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.
Author: Emily (Outreach)
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 RefSeq column on our gene pages has changed.
We’re moving towards a more unified gene-set with RefSeq, with biologically important transcripts being highlighted as MANE. This means displays you’re used to seeing will be updated to reflect these changes, and this may affect the way you have been working with Ensembl.
We’re fortunate to be part of the EMBL European Bioinformatics Institute (EBI), which puts us alongside stellar bioinformaticians and resources in every discipline. From this, great collaborations can grow. We’ve already worked with our colleagues at Gene Expression Atlas and Reactome to embed widgets in Ensembl for viewing baseline gene expression and biochemical pathways respectively, but our latest collaboration is with the Protein Data Bank in Europe (PDBe) to show genetic variation on protein structures.
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.
As the community’s capacity for genome sequencing expands, so do its ambitions. Recently, many exciting global genomics projects have been launched, including the Vertebrate Genomes Project (VGP), Darwin Tree of Life (DToL), Earth Biogenome Project EBP, i5K (insects) and 10KP (plants). Between them, they aim to sequence the genomes of every eukaryote on Earth, and Ensembl are excited to take on the annotation of some of those genomes.
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.
Identifying the causal variants from a GWAS generally involves identifying the haplotype blocks that contain your variant of interest, rather than the variant and the gene it is affecting itself. To find the actual genes involved, you need to consider all variants in LD with your identified associations. Ensembl Post-GWAS analysis pipeline (PostGAP) can provide automatic fine-tuning of your GWAS variants, incorporating regulatory information and population-wide LD calculations, along with your VEP results.