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MuTect specifications


Unique identifier OMICS_00087
Name MuTect
Alternative name MuTect2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Gad Getz <>

Publication for MuTect

MuTect citations


Muver, a computational framework for accurately calling accumulated mutations

PMCID: 5944071
PMID: 29743009
DOI: 10.1186/s12864-018-4753-3

[…] but more directly, we called mutations after splitting reads from a single sample (tak137) into virtual outgrowth and t0 samples, using the “virtual tumor” method as applied by the authors of mutect []. as reads were derived from the same source, no mutations should be called. of the three tools, only varscan reported mutations passing all filters (a total of 9). the wt mutation […]


Characterization and remediation of sample index swaps by non redundant dual indexing on massively parallel sequencing platforms

PMCID: 5941783
PMID: 29739332
DOI: 10.1186/s12864-018-4703-0

[…] it can lead to spurious results when looking for rare transcripts or fusion events in rna-seq (as seen in fig. ) and in low allele fraction somatic analysis. while mutation callers such as mutect have filters for many common artifacts that occur during the sequencing process, index swapped reads are unique as they are high quality reads, not errors, that are assigned to the wrong […]


Recurrent hotspot mutations in HRAS Q61 and PI3K AKT pathway genes as drivers of breast adenomyoepitheliomas

PMCID: 5940840
PMID: 29739933
DOI: 10.1038/s41467-018-04128-5

[…] aligner. local realignment, de-duplication, and quality score recalibration were performed using the genome analysis toolkit (gatk). somatic single nucleotide variants (snvs) were identified using mutect; small insertions and deletions (indels) were identified using strelka and varscan 2,, and further curated by manual inspection. variants found with >5% global minor allele frequency […]


Distinct mutational signatures characterize concurrent loss of polymerase proofreading and mismatch repair

PMCID: 5931517
PMID: 29717118
DOI: 10.1038/s41467-018-04002-4

[…] calls for our principal cohort of endometrial samples, alignments (bam files) of the 547 tcga exomes were downloaded from the genome data commons (gdc). somatic point mutations were called using mutect and filtered using d-toxog, and indels were called using indelocator (all available at all calls were filtered using a panel of normals. indels […]


Whole exome sequencing of cell free DNA and circulating tumor cells in multiple myeloma

PMCID: 5923255
PMID: 29703982
DOI: 10.1038/s41467-018-04001-5

[…] were manually reviewed for tumor fraction estimation., the wes output was analyzed by the broad picard pipeline, resulting in bam files aligned to hg19 with calibrated quality scores,. we used mutect within the firehose framework to call somatic mutations in tumor biopsies, cfdna, and ctc samples,. we assessed cross-sample contamination levels using contest and filtered out potential […]


An integrated clinical and genomic information system for cancer precision medicine

PMCID: 5918454
PMID: 29697362
DOI: 10.1186/s12920-018-0347-9

[…] from whole transcriptome sequencing (wts, a.k.a. rna-seq) data. we calculate the somatic single nucleotide variants (snvs), insertions and deletions (indels), and copy number variations (cnvs) using mutect [], strelka [], and excavator [], respectively. the mapsplice-rsem [, ] pipeline was used for rna-seq quantification to warrant accuracy in spite of long computation time. galaxy [] pipelines […]

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MuTect institution(s)
The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Division of Health Sciences and Technology, MIT, Cambridge, MA, USA; Divisions of Medical Oncology and Cancer Biology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA; MIT Department of Biology, Cambridge, MA, USA; Massachusetts General Hospital Cancer Center and Department of Pathology
MuTect funding source(s)
Supported by grants from the National Human Genome Research Institute (U54HG003067) and the National Cancer Institute (U24CA143845).

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