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# Barcoded BAMs

The cellranger vdj pipeline outputs several indexed BAM files. These files are primarily provided for use with a BAM visualization tool such as the Integrated Genome Viewer (IGV).

File Records Reference Description
all_contig.bam Reads Assembled contigs Reads aligned to assembled contigs, per cell barcode. This file demonstrates how the reads and UMIs support the assembled contigs within a cell barcode. Reads are not aligned across cell barcode boundaries. Please note that this BAM excludes reads whose barcodes don't match the whitelist, so it is not suitable as an archive of every single input read.
consensus.bam Contigs Clonotype consensus Each "reference" sequence is a clonotype consensus sequence, and each record is an alignment of a single cell's contig against this consensus. This file shows, for a clonotype consensus sequences, how the constituent per-cell assemblies support the consensus.
concat_ref.bam Contigs Concatenated germline segments Each reference sequence is, for each clonotype consensus, the annotated germline segments concatenated together. This file shows how both the per-cell contigs and the clonotype consensus contig relate to the germline reference. This file is expected to reveal polymorphisms, somatic mutations, and recombination-induced differences such as non-templated nucleotide additions.

The following assumes basic familiarity with the BAM format. More details on the SAM/BAM standard are available online.

## BAM Barcode Tags

Chromium cell barcode and UMI information for each read is stored as TAG fields:

TagTypeDescription
CBZChromium cell barcode sequence that is error-corrected and confirmed against a list of known-good barcode sequences.
CRZChromium cell barcode sequence as reported by the sequencer.
CYZChromium cell barcode read quality. Phred scores as reported by sequencer.
UBZChromium UMI sequence that is error-corrected among other UMIs with the same cell barcode and gene alignment.
URZChromium UMI sequence as reported by the sequencer.
UYZChromium UMI read quality. Phred scores as reported by sequencer.
BCZSample index read.
QTZSample index read quality. Phred scores as reported by sequencer.

The cell barcode CB tag includes a suffix with a dash separator followed by a number:

AGAATGGTCTGCAT-1

This number denotes what we call a GEM group, and is used to virtualize barcodes in order to achieve a higher effective barcode diversity when combining samples generated from separate GEM chip channel runs. Normally, this number will be "1" across all barcodes when analyzing a sample generated from a single GEM chip channel. It can either be left in place and treated as part of a unique barcode identifier, or explicitly parsed out to leave only the barcode sequence itself.

## BAM CIGAR String

The cellranger vdj pipeline uses the = and X CIGAR string operations to indicate matches and mismatches, respectively. This contrasts with most aligners which simply report M for match/mismatch. The SAM/BAM standard supports both CIGAR formats. For more details please refer to the SAM/BAM standard.