1. NGS.git
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  bin escaped spaces in tt a name var; changed production env flag to deployment 12 years ago
  environments 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 12 years ago
  lib 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
  public added bootswatch spacelab css; added bootstrap table styles 12 years ago
  script 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
  t skipped 002_data.t test for 404 error unless D2 versrion > 0.04 - didn't handle 404 error properly 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
  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