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Table 2 Comparison of somatic mutation prediction methods

From: BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity

 

MuTect

Strelka

VarScan2

Shimmer

BAYSIC

# of somatic mutations

9977

6887

79313

8222

7194

Positions on chip

2

2

120

23

3

Agreement with chip (SM on chip/SM with genotype agreeing with chip)

100% (2/2)

100% (2/2)

100% (104/104)

100% (10/10)

100% (3/3)

# in COSMIC

330

179

165

222

510

% in COSMIC

3.3%

2.6%

0.2%

2.7%

7.1%

% unique somatic mutations

36%

8%

83%

51%

-

# of somatic mutations causing coding changes

58

58

458

113

164

  1. Somatic mutations from exome data from a single patient were predicted using Mutect, Strelka, Varscan2 and Shimmer and these four sets of somatic mutation calls were combined using BAYSIC with a posterior probability cutoff of 0.8. The total number of somatic mutations detected by each program, as well as the agreement of these somatic mutations with those COSMIC and with sets determined by chip are shown.