The Sequence Alignment/Map (SAM) format is a generic alignment format for storing reads aligned to a reference genome, 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 the same information as SAM, but in a compressed, binary format that is only machine readable.
BAM files show alignments. Use them for direct interpretation or as a starting point for further analysis with downstream analysis tools that are compatible with BAM. BAM files are suitable for viewing with an external viewer such as IGV or the UCSC Genome Browser.
If you use an app in BaseSpace that uses BAM files as input, the app locates the file when launched. If using BAM files in other local tools, download the file to use it in the external tool.
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