ToolSEG: A Tool for DNA Copy Number Segmentation

Abstract

To perform segmentation to identify regions of constant copy number is an important key for discovering structural variation in the human genome. It calls for a uniform pipeline to integrate various segmentation methods in a flexible software toolbox for conveniently evaluating outcome. We propose such toolbox and implement an open source Java package called ToolSEG to generate realistic DNA copy number profiles with known truth. Five typical methods have been assessed on synthetic data and real copy number profiles: HMM, CBS, PCF, Lasso, CLT.