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: 92.1
• Added: February, 2017
• Updated: April, 2018
• Link: http://www.ensembl.org/info/docs/tools/vep/index.html
• Annotations: /export/apps/vep/92.1/cache

See versions of VEP which are available:

$ module avail vep

Load one version into your environment and run it:

$ module load vep/92.1
$ vep --cache /export/apps/vep/92.1/cache

N.B. The VEP cache is installed in /export/apps/vep/92.1/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/92.1.zip
$ unzip 92.1.zip
$ sudo yum install perl-DBI perl-DBD-mysql perl-JSON perl-perlIO-gzip
$ module load htslib/1.6
$ cd ensembl-vep-release-92.1
$ cpanm -l . Set::IntervalTree
$ mkdir cache
$ PERL5LIB=lib/perl5 perl INSTALL.pl --NO_HTSLIB --CACHEDIR cache
$ sudo mkdir -p /export/apps/vep/92.1
$ sudo cp -r * /export/apps/vep/92.1