Manual pages

Documentation for BCFtools, SAMtools, and HTSlib’s utilities is available by using man command on the command line. The manual pages for several releases are also included below — be sure to consult the documentation for the release you are using.

File formats

SAMtools conforms to the specifications produced by the GA4GH File Formats working group. Details of the current specifications are available on the hts-specs page.

HTSlib also includes brief manual pages outlining aspects of several of the more important file formats. These are available via man format on the command line or here on the web site:

Benchmarks

Publications