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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

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Maintainer


  • person_outline Gad Getz <>

Publication for MuTect

MuTect in pipelines

 (31)
2018
PMCID: 5768770
PMID: 29335443
DOI: 10.1038/s41467-017-02584-z

[…] tools after which realignment around known indels and base quality recalibration was performed at an individual sample level using gatk 2.7 version., somatic mutation calling was performed using mutect allowing up to 5 reads supporting the variant allele in the normal sample up to a maximum of 0.05 allele frequency. the passed variants were further filtered using the described criteria […]

2018
PMCID: 5839396
PMID: 29515765
DOI: 10.18632/oncotarget.23882

[…] toolkit (https://www.broadinstitute.org/gatk/guide/best-practices?bpm=dnaseq). the resulting bam [] files were preprocessed and base substitutions and small insertions/deletions were called using mutect [] and pindel [], respectively. to overcome the lack of matched normal sample, we generated virtual common normal sequence using in-house pooled normal sequence. this method has been shown […]

2018
PMCID: 5843664
PMID: 29520031
DOI: 10.1038/s41467-018-03121-2

[…] following the gatk best practices of duplicate removal, indel realignment, and recalibration. somatic single-nucleotide variations (snvs) and small insertions and deletions (indels) were detected by mutect and pindel, respectively. in addition, variants were filtered against the exac database using a cut-off of 0.1%. snvs and indels were annotated using snpeff based on ucsc known genes. […]

2018
PMCID: 5844869
PMID: 29523855
DOI: 10.1038/s41598-018-22473-9

[…] low quality sequences using cutadapt (version 1.8.3); and aligned to the reference genome (grch37/hg19 assembly) using bwa mem (version 0.7.13). pairs of normal and tumor samples were provided to mutect pipeline (version 1.1.7) along with dbsnp (hg19) and cosmic (version 80) variant files. all candidate mutations that were not rejected as somatic variants by mutect were retained. vcftool […]

2017
PMCID: 5333358
PMID: 28240289
DOI: 10.1038/ncomms14565

[…] sequence data then follow through base quality recalibration and realignment using the genome analysis tool kit. somatic variants were called comparing tumour against normal using the mutect programme (version 1.1.4) (). using sequenom platform (a mass spectrometry-based technology), a small subset of somatic variants were experimentally validated (). copy number alterations […]


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MuTect in publications

 (426)
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 […]

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 […]

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 […]

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 http://www.broadinstitute.org/cancer/cga). all calls were filtered using a panel of normals. indels […]

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 […]


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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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