Extracting split-mappings with BWA-SW

Question

[novice]

I aligned a draft genome onto a reference with BWA-SW and would like to extract split-mappings. Specifically, I'd like to extract split mappings with more than 30 bp of non-overlap. Do you know how to do this?

My purpose is to find SV breakpoints.

Answer 1

[igor]

You probably don't want to reinvent the wheel. There are a lot of existing tools. See previous discussion here: How to find structural variants .

Also, a recent review: http://journal.frontiersin.org/article/10.3389/fbioe.2015.00092/full