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# [SAMtools] Sort by coordinates

This wrapper for SAMtools sort sorts entries in a BAM file by their coordinates by running the command

    samtools sort - tmp -o

and has no additional options. Sorting uses a temporary file with prefix `tmp` that will briefly occupy additional storage space in the current work directory if the whole alignment does not fit into memory.

See also

http://samtools.sourceforge.net/samtools.shtml

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