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Variant Effect Predictor Command line VEP


Quick start
  1. Download
    git clone https://github.com/Ensembl/ensembl-vep.git
  2. Install
    cd ensembl-vep
    perl INSTALL.pl
  3. Test
    ./vep -i examples/homo_sapiens_GRCh38.vcf --cache

Use VEP to analyse your variation data locally. No limits, powerful, fast and extendable, command line VEP is the way to get the most out of VEP and Ensembl.

VEP is a powerful and highly configurable tool - have a browse through the documentation. You might also like to read up on the data formats that VEP uses, and the different ways you can access genome data. The VEP script can annotate your variants with custom data, be extended with plugins, and use powerful filtering to find biologically interesting results.

Beginners should have a run through the tutorial, or try the web interface first.

If you use VEP in your work, please cite our latest publication McLaren et. al. 2016 (doi:10.1186/s13059-016-0974-4)

Any questions? Send an email to the Ensembl developers' mailing list or contact the Ensembl Helpdesk.

What's new in release 98?