i have identified softclipped 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 softclipped 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?