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A (Binary Alignment Map) BAM file is an alignment file in a compressed binary format that is machine readable only. Alignment files store reads aligned to a reference genome. Reads can be short or long (up to 128 Mp) and are produced by different sequencing platforms.
Use BAM files 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 a BaseSpace Sequence Hub app that uses BAM files as input, the app locates the file when it is launched. If using BAM files in other local tools, download the file to use it in the external tool.