Changing RGSM without changing any RGID, RGPL etc

[akhattri]

Hi there,
I have a bam file which was created by merging the two bam files – each a different run of same sample. Somehow while adding the read group information I added the wrong sample name to it.

Now I want to replace the Sample Name to correct sample name. I know I can use picard tool 'AddOrReplaceReadGroup' or samtools but it changes all the read group info. What I want is replacing new SM info only

What I have is:
@RG ID:A PL:ILLUMINA LB:250BP SM:X
@RG ID:B PL:ILLUMINA LB:250BP SM:X

What I want is:

@RG ID:A PL:ILLUMINA PU:NA LB:250BP SM:Y
@RG ID:B PL:ILLUMINA PU:NA LB:250BP SM:Y

Let me know if this can be done easily without going back to the original bam files and merging them again after changing the SM info in each
Thanks

[gringer]

I'm not quite sure if I get the question that you're asking. There's a 'samtools reheader' function that allows you to replace headers in a BAM file with the header from a [possibly empty] SAM file.

FWIW, the read groups specified on the mapping lines must link back to a read group line in the header -- in the BAM representation, this is an integer lookup, while in the SAM representation this is a unique ID. See SAM Specification, page 3:

Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section

[akhattri]

Thanks gringer. I found a post describing the similar way to do it:

samtools view -H mybamfile.bam | sed -e 's/SM:X/SM:Y/' | samtools reheader - mybamfile.bam > mybamfile.reheadered.bam


I validated the output BAM file with ValidateSAM. Seems like it has worked. But I will post here if I encounter any problem with this file.
Thanks