These soft-clipped reads often indicate reads with split mappings and so can be used to localize translocations with single-base accuracy. CREST and ClipCrop are two algorithms that make use of soft-clipping information to detect split reads (30,31). SLOPE is another method for detection of translocations by split reads (32). Instead of using soft clips, however, it performs a local realignment of the unmapped “orphaned” mates in the vicinity of the uniquely mapped mate and looks for single breakpoints supported by many split reads.
