SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
Software Category: bio

For detailed information, visit the SAMTools website.

Available Versions

To find the available versions and learn how to load them, run:

module spider samtools

The output of the command shows the available SAMTools module versions.

For detailed information about a particular SAMTools module, including how to load the module, run the module spider command with the module’s full version label. For example:

module spider samtools/1.4.1
ModuleVersion Module Load Command
samtools1.4.1 module load gcc/9.2.0 samtools/1.4.1
samtools0.1.20 module load samtools/0.1.20
samtools1.10 module load samtools/1.10
samtools1.4.1 module load samtools/1.4.1
samtools1.7 module load samtools/1.7
samtools1.9 module load samtools/1.9

Build Your Own Version

Users may build their own versions of SAMTools if they wish to use a different compiler or software version. Instructions are available on the SAMTools website.

SLURM Script Example

To run SAMTools on Rivanna, a script similar to the following can be used. SAMTools has many options so only a basic example is shown.