To test the effectiveness of joint updating of the transition matrices we artificially generated data for 1000 assays of a 500 SNP long chromosome containing a single 5 SNP aberrant region. We then applied QuantiSNP independently to each individual assay and then QuantiSNP, in its multi-sample analysis mode (we manually set K = 100), to the entire dataset. This procedure was repeated 100 times. We then assessed the performance by counting the number of deleted SNPs that were correctly called by the single- and multi-sample analysis modes and computing the average over the 100 iterations. Figure 3 shows the improved detection of a small deletion and duplication region shared by 1000 individuals.
