Allele-specific multi-sample copy number segmentation in ASCAT.

MOTIVATION: Allele-specific copy number alterations are commonly used to trace the evolution of tumours. A key step of the analysis is to segment genomic data into regions of constant copy number. For precise phylogenetic inference, breakpoints shared between samples need to be aligned to each other. RESULTS: Here we present asmultipcf, an algorithm for allele-specific segmentation of multiple samples that infers private and shared segment boundaries of phylogenetically related samples. The output of this algorithm can directly be used for allele-specific copy number calling using ASCAT. AVAILABILITY: asmultipcf is available as part of the ASCAT R package (version ≥ 2.5) from github.com/Crick-CancerGenomics/ascat/.