I would use Picard tools to merges the BAM files. Picard tools keeps the
read groups
On Mon, Dec 8, 2014 at 10:39 PM, Martin, Jessica L. <
jessica.mar...@tufts.edu> wrote:
> Hello,
>
> I have a bunch of bam files with read groups that I am hoping to merge
> with the goal of using GATK in the next steps. I have been using this
> command to merge them: samtools merge -rh rg.txt merge.bam *_q20_sort.bam
> where rg.txt is a tab delimited file that contains the read group
> information for each of the bam files. (I am following instructions found
> in the Simple Fool's Guide to Population Genomics at
> http://sfg.stanford.edu/guide.html) However, when I do this, there are no
> read groups in the header of the merged file, and GATK consequently doesn't
> work. (GATK gives me the error message "SAM/BAM file merged.bam is
> malformed: SAM file doesn't have any read groups defined in the header.")
>
> Any advice would be much appreciated!
>
> Thanks,
> Jessie
>
>
>
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