1samtools-head(1)             Bioinformatics tools             samtools-head(1)
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NAME

6       samtools head - view SAM/BAM/CRAM file headers
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SYNOPSIS

10       samtools head [-h INT] [-n INT] [FILE]
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DESCRIPTION

14       By  default,  prints all headers from the specified input file to stan‐
15       dard output in SAM format.  The input alignment file  may  be  in  SAM,
16       BAM,  or  CRAM  format; if no FILE is specified, standard input will be
17       read.  With appropriate options, only some of the headers and/or  addi‐
18       tionally some of the alignment records will be printed.
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20       The samtools head command outputs SAM headers exactly as they appear in
21       the input file; in particular, it never  adds  an  @PG  header  itself.
22       (Other  samtools commands add such @PG headers to facilitate provenance
23       tracking in analysis pipelines, but because samtools head never outputs
24       more  than  a  handful of alignment records it is unsuitable for use in
25       such contexts anyway.)
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OPTIONS

29       -h, --headers INT
30           Display only the first INT header lines.  By  default,  all  header
31           lines are displayed.
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33       -n, --records INT
34           Also  display  the  first  INT  alignment  records.  By default, no
35           alignment records are displayed.
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AUTHOR

39       Written by John Marshall from the University of Glasgow.
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SEE ALSO

43       samtools(1), samtools-view(1)
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47samtools-1.15.1                  7 April 2022                 samtools-head(1)