Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
The Francis Crick Institute, London NW1 1AT, UK.
Bioinformatics. 2021 Jul 27;37(13):1909-1911. doi: 10.1093/bioinformatics/btaa538.
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.
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.
asmultipcf is available as part of the ASCAT R package (version ≥2.5) from github.com/Crick-CancerGenomics/ascat/.
等位基因特异性拷贝数改变常用于追踪肿瘤的进化。分析的关键步骤是将基因组数据分割成具有恒定拷贝数的区域。为了进行精确的系统发育推断，需要将样本之间的断点相互对齐。
在这里，我们提出了 asmultipcf，这是一种用于对多个样本进行等位基因特异性分割的算法，该算法可以推断出系统发育相关样本的私有和共享片段边界。该算法的输出可以直接用于使用 ASCAT 进行等位基因特异性拷贝数调用。
asmultipcf 作为 ASCAT R 包（版本≥2.5）的一部分，可从 github.com/Crick-CancerGenomics/ascat/ 获得。
