http://www.ensembl.org/info/docs/variation/vep/vep_script.html Setup/update - extract variant_effect_predictor.tar.gz and run INSTALL.pl - skip cache if already installed - cache can be manually updated from (and needs to match VEP version): ftp://ftp.ensembl.org/pub/release-72/variation/VEP/ Cache directory structure: vep dir containing core & refseq dirs, each with homo_sapiens/72 cache on dev box - symlink /home/raj/.vep -> /media/sf_WIN_DRIVE/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