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?
<p>Hi,</p> <p>As it mentioned in <a href='http://www.broadinstitute.org/files/shared/mpg/nextgen2010/nextgen_poplin.pdf'>here</a>, the reported base quality scores (the QUAL column in <a href='http://samtools.sourceforge.net/SAM1.pdf'>BAM</a> file) before Base Quality Score Recalibration(BQSR) are …