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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.



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
$ unzip
$ 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
$ PERL5LIB=lib/perl5 perl --NO_HTSLIB --CACHEDIR cache
$ sudo mkdir -p /export/apps/vep/109.3
$ sudo cp -r * /export/apps/vep/109.3
vep-software.txt · Last modified: 2023/05/22 06:10 by aorth