title: cgpPindel: Identifying Somatically Acquired Insertion and Deletion Events from Paired End Sequencing.
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.
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Keiran M
authors.initials: KM
authors.lastname: Raine
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Hinton
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Adam P
authors.initials: AP
authors.lastname: Butler
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Jon W
authors.initials: JW
authors.lastname: Teague
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Helen
authors.initials: H
authors.lastname: Davies
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Patrick
authors.initials: P
authors.lastname: Tarpey
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Serena
authors.initials: S
authors.lastname: Nik-Zainal
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Campbell
mesh_terms: D030541:Databases, Genetic; D006801:Humans; D054643:INDEL Mutation / Q000235:genetics*; D009369:Neoplasms / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
keywords: Pindel; cancer; sequencing; somatic