User Tools

Site Tools


This is an old revision of the document!

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


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 --DESTDIR /export/apps/vep/87 --NO_HTSLIB 
$ PERL5LIB=$PERL5LIB:/export/apps/vep/87 perl --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 --DESTDIR /export/apps/vep/87 --CACHEDIR /export/data/bio/vep --NO_HTSLIB
$ sudo chown -R root:root /export/data/bio/vep
vep-software.1486416888.txt.gz · Last modified: 2017/02/06 21:34 by joguya