What does the label 'complicated' mean? about mumandco

[SAMtoBAM]

Hi @Leona123151

It has been on my mind to properly explain this tag!
As you can see with your output these two events have the same coordinates, however it appears that there is a deletions and an insertion detected in this region. So essentially complicated is just a warning that this may be a complex event

In this case they are kept because the size of the events are very different, therefore making it less likely to be an anomaly of alignment. However when the sizes are also the same they are used to potentially verify inversions (as in some MUMmer processing scripts inversions can be essentially ignored, which makes it look like a gap in both the query and the reference, i.e. looking like a deletion and insertion but they are of the same size, so I use this to verify potential inverted alignments as inversions) and then removed.

Does this help at all?

Thanks

[Leona123151]

I think I've got it through your explanation. Thank you very much!