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schneebergerlab / syri

Synteny and Rearrangement Identifier
https://schneebergerlab.github.io/syri/
MIT License
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INV vs INVDUP #250

Closed mparker2 closed 1 month ago

mparker2 commented 1 month ago

Hi again @mnshgl0110,

sorry for opening so many issues today... I also noticed that minimap2 can sometimes produce alignments where short-ish inversions are represented as a deletion and a supplementary alignment, for example:

image

Syri currently identifies these as INVDUPs/copygains since they are involved in two alignments, but this is somewhat misleading since the sequence is not actually duplicated. Would it be possible to consider inverted alignments wholly contained within deletions as INVs instead?

mparker2 commented 1 month ago

Similarly (although less important for me personally), there is an argument to be made that this is a translocation with duplicated ends, not wholly a duplication:

image

mparker2 commented 1 month ago

sorry I realised both examples actually have multiple 2ndary alignments lol

This stuff hurts my brain