The overall workflow of SCNVSim. A) A personal genome with normal diploid status is generated by simulating SNV and INDEL against reference genome sequence. SNV/INDEL ratio, transition/transversion ratio, Heterozygous/Homozygous ratio and INDEL size distribution are considered (left). B) For tumor genome simulation, ploidy is first determined, followed by SV generations of different types and mechanisms (Non-homology or homology mediated). Heterogeneity is also implemented (right). The outputs include a simulated personal genome with normal diploid status in FASTA format, germline SNVs and INDELs in variant call format (VCF), and the following for each simulated tumor clone: 1) simulated SVs in terms of events and breakpoints, 2) copy number status for each individual segment, 3) BAF and LOH status of each segment, 4) FASTA format of cancer genome with somatic SV/CNV events as input for NGS reads simulation. By mixing the simulated genomes from the normal sample and tumor clones into a ratio specified by the user, a realistic and complicated cancer genome data set with varying levels of tumor heterogeneity and purity can be obtained.