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Plugins for the Ensembl Variant Effect Predictor (VEP)
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config/Condel add Condel configuration Mar 16, 2012
.hgignore added RefSeqHGVS Feb 16, 2012
AncestralAllele.pm Added support for 5.26 Jun 18, 2019
Blosum62.pm Yearly copyright update - 2019 Feb 14, 2019
CADD.pm Yearly copyright update - 2019 Feb 14, 2019
CCDSFilter.pm Yearly copyright update - 2019 Feb 14, 2019
CSN.pm Yearly copyright update - 2019 Feb 14, 2019
Carol.pm Yearly copyright update - 2019 Feb 14, 2019
Condel.pm Yearly copyright update - 2019 Feb 14, 2019
Conservation.pm Updates to Conservation to support 5.26 Apr 3, 2019
DAS.pm remove personal email Aug 14, 2017
Downstream.pm Yearly copyright update - 2019 Feb 14, 2019
Draw.pm Yearly copyright update - 2019 Feb 14, 2019
ExAC.pm Yearly copyright update - 2019 Feb 14, 2019
ExACpLI.pm Yearly copyright update - 2019 Feb 14, 2019
ExACpLI_values.txt Add plugin for pLI on ExAC data Feb 16, 2017
FATHMM.pm Yearly copyright update - 2019 Feb 14, 2019
FATHMM_MKL.pm Yearly copyright update - 2019 Feb 14, 2019
FlagLRG.pm Added FlagLRG plugin Oct 16, 2018
G2P.pm revert May 24, 2019
GO.pm Yearly copyright update - 2019 Feb 14, 2019
GXA.pm Yearly copyright update - 2019 Feb 14, 2019
GeneSplicer.pm Yearly copyright update - 2019 Feb 14, 2019
HGVSIntronOffset.pm Updated contact details Sep 28, 2018
HGVSReferenceBase.pm Yearly copyright update - 2019 Feb 14, 2019
LD.pm Yearly copyright update - 2019 Feb 14, 2019
LICENSE Yearly copyright update - 2019 Feb 14, 2019
LOVD.pm Yearly copyright update - 2019 Feb 14, 2019
LoFtool.pm Yearly copyright update - 2019 Feb 14, 2019
LoFtool_scores.txt add LoFtool plugin and scores file Jun 12, 2015
LocalID.pm Yearly copyright update - 2019 Feb 14, 2019
MPC.pm Yearly copyright update - 2019 Feb 14, 2019
MTR.pm Remove the # character from the header Apr 4, 2019
MaxEntScan.pm Yearly copyright update - 2019 Feb 14, 2019
NearestExonJB.pm Adding NearestExonJB.pm to postreleasefix/96 Mar 1, 2019
NearestGene.pm Yearly copyright update - 2019 Feb 14, 2019
NonSynonymousFilter.pm Yearly copyright update - 2019 Feb 14, 2019
PON_P2.pm Move Contact Perldoc Nov 12, 2018
Phenotypes.pm fix config for rest calls Apr 8, 2019
PolyPhen_SIFT.pm Yearly copyright update - 2019 Feb 14, 2019
PostGAP.pm fix fetch position May 23, 2019
ProteinSeqs.pm Merge pull request #164 from aparton/origin/proteinseqsupdate May 8, 2019
README Yearly copyright update - 2019 Feb 14, 2019
REVEL.pm Yearly copyright update - 2019 Feb 14, 2019
RankFilter.pm Yearly copyright update - 2019 Feb 14, 2019
RefSeqHGVS.pm fixed POD problem Feb 16, 2012
ReferenceQuality.pm Yearly copyright update - 2019 Feb 14, 2019
SameCodon.pm Yearly copyright update - 2019 Feb 14, 2019
SingleLetterAA.pm Yearly copyright update - 2019 Feb 14, 2019
SpliceRegion.pm Yearly copyright update - 2019 Feb 14, 2019
SubsetVCF.pm Adding contact and licence details Dec 27, 2017
TSSDistance.pm Yearly copyright update - 2019 Feb 14, 2019
dbNSFP.pm Remove the # character from the header Apr 4, 2019
dbNSFP_replacement_logic File stores replacement logic Jan 30, 2018
dbscSNV.pm Yearly copyright update - 2019 Feb 14, 2019
gnomADc.pm For insertions, report on the normalized position Nov 2, 2018
miRNA.pm Yearly copyright update - 2019 Feb 14, 2019
plugin_config.txt update config for phenotypes Feb 1, 2019

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 [2016-2019] 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

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