BAM Files

A BAM file (*.bam) is the compressed binary version of a SAM (sequence alignment map) file that is used to represent aligned sequences up to 128 Mb. BAM files use the file naming format of SampleName_S#.bam. # 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 the match descriptor string.

The alignments section includes the following information for each read or read pair:

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AS: Paired-end alignment quality.

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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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XC: Match descriptor string.

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XN: Amplicon name tag, which records the amplicon ID associated with the read

BAM index files (*.bam.bai) provide an index of the corresponding BAM file.