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Table 2 Comparison of TT-Mars and GIAB benchmarks on HG002. The two methods have the same classification results on more than 96% of the analyzed calls, while TT-Mars analyzed more candidate calls on all the four callsets. A length filter (50 bp to 10 Mbp) is applied, and only deletions and insertions are included to match the truvari parameter settings

From: TT-Mars: structural variants assessment based on haplotype-resolved assemblies

  

TT-Mars

  

Wham

LUMPY

  

TP

FP

NA

Sum

TP

FP

NA

Sum

 

TP

882

3

21

906

2091

8

51

2150

GIAB

FP

1

13

0

14

22

218

3

243

 

NA

118

24

20

162

582

215

99

896

 

Sum

1001

40

41

1082

2695

441

153

3289

  

DELLY

pbsv

  

TP

FP

NA

Sum

TP

FP

NA

Sum

 

TP

2927

11

57

2995

8903

94

191

9188

GIAB

FP

4

412

6

422

286

165

16

467

 

NA

1179

360

145

1684

9710

1463

721

11,894

 

Sum

4110

783

208

5101

18,899

1722

928

21,549