NAME

       samtools-split - splits a file by read group.

SYNOPSIS

       samtools split [options] merged.sam|merged.bam|merged.cram

DESCRIPTION

       Splits  a  file by read group, producing one or more output files matching a common prefix
       (by default based on the input filename) each containing one read-group.

       The -u option may be used to specify the output filename for any  records  without  an  RG
       tag.

OPTIONS

       -u FILE1      Put reads with no RG tag or an unrecognised RG tag into FILE1

       -h FILE2      Use  the  header  from  FILE2  when writing the file given in the -u option.
                     This header completely replaces the one from the input  file.   It  must  be
                     compatible  with  the  input  file header, which means it must have the same
                     number of references listed in the @SQ lines and the references must  be  in
                     the same order and have the same lengths.

       -f STRING     Output filename format string (see below) ["%*_%#.%."]

       -v            Verbose output

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

       Format string expansions:

                                 %%   %
                                 %*   basename
                                 %#   @RG index
                                 %!   @RG ID
                                 %.   output format filename extension

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

AUTHOR

       Written by Martin Pollard from the Sanger Institute.

SEE ALSO

       samtools(1), samtools-addreplacerg(1)

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