Variant Effect Predictor (VEP)

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

• Latest Version: 109.3
• Added: February, 2017
• Updated: May, 2023
• Link: https://github.com/Ensembl/ensembl-vep
• Annotations: /export/apps/vep/109.3/cache

See versions of VEP which are available:

$ module avail vep

Load one version into your environment and run it:

$ module load vep/109.3
$ vep --cache /export/apps/vep/109.3/cache

N.B. The VEP cache is installed in /export/apps/vep/109.3/cache, so make sure to specify this when working with VEP. Contact Alan or Jean-Baka if you need more databases installed.

Notes from the sysadmin during installation:

$ cd /tmp
$ curl -L -O https://github.com/Ensembl/ensembl-vep/archive/release/109.3.zip
$ unzip 109.3.zip
$ sudo dnf install perl-DBI perl-DBD-mysql perl-JSON perl-perlIO-gzip
$ cd ensembl-vep-release-109.3
$ cpanm -l . Set::IntervalTree
$ mkdir cache
$ module load htslib/1.9 # use our own, instead of the one installed by INSTALL.pl
$ PERL5LIB=lib/perl5 perl INSTALL.pl --NO_HTSLIB --CACHEDIR cache
$ sudo mkdir -p /export/apps/vep/109.3
$ sudo cp -r * /export/apps/vep/109.3