classification of inversion may be translocation

[emikana]

Hi! In the hic_breakfinder outputs, many are classified as inversions. However, when I look at the Hi-C map, it looks like some should be defined as "intra-chromosomal translocations". (not flipping of the segments, but translocation of the segments within the same chromosome)

Let's say I just marked these as "translocation" in the input data for assemble-complexSVs. WOuld the pipeline handle it correctly?

Thanks in advance!

[XiaoTaoWang]

Hi! The annotation label (e.g., inversion vs. translocation) doesn’t influence the pipeline’s behavior. What really matters for processing is the SV strand information.

[emikana]

Hello XiaoTaoWang, Thank you very much for your prompt reply!
Really appreciate it. Also thank you for providing the nice pipeline!