bugfix to _prediction_and_score() - needed to skip undef vars; colour-coded results if deleterious or damaging; truncated long (>30 char) variation results; re-ordered results cols for clarity
renamed vep orphans to non-CDS regions; added new ref entry to sqlite db; results page displays input src filename
12 years ago
README.txt
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
