NAME

       sambamba-sort - tool for sorting BAM files

SYNOPSIS

       sambamba sort OPTIONS <input.bam>

DESCRIPTION

       BAM files can have either ´coordinate´ sort order, or ´qname´ one.

       The first one means to sort the file by (integer) reference ID, and for each reference sort corresponding
       reads by start coordinate.

       ´qname´ sorting order is when reads are sorted lexicographically by their names.

       sambamba sort does an external stable-type sort on input file. That means it reads the source BAM file in
       chunks  that fit into memory, sorts them and writes to a temporary directory, and then merges them. After
       merging temporary files are removed automatically.

       Both sorting orders are supported. Default one is ´coordinate´ because this is the one used for  building
       index later. In order to switch to ´qname´ sorting order, use -n|--sort-by-name flag.

OPTIONS

       -m, --memory-limit=LIMIT
              Sets  an  upper  bound for used memory. However, this is very approximate. Default memory limit is
              512MiB. Increasing it will allow to make chunk sizes larger and also reduce amount  of  I/O  seeks
              thus improving the overall performance.

              LIMIT  must  be  a  number  with  an optional suffix specyfying unit of measumerent. The following
              endings are recognized: K, KiB, KB, M, MiB, MB, G, GiB, GB.

       --tmpdir=TMPDIR
              Use TMPDIR to output sorted chunks. Default behaviour is to use system temporary directory.

       -o, --out=OUTPUTFILE
              Output file name. If not provided, the result is written to a file with .sorted.bam extension.

       -n, --sort-by-name
              Sort by read name instead of doing coordinate sort.

       -l, --compression-level=COMPRESSION_LEVEL
              Compression level to use for sorted BAM, from 0 (known as uncompressed BAM in samtools) to 9.

       -u, --uncompressed-chunks
              Write sorted chunks as uncompressed BAM. Default behaviour is to write them with compression level
              1, because that reduces time spent on I/O, but in some cases using this  option  can  give  you  a
              better  speed.  Note,  however, that the disk space needed for sorting will typically be 3-4 times
              more than without enabling this option.

       -p, --show-progress
              Show wget-like progressbar in STDERR (in fact, two of  them  one  after  another,  first  one  for
              sorting, and then another one for merging).

       -t, --nthreads=NTHREADS
              Number of threads to use.

SEE ALSO

       For  more  information  on  the  original  samtools  SORT behaviour, check out the samtools documentation
       http://samtools.sourceforge.net/samtools.shtml.

BUGS

       At the moment, the memory is used quite ineffectively for really large files.

                                                  February 2015                                 SAMBAMBA-SORT(1)