Certain downstream tools, particularly duplicate markers/removers e.g. fgbio GroupReadsByUmi, rely on the mate CIGAR (MC:Z) and mate quality (MQ:i) tags. They can be added via samtools fixmate or a similar tool, but this adds an unnecessary step. In fact the fgumi Best Practices suggests the possibility of eliminating samtools from the pipeline entirely and using only fgumi and an aligner - but this is only possible if these tags are present in the aligner output. Notably recent versions of bwa and minibwa add both tags.
Certain downstream tools, particularly duplicate markers/removers e.g. fgbio GroupReadsByUmi, rely on the mate CIGAR (MC:Z) and mate quality (MQ:i) tags. They can be added via samtools fixmate or a similar tool, but this adds an unnecessary step. In fact the fgumi Best Practices suggests the possibility of eliminating samtools from the pipeline entirely and using only fgumi and an aligner - but this is only possible if these tags are present in the aligner output. Notably recent versions of bwa and minibwa add both tags.