How to identify translocations

[athitheo]

Hi,

Could you please extrapolate how to identify translocations from the NAIBR output bedpe format? I am looking for a known assumed balanced translocation within the results and need to know how this would appear in the bedpe format when 1) in a different chromosome 2) within the same chromosome (I presume the break2 chromosome would be the different one but need to confirm this). Also how would the orientation be presented?

Thanks,
Athina

[pontushojer]

I have briefly described the output here in my fork of this repo.You are also welcome to try this fork out on your as it has produce better results than this repo in my hands.

The orientation of breakpoints is discussed in this issue #11