SAMtoBAM

So there is only a 3kb region identified as a match between these two genomes which explains the issue I would guess therefore that the step that is failing is...

So nucmer can be adjusted for more distant genomes but you would have to do it yourself and it isn't really clear on how to do it effectively You can...

Hi there, That definitely happens on occasion and you are right that it is unusual. Why this happens with MUM&Co is it attempts to find the closest alignment on the...

> As the situation you described, isn't it a translocation variation that the TE in reference move to another place and the query TE inserted into the reference position where...

> In what I have learned, there shouldn't be the unaligned region in the reference for the insertion or in the query for the deletion, it should be a specific...

> But how it occurred in the actual genome? I think it is a chimeric phenomenon that in some cells it is the normal insertion, but in other cells, it...

Hi Gabriele, Thanks for using MUM&Co For duplications: Technically that is how it should function, the duplications are to be from haplotype1. MUM&Co doesn't predict 'expansions' and 'contractions' so duplications...

Ok so that confirms what I was saying, that duplications only detect expansions within the query and not contractions. Although I could technically invert the detection using the reciprocal alignment...

Hi there, Sorry for taking a couple days Essentially I have just reverted the parsing of the alignment for duplications onto the reciprocal alignment instead, and therefore this should find,...

Unfortunately I don't have any idea at the moment why some duplications are not labelled as contractions in the opposite as it should be performing the same analysis on essentially...