Manual page from samtools-1.15
released on 21 February 2022


samtools head – view SAM/BAM/CRAM file headers


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


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.)


-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.


Written by John Marshall from the University of Glasgow.


samtools (1), samtools-view (1)