Comments (5)
Hi @shaka-emperor,
That means that bwa is skipping the FF,RF and RR reads when to calculate the insert size distribution. Those are common warnings. I do not think you have anything to worry about.
Best,
Iñigo
from circle-map.
So when analyzing structural variations (like ecDNA), these FF/RF/RR reads are included? (They are neglected only in insertion size distribution?)
from circle-map.
As far as I am aware, yes. BWA neglects them for the insert size distribution calculations, but flags them correctly when they have non-concordant orientations.
Best,
Iñigo
from circle-map.
Thank you very much~~
from circle-map.
Wonderful. Feel free to open a new issue if you have more question, and have a happy circle hunt!
from circle-map.
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