dRanger

dRanger is a tool to identify somatic rearrangements as clusters of aberrant paired-end sequencing reads in a tumor sample where the the normal sample has read-pairs consistent with the reference. Candidate rearrangement breakpoints from dRanger are passed into Breakpointer, which applies a modified Smith-Waterman algorithm to all reads in the region to identify split-read support for  the rearrangement. 

Contact: 
http://www.broadinstitute.org/cancer/cga/cga_forums