An algorithm for identifying haplotype heterogeneity in cancer genomes is proposed to consider somatic mutational events carried by multiple sub-clones.The algorithm is based on the genomic sequencing data with multiple libraries of tumor tissue and extracts the features from both the multi-library and the constraints of paired-end reads.A priori number of sub-clones is roughly estimated by clustering the allelic variant frequency of each somatic loci.A contig-andextension algorithm is designed,and the hapl...