Question: [samtools reheader] Can't change chromosome name
gravatar for madkitty
6.5 years ago by
madkitty620 wrote:

I have a BAM file (containing reads mapped to only one chromosome), that has a very long header. I need to replace the long header of the chromosome by "chrM" and did the following:


  1. samtools view -H my.bam > header.sam
  2. sed "s/longheader/chrM/" header.sam > header_corrected.sam # (longheader stands for the long header..)
  3. samtools reheader  header_corrected.sam my.bam


Both header.sam and header_corrected.sam have the appropriate header. This query doesn't work and only displays a bunch of unreadable characters just as is I didn't use samtools to read the bam file.. what's wrong with my query? Is there another way to substitute "longheader" with "chrM" ? 



samtools bam reheader • 2.8k views
ADD COMMENTlink modified 6.5 years ago by cts1.6k • written 6.5 years ago by madkitty620
gravatar for cts
6.5 years ago by
cts1.6k wrote:

My guess would be that samtools reheader outputs a bam file which is a binary representation of the text from a sam file. That is why you're getting all those unreadable characters on your screen. To test this out try to redirect the output to a file and then use samtools view to see the text representation.

$ samtools reheader header_corrected.sam my.bam >new.bam
$ samtools view new.bam
ADD COMMENTlink modified 10 months ago by _r_am31k • written 6.5 years ago by cts1.6k

Your guess is correct. Samtools will never modify a file in place, since that would almost certainly lead to a corrupted file.

ADD REPLYlink written 6.5 years ago by Devon Ryan97k

It worked well, thanks :)

ADD REPLYlink written 6.5 years ago by madkitty620
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