Fig. 7

Simulation pipeline. Given the reference genome GRCh37, Single-Nucleotide-Variants (SNVs) from the 1000 Genomes project, and a set of randomly-designed CNAs to be added to the tumor cell genome, our pipeline first calls EAGLE to generate three different bam files containing simulated reads for the normal cell (the leftmost column) in the normal sample, the normal cell in the tumor sample, and the tumor cell in the tumor sample respectively. Besides random sequencing errors, EAGLE introduces point-mutations to simulated reads at the given SNV loci. Excluding the sequencing errors, the locations of the SNVs in the three different bam files are identical. The tumor cell may lose one or both SNV alleles in copy-loss regions. To simulate a tumor sample that contains subclones, we design a different set of CNAs that share some CNAs with the first tumor clone and generates another bam file for the second (or third and so forth) tumor subclone. The sequencing reads of the normal cell and tumor cell(s) that belong to the same tumor sample are mixed proportionately to generate the final bam file for one tumor sample