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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

From: Truvari: refined structural variant comparison preserves allelic diversity

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