NAME

       samtools-reheader - replaces the header in the input file

SYNOPSIS

       samtools reheader [-iP] [-c CMD | in.header.sam] in.bam

DESCRIPTION

       Replace  the  header  in  in.bam  with  the header in in.header.sam.  This command is much
       faster than replacing the header with a BAM→SAM→BAM conversion.

       By default this command outputs the BAM or CRAM file to standard output (stdout), but  for
       CRAM  format files it has the option to perform an in-place edit, both reading and writing
       to the same file.  No validity checking is  performed  on  the  header,  nor  that  it  is
       suitable to use with the sequence data itself.

OPTIONS

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

       -i, --in-place
               Perform  the header edit in-place, if possible.  This only works on CRAM files and
               only if there is sufficient room to store the new header.   The  amount  of  space
               available will differ for each CRAM file.

       -c, --command CMD
               Allow  the  header  from  in.bam to be processed by external CMD and read back the
               result. When used in this manner, the external header file in.header.sam has to be
               omitted.

               CMD  must  take  the  original  header  through stdin in SAM format and output the
               modified header to stdout.  CMD is passed to the  system's  command  shell.   Care
               should  be taken to ensure the command is quoted correctly to avoid unwanted shell
               expansions (for example of $ variables).

               CMD must return an exit status of zero.

EXAMPLES

       • Remove comment lines

           samtools reheader -c 'grep -v ^@CO' in.bam

       • Add “Chr” prefix to chromosome names.  Note extra backslashes  before  dollar  signs  to
         prevent unwanted shell variable expansion.

           samtools reheader -c 'perl -pe "s/^(@SQ.*)(\tSN:)(\d+|X|Y|MT)(\s|\$)/\$1Chr\$2\$3/"' in.bam

       • Remove “Chr” prefix

           samtools reheader -c 'perl -pe "s/^(@SQ.*)(\tSN:)Chr/\$1\$2/"' in.bam

AUTHOR

       Written  by  Heng  Li  with modifications by James Bonfield and Valeriu Ohan, all from the
       Sanger Institute.

SEE ALSO

       samtools(1)

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