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. 2017 May 16;38(7):889–897. doi: 10.1002/humu.23237

Figure 3.

Figure 3

Strengths and weaknesses of all methods analyzed. In general, “+++” indicates the best possible performance, whereas “++” means the method is close to the best, “+” is acceptable, but not very good, and “−” signals failure or missing feature. For the two detection performance measures (i.e., sensitivity and specificity), 100% is indicated by “+++.” A single FN or FP is indicated by “++” in the corresponding sensitivity or specificity row. More than one false classification but an overall sensitivity or specificity greater than 95% is indicated by “+.” “No‐call rate” stands for the fraction of ROIs classified as low quality (see the section “Evaluation criteria”). “+++” means no‐call rate of 0, “++” means less than 0.01, “+” means less than 0.1, and “−” means no‐call rate larger than 0.1. Programs with QC for samples and ROIs are marked as “+++,” whereas programs with QC only for samples are marked as “+.” For “CNVs <1 ROI,” each plus sign symbolizes one successful detection of a CNV that affected only part of a ROI (see the section “Small CNVs”). The row “Whole‐gene CNVs” especially concerns CNVs that affect all ROIs that are within the gene of interest for a patient. “+++” indicates that all of them were detected, whereas “++” indicates that some of them were detected and others classified as low quality. If the CNVs affecting the entire gene of interest are not fully detected, this is indicated by “+,” whereas “−” means that these CNVs can only be detected while risking incidental findings. While “+” in the row “Incidental findings” indicates that incidental findings can be avoided, but only at the risk of missing CNVs that affect all ROIs analyzed, “+++” means that the method avoids incidental findings without loss of power. “−” reflects that the CNV tool offers no option to filter the results for genes of interest and, therefore, for avoiding incidental findings. The row “Runtime” indicates the runtime of the CNV detection algorithm measured as described in the section “Runtime.” The thresholds for “+++,” “++,” “+,” and “−” are less than 10 min, less than 1 hr, less than 6 hr, and more than 6 hr, respectively. Classes for the row “GUI” are: “+++” if there is an easy‐to‐use graphical user interface (GUI), “++” if the GUI is not easy to use, and “−” if there is no GUI at all. Since only two of the programs are commercial, they were marked “−” in the corresponding row, whereas all others have “+++”