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 added col headers to csv output 11 years ago
  lib added col headers to csv output 11 years ago
  public new route - app version history; replaced system calls with CPAN Git library; exon links jump directly to selected gene/feature in vep results table 11 years ago
  script added ability to set max x & y-axis values in chartdirector output; 02-vcf-analysis script loads ngs.locations db table for use in start position exclusions 11 years ago
  t new tests files for scripts 11 years ago
  views moved all db queries to NGS::DB; added download facility for processed data; new MySQL ngs db for download data 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 moved all db queries to NGS::DB; added download facility for processed data; new MySQL ngs db for download data 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 bugfix - recent change to locations table didn't take effect; moved _run_vep() %vep_cols to global var %VEP_COLS 11 years ago
  ngs_setup.sql 1kB moved all db queries to NGS::DB; added download facility for processed data; new MySQL ngs db for download data 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