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

Table 1 Benchmarking metrics for SNPs within coding exons of ~ 7000 clinically relevant genes (as specified in “Methods” section)

GIAB genome/NIST ID	Number of bases	Truth total	TP	FP	FN	TN	NPA	Precision	Recall
NA12878	13,728,555	7803	7781	4	22	13,720,748	100	99.95	99.72
NA24143	12,549,224	7470	7460	14	10	12,541,740	100	99.81	99.87
NA24149	12,538,042	7495	7485	19	9	12,530,529	100	99.75	99.88
NA24385	12,626,866	7452	7436	0	16	12,619,414	100	100	99.79
NA24631	12,808,688	7591	7581	6	10	12,801,091	100	99.92	99.87

ISSN: 1471-2105