User Tools

Site Tools


vep-software

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.

Information

Usage

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, Jean-Baka, Joyce, or Dedan if you need more databases installed.

Installation

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
vep-software.txt · Last modified: 2018/04/16 00:04 by aorth