question about read group... confused!

[caswater]

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).

The 2 bam files were then merged as a single multi-sample bam, and used GATK to call variants for the two samples with the multi-sample bam. I am just a bit unsure, if the two samples are with the same LB id... will this affect variant calls? all the caller can distinguish them by their different sample IDs?

Thank you very much for your kind guidance!

[vivek_]

I think GATK considers the sample IDs and treats them differently. If you do multi-sample calling the genotyper would produce GTs separately for each sample.

Is there any reason to merge the bams together? YOu can as well specify each bam in the command line separately for GATK and do the same analysis.

[caswater]

it is a comparison between case and conrol.. so i feed the bam files separately into GATK, and the program merge them by itself.
Thank you for your help!