MutSig (for “Mutation Significance”) is a package of tools for analyzing mutation data. It operates on a cohort of patients and identifies mutations, genes, and other genomic elements predicted to be driver candidates. MutSig was developed for the use case of somatic mutations, i.e. mutations that occurred during the development of cancer, and this documentation uses language specific to somatic mutations. However, MutSig has also been used for analysis of germline mutations and is completely applicable to that use case also.
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Shantanu Banerji,et al.
Sequence analysis of mutations and translocations across breast cancer subtypes
Nature 486, 405–409 (21 June 2012) doi:10.1038/nature11154