SAMtools

Category

Bioinformatics

Description

Samtools is a set of utilities that manipulate alignments in the BAM format. It imports from and exports to the SAM (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows to retrieve reads in any regions swiftly. It is designed to work on a stream. It regards an input file `-' as the standard input (stdin) and an output file `-' as the standard output (stdout). Several commands can thus be combined with Unix pipes. Samtools always output warning and error messages to the standard error output (stderr). Samtools is also able to open a BAM (not SAM) file on a remote FTP or HTTP server if the BAM file name starts with `ftp://' or `http://'. Samtools checks the current working directory for the index file and will download the index upon absence. Samtools does not retrieve the entire alignment file unless it is asked to do so.

Available versions (Euler, old software stack)

Legacy versions	Supported versions	New versions
	1.1, 1.2

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

Environment modules (Euler, old software stack)

Version	Module load command	Additional modules loaded automatically
1.1	module load gcc/4.8.2 samtools/1.1	legacy centos_cruft/6
1.2	module load gcc/4.8.2 samtools/1.2	legacy centos_cruft/6

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

How to submit a job

You can submit a SAMtools job in batch mode with the following command:

sbatch [Slurm options] --wrap="samtools [samtools options]"

Here you need to replace [samtools options] with SAMtools command line options (please run the command samtools for getting a list of all command line options) and [Slurm options] with Slurm parameters for the resource requirements of the job. Please find a documentation about the parameters of sbatch on the wiki page about the batch system.

License information

BSD license,MIT license

Links

http://www.htslib.org

https://github.com/samtools/samtools
http://samtools.sourceforge.net
https://en.wikipedia.org/wiki/SAMtools
http://biobits.org/samtools_primer.html