A read group corresponds to some physical pool of reads. In older sequencing machines, WGS data (and even WXS) requires combination of many read groups to reach the desired coverage. The newer platform normally enables much larger read group, so this is often not necessary, or much less read groups are needed.
Another complication is that some sequencing centers are contracted to provide a certain coverage to get paid. In order to not "waste" their reagent and sequencing capacity, they might intentionally make smaller "top-off" read groups in order to satisfy the total coverage requirements.
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Zhenyu Zhang
Thanh, it is likely that the bam files need to be merged when they are sorted. This is don e automatically when the merge/sort options are rendered following which all filenames with suffix .0001.bam, .0002.bam etc. would be combined to one bam file.
And I see there is no point on read groups here unless you are doing a WTSS.