```
samtools collate
```
Usage: samtools collate [options...] <in.bam> [<prefix>]

Options:
      -O       Output to stdout
      -o       Output file name (use prefix if not set)
      -u       Uncompressed BAM output
      -f       Fast (only primary alignments)
      -r       Working reads stored (with -f) [10000]
      -l INT   Compression level [1]
      -n INT   Number of temporary files [64]
      -T PREFIX
               Write temporary files to PREFIX.nnnn.bam
      --no-PG  do not add a PG line
      --input-fmt-option OPT[=VAL]
               Specify a single input file format option in the form
               of OPTION or OPTION=VALUE
      --output-fmt FORMAT[,OPT[=VAL]]...
               Specify output format (SAM, BAM, CRAM)
      --output-fmt-option OPT[=VAL]
               Specify a single output file format option in the form
               of OPTION or OPTION=VALUE
      --reference FILE
               Reference sequence FASTA FILE [null]
  -@, --threads INT
               Number of additional threads to use [0]
      --verbosity INT
               Set level of verbosity
  <prefix> is required unless the -o or -O options are used.