NAME

       samtools-collate - shuffles and groups reads together by their names

SYNOPSIS

       samtools collate [options] in.sam|in.bam|in.cram [<prefix>]

DESCRIPTION

       Shuffles  and  groups reads together by their names.  A faster alternative to a full query
       name sort, collate ensures that reads of the same name are grouped together in  contiguous
       groups, but doesn't make any guarantees about the order of read names between groups.

       The  output from this command should be suitable for any operation that requires all reads
       from the same template to be grouped together.

       Temporary files are written to <prefix>, specified either as the last argument or with the
       -T option.  If prefix is unspecified then one will be derived from the output filename (-o
       option).  If no output file was given then the TMPDIR environment variable will  be  used,
       and finally if that is unset then "/tmp" is used.

       Conversely,  if  prefix is specified but no output filename has been given then the output
       will be written to <prefix>.<fmt> where <fmt> is appropriate to the  file  format  is  use
       (e.g. "bam" or "cram").

       Using  -f  for fast mode will output only primary alignments that have either the READ1 or
       READ2 flags set (but not both).  Any other alignment records will be  filtered  out.   The
       collation will only work correctly if there are no more than two reads for any given QNAME
       after filtering.

       Fast mode keeps a buffer of alignments in memory so that it can write out  most  pairs  as
       soon as they are found instead of storing them in temporary files.  This allows collate to
       avoid some work and so finish more quickly compared to the standard mode.  The  number  of
       alignments  held  can  be  changed  using -r, storing more alignments uses more memory but
       increases the number of pairs that can be written early.

       While collate normally randomises  the  ordering  of  read  pairs,  fast  mode  does  not.
       Position-dependent  biases that would normally be broken up can remain in the fast collate
       output.  It is therefore not a good idea to use fast mode when preparing data for programs
       that  expect randomly ordered paired reads.  For example using fast collate instead of the
       standard mode may lead to significantly different  results  from  aligners  that  estimate
       library insert sizes on batches of reads.

OPTIONS

       -O      Output to stdout.  This option cannot be used with -o.

       -o FILE Write  output to FILE.  This option cannot be used with -O.  If unspecified and -O
               is not set, the temporary file <prefix> is used, appended by the  the  appropriate
               file-format suffix.

       -T PREFIX
               Use PREFIX for temporary files.  This is the same as specifying PREFIX as the last
               argument on the command line.   This  option  is  included  for  consistency  with
               samtools sort.

       -u      Write uncompressed BAM output

       -l INT  Compression level.  [1]

       -n INT  Number of temporary files to use.  [64]

       -f      Fast mode (primary alignments only).

       -r INT  Number of reads to store in memory (for use with -f).  [10000]

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

       -@, --threads INT
               Number of input/output compression threads to use in addition to main thread [0].

AUTHOR

       Written by Heng Li from the Sanger Institute and extended by Andrew Whitwham.

SEE ALSO

       samtools(1), samtools-sort(1)

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