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The Ensembl Genome Browser

Variant Effect Predictor (Ve!P)

To access Ve!P, click on the Ve!P logo from the Ensembl homepage, or, from any Ensembl page, click the Tools menu at the top of the page, then click the Ve!P logo from the tools page.

From this page, you can use the REST API, download the Perl script, or use the web interface. Click the Lauch Ve!P button to launch the web interface.

There are lots of features and options in the Ve!P. Select your species of choice, give the project a name (optional), then upload your data. The Ve!P accepts Ensembl format files, variant call format (VCF) files, simple lists of variant IDs (like dbSNP IDs), HGVS notations, and pileup formats. Paste or upload your file.

Now select from the many options for output fields. Click the small "+" sign next to the optional fields below the Output options header to see all your choices.

Once you have made your output choices, click the Run button. Your job will enter a queue. When it's done, you'll see a green Done flag and a link to view results.

 

Screen shot of Variant Effect Predictor results.

 

After your job is done you will see a pie chart of the distribution of variant types from your file, followed by a table of the predicted variants and thier consequences, if known.

  • Filter your output file by column type by using the Filters menu above the table
  • Download your results file as VCF, VEP or plain text
  • Alternately, you can send all the result identifiers for your predicted genes or variants to BioMart