BAM Files

The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mb) produced by different sequencing platforms. SAM is a text format file that is human-readable. The Binary Alignment/Map (BAM) keeps exactly the same information as SAM, but in a compressed, binary format that is only machine-readable.

If you use an app in BaseSpace that uses BAM files as input, the app will locate the file when launched. If using BAM files in other tools, download the file to use it in the external tool.

Go to http://samtools.sourceforge.net/SAM1.pdf to see the exact SAM specification.