VAGrENT: Variation Annotation Generator

Andy Menzies1, Jon W. Teague1, Adam P. Butler1, Helen Davies1, Patrick Tarpey1, Serena Nik‐Zainal1, Peter J. Campbell1

1 Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 15.8
DOI:  10.1002/0471250953.bi1508s52
Online Posting Date:  December, 2015
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Abstract

VAGrENT is a tool that provides biological context and effect prediction for genomic sequence variants. It annotates single base substitutions and small insertions and deletions by comparing them to reference information within or close to genes or other transcribed elements. This information provides the critical insight required to inform the biological or clinical significance of variant data generated from sequencing studies. The software has been optimized to run efficiently against the large numbers and diverse classes of variants that are typically generated from next generation sequencing technologies. This unit describes how to configure and use VAGrENT and also contains support protocols for extending and adapting its default behavior. © 2015 by John Wiley & Sons, Inc.

Keywords: variant annotation; substitution; insertion; deletion

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Using VAGrENT to Annotate a VCF File
  • Alternate Protocol 1: Altering VAGrENT's Behavior to Suit Your Own Needs
  • Support Protocol 1: Installation of VAGrENT
  • Support Protocol 2: Creating/Generating VAGrENT Cache Files
  • Guidelines for Understanding Results
  • Commentary
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
  den Dunnen, J.T. and Antonarakis, S.E. 2000. Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion. Hum. Mutat. 15:7‐12. doi: 10.1002/(SICI)1098-1004(200001)15:1%3c7::AID-HUMU4%3e3.0.CO;2-N.
  Eilbeck, K., Lewis, S.E., Mungall, C.J., Yandell, M., Stein, L., Durbin, R., and Ashburner, M., 2005. The sequence ontology: A tool for the unification of genome annotations. Genome Biol. 6:r44. doi: 10.1186/gb-2005-6-5-r44.
  Li, H. 2011. Tabix: Fast retrieval of sequence features from generic TAB‐delimited files. Bioinformatics 27:718‐719. doi: 10.1093/bioinformatics/btq671.
Internet Resources
  https://github.com/cancerit/VAGrENT
  The VAGrENT GitHub repository
  https://github.com/cancerit
  Repository for Wellcome Trust Sanger Institute Cancer Genome Project public projects
  http://samtools.github.io/hts‐specs/VCFv4.1.pdf
  VCF format 4.1 specification
  http://www.sequenceontology.org
  The Sequence Ontology Project
  http://www.hgvs.org
  Human Genome Variation Society
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