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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 ( This unit describes both 'one-shot' execution and approaches more suitable for large-scale compute farms. © 2016 by John Wiley & Sons, Inc.

Original publication




Journal article


Curr Protoc Bioinformatics

Publication Date





15.9.1 - 15.9.17


cancer, copy-number, sequencing, somatic, Algorithms, Computational Biology, DNA Copy Number Variations, Databases, Genetic, Genome, Humans, Neoplasms