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Table 1 Results of different metrics used to assess phasing quality in both scenarios. Median values of switch error counts (SEC), switch error rates (SER, %), quality adjusted (QA) haplotype block length (bp), and QAN50 (bp), obtained with AlphaPhase1.3, Beagle4.1, Beagle5.2, Eagle2.4, FImpute3.0 and ShapeIT4.1, computed for the 98 validation individuals in each scenario (scenario 1: using the 98 validation individuals; scenario 2: using the 264 sequenced individuals)

From: Benchmarking phasing software with a whole-genome sequenced cattle pedigree

Metric

Median

SEC

Median

SER (%)

Median QA

haplotype block length (bp)

QAN50 (bp)

Scenario

1

2

1

2

1

2

1

2

AlphaPhase1.3

4612

3548

0.2412

0.1834

10,653

55,973

2,505,672

2,719,430

Beagle4.1

2769

359

0.1404

0.0183

484

45,729

18,212,951

44,254,507

Beagle5.2

191

55

0.0093

0.0027

12,334

6,953,676

47,895,001

62,687,474

Eagle2.4

4901

882

0.2485

0.0451

172

161

5,771,337

22,281,097

FImpute3.0

4477

115

0.2256

0.0059

583

27,490

6,114,640

79,974,276

ShapeIT4.1

386

50

0.0192

0.0026

2134

4,738,542

48,437,671

69,002,979