Comprehensive evaluation of structural variant genotyping methods based on long-read sequencing data

BMC Genomics

Table 4 F1 scores of SV genotyping methods based on different aligners and sequencing data

SV genotyping method	Aligner	Sequencing data			Max-Min
SV genotyping method	Aligner	CLR	ONT	CCS	Max-Min
cuteSV	minimap2	0.89	0.93	0.93	0.06
cuteSV	NGMLR	0.87	0.91	0.91	0.06
LRcaller	minimap2	0.86	0.85	0.88	0.03
LRcaller	NGMLR	0.87	0.87	0.87	0.03
Sniffles	minimap2	0.68	0.81	0.83	0.18
Sniffles	NGMLR	0.65	0.73	0.76	0.18
SVJedi	minimap2	0.86	0.81	NA	0.05
VaPoR	minimap2	0.67	0.71	0.71	0.04
VaPoR	NGMLR	0.67	0.71	0.71	0.04

Impact of aligner (minimap2 and NGMLR) and sequencing data (PacBio CLR, PacBio CCS, and ONT) on the F1 score of each genotyping method based on the HG002 Tier 1 dataset. Performance was evaluated on 30× HG002 sequencing data. SVJedi does not support the output from NGMLR. “NA” indicates the data is not available. The bold black number is the highest F1 score for each SV genotyping method. The “Max-Min” column represents the maximum F1 score minus the minimum F1 score for each SV genotyping method under different combinations of aligners and sequencing data

ISSN: 1471-2164