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samtools-reheader(1) Bioinformatics tools samtools-reheader(1) 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 com- mand is much faster than replacing the header with a BAM->SAM->BAM conver- sion. 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 check- ing is performed on the header, nor that it is suitable to use with the se- quence 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 sys- tem'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 dol- lar 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 website: <http://www.htslib.org/> samtools-1.23.1 18 March 2026 samtools-reheader(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXAMPLES | AUTHOR | SEE ALSO
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