This is a wrapper node for AnalyzeCovariates, BaseRecalibrator and PrintReads of the Genome Analysis Toolkit (GATK).
This node addresses the problem of systematic errors in the base quality score emitted by sequencing machines.
As these base qualities are used by many variant calling tools removing the bias leads to more accurate variant calls.
The process of recalibration consists of 3 steps.
Step 1: A machine learning device is trained to build a model of covariation which is generated from the actual data and from known sites of genetic variation. (walkers: BaseRecalibrator)
Step 2: This optional step builds a second model and compares it to the first one. The comparison allows to generate before/after plots of the quality values. (walkers: BaseRecalibrator + AnalyzeCovariates).
Step 3: Finally, the model is applied to the alignment data and the base qualities are adapted to the biases found. (walkers: PrintReads)
For further information, see the GATK documentation of the BaseRecalibrator, the AnalyzeCovariates and the PrintReads walkers.
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