This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How To Get Split-Reads From Breakdancer Output

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?

structural variation genome alignment
• 2,826 views • link
updated by ernfrid ernfrid • written by gundalav gundalav

1 answer

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.

• 292 views • link
written by ernfrid ernfrid

Log in to answer this question.

More posts like this