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Table 2 Relaxing MuTect parameters increases the number of false positive calls. Number of variants found by MuTect, before and after relaxing the ΘT and ΘN parameters for six Acute Myeloid Leukemia (AML) normal-cancer sample pairs

From: Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data

Patients MuTect MuTect Adapteda
a1024 11 39
a1025 31 41
b1014 22 54
b2002 10 25
b2035 43 419
b2042 58 338
  1. aApplying the computation of ΘT and ΘN, from the MuTect algorithm, with lowered threshold values (4.5 and 3, respectively) downstream to the GATK analysis