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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