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: 87
• Added: February, 2017
• Link: http://www.ensembl.org/info/docs/tools/vep/index.html
• Annotations: /export/data/bio/vep/

See versions of VEP which are available:

$ module avail vep

Notes from the sysadmin during installation:

- install vep-script
$ sudo mkdir -p /export/apps/vep/87/
$ sudo chown -R joguya:joguya /export/apps/vep/87/
$ cd scripts/variant_effect_predictor
$ module load perl/5.22.3
$ scl enable devtoolset-3 bash
$ cpanm File::Copy::Recursive Archive::Extract LWP::Simple LWP::Protocol::https CGI
$ module load htslib/1.3.2
$ mkdir /export/apps/vep/87/cache
$ perl INSTALL.pl --DESTDIR /export/apps/vep/87 --NO_HTSLIB 
$ PERL5LIB=$PERL5LIB:/export/apps/vep/87 perl INSTALL.pl --DESTDIR /export/apps/vep/87 --NO_HTSLIB
$ cp *.pl *.vcf /export/apps/vep/87/
$ sudo chown -R root:root /export/apps/vep/87/

- download cattle annotation data to /export/data/ for use by VEP in /export/data/bio
$ sudo mkdir /export/data/bio/vep
$ sudo chown joguya:joguya /export/data/bio/vep
$ PERL5LIB=$PERL5LIB:/export/apps/vep/87 perl INSTALL.pl --DESTDIR /export/apps/vep/87 --CACHEDIR /export/data/bio/vep --NO_HTSLIB
$ sudo chown -R root:root /export/data/bio/vep