How does bambu handle secondary/supplementary alignmets, low MAPQ, and MAPQ=0 (reads that align equally well to 2+ loci)?

[bernardo-heberle]

Hello,

I was wondering how Bambu handles these three alignment cases:

1. Secondary and Supplementary alignments in a bam file? Does Bambu do anything with those or just ignores them?

2. Low MAPQ score? Is there a threshold where Bambu stops taking a read alignment into account if the MAPQ is too low?

3. MAPQ=0? From my understanding when a read aligns equally well to two or more different loci in the reference genome Minimap2 gives it a MAPQ=0 and randomly assigns the read to one of the loci. Does Bambu take those alignments into account or filters them out?

Thank you for your time.