oracular (1) sambamba-sort.1.gz

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)