Figure 2.

Phase II of the RIG workflow. Phase II of the RIG workflow determines whether VQSR, BQSR, or both are appropriate, given the entities defined in Phase I. The workflow always proceeds through an analysis pipeline, characterized as the naive, the initial informed, and the informed pipelines shown in Figure 3. The end result of the workflow is the production of a variant resource that can be used in future analyses. RIG, Recalibration and Interrelation of genomic sequence data with the GATK; VQSR, Variant Quality Score Recalibration; BQSR, Base Quality Score Recalibration.