Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays

Table 2 Benchmarking metrics for SNPs in whole exome regions, including non-coding exons, splice sites (± 20 bp) and clinically relevant deep intronic regions

GIAB genome/NIST ID	Number of bases	Truth total	TP	FP	FN	TN	NPA	Precision	Recall
NA12878	71,152,019	57,822	57,024	491	776	71,093,728	100	99.15	98.66
NA24143	65,657,646	55,975	55,340	669	611	65,601,026	100	98.81	98.91
NA24149	65,597,266	55,518	54,827	669	669	65,541,101	100	98.79	98.79
NA24385	65,948,744	56,068	55,329	389	705	65,892,321	100	99.30	98.74
NA24631	66,988,987	56,948	56,303	394	643	66,931,647	100	99.31	98.87

ISSN: 1471-2105