Man page - samtools-head(1)

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samtools

Manual

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 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.