Variant Effect Predictor

About | Data formats | Web version | Perl script | Frequently asked questions

About

Ensembl provides the facility to predict the functional consequences of variants using the Variant Effect Predictor (VEP). There are three primary ways to use the functionality of the VEP:

The web version is suitable for users with small volumes of data or those who prefer not to use command-line utilities. The script version is the most flexible of the VEP, and allows users to process large volumes of data using their own compute resources. The API is suitable for perl programmers looking to incorporate features of the VEP into their own code.

Data formats

Both the web and script versions of the VEP use the same data formats as input and output. For input, the default is a simple tab-delimited format, as is the output format. The popular VCF (version 4.0) and pileup formats are also supported as input.

Web version

The web version of the VEP can be accessed via the Tools link at the top of each Ensembl web page, or via the "Manage your data" link on any species-specific page.

Upload form

When you reach the VEP web interface, you will be presented with a form to enter your data. Data can be uploaded in one of three ways:

It is then possible to configure other options. The VEP will run fine with the default options; click the blue "Next" button at the bottom of the panel to continue when you are happy with the options.

The following options are currently available for human only.

Select output format

After clicking "Next", you are then asked to select either HTML or Text output. Both formats contain the same information:

Viewing your results in the browser

Any data uploaded via the VEP web tool can be viewed on the Ensembl location view; to view your data, either click a link in the Location column of the HTML output, or switch on the track on location view (click "Configure this page", then "User attached data" on Region in detail view to see uploaded tracks).