MutSig specifications

Information


Unique identifier OMICS_00155
Name MutSig
Alternative name Mutation Significance
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A list of mutations (and indels) from a set of samples (patients) that were subjected to DNA sequencing, a coverage file that contains information about the sequencing coverage achieved for each gene and patient/tumor, a covariate file that contains the genomic covariate data for each gene.
Input format MAF, TSV
Output data A tab-delimited report of significant mutations, listed in descending order from most significant to least significant.
Output format TSV
Operating system Unix/Linux
Programming languages MATLAB
Computer skills Advanced
Version 1.3.01
Stability Stable
Maintained Yes

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MutSig article

MutSig citations

 (2)
2018
PMCID: 5858179

[…] copy number change and gene expression data were obtained from tcga data portal., we identified significantly mutated genes (smgs) with three algorithms using mutsigcv, mutsigcl and mutsigfn. mutsigcv quantifies significance of non-silent mutations in a gene based on background mutation rate estimated by silent mutations with other confounding covariates taken into account. mutsigcl […]

2017
PMCID: 5562225

[…] gene mutation frequencies that differed with respect to low and high mutation load and racial status (caucasians versus aa). the hochberg (1988) approach was used to adjust for multiple testing 19. mutsig algorithm, mutsigcv, was used to evaluate the significance of mutated genes. all analyses were performed with r statistical computing software version 3.3.0 20. mutagenic processes and tumor […]

MutSig institution(s)
The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Instituto Nacional de Medicina Genómica, Mexico City, Mexico; Yale Cancer Center, Department of Hematology, New Haven, CT, USA; Massachusetts General Hospital, Boston, MA, USA; Brigham and Women’s Hospital, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel; Boston Children’s Hospital, Boston, MA, USA; Children’s Hospital, Philadelphia, PA, USA; Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC, USA; Department of Pediatric Oncology, Hospital Sant Joan de Déu, Barcelona, Spain; Genome Sciences, University of Washington, Seattle, WA, USA
MutSig funding source(s)
This work was supported as part of The Cancer Genome Atlas (TCGA), a project of the National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI) and as part of the Slim Initiative for Genomic Medicine (SIGMA), a joint U.S.-Mexico project founded by the Carlos Slim Health Institute, and the Intramural Research Program of the NIEHS (NIH, DHHS) project ES065073.

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