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Table 1 Indel results for HG003 Whole Genome Sequencing (WGS), Illumina

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

 

GATK

DeepVariant

HELLO

Precision

Recall

Errors

Precision

Recall

Errors

Precision

Recall

Errors

20x

0.977132

0.962505

30,699

0.980459

0.971863

24,345

0.986638

0.973921

20,052

30x

0.987019

0.981851

15,934

0.991070

0.987324

11,067

0.994046

0.987738

9284

40x

0.990826

0.988121

10,801

0.994484

0.991528

7164

0.996235

0.990973

6516

50x

0.992820

0.991235

8191

0.996153

0.993191

5451

0.997263

0.992274

5325

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

ISSN: 1471-2105

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