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Table 2 Validation results by call set

From: A simple consensus approach improves somatic mutation prediction accuracy

 

MJS

MJ

MS

JS

M

J

S

Overall

Variants assesseda

181

13

37

28

31

26

48

364

True positives b (% true positive)

179 (98.9%)

5 (38.5%)

29 (78.4%)

10 (35.7%)

4 (12.9%)

1 (3.8%)

1 (2.1%)

229 (62.9%)

Germlinec

1

0

5

3

15

4

11

39

Did not validatec

1

8

3

15

12

21

36

97

  1. Abbreviations: J, JointSNVMix2; JS, JointSNVMix2 + SomaticSniper; M, MuTect, MJ, MuTect + JointSNVMix2; MJS, MuTect + JointSNVMix2; + SomaticSniper; MS, MuTect + SomaticSniper; NRAF, non-reference allele frequency; S, SomaticSniper; SNV, single nucleotide variant.
  2. aNumber of sites that were successfully amplified and Sanger sequenced.
  3. bIndicates the number of SNVs that were confirmed as somatic.
  4. cFalse-positive SNVs were either detected in the matched germline (normal) sample ('Germline’) or did not validate in the tumor sample ('Did not validate’).