1. NGS.git
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  bin needed FindBin in app.pl after update to D2 v0.09; bootstrap 3.0.0 spacelabs theme 12 years ago
  environments changed script/variant_effect_predictor.pl file to symlink to same file inside variant_effect_predictor dir for ease of updating vep version - now just download, extract & run new v_e_p.tar.gz 12 years ago
  lib fixed error in previous commit 12 years ago
  public needed FindBin in app.pl after update to D2 v0.09; bootstrap 3.0.0 spacelabs theme 12 years ago
  script changed script/variant_effect_predictor.pl file to symlink to same file inside variant_effect_predictor dir for ease of updating vep version - now just download, extract & run new v_e_p.tar.gz 12 years ago
  t needed FindBin in app.pl after update to D2 v0.09; bootstrap 3.0.0 spacelabs theme 12 years ago
  views added transcription db = refseq option; fix for FLT3-ITD 1 variant; tests for invalid variant format 12 years ago
  README.txt 722B 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
  config.yml 913B initial working project 13 years ago
  module_build.pl 287B decoupled NGS::DB from LIMS - moved DBI handling to Local::DB; added module_build.pl 12 years ago
  ngs.sqlite 16kB 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 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