cgpPindel: Identifying Somatically Acquired Insertion and Deletion Events from Paired End Sequencing

Keiran M. Raine1, Jonathan Hinton1, Adam P. Butler1, Jon W. Teague1, Helen Davies1, Patrick Tarpey1, Serena Nik‐Zainal1, Peter J. Campbell1

1 Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 15.7
DOI:  10.1002/0471250953.bi1507s52
Online Posting Date:  December, 2015
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Abstract

cgpPindel is a modified version of Pindel that is optimized for detecting somatic insertions and deletions (indels) in cancer genomes and other samples compared to a reference control. Post‐hoc filters remove false positive calls, resulting in a high‐quality dataset for downstream analysis. This unit provides concise instructions for both a simple ‘one‐shot’ execution of cgpPindel and a more detailed approach suitable for large‐scale compute farms. © 2015 by John Wiley & Sons, Inc.

Keywords: somatic; sequencing; Pindel; cancer

     
 
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Table of Contents

  • Introduction
  • Strategic Planning
  • Basic Protocol 1: Calling Indels with a Single Command for a Tumor/Normal Sample Pair
  • Alternate Protocol 1: Processing Other Sequencing Types
  • Alternate Protocol 2: Using cgpPindel with Compute Farm Infrastructure
  • Support Protocol 1: Installation of cgpPindel and Dependencies
  • Support Protocol 2: Static Reference Files
  • Guidelines for Understanding Results
  • Commentary
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
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Internet Resources
  https://github.com/cancerit
  Repository for Wellcome Trust Sanger Institute Cancer Genome Project public projects.
  http://gmt.genome.wustl.edu/packages/pindel
  Core Pindel site.
  https://genome.ucsc.edu/cgi‐bin/hgTables
  UCSC Genome Browser Table Browser.
  http://vcftools.github.io/specs.html
  VCF file format specification.
  https://samtools.github.io/hts‐specs/SAMv1.pdf
  SAM format specification.
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