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What is MuTect?

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
edited December 2015 in MuTect v1 Documentation

Please note that this article refers to the original standalone version of MuTect. A new version is now available within GATK (starting at GATK 3.5) under the name MuTect2. This new version is able to call both SNPs and indels. See the GATK version 3.5 release notes and the MuTect2 tool documentation for further details.

MuTect is a tool developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes. It is built on top of the GenomeAnalysisToolkit (GATK), which is also developed at the Broad Institute, so it uses the same command-line conventions and (almost all) the same input and output file formats.

MuTect operates on sequencing data for matched normal and tumor tissue samples, and it outputs mutation calls as well as optional coverage results.

In a nutshell, the analysis itself consists of three steps:

  1. Pre-processing the aligned reads in the tumor and normal sequencing data
  2. Statistical analysis to identify sites that are likely to carry somatic mutations with high confidence
  3. Post-processing of candidate somatic mutations

For complete details, please see the method documentation as well as our 2013 publication in Nature Biotechnology:

Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnology (2013).doi:10.1038/nbt.2514

Post edited by Geraldine_VdAuwera on


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