SAMtools 1.8

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that:

  • Is flexible enough to store all the alignment information generated by various alignment programs;
  • Is simple enough to be easily generated by alignment programs or converted from existing alignment formats;
  • Is compact in file size;
  • Allows most of operations on the alignment to work on a stream without loading the whole alignment into memory;
  • Allows the file to be indexed by genomic position to efficiently retrieve all reads aligning to a locus.

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

Accessing the software

To load the module:

$ module load SAMtools/1.8-iomkl-2018a
$ module load SAMtools/1.8-foss-2018a

To view command-line options, run the following command:

$ samtools --help

Example: SAMtools Job

An example can be found at ${BB_EXAMPLES}/SAMtools/1.4/ The example can be copied to a test directory and submitted to the batch system using sbatch.

$ cp -r ${BB_EXAMPLES}/SAMtools/1.4 ~/samtools-test
$ cd ~/samtools-test

Edit the script according to your needs, then do:

$ sbatch

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

The following previous versions are available on this service:

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the SAMtools website for more information regarding this application.

Last modified: 14 August 2018