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:

For detailed information, visit the SAMTools website.

Available Versions

The current installation of SAMTools incorporates the most popular packages. 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

Module Version Module Load Command
samtools 1.4.1 module load gcc/7.1.0 samtools/1.4.1
samtools 0.1.20 module load samtools/0.1.20
samtools 1.4.1 module load samtools/1.4.1
samtools 1.7 module load samtools/1.7
samtools 1.9 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.