Ensembl VEP integrates information from many different resources to help you interpret the functional impact of your variants. It now reports when variants fall in sites with evidence of impact on protein interactions, as described in the IntAct database.
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Cool stuff Ensembl VEP can do: run faster with Nextflow
Ensembl VEP is now wrapped in a Nextflow pipeline which means you can analyse large variant sets more quickly using simple parallelisation.
Continue readingCool stuff Ensembl VEP can do: flagging variants predicted to allow NMD escape
A new plugin was released in Ensembl VEP version 105 which reports when a variant introducing a premature stop codon may allow the transcript to escape nonsense-mediated decay (NMD).
Continue readingUpdated G2P terms supported in Ensembl VEP
Recent changes to the terms used in the G2P database are aligned with global standards, but are not compatible with old versions of the VEP G2P plugin. We’ve updated the latest version of the VEP G2P plugin (Ensembl 105) to be compatible with both the old and new formats.
Continue readingCool stuff Ensembl VEP can do: protein annotations from neXtProt
Together with the neXtProt team, we’ve created a plugin for the command-line VEP tool to retrieve and report information about the protein location of missense and stop gained variants.
Continue readingUsing Ensembl VEP with Windows 10
Ensembl VEP has been developed for use on Linux systems and we recommend installing on a Linux system for the optimal installation and usage experience. However, we occasionally receive queries about using VEP in the Windows environment – this guide will help you get going if you are using Windows 10.
Continue readingCool stuff the VEP can do: Singularity
The quickest and most flexible way to run Ensembl VEP on large scale variant sets is to install and run it locally. Depending on the use case, the underlying architecture, and the available permissions, installing VEP prerequisites is prone to complications. To aid with this, we have made the VEP available with containers.
Continue readingCool stuff Ensembl VEP can do: disease information from DisGeNET
To better understand how your variants might be linked to disease, you can add information from DisGeNET to your VEP analysis. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models and the scientific literature, to provide disease associations with genes and variants.
Continue readingCool stuff Ensembl VEP can do: links to variation databases
When you find a variant you are interested in, you will want to thoroughly investigate all current knowledge about it. For each Ensembl release we update our variation databases with the latest public information from a wide range of resources and make summary information available in VEP. We now make it easier to link to fuller details in these resources by providing lists of names used for each variant in each.
Continue readingCool stuff the VEP can do: publication data from Mastermind
With absolutely tons of publication data out there, finding relevant information about your variants and genes of interest can be a struggle. We’ve been working with Genomenon to integrate Mastermind, the Genomic Search Engine, into VEP results, bringing you publication data about genes, variants, phenotypes, diseases and therapy evidence.
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