ascatNgs: Identifying Somatically Acquired Copy-Number Alterations from Whole-Genome Sequencing Data.
Raine KM., Van Loo P., Wedge DC., Jones D., Menzies A., Butler AP., Teague JW., Tarpey P., Nik-Zainal S., Campbell PJ.
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.