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  variant_effect_predictor.pl 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
  vcf new vcf-to-vep.pl script; adapted NGS::DB to find sqlite db from t/ and scripts/vcf 11 years ago
  README.txt 545B new vcf analysis section; moved ChartMaker to NGS::ChartMaker 12 years ago
  sqlite_input.pl 1kB new vcf-to-vep.pl script; adapted NGS::DB to find sqlite db from t/ and scripts/vcf 11 years ago
  vep.ini 883B fixed refseq selection function - required separate cache dir & use of --dir option 12 years ago
  README.txt
to update vep: 1) delete variant_effect_predictor dir (leave symlink intact) 2) download latest version from: http://www.ensembl.org/info/docs/tools/vep/index.html 3) run INSTALL.pl - skip cache (done manually below) 4) rename local Bio to eg Bio.v7x, move to ~/perl-lib and update Bio symlink in ~/perl5/lib/perl5 5) download & extract matching databases into ~/.vep/core & ~/.vep/refseq using ftp://ftp.ensembl.org/pub/release-<xx>/variation/VEP/ *) main difference after upgrade is Bio::EnsEMBL classes - other Bio:: classes same