Figure 3

Overview of trimming algorithm of ChopSticks. Schematic illustration of the trimming algorithm of ChopSticks. ChopSticks trims ends of deletion calls that are not likely to be parts of deletions, according to their coverage. First, it trims high-coverage regions at the ends of deletion calls. Here, a high-coverage region is a region whose coverage is greater than a given parameter k. Second, it recognizes a high-coverage region separated by a low-coverage region and trims these regions if their joint coverage is deeper than kf, where f is another parameter. The second step is repeatedly conducted until the joint coverage becomes less than kf.