Skip to main content

Table 3 The GATK-LODN method increases the GATK performance for both mutation detection and classification. The Sanger sequencing validation was performed in two rounds: in the first round we tested whether the methods correctly detected the mutation and in the second one we assessed whether the methods correctly classified the mutations as somatic events. The variant subsets tested (AML datatset) presented variants method specific and variants detected by one or more methods

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

  Mutation Detectiona Mutation Classificationb
  Tested Validated Tested Validated
GATK-LODN - specific 4 1 2 2
GATK-LODN (All variants) 9 6 4 3
GATK (without LODN) - specific 37 11 9 2
GATK (without LODN) (All Variants) 48 18 14 5
MuTect - specific 22 21 8 8
MuTect (All Variants) 29 27 11 10
MuTect & GATK 7 6 3 2
  1. avariants tested for correct mutation detection
  2. bvariants tested for correct classification as somatic events