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samtools-head(1) Bioinformatics tools samtools-head(1) 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 appro- priate 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 sam- tools 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 any- way.) 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-1.23.1 18 March 2026 samtools-head(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO
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