Algorithms for identification of insertion sites using split reads

Question

[xieshaojun0621]

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.

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

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

Answer 1

[harold.smith.tarheel]

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

[xieshaojun0621]

Thanks. I'll try it.

Answer 2

[Vitis]

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

C: Identification of the sequence insertion site in the genome