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

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?

sequencing rna-seq
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updated by Kevin Blighe Kevin Blighe • written by ElUretsky • ElUretsky

1 answer

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]

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written by Kevin Blighe Kevin Blighe

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