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)