edit RGID in header

[shawpa]

I assigned RGID's to 4 different sets of files. I labeled them L1, L2, L3, L4 to indicate which lane they were from. I was having issues after samtools merge and I think the problem is that the first in.bam header overwrote the other headers (this is in the samtools manual). Basically I have orphan reads now because they have a RGID that isn't in the header. All the other RG tags are identical in the bam files. I was told that I needed to add the other ID's to my header in the merged file. So I guess the header needs to say something like RGID: L1, L2, L3, L4 for it to work properly but I don't think you can put comma's. I don't really know how to reformat text files and on a scale of 1-10 in programming knowledge, I would put myself at a 2. Can someone please give me an example code for how to edit this header? I will attach the header of my existing file below if that helps.

[Richard Finney]

I think various RGs need to be on separate lines.
You can use text editor to get the header you want, no "programming" involved using gedit/vim/emacs.
It you did want to program, using the Unix tools sed,grep,cat and so in a script could solve the problem.
When you get the header you want, try the samtools "reheader" option.

[kmcarr]

In the future you might want to use Picard Tools MergeSamFiles. It merges header information in addition to the alignment portions of the BAM files.

[shawpa]

I think various RGs need to be on separate lines.
You can use text editor to get the header you want, no "programming" involved using gedit/vim/emacs.
It you did want to program, using the Unix tools sed,grep,cat and so in a script could solve the problem.
When you get the header you want, try the samtools "reheader" option.

I think I wasn't clear when I said I couldn't program very well. I actually meant I couldn't program as well as do what you are describing.

[Alex Renwick]

I think I wasn't clear when I said I couldn't program very well. I actually meant I couldn't program as well as do what you are describing.

There's no programming involved. You need to edit the header to add lines for samples L2, L3, and L4.

Right now your header has only L1:

@RG     ID:L1   PL:ILLUMINA     PU:D0DHVACXX    LB:ryan SM:ryan

You need all four in the header, and they need to have different sample names (SM):

@RG     ID:L1   PL:ILLUMINA     PU:D0DHVACXX    LB:ryan SM:ryan1
@RG     ID:L2   PL:ILLUMINA     PU:D0DHVACXX    LB:ryan SM:ryan2
@RG     ID:L3   PL:ILLUMINA     PU:D0DHVACXX    LB:ryan SM:ryan3
@RG     ID:L4   PL:ILLUMINA     PU:D0DHVACXX    LB:ryan SM:ryan4

You could use samtools view -h to make a sam file from the merged bam and then edit that file directly, but that's probably a bad idea since the file might be huge.

The method Richard Finney suggests is to use samtools reheader:

samtools view -H file.bam > header.txt
...edit header.txt using any text editor...
samtools reheader header.txt file.bam > file.fixedheader.bam

[shawpa]

Thanks so much. This is exactly what I needed.