SAMtools

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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

Legacy versions Supported versions New versions
1.1, 1.2

Environment modules

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

How to submit a job

You can submit a SAMtools job in batch mode with the following command:
bsub [LSF options] "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 [LSF options] with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of bsub 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