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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’).