Cap base quality in bam file

Question

[junnna]

Hello,

I would like to change the base quality scores in PacBio HiFi bam files, such that the base qualities are capped to 33. Is there a tool that can do this?

Thanks in advance!

Answer 1

[h.mon]

You can try reformat.sh from the BBTools package:

reformat.sh in=reads.bam out=capped.bam maxcalledquality=33