title: ascatNgs: Identifying Somatically Acquired Copy-Number Alterations from Whole-Genome Sequencing Data.
abstract: We have developed ascatNgs to aid researchers in carrying out Allele-Specific Copy number Analysis of Tumours (ASCAT). ASCAT is capable of detecting DNA copy number changes affecting a tumor genome when comparing to a matched normal sample. Additionally, the algorithm estimates the amount of tumor DNA in the sample, known as Aberrant Cell Fraction (ACF). ASCAT itself is an R-package which requires the generation of many file types. Here, we present a suite of tools to help handle this for the user. Our code is available on our GitHub site (https://github.com/cancerit). This unit describes both 'one-shot' execution and approaches more suitable for large-scale compute farms. © 2016 by John Wiley & Sons, Inc.
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.|The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, United Kingdom.
authors.forename: Peter
authors.initials: P
authors.lastname: Van Loo
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.|Oxford Big Data Institute, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.
authors.forename: David C
authors.initials: DC
authors.lastname: Wedge
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: David
authors.initials: D
authors.lastname: Jones
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Andrew
authors.initials: A
authors.lastname: Menzies
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: 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: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D056915:DNA Copy Number Variations / Q000235:genetics*; D030541:Databases, Genetic; D016678:Genome; D006801:Humans; D009369:Neoplasms / Q000235:genetics
keywords: cancer; copy-number; sequencing; somatic