1. NGS.git
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  data NGS::VEP refactor - changed exon identifier to accomodate multiple point mutations at same locus; all tests pass 12 years ago
  001_base.t 68B initial working project 13 years ago
  002_index_route.t 757B skipped 002_data.t test for 404 error unless D2 versrion > 0.04 - didn't handle 404 error properly 12 years ago
  003_data.t 2kB 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
  004_data.t 1kB added errors & alerts display to results output; checks all exon names in src data are in vep input data; updated test scripts with results output format 12 years ago
  005_data.t 1kB added errors & alerts display to results output; checks all exon names in src data are in vep input data; updated test scripts with results output format 12 years ago
  006_data.t 1kB added errors & alerts display to results output; checks all exon names in src data are in vep input data; updated test scripts with results output format 12 years ago
  007_data.t 1kB added errors & alerts display to results output; checks all exon names in src data are in vep input data; updated test scripts with results output format 12 years ago
  008_data.t 1kB added errors & alerts display to results output; checks all exon names in src data are in vep input data; updated test scripts with results output format 12 years ago
  009_data.t 1kB added errors & alerts display to results output; checks all exon names in src data are in vep input data; updated test scripts with results output format 12 years ago
  010_data.t 1kB added errors & alerts display to results output; checks all exon names in src data are in vep input data; updated test scripts with results output format 12 years ago
  011_data.t 4kB added errors & alerts display to results output; checks all exon names in src data are in vep input data; updated test scripts with results output format 12 years ago
  012_data.t 2kB added errors & alerts display to results output; checks all exon names in src data are in vep input data; updated test scripts with results output format 12 years ago
  013_data.t 2kB added transcription db = refseq option; fix for FLT3-ITD 1 variant; tests for invalid variant format 12 years ago
  014_data.t 2kB 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
  015_data.t 1kB needed FindBin in app.pl after update to D2 v0.09; bootstrap 3.0.0 spacelabs theme 12 years ago
  test-lib.pl 2kB added errors & alerts display to results output; checks all exon names in src data are in vep input data; updated test scripts with results output format 12 years ago
  README.txt
http://www.ensembl.org/info/docs/variation/vep/vep_script.html Setup/update VEP - delete scripts/variant_effect_predictor dir extract variant_effect_predictor.tar.gz into scripts dir run scripts/variant_effect_predictor/INSTALL.pl - skip cache. Cache manually installed/updated (needs to match VEP version) from: ftp://ftp.ensembl.org/pub/release-<xx>/variation/VEP/ see README.txt in NGS/script dir for more details Cache directory structure: vep dir containing core & refseq dirs, each with homo_sapiens/xx 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