NAME

       samtools-head - view SAM/BAM/CRAM file headers

SYNOPSIS

       samtools head [-h INT] [-n INT] [FILE]

DESCRIPTION

       By  default,  prints  all  headers from the specified input file to standard output in SAM
       format.  The input alignment file may be in SAM, BAM,  or  CRAM  format;  if  no  FILE  is
       specified,  standard  input  will  be  read.   With  appropriate options, only some of the
       headers and/or additionally some of the alignment records will be printed.

       The samtools head command outputs SAM headers exactly as they appear in the input file; in
       particular,  it  never  adds  an @PG header itself.  (Other samtools commands add such @PG
       headers to facilitate provenance tracking in analysis pipelines, but because samtools head
       never  outputs  more  than a handful of alignment records it is unsuitable for use in such
       contexts anyway.)

OPTIONS

       -h, --headers INT
           Display only the first INT header lines.  By default, all header lines are displayed.

       -n, --records INT
           Also display the first INT alignment records.  By default, no  alignment  records  are
           displayed.

AUTHOR

       Written by John Marshall from the University of Glasgow.

SEE ALSO

       samtools(1), samtools-view(1)