when I run the SplitNcigarReads command, it occurs the error that "SAM/BAM/CRAM file [email protected]e18309e appears to be using the wrong encoding for quality scores: we encountered an extremely high quality score of 65." What's that means?
It means that your data may be using the wrong scale for quality scores. This often happens with older datasets, although we have also seen it happen more recently with some binned Illumina files. Can you tell us more about your dataset and where it comes from?