Question: BQSR on one sample vs. all samples in a run
gravatar for ari.nazarian
2.0 years ago by
ari.nazarian10 wrote:

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.

miseq bsqr • 839 views
ADD COMMENTlink modified 2.0 years ago by cpad011211k • written 2.0 years ago by ari.nazarian10
gravatar for cpad0112
2.0 years ago by
cpad011211k wrote:

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.

ADD COMMENTlink written 2.0 years ago by cpad011211k
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