Dear GATK Team,
In the Base Quality Score Recalibration (BQSR) documentation, the following is described:
We usually expect to see more than 100M bases per read group; as a rule of thumb, larger numbers will work better.
With default read filters (listed below) being applied when running BaseRecalibrator and ApplyBQSR, should the number of bases per read group be calculated after these read filters are applied to the data? If so, how do I calculate this figure to check enough data is present to run BQSR, taking into account the read filters?
Thank you for your time and help.
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