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Table 2 Indel verification results

From: A cancer cell-line titration series for evaluating somatic classification

Verification result Phase 1 Phase 2 Strelka GATK + In-house VarScan2
Somatic 17 2 11 12 2
Germline 38 8 0 2 3
Wildtype 26 62 0 4 3
Inconclusive 22 21 3 10 0
  1. Verification results for Phase 1 and 2 of indel verification, as well as the performance of the individual tools on BWA aligned reads with no GATK recalibration. Calls verified as Somatic are true positives, while calls verified to be Germline or Wildtype are false positives. 43 indels were removed from consideration as their verification was inconclusive due to insufficient coverage, marginal allele frequency or the presence of both insertion and deletion calls at the position. All tools were run with default settings