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| samtools-head(1) | Bioinformatics tools | samtools-head(1) |
NAME
samtools head - view SAM/BAM/CRAM file headersSYNOPSIS
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.SEE ALSO
samtools(1), samtools-view(1)| 21 February 2022 | samtools-1.15 |
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