Both simple and advanced tools are provided, supporting complex tasks like variant calling and alignment viewing as well as sorting, indexing, data extraction and format conversion.

[3] SAM files can be very large (tens of Gigabytes is common), so compression is used to save space.

Although the final output can be very complex, only a limited number of simple commands are needed to produce it.

Data sent to stdout are printed to the screen by default but are easily redirected to another file using the normal Unix redirectors (> and >>), or to another command via a pipe (|).

These headers include a description of the reference that the reads in sample_sorted.bam were aligned to and will be needed if the tiny_sorted.bam file is to be used with some of the more advanced SAMtools commands.

Start an interactive viewer to visualize a small region of the reference, the reads aligned, and mismatches.

brings up help information for scroll movement, colors, views, ... Set start position and compare.