Table 1: Multi-Sample SV Genotyping Performance.

Average performance of genotypers across 47 samples when given a multi-sample VCF of assembly-derived SVs and 32x long-read coverage. SV matching was performed using truvari bench and is detailed in Methods: Measuring Genotyping Performance.

Program	GT Concordance	TP-base	TP-comp	FP	FN	precision	recall	f1
kanpig	86.6%	22,671	21,640	598	1,129	0.973	0.953	0.963
SVJedi	42.8%	25,153	25,317	19,515	327	0.564	0.987	0.718
cuteSV-fc	12.8%	22,928	22,981	104,495	1,051	0.180	0.956	0.303
sniffles-fc	12.3%	24,886	24,986	121,394	763	0.171	0.970	0.290