How To Get Split-Reads From Breakdancer Output

Question

[gundalav]

BreakDancer output gives the following files: CFG, CTX, BED and OUT. How can I find the 'split-reads' output from these files? Is there a way to infer that from the supporting reads?

Answer 1

[ernfrid]

No, the BreakDancer program does not have any concept of split reads. You could attempt to assemble a putative breakpoint (with TIGRA or another assemble) and map the reads back to the contigs to recover breakpoint supporting reads.