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Protocols

MuTect specifications

Information


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

Versioning


No version available

Maintainer


  • person_outline Gad Getz

Publication for MuTect

MuTect citations

 (384)
library_books

Outlier response to anti PD1 in uveal melanoma reveals germline MBD4 mutations in hypermutated tumors

2018
Nat Commun
PMCID: 5951831
PMID: 29760383
DOI: 10.1038/s41467-018-04322-5

[…] //broadinstitute.github.io/picard/; HaplotypeCaller, https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php; MuTect2, https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php; SAMtools mpileup, http://samtools.sourceforge.net/; ANNOVA […]

library_books

Muver, a computational framework for accurately calling accumulated mutations

2018
BMC Genomics
PMCID: 5944071
PMID: 29743009
DOI: 10.1186/s12864-018-4753-3

[…] t_allele_in_normal. Mutations flagged as “alt_allele_in_normal”, “clustered_events”, or “str_contraction” were accepted, as no such filters are applied by muver. An additional step was applied to the MuTect2 results: mutations were filtered whose outgrowth alternate allele frequency fell below 0.4 or above 0.6. This was performed to filter down to clonal-only mutations to facilitate comparisons wi […]

library_books

VAReporter: variant reporter for cancer research of massive parallel sequencing

2018
BMC Genomics
PMCID: 5954270
PMID: 29764369
DOI: 10.1186/s12864-018-4468-5

[…] d visual interpretation of the genetic variants. VAReporter has the ability to accept heterogeneous variant call file (VCF) formats from state-of-the-art variant callers, such as GATK [], VarScan [], MuTect [] and VarDict [], and provides the most comprehensive list of support formats with respect to single and paired samples. A wide variety of biomedical databases, including dbSNP [], 1000 Genome […]

call_split

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

2018
Nat Commun
PMCID: 5940840
PMID: 29739933
DOI: 10.1038/s41467-018-04128-5
call_split See protocol

[…] er 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 in dbSNP ( […]

library_books

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

2018
Nat Commun
PMCID: 5923255
PMID: 29703982
DOI: 10.1038/s41467-018-04001-5

[…] samples 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 artifa […]

library_books

An integrated clinical and genomic information system for cancer precision medicine

2018
BMC Med Genomics
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 f […]

Citations

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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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