GATK Base Quality Score Recalibration (BQSR) for merged sequencing runs

Question

[ElUretsky]

I have a BAM file with 10 different read groups all from the same sample:

• 2 of those were test libraries sequenced in a MiSeq.
• The remaining 8 are from a HiSeq and are much more abundant.

Can GATK recognize that the input quality scores will have a different profile for each read group? Should I split my BAM file with respect to sequencing platform or even on a per read group basis?

Answer 1

[Kevin Blighe]

Can GATK recognize that the input quality scores will have a different profile for each read group?

The BQSR calibration is indeed read-group aware, so, the answer to your question is 'yes'.

Should I split my BAM file with respect to sequencing platform or even on a per read group basis?

Keep them in the same BAM. The GATK will identify them by read-group.

[Source: Geraldine at GATK Forum]