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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.