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Cap base quality in bam file

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!

bam hifi

1 answer

You can try reformat.sh from the BBTools package:

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

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