Bwa Soft Clipped Indels Realignment

Question

[stolarek.ir]

Hi guys

I generated a sam file by aligning single end reads with bwa-mem.

i have identified soft-clipped fragments which suggest indels at their breakpoints. Now I wanted to select those fragments and realign around those regions. And here is my question:

Should I take left and right breakpoint soft-clipped fragments putting them together in one file as one would normally do for pair-end data? And them using those 2 files to realign against reference file composed of the regions around the breakpoints?

I never tried indel realignment. And my idea is utilizing soft clipped fragments, which to complicate matters more come from single end reads.

Can any one suggest anything?

Answer 1

[Ashutosh Pandey]

Have you ever tried using SVMerge (http://svmerge.sourceforge.net/). It exactly does what you are looking for. Little complicated to use but it does the local realignment around the softclipped reads to get you the exact breakpoints.

[stolarek.ir]

Hmm actually it depends on the calls made by other tools in the first step. Only Pindel is using proper split read approach in which I'm interested (but don't know if for single end ones). Other tools are no good for me, as my pipeline has much greater sensitivity and base pair resolution in first step of analyzing SAM file.

I now it sounds very geeky, that I'm writing almost everything from scratch, but well, that's the best way to learn something.

I think that it shouldn't matter now if I will use soft clipped parts as pair end or just dump into one file. Proper naming will resolve this problem, and adding +- 1k bp either side of the breakpoint in reference should give nice specificity

Anyways, thanks for the SVMerge