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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.
The SAMtools package has been installed under /global/software/samtools/samtools13. Initialize your environment to run Samtools with:
module load samtools/1.3
for documentation for the various utilities provided with the SAMtools package.
for a brief summary of command line arguments for the samtools executable.
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.
For More Information
2015-06-24: Page created.
2015-12-23: - Updated for SAMtools 1.3 on Breezy.