---
name: "samtools-head"
section: "1"
platform: "linux"
package: "samtools"
version: "1.21-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/samtools-head"
---

# samtools-head(1)

view SAM/BAM/CRAM file headers

## 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/1.md), [*samtools-view*(1)](/samtools-view/1.md)