patched VEP::_get_hmds_refs to return error if col header doesn't look like lab number; 015_data.t to test
12 years ago
README.txt
http://www.ensembl.org/info/docs/variation/vep/vep_script.html
Setup/update VEP - extract variant_effect_predictor.tar.gz into scripts dir and run
INSTALL.pl - skip cache. Cache manually installed/updated (needs to match
VEP version) from: 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
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
