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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
#----------------------------------#
# ENSEMBL VARIANT EFFECT PREDICTOR #
#----------------------------------#

...

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

...

VEP Database Configuration on Apocrita

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

More information and the data download instructions can be found here: http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html

The --offline flag has to be added to the vep command with --dir <path_to_the_downloaded_data> and --cache_dir <path_to_the_downloaded_data> options

Example jobs

Here is an example job running with 1 core and 15G memory on a nxv node:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -l h_rt=2:00:00
#$ -l h_vmem=15G
#$ -l node_type=nxv

module load ensembl-vep

vep -i homo_sapiens_GRCh38.vcf \
    --offline \
    --fasta data/homo_sapiens/89_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz \
    --dir data \
    --output_file results \

References