Fig. 1
From: Accurate sequence variant genotyping in cattle using variation-aware genome graphs
Schematic representation of the three sequence variant discovery and genotyping methods evaluated. According to the best practice recommendations for sequence variant discovery using GATK, the VQSR module should be applied to distinguish between true and false positive variants. Because this approach requires a truth set of variants, which is not (publicly) available for cattle, the VQSR module was not considered in our evaluation