ACE: Absolute Copy number Estimation from low-coverage whole-genome sequencing data

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Summary: Chromosomal copy number aberrations can be efficiently detected and quantified using low-coverage whole-genome sequencing (lcWGS), but analysis is hampered by the lack of knowledge on absolute DNA copy numbers and tumor purity. Here we describe an analytical tool for Absolute Copy number Estimation, ACE, which scales relative copy number signals from chromosomal segments to optimally fit absolute copy numbers, without the need for additional genetic information, such as SNP data. In doing so, ACE derives an estimate of tumor purity as well. ACE facilitates analysis of large numbers of samples, while maintaining the flexibility to customize models and generate output of single samples.

Availability and implementation: ACE is freely available via and at

Supplementary information: Supplementary methods and data are available at Bioinformatics online. Documentation, example data, and a vignette, are included in the R package of ACE.

Original languageEnglish
Pages (from-to)2847-2849
Issue number16
Publication statusPublished - 15 Aug 2019

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