We know that installing the VEP is not always trivial – there are dependencies and modules that you may or may not have already, and your existing setup may require different module versions. It’s also designed for a Linux system and installing on, for example, Windows, can be complex. To get around this, the VEP and all its dependencies are available in a Docker image, so that you can install everything with just a few simple commands.

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Plugins can be an excellent way to extend the functionality of the VEP. They can be used to look-up information in external databases or use the Ensembl API to add to or filter your VEP output. Many plugins have already been written, both by us and external groups, but with a bit of Perl you can easily write your own.

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In early March the EMBL-EBI data centre will be migrating to a new physical location. This will impact on the services that we can offer that are provided by the data centre during this time. There will be a complete shut-down of some services for over a week as the servers are disconnected, moved and reconnected in their new location, and there may be continued impacts as we reconfigure the services afterwards.

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The interpretation of non-coding variants is more challenging than that of coding variants as less prediction methods and reference data are available. On top of the annotation provided for human and mouse in the Ensembl Regulatory Build, the Ensembl Variant Effect Predictor (VEP) also integrates two other human-specific datasets providing information about how variants can affect gene expression. The plugins, satMutMPRA and FunMotifs, are available for use with command-line VEP. One provides detailed information on the impact on expression of variants in the regulatory regions of disease-associated genes; the other an alternative set of genome-wide transcription factor binding motifs.

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As Ensembl continues to rapidly grow in terms of the number of supported species, we continually assess our provided resources effectively match the scientific needs of the researchers using them. 

In order to maintain our BioMart service at its current performance level, we will be making changes to data availability in BioMart starting with the upcoming e99 release. 

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Following our consultation on simplifying our GRCh37 services, we have decided to remove all support for non-human data from our dedicated GRCh37 database from release 100 onwards in early 2020. This will impact the website at grch37.ensembl.org, the REST server at grch37.rest.ensembl.org and the database at ensembldb.ensembl.org:3337. Non-human data will still be supported on the e75.ensembl.org archive.

In response to feedback during consultation, access to the full data currently provided by the existing GRCh37 REST services will also be made available for at least a year.

Please see our longer post for more details.

Some missense variants have significant impact on the protein function, some do not. In the absence of global comprehensive functional assays of missense variants, the next best way to assess if a missense variant is likely to be pathogenic is through prediction tools which take into account factors like the chemical properties of amino acids, functional protein domains and protein conservation to predict how likely it is that a missense variant will impact function. A number of different missense pathogenicity predictors are available for human through Ensembl VEP, and these are are optimised for different purposes.

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