Annotate BAM
If enabled, the BAM file output by STAR and bwa-mem2 (for ATAC-Seq) is further annotated to summarize the results of the BD Rhapsody™ Sequence Analysis Pipeline. See BAM and BAM Index in the output files section for more detail on tags added to BAM records.
See also:
samtools.github.io/hts-specs/SAMv1.pdf
bwa-mem2 man page (note that usage is same as original bwa-mem)