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What tags are included in an Optimus BAM file?

The Optimus Pipeline outputs a barcoded BAM file of aligned reads. There are multiple tags within the BAM file, including standard tags from 10X genomics and Sequence Alignment Map (SAM) files. The table below details the tags used by the Optimus Pipeline and the relevant sources/tools from which the pipeline obtains the tags.

Optimus Pipeline BAM TagDetailsSource
ASAlignment score generated by alignerSAM
CBChromium cellular barcode sequence that is error-corrected and confirmed against a list of known-good barcode sequences10X Genomics
CRChromium cellular barcode sequence as reported by the sequencer10X Genomics
CYChromium cellular barcode read quality. Phred scores as reported by sequencer10X Genomics
GXGene IDSTAR aligner
GNGene namesSTAR aligner
GSReserved for backwards compatibility reasonsSAM
HIQuery hit indexSAM
MDString for mismatching indexesSAM
NHNumber of reported alignments that contain the query in the current recordSAM
NMEdit difference to the referenceSAM
RGRead groupSAM
UBChromium molecular barcode sequence that is error-corrected among other molecular barcodes with the same cellular barcode and gene alignment10X Genomics
UGRead group IDUmi-tools
URChromium molecular barcode sequence as reported by the sequencer10X Genomics
UYChromium molecular barcode read quality. Phred scores as reported by sequencer10X Genomics
XFExtra alignment flags10X Genomics
jI[jI:B:I,Start1,End1,Start2,End2,...] Start and End of introns for all junctions (1-based)STAR
jM[jM:B:c,M1,M2,...] Intron motifs for all junctions (i.e. N in CIGAR)STAR
nMThe number of mismatches per (paired) alignmentSTAR