Table 1.

Merges’ pVCF performance on GIAB CMRG SV benchmark of NA24385 for GRCh38. Hardy-Weinberg equilibrium (HWE) and excess heterozygosity (ExcHet) scores less than 0.05 were counted for true positives across all 36 samples’ genotypes

Merge	TP	FP	FN	Precision	Recall	f1	Call cnt	gt_concordance	HWE < 0.05	ExcHet < 0.05
BCFtools	201	5	15	0.976	0.931	0.953	206	0.950	39	1
Truvari	200	5	16	0.976	0.926	0.950	205	0.950	17	4
Jasmine	196	10	20	0.951	0.907	0.929	206	0.949	17	4
Naive	171	22	45	0.886	0.792	0.836	193	0.947	26	18
SURVIVOR	160	28	56	0.851	0.741	0.792	188	0.956	24	20