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.)
-
-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.
samtools(1),
samtools-view(1)