1. NGS.git
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  bin moved ngs.pl startup script stderr & stdout to go to NGS/logs/deployment.log; made path to debug.txt explicit in NGS::VEP 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 bugfix: optional lab number prefix needs to be specified as A-Z not \w 11 years ago
  public added new counters for vep input rows and raw src_file rows; patched lab number regex to allow optional letter prefix; fixed test scripts to report vep input row count instead of 'accepted' rows 11 years ago
  script adapted NGS::VEP to accept vcf files - imported vcf-to-vep.pl script code 11 years ago
  t added new counters for vep input rows and raw src_file rows; patched lab number regex to allow optional letter prefix; fixed test scripts to report vep input row count instead of 'accepted' rows 11 years ago
  views added new counters for vep input rows and raw src_file rows; patched lab number regex to allow optional letter prefix; fixed test scripts to report vep input row count instead of 'accepted' rows 11 years ago
  .gitignore 169B new vcf analysis section; moved ChartMaker to NGS::ChartMaker 12 years ago
  README.txt 1kB added new counters for vep input rows and raw src_file rows; patched lab number regex to allow optional letter prefix; fixed test scripts to report vep input row count instead of 'accepted' rows 11 years ago
  config.yml 917B adapted NGS::VEP to accept vcf files - imported vcf-to-vep.pl script code 11 years ago
  module_build.pl 438B updated module_build.pl 12 years ago
  ngs.sqlite 40kB adapted NGS::VEP to accept vcf files - imported vcf-to-vep.pl script code 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 -i=/tmp/20_06_14.vep -config=/home/raj/apps/NGS/script/vep.ini --dir=/home/raj/.vep/refseq --polyphen=b --sift=b --check_existing --coding_only --regulatory > foo.txt