BreakPointer

What is BreakPointer?

BreakPointer is a tool to pinpoint rearrangement breakpoints using paired end reads.

How does it work?

In brief, BreakPointer consists of five steps, shown in the sketch below:

  1. dRanger predicts approximate somatic rearrangement.
  2. BreakPointer fishes for reads that span both sides of a putative breakpoint.
  3. The reads are aligned by a modified Smith-Waterman algorithm.
  4. Each breakpoint is called and assigned quality score, and the segments are fused acorrdingly to deduce the cancer genome.
  5. All the candidate split reads in the list are being aligned to the newly fused sequence. Breakpoints, fused sequences and the reads that support them are reported, and exported to IGV for easy view (actual IGV example is shown at the bottom)

 

How to Cite BreakPointer?

BreakPointer users may publish or otherwise publicly disclose the results of using BreakPointer. Please acknowledge BreakPointer in your publications by citing the following reference:

Drier Y, Lawrence MS, Carter SL, Stewart C, Gabriel SB, Lander ES, Meyerson M, Beroukhim R, Getz G. Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability. Genome Research 2013, 23(2): 228-235

How do I get BreakPointer?

How do I run BreakPointer?

How do I interpert BreakPointer Output?

Additional questions?

Email us at breakpointer-help@broadinstitute.org anytime!