UNIT 15.7 cgpPindel: Identifying Somatically Acquired Insertion and Deletion Events from Paired End Sequencing. Issue 1 (17th December 2015)

• Record Type: Journal Article
• Authors: Raine, Keiran M.; Hinton, Jonathan; Butler, Adam P.; Teague, Jon W.; Davies, Helen; Tarpey, Patrick; Nik‐Zainal, Serena; Campbell, Peter J.
• Is Part Of: Current protocols in bioinformatics. Volume 52:Issue 1(2015)
• Page Start: 15.7.1
• Page End: 15.7.12
• Publication Date: 2015-12-17
• Subjects: somatic -- sequencing -- Pindel -- cancer; Bioinformatics -- Laboratory manuals; Nucleotide sequence -- Laboratory manuals; Amino acid sequence -- Laboratory manuals; Base Sequence; Amino Acid Sequence; Computational Biology -- methods; Databases, Genetic; Proteins -- analysis; Sequence Analysis -- methods; Sequence Homology; Amino acid sequence; Bioinformatics; Nucleotide sequence; Laboratory Manuals; Laboratory manuals; 570.285
• DOI: 10.1002/0471250953.bi1507s52
• Languages: English
• ISSNs: 1934-3396

Abstract

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.