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.
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Using 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.
Continue readingCool stuff Ensembl VEP can do: one click BioMart
The web VEP tool gives you a lot of useful information about your variants, but you may want more details, for example about the genes your variants overlap: maybe you want to fetch their sequences, homologues or protein domains. With a single click, you can go straight to BioMart, using your list of genes or known variants as your filter.
Continue readingCool stuff Ensembl VEP can do – What’s in the cache and how does VEP use it?
We often get questions about Ensembl VEP caches – the compressed data files we create for each new Ensembl release, which can be automatically installed with the VEP installer script – so here’s a quick introduction to these handy data bundles.
Continue readingCool stuff the Ensembl VEP can do: getting and using allele frequency data
Allele frequency data is important for variant prioritisation – it helps to identify variants that are less likely to be causing a phenotype or disease. With the Ensembl VEP, you can get allele frequencies for variants that are identical with the variants you analysed and you can use allele frequencies to filter the results of your analysis.
Continue readingCool stuff the Ensembl VEP can do: annotating SARS-CoV-2 variants
We had a number of queries about the Ensembl VEP related to its support for SARS-CoV-2. Here, we talk about how you can use the command line VEP to analyse your variants against the SARS-CoV-2 gene set from Ensembl.
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