Figure 3.

RIG pipelines. These are analysis pipelines that are traversed as part of Phase II of the RIG workflow. They correspond to cases where neither BQSR nor VQSR are appropriate (naive pipeline), where only VQSR is appropriate (initial informed pipeline), or where both BQSR and VQSR are appropriate (informed pipeline). When traversed, the informed pipeline emulates the GATK’s Best Practices (Van Der Auwera et al. 2013). RIG, Recalibration and Interrelation of genomic sequence data with the GATK; BQSR, Base Quality Score Recalibration; VQSR, Variant Quality Score Recalibration; GATK, Genome Analysis Toolkit.