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Table 2 GATK and CASAVA comparison in diseased Family 1

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

Pipelines

CASAVA all

GATK all

  

HRC

 

HRC

 

Total

Total

HRC by CASAVA but not by GATK

Total

Total

HRC by GATK but not by CASAVA

Total number of variant

6082624

61497

409

6337108

63774

1349

TsTv Ratio

2.00

2.09

1.88

1.88

2.03

1.07

Mendelian Violation

290985

0

0

187920

0

0

In dbSNP

5562308

60769

268

5609116

62277

643

In interGenic

3682138

35416

257

3790849

36884

846

In CDS

65785

650

2

64452

638

2

In ‘3 UTR

77701

849

16

82211

853

11

In ‘5 UTR

18552

240

0

20093

246

4

In Intronic

4113210

47220

218

4412928

48805

818

In Non_coding_intronic

214239

1826

26

217104

1839

40

In Exonic

57842

580

1

56762

579

3

In Non_coding_exonic

16356

110

0

15196

106

0

In Putative Promoter Region

12780

135

0

15517

141

1

Non-Synonymous Coding

19080

159

1

18299

161

2

Common Variant

5395888

60389

205

5905677

62830

1335

Common Homozygougs Minor Variant in 1000genome

4777175

56874

104

4792920

57620

194

Common Homozygougs Minor Variant in Q108

4727231

57643

142

4915274

60169

1293

Common Het (>5%) Variant in 1000genome

4479609

56407

99

4494483

57151

189

Common Het(>5) Variant in Q108

4895168

59296

63

5422841

62027

1332

  1. Comparison between the pipelines have been done for unfiltered sets (CASAVA ALL, GATK ALL), and subset of variants fulfilling the criteria of Homozygous Recessive Conditions (HRC).