NAME

       samtools sort - sorts SAM/BAM/CRAM files

SYNOPSIS

       samtools sort [-l level] [-m maxMem] [-o out.bam] [-O format] [-n] [-t tag] [-T tmpprefix]
       [-@ threads] [in.sam|in.bam|in.cram]

DESCRIPTION

       Sort alignments by leftmost coordinates, or by read name when -n is used.  An  appropriate
       @HD-SO sort order header tag will be added or an existing one updated if necessary.

       The  sorted  output  is  written  to  standard output by default, or to the specified file
       (out.bam) when -o is used.  This command will also create temporary files tmpprefix.%d.bam
       as  needed when the entire alignment data cannot fit into memory (as controlled via the -m
       option).

       Consider using samtools collate instead if you need name  collated  data  without  a  full
       lexicographical sort.

OPTIONS

       -l INT     Set  the  desired  compression  level for the final output file, ranging from 0
                  (uncompressed) or 1 (fastest but minimal compression) to  9  (best  compression
                  but slowest to write), similarly to gzip(1)'s compression level setting.

                  If -l is not used, the default compression level will apply.

       -m INT     Approximately the maximum required memory per thread, specified either in bytes
                  or with a K, M, or G suffix.  [768 MiB]

                  To prevent sort from creating a huge number of temporary files, it  enforces  a
                  minimum value of 1M for this setting.

       -n         Sort  by  read  names  (i.e.,  the  QNAME  field)  rather  than  by chromosomal
                  coordinates.

       -t TAG     Sort first by the value in the alignment tag TAG, then by position or name  (if
                  also using -n).

       -o FILE    Write the final sorted output to FILE, rather than to standard output.

       -O FORMAT  Write the final output as sam, bam, or cram.

                  By  default,  samtools  tries  to  select  a  format  based  on the -o filename
                  extension; if output is to standard output or no format can be deduced, bam  is
                  selected.

       -T PREFIX  Write  temporary  files  to  PREFIX.nnnn.bam,  or if the specified PREFIX is an
                  existing  directory,  to  PREFIX/samtools.mmm.mmm.tmp.nnnn.bam,  where  mmm  is
                  unique to this invocation of the sort command.

                  By  default,  any  temporary  files  are  written alongside the output file, as
                  out.bam.tmp.nnnn.bam, or if output  is  to  standard  output,  in  the  current
                  directory as samtools.mmm.mmm.tmp.nnnn.bam.

       -@ INT     Set  number  of  sorting  and  compression  threads.   By default, operation is
                  single-threaded.

       --no-PG    Do not add a @PG line to the header of the output file.

       Ordering Rules

       The following rules are used for ordering records.

       If option -t is in use, records are first sorted by the value of the given alignment  tag,
       and then by position or name (if using -n).  For example, “-t RG” will make read group the
       primary sort key.  The rules for ordering by tag are:

       •   Records that do not have the tag are sorted before ones that do.

       •   If the types of the tags are different, they will be sorted so that  single  character
           tags  (type A) come before array tags (type B), then string tags (types H and Z), then
           numeric tags (types f and i).

       •   Numeric tags (types f and  i)  are  compared  by  value.   Note  that  comparisons  of
           floating-point values are subject to issues of rounding and precision.

       •   String tags (types H and Z) are compared based on the binary contents of the tag using
           the C strcmp(3) function.

       •   Character tags (type A) are compared by binary character value.

       •   No attempt is made to compare tags of other types — notably type B array  values  will
           not be compared.

       When  the  -n  option is present, records are sorted by name.  Names are compared so as to
       give a “natural” ordering — i.e. sections consisting of digits  are  compared  numerically
       while  all  other  sections are compared based on their binary representation.  This means
       “a1” will come before “b1” and “a9” will come before “a10”.  Records with  the  same  name
       will be ordered according to the values of the READ1 and READ2 flags (see flags).

       When  the  -n option is not present, reads are sorted by reference (according to the order
       of the @SQ header records), then by position in the reference, and  then  by  the  REVERSE
       flag.

       Note

       Historically  samtools  sort also accepted a less flexible way of specifying the final and
       temporary output filenames:

              samtools sort [-f] [-o] in.bam out.prefix

       This has now been removed.  The previous out.prefix  argument  (and  -f  option,  if  any)
       should be changed to an appropriate combination of -T PREFIX and -o FILE.  The previous -o
       option should be removed, as output defaults to standard output.

AUTHOR

       Written by Heng Li from the Sanger Institute with numerous subsequent modifications.

SEE ALSO

       samtools(1), samtools-collate(1), samtools-merge(1)

       Samtools website: <http://www.htslib.org/>