BAM File Format
A BAM file (*.bam) is the compressed binary version of a SAM file that is used to represent aligned sequences. SAM and BAM formats are described in detail at samtools.github.io/hts-specs/SAMv1.pdf.
BAM files use the file naming format of SampleName_S#.bam, in which # is the sample number determined by the order that samples are listed for the run. In multinode mode, the S# is set to S1, regardless of the order of the sample.
BAM files contain a header section and an alignment section:
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Header—Contains information about the entire file, such as sample name, sample length, and alignment method. Alignments in the alignments section are associated with specific information in the header section. |
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Alignments—Contains read name, read sequence, read quality, alignment information, and custom tags. The read name includes the chromosome, start coordinate, alignment quality, and match descriptor string. |
The alignments section includes the following information for each read or read pair:
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RG—Read group, which indicates the number of reads for a specific sample. |
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BC—Barcode tag, which indicates the demultiplexed sample ID associated with the read. |
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SM—Single-end alignment quality. |
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NM—Edit distance tag, which records the Levenshtein distance between the read and the reference. |
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XU—Identifies the UMI BAM tag. |
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XB—Identifies the bead-barcode BAM tag. |
BAM index files (*.bam.bai) provide an index of the corresponding BAM file.