ascatNgs: Identifying Somatically Acquired Copy-Number Alterations from Whole-Genome Sequencing Data

Curr Protoc Bioinformatics. 2016 Dec 8:56:15.9.1-15.9.17. doi: 10.1002/cpbi.17.

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.

Keywords: cancer; copy-number; sequencing; somatic.

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • DNA Copy Number Variations / genetics*
  • Databases, Genetic*
  • Genome
  • Humans
  • Neoplasms / genetics