1. NGS.git
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  bin major version change: refactored _run_vep() to select consequence, variation, sift & polyphen values from specified gene/feature combination (multiple entries for same exon_id from vep, with varying sift, polyphen, consequence & variation vals taken into hashref meant last one wins); added cds and protein annotation vals; vep data row skipped & warning issued if ENSG0000* gene id not present in transcripts db 11 years ago
  environments args to Local::DB either dsn or dbname; integration with other apps and Local::QueryLogger; switched off query logging for test scripts 10 years ago
  lib patched miseq_vcf() unlink block to skip non-file items - Archive::Extract ->files includes directory as a file for linux .zip 10 years ago
  public wrapped call to NGS::VEP in try/catch to handle die via 500.tt - works for tests as well; test for invalid filename; display list of valid filenames in upload page 11 years ago
  script new script to populate locations.sqlite table; new locations data 10 years ago
  t simplified args passed in NGS.pm method calls - src_data & data_file are equivalent so replaced all refs to former with latter; simplified config block in _parse() 11 years ago
  views simplified args passed in NGS.pm method calls - src_data & data_file are equivalent so replaced all refs to former with latter; simplified config block in _parse() 11 years ago
  .gitignore 492B major upgrade - app uses vep api_version to look for available cache types (ensembl, refseq, merged) and disables any from selection if not available; results page displays api version and selected cache database; vep wrapper captures vep.pl stderr for display on results page; added vcf 'filter' col to results page; enabled HGVS notation function 11 years ago
  README.txt 2kB changed method of finding sqlite db in NGS::DB from search of @INC to using D2::FileUtils::path(); added functionality to create separate vep inputs per chromosome - not in use 11 years ago
  config.yml 1kB wrapped call to NGS::VEP in try/catch to handle die via 500.tt - works for tests as well; test for invalid filename; display list of valid filenames in upload page 11 years ago
  module_build.pl 890B moved all db queries to NGS::DB; added download facility for processed data; new MySQL ngs db for download data 11 years ago
  ngs.sqlite 52kB new script to populate locations.sqlite table; new locations data 10 years ago
  ngs_setup.sql 2kB increased max lengthg of sample_data.cds to 255 chars; amended recent transcripts gene feature entry 11 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 or: perl script/variant_effect_predictor.pl -config=/home/raj/apps/NGS/script/vep.ini \ -o=output.txt --dir=/home/raj/.vep/refseq --polyphen=b --sift=b --check_existing \ --coding_only --regulatory -i=/tmp/20_06_14.vep PERFORMANCE: a) 4055-row vep input with unsorted chromosome order on 163.160.171.48: fork=0 255 sec fork=2 580 sec fork=4 620 sec b) 1028-row vep input with alpha-numerically sorted chromosome order on 163.160.171.48: fork=0 95 sec fork=2 65 sec (optimal) fork=3 68 sec fork=4 70 sec fork=5 75 sec fork=6 75 sec performance much WORSE on dev server with fork enabled splitting a 1110-row vep input into separate chromosome input files slightly REDUCED performance (77sec vs 66sec) on dev