Plugins for the Ensembl Variant Effect Predictor (VEP)
Perl
Latest commit d090750 May 22, 2017 @willmclaren willmclaren committed on GitHub Merge pull request #45 from mimadrid/fix/NearestGene
NearestGene: Fix "ERROR: Could not get gene adaptor"
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config/Condel add Condel configuration Mar 16, 2012
Blosum62.pm Change script name to vep Feb 28, 2017
CADD.pm Change script name to vep Feb 28, 2017
CCDSFilter.pm Change script name to vep Feb 28, 2017
CSN.pm Change script name to vep Feb 28, 2017
Carol.pm Change script name to vep Feb 28, 2017
Condel.pm Change script name to vep Feb 28, 2017
Conservation.pm Change script name to vep Feb 28, 2017
DAS.pm Change script name to vep Feb 28, 2017
Downstream.pm Change script name to vep Feb 28, 2017
Draw.pm Change script name to vep Feb 28, 2017
ExAC.pm Change script name to vep Feb 28, 2017
ExACpLI.pm Change script name to vep Feb 28, 2017
ExACpLI_values.txt Add plugin for pLI on ExAC data Feb 16, 2017
FATHMM.pm Change script name to vep Feb 28, 2017
FATHMM_MKL.pm Change script name to vep Feb 28, 2017
G2P.pm Change script name to vep Feb 28, 2017
GO.pm Change script name to vep Feb 28, 2017
GXA.pm Change script name to vep Feb 28, 2017
GeneSplicer.pm Change script name to vep Feb 28, 2017
HGVSshift.pm Change script name to vep Feb 28, 2017
LD.pm speed improvements Mar 31, 2017
LICENSE Correction to copyright notices Jan 17, 2017
LOVD.pm Change script name to vep Feb 28, 2017
LoFtool.pm Change script name to vep Feb 28, 2017
LoFtool_scores.txt add LoFtool plugin and scores file Jun 12, 2015
MaxEntScan.pm fix for sequence fetching on -ve strand transcripts Apr 19, 2017
NearestGene.pm NearestGene: Fix "ERROR: Could not get gene adaptor" May 16, 2017
NonSynonymousFilter.pm Change script name to vep Feb 28, 2017
PON_P2.pm Change script name to vep Feb 28, 2017
Phenotypes.pm Change script name to vep Feb 28, 2017
PolyPhen_SIFT.pm Change script name to vep Feb 28, 2017
ProteinSeqs.pm Change script name to vep Feb 28, 2017
README Correction to copyright notices Jan 17, 2017
RankFilter.pm Change script name to vep Feb 28, 2017
SameCodon.pm Change script name to vep Feb 28, 2017
SpliceRegion.pm add SpliceRegion plugin May 3, 2017
TSSDistance.pm Change script name to vep Feb 28, 2017
UpDownDistance.pm Change script name to vep Feb 28, 2017
VEPbrowse.pm Change script name to vep Feb 28, 2017
dbNSFP.pm Change script name to vep Feb 28, 2017
dbscSNV.pm Change script name to vep Feb 28, 2017
miRNA.pm Change script name to vep Feb 28, 2017
plugin_config.txt add PolyPhen_SIFT to config May 10, 2017

README

This repository contains several perl plugin modules for the Ensembl
Variant Effect Predictor (VEP). Please refer to the documentation at 
the top of each file for details of what each plugin does and how to 
run it, though for most you will just need to put the module in your
~/.vep/Plugins directory (or elsewhere on your $PERL5LIB) and then
run the VEP with the argument --plugin <module name>.

More documentation on VEP plugins, and on the VEP itself, can be 
found on the Ensembl website:

http://www.ensembl.org/info/docs/tools/vep/script/index.html

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2017] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

http://www.ensembl.org/info/about/code_licence.html