Background: Various aberrations such as amplification, deletion and translocation of segmental regions are common features of cancer genomes and play an important role in tumourigenesis and progression.Whole-genome sequencing of tumor samples has been demonstrated as an efficient approach for comprehensive analysis of genomic aberrations in cancer genome.Critical issues such as tumor impurity and aneuploidy, GC-content and mappability bias have been reported to complicate identification of copy number alteration and loss of heterozygosity in complex tumor samples.Therefore efficient computational methods are required to address these issues.