CNVnator results improved by ChopSticks. Box-and-whisker plots of upstream differences of deletion calls obtained by CNVnator and those improved by ChopSticks. The format of this plot is exactly the same as that in Figure 6. We expanded the original deletion calls of CNVnator outward by the window size (50 bp) because ChopSticks assumes that predicted breakpoints are outside true deletions. The results in this figure indicate that ChopSticks can improve the resolution of CNVnator results if predicted positions of breakpoints are within a few hundreds of bases from true breakpoints.