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Service note: Geraldine is on vacation this week; other members of GSA will be responding to questions, but they have a lot of work besides this, so be aware that responses may be a little slower than usual. Thank you for your patience.

about the info from read group

caswatercaswater Posts: 5Member ✭
in Ask the team

Hi, I have two bam files from one case and one control. They were both mapped with bwa. In their bam files, their readgroup tags are with different sample ID (SM), but with the same library ID (LB).

I then fed the two bam files into GATK together for realignment, and the output is a merged bam for the two samples. I am just a bit unsure, if the two samples with the same LB id will affect the downstream variant calls? can the caller can distinguish them by their different sample IDs?

Thank you very much for your kind guidance!

Post edited by Geraldine_VdAuwera on
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