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samtools-head(1) Bioinformatics tools samtools-head(1)


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.)


Display only the first INT header lines. By default, all header lines are displayed.
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)

12 December 2023 samtools-1.19