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)

samtools-1.21                                   12 September 2024                               samtools-head(1)