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1 Laboratory for Medical Science Mathematics, RIKEN Center for Integrative ... SAMtools. WGS or WES. Caller*. Examined. Verified (genotype discordance).

Supplementary Information

A practical method to detect SNVs and indels from whole genome and exome sequencing data Daichi Shigemizu1*, Akihiro Fujimoto1*, Shintaro Akiyama1, Tetsuo Abe1, Kaoru Nakano2, Keith A Boroevich1, Yujiro Yamamoto2, Mayuko Furuta2, Michiaki Kubo3, Hidewaki Nakagawa2 and Tatsuhiko Tsunoda1†

1

Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical

Sciences, Yokohama, Japan. 2

Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical

Sciences, Tokyo, Japan. 3

Laboratory for Genotyping Development, RIKEN Center for Integrative Medical

Sciences, Yokohama, Japan.

*These authors contributed equally to this project and should be considered co-first authors † Correspondence

should be addressed to T.T. ([email protected])

Supplementary Tables

Supplementary Table S1. Comprison of SNV calling among VCMM, GATK and SAMtools. Number WGS or

Sample

WES

ID

WES

NA12878

NA12891

NA12892

WGS

Ratio (%)

RK001

VCMM

GATK

SAMtools

VCMM

GATK

SAMtools

Concordant

45,641

45,585

44,489

99.28

99.16

96.77

FN

92

137

1,253

0.20

0.30

2.75

FP

239

250

230

0.52

0.55

0.50

Concordant

45,419

45,365

44,085

99.24

99.13

96.33

FN

111

147

1,472

0.28

0.37

3.82

FP

235

253

208

0.60

0.65

0.53

Concordant

38,916

38,888

36,891

99.40

99.33

94.23

FN

56

75

2,107

0.14

0.19

5.38

FP

180

189

154

0.46

0.48

0.39

Concordant

639,462

638,912

636,410

99.64

99.59

98.78

FN

2,031

2,568

5,088

0.17

0.21

0.79

FP

126

139

121

0.015

0.021

0.019

Supplementary Table S2. Comparison of indel calling among VCMM, GATK and SAMtools. WGS or WES

Caller*

Examined

Verified (genotype discordance)

WES

G

1

0 (1)

S

11

0 (4)

V and S

12

9 (1)

V, G and S

37

36

G

1

1

S

4

2 (1)

V and S

2

2

G and S

1

0

V, G and S

14

14

WGS

*: V; VCMM, G; GATK, S; SAMtools