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, SampleName
BAM files contain a header section and an alignment section:
| • | 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. |
| • | 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:
| • | RG—Read group, which indicates the number of reads for a specific sample. |
| • | BC—Barcode tag, which indicates the demultiplexed sample ID associated with the read. |
| • | SM—Single-end alignment quality. |
| • | NM—Edit distance tag, which records the Levenshtein distance between the read and the reference. |
| • | MD—Mismatching positions/bases (BWA only). |
BAM files are suitable for viewing with an external viewer such as IGV or the UCSC Genome Browser.
BAM index files (*.bam.bai) provide an index of the corresponding BAM file.
NOTE
BAM files are not available for runs that performed fusion calling.