---
name: "samtools-reheader"
section: "1"
platform: "linux"
package: "samtools"
version: "1.21-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/samtools-reheader"
---

# samtools-reheader(1)

replaces the header in the input file

## NAME

samtools-reheader - replaces the header in the input file

## SYNOPSIS

samtools reheader \[**-iP**\] \[**-c** *CMD* \| *in.header.sam*\] *in.bam*

## DESCRIPTION

Replace the header in *in.bam* with the header in *in.header.sam*. This command is much faster than replacing the header with a BAM→SAM→BAM conversion.

By default this command outputs the BAM or CRAM file to standard output (stdout), but for CRAM format files it has the option to perform an in-place edit, both reading and writing to the same file. No validity checking is performed on the header, nor that it is suitable to use with the sequence data itself.

## OPTIONS

- **-P, --no-PG**

  Do not add a @PG line to the header of the output file.

- **-i, --in-place**

  Perform the header edit in-place, if possible.  This only works on CRAM files and only if there is sufficient room to store the new header. The amount of space available will differ for each CRAM file.

- **-c, --command** *CMD*

  Allow the header from  *in.bam* to be processed by external  *CMD* and read back the result. When used in this manner, the external header file *in.header.sam* has to be omitted.

  *CMD* must take the original header through stdin in SAM format and output the modified header to stdout. *CMD* is passed to the system's command shell. Care should be taken to ensure the command is quoted correctly to avoid unwanted shell expansions (for example of $ variables).

  *CMD* must return an exit status of zero.

## EXAMPLES

- •

  Remove comment lines

  ```
  samtools reheader -c 'grep -v ^@CO' in.bam
  ```

- •

  Add “Chr” prefix to chromosome names.  Note extra backslashes before dollar signs to prevent unwanted shell variable expansion.

  ```
  samtools reheader -c 'perl -pe "s/^(@SQ.*)(\tSN:)(\d+|X|Y|MT)(\s|\$)/\$1Chr\$2\$3/"' in.bam
  ```

- •

  Remove “Chr” prefix

  ```
  samtools reheader -c 'perl -pe "s/^(@SQ.*)(\tSN:)Chr/\$1\$2/"' in.bam
  ```

## AUTHOR

Written by Heng Li with modifications by James Bonfield and Valeriu Ohan, all from the Sanger Institute.

## SEE ALSO

[*samtools*(1)](/samtools/1.md)

Samtools website: \<http://www.htslib.org/\>