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
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