Cap base quality in bam file
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3 months ago
junnna ▴ 10

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!

HiFi bamfile • 217 views
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Entering edit mode
3 months ago
h.mon 34k

You can try reformat.sh from the BBTools package:

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