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SAMtools and HTSlib utilities

Table of Contents


SAMtools is a set of utiltiies for manipulation of genetic sequence data stored in files with SAM (Sequence Alignment/Map), BAM or CRAM formats.  (See BCFtools for tools to manipulate VCF or BCF files).  The HTSlib commands tabix, bgzip and htsfile are also included in the package.

See the Software Versions tab for a list of systems on which Samtools have been installed.

Using SAMtools on Breezy

The SAMtools package has been installed under /global/software/samtools/samtools13.  Initialize your environment to run Samtools with:

module load samtools/1.3


man samtools

for documentation for the various utilities provided with the SAMtools package.


samtools --help

for a brief summary of command line arguments for the samtools executable.

Using SAMtools libraries on Bugaboo

If you want to link your program with libbam which comes with SAMtools you need to add:

-L/usr/local/samtools-$version/lib -Wl,-rpath /usr/local/samtools-$version/lib -lbam -lhts

where $version is the SAMtools version number that has been installed on Bugaboo.


2015-06-24: Page created.
2015-12-23: - Updated for SAMtools 1.3 on Breezy.