BQSR on one sample vs. all samples in a run

Question

[ari.nazarian]

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.

Answer 1

[cpad0112]

To my understanding, it simply needs a RG field appended to your sample. But you have a different question though: Does BQSR vary between single sample in one RG vs multiple samples in one RG.