The performance of Churchill does not come at the sacrifice of data quality. The final VCF output of Churchill (green), GATK-Queue (blue) and HugeSeq (red) was compared and evaluated against the National Institute of Standards and Technology (NIST) benchmark SNP and indel genotype calls generated by the Genome in a Bottle Consortium (GIAB) . The Venn diagram shows a high degree of concordance between the three pipelines. Churchill identified the highest number of validated variants from the approximately 2.9 million calls in the GIAB dataset, for both SNPs (99.9%) and indels (93.5%), and had the highest overall sensitivity (99.7%) and accuracy (99.9988%). The Youden index (or J statistic), a function of sensitivity (true positive rate) and specificity (true negative rate), is a commonly used measure of overall diagnostic effectiveness .