ILRI Research Computing

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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.

===== Information =====

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

===== Usage =====

See versions of VEP which are available:
<code>$ module avail vep</code>

Load one version into your environment and run it:
<code>$ module load vep/109.3
$ vep --cache /export/apps/vep/109.3/cache</code>

**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.

===== Installation ======
Notes from the sysadmin during installation:

<code>$ 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</code>