http://www.ensembl.org/info/docs/variation/vep/vep_script.html Setup/update VEP - delete scripts/variant_effect_predictor dir extract variant_effect_predictor.tar.gz into scripts dir run scripts/variant_effect_predictor/INSTALL.pl - skip cache. Cache manually installed/updated (needs to match VEP version) from: ftp://ftp.ensembl.org/pub/release-<xx>/variation/VEP/ see README.txt in NGS/script dir for more details Cache directory structure: vep dir containing core & refseq dirs, each with homo_sapiens/xx cache * on dev box - symlink /home/raj/.vep -> /media/sf_WIN_DRIVE/vep * on deployment - /home/raj/.vep to run from command-line: perl script/variant_effect_predictor.pl -config=script/vep.ini \ -i=t/data/myeloid_variants.vep -o=output.txt --polyphen=b --sift=b \ --check_existing --coding_only --regulatory --dir=refseq/core