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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
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BMC Bioinformatics

ISSN: 1471-2105

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