Skip to content

Ensembl-VEP

VEP determines the effect of your variants (insertions, deletions and structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

Ensembl-VEP is available as a module on Apocrita.

Usage

To run the latest installed version of Ensembl-VEP, simply load the ensembl-vep module:

$ module load ensembl-vep
$ vep

Usage:
./vep [--cache|--offline|--database] [arguments]

Basic options
=============

--help                 Display this message and quit

-i | --input_file      Input file
-o | --output_file     Output file
--force_overwrite      Force overwriting of output file
--species [species]    Species to use [default: "human"]

--everything           Shortcut switch to turn on commonly used options. See web
                       documentation for details [default: off]
--fork [num_forks]     Use forking to improve script runtime

For full option documentation see here.

VEP Database Configuration on Apocrita

There are no databases or cache files for Ensembl-VEP available on Apocrita. The required data for each run must be downloaded in advance.

Instructions on how to download and use cached files can be found here.

To enable offline mode and use of the cache, pass the --offline and --cache flags.

Example job

Serial job

Here is an example job running on 1 core and 1GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load ensembl-vep

vep -i homo_sapiens_GRCh38.vcf \
    --cache \
    --offline \
    --output_file results

References