Table 3 The GATK-LOD_N 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