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samtools-head - Man Page

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.

See Also

samtools(1), samtools-view(1)

Referenced By


7 April 2022 samtools-1.15.1 Bioinformatics tools