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Table 9 Indel results for HG003 chr21-22, PacBio

From: HELLO: improved neural network architectures and methodologies for small variant calling

 

GATK

DeepVariant

HELLO

Precision

Recall

Errors

Precision

Recall

Errors

Precision

Recall

Errors

15x

0.862101

0.857818

3903

0.943052

0.937196

1666

0.964158

0.950716

1179

30x

0.902858

0.895181

2812

0.977656

0.979065

606

0.989340

0.986043

343

60x

0.909926

0.904776

2585

0.990084

0.989460

286

0.996480

0.994912

120

  1. Values in bold indicate the best operating point for each tool for the corresponding metric