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

Detecting somatic mutations for profiling cancer development and chemotherapy resistance.

Authors: do Valle ÍF, Giampieri E, Simonetti G, Padella A, Manfrini M, Ferrari A, Papayannidis C, Zironi I, Garonzi M, Bernardi S, Delledonne M, Martinelli G, Remondini D, Castellani G.
BMC Bioinformatics. 2016 Nov 8;17(Suppl 12):341.

We aimed to develop a pipeline which detects a wide range of single nucleotide mutations with high validation rates. We combined two standard tools – Genome Analysis Toolkit (GATK) and MuTect – to create the GATK-LODN method. Experiments in simulated data demonstrated that GATK-LODNincreased both specificity and sensitivity of GATK results. We presented a pipeline that detects a wide range of somatic single nucleotide variants. This pipeline can be helpful in discovery studies aimed to profile the somatic mutational landscape of cancer genomes.

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