Fig. 3

Overall performance of ConanVarvar, CNVnator/CNVpytor, Control-FREEC and Manta on the test dataset based on the merged output of each tool for NA12878 and the 4 clinical and 9 simulated single-chromosome samples. A CNV was considered a false positive if it was not present in the simulated or clinical samples. “1-Recall” is also known as False Negative Rate (FNR). Absence of a bar indicates that the corresponding metric has the value of zero, e.g., ConanVarvar, CNVnator/CNVpytor and Control-FREEC all had the FNR of zero (perfect recall). Manta’s output was filtered to include only those variants that were at least 50 kb in size