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how to add read group to the bam file using PICARD generated from GS reference mapper BAM file?
That's a questIon for Picard, not for GATK...
Geraldine Van der Auwera, PhD
well thanks for the reply, I wonder why my question was not edited even though I edited it quickly once I put up the question.anyway, my task was to call SNPs using GATK pipeline from the .bam file of GS reference mapper but it did not work out because .bam file was devoid of any READ GROUP now my problem is to add read group so that I can process it using GATK. Waiting for your reply..
Yes, I understand your question, and my answer is still the same: if you want to use Picard software to add read groups (which is the right thing to do) you should ask the Picard team how to do this (or better yet, read their excellent documentation). We do not provide support for using software other than GATK.