BreakDancer results improved by ChopSticks. Box-and-whisker plots of upstream differences of deletion calls obtained by BreakDancer and those improved by ChopSticks. The red, green, blue, light blue, and magenta boxes correspond to k values of 1, 2, 3, 4, and 5, respectively, and the rightmost yellow box corresponds to the original results of BreakDancer. Among boxes of the same color, from left to right, f=0.1, 0.2, …, 1.0. Brown horizontal dashed lines indicate the values of 25%, 50%, and 75% tiles of differences of original deletion calls from below to above, respectively. The results in this figure indicate that ChopSticks clearly improved the resolution of the original BreakDancer results. When the coverage was low, small k values were effective in improving the resolution. When coverage was high, the resolution was also improved for large k values. Therefore, when the coverage is high, we recommend using large k values to avoid erroneous alignments of NGS reads and the genome. We omitted the results for coverage=15 because they were similar to those for coverage=20.