'\" t
.TH samtools-head 1 "2 September 2022" "samtools-1.16.1" "Bioinformatics tools"
.SH NAME
samtools-head \- view SAM/BAM/CRAM file headers
.\"
.\" Copyright (C) 2021 University of Glasgow.
.\"
.\" Author: John Marshall <jmarshall@hey.com>
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.SH SYNOPSIS
.B samtools head
.RB [ -h
.IR INT ]
.RB [ -n
.IR INT ]
.RI [ FILE ]

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

.SH OPTIONS
.TP 4n
.BI "-h, --headers " INT
Display only the first \fIINT\fR header lines.
By default, all header lines are displayed.
.TP
.BI "-n, --records " INT
Also display the first \fIINT\fR alignment records.
By default, no alignment records are displayed.

.SH AUTHOR
Written by John Marshall from the University of Glasgow.

.SH SEE ALSO
.IR samtools (1),
.IR samtools-view (1)