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Table 1 Summary of GATK and CASAVA comparison

From: Evaluation of SNP calling using single and multiple-sample calling algorithms by validation against array base genotyping and Mendelian inheritance

Data sets

CASAVA

GATK

Common

 

Variant count

TsTv ratio

Variant count

TsTv ratio

Variant count

TsTv ratio

Omni Array Genotyping Data

      

108 unrelated (per sample)

All

SNP by pipelines

708,089 ± 4,516

3.56 ± 0.003

715,033 ± 4,551

3.53 ± 0.003

706,378 ± 4502

3.57 ± 0.003

GT Matched SNP

705,749 ± 4468

3.58 ± 0.003

703,608 ± 4479

3.59 ± 0.003

698,910 ± 4437

3.60 ± 0.003

Ref or missing by pipeline

1661347 ± 4538

 

1654613 ± 4573

 

1649566 ± 4567

 

False positive

988 ± 20

1.46 ± 0.020

6320 ± 112

1.61 ± 0.039

489 ± 13

1.92 ± 0.031

False negative

23283 ± 90

 

22076 ± 58

 

20550 ± 59

 

PASS

SNP by pipelines

707,128 ± 4506

3.57 ± 0.003

696,960 ± 4480

3.60 ± 0.003

695,589 ± 4456

3.60 ± 0.003

GT Matched SNP

705,106 ± 4459

3.58 ± 0.003

693,135 ± 4434

3.63 ± 0.003

689,330 ± 4394

3.63 ± 0.003

Ref or missing by pipeline

1662325 ± 4528

 

1672894 ± 4501

 

1657868 ± 4533

 

False positive

810 ± 17

1.33 ± 0.019

277 ± 20

2.23 ± 0.054

229 ± 10

2.12 ± 0.054

False negative

24067 ± 134

 

33985 ± 96

 

22735 ± 65

 

NGS Data Set

      

108 unrelated (per sample)

All

4,025,625 ± 44,102

2.02 ± 0.001

4,331,336 ± 45,896

1.86 ± 0.002

3,792,293 ± 43,122

2.07 ± 0.000

PASS

3,894,810 ± 43,388

2.04 ± 0.001

3,438,203 ± 41205

2.13 ± 0.001

3,401,091 ± 40317

2.15 ± 0.001

19 trios ( per trio)

ALL

5,235,184 ± 47,790

2.01 ± 0.001

7,003,439 ± 56,488

1.88 ± 0.003

4,945,042 ± 46,650

2.06 ± 0.002

PASS

4,786,871 ± 47,564

2.07 ± 0.002

5,125,002 ± 48,717

2.13 ± 0.001

4,320,414 ± 43,062

2.14 ± 0.001

Family 1

ALL

6,082,624

2.00

6,337,108

1.88

5,635,183

2.04

PASS

5,438,393

2.07

5,004,048

2.12

4,898,126

2.13

Family 2

ALL

5,192,891

1.99

5,459,725

1.84

4,752,193

2.03

PASS

4,526,291

2.07

4,205,995

2.12

4,104,343

2.13

  1. Comparison between the pipelines have been done for unfiltered sets (CASAVA ALL, GATK ALL), and for quality filtered sets (CASAVA PASS, GATK PASS).