Extracting split-mappings with BWA-SW
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.
1 answer
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
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