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!