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Algorithms for identification of insertion sites using split reads

Imaging I have a big insertion in the genome. Then if I sequence the sample and align the reads to the reference genome, I will get some split reads. I showed one example here. Image and video hosting by TinyPic

My plan is to identify the insertion site using these split reads.

Could anyone give me some suggestions of how to do this?

split read next generation sequencing data
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updated by Vitis Vitis • written by xieshaojun0621 xieshaojun0621

2 answers

We've had reasonably good success using LUMPY, which takes advantage of split reads.

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written by harold.smith.tarheel harold.smith.tarheel

A lot of approaches to tackle this problem. A very good discussion here:

C: Identification of the sequence insertion site in the genome

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written by Vitis Vitis

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