I'm trying to run BQSR on a sample from a miSeq run, but received an error saying that I need to add read groups. Since this sample was one of 40-something samples multiplexed during a run, should I merge all the samples on one BAM before running BQSR, so that BQSR is more accurate/effective? I read this on the GATK article on read groups, which prompted my question:

Use for BQSR: ID is the lowest denominator that differentiates factors contributing to technical batch effects: therefore, a read group is effectively treated as a separate run of the instrument in data processing steps such as base quality score recalibration, since they are assumed to share the same error model.