MuTect 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 No

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Publication for MuTect

MuTect IN pipelines

 (12)
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 version54., somatic mutation calling was performed using mutect55 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 [34] files were preprocessed and base substitutions and small insertions/deletions were called using mutect [35] and pindel [36], 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

[…] the gatk best practices of duplicate removal64, indel realignment, and recalibration. somatic single-nucleotide variations (snvs) and small insertions and deletions (indels) were detected by mutect65 and pindel66, respectively. in addition, variants were filtered against the exac67 database using a cut-off of 0.1%. snvs and indels were annotated using snpeff68 based on ucsc known genes. […]

2017
PMCID: 5253631
PMID: 28098136
DOI: 10.1038/ncomms14121

[…] files are deposited european nucleotide archive (ena) (accession number prjeb12830, wgs of matched normal and tumour samples of npc patients). identification of somatic snv and sv was conducted by mutect27 and manta31, respectively. to evaluate the sensitivity of somatic sv results, we used only one sv result when different calls share breakpoints within 1,000 base pairs. we predicted somatic […]

2017
PMCID: 5522028
PMID: 28611298
DOI: 10.18632/oncotarget.18355

[…] radseq data (see removing pcr duplicates above). reads were aligned to the zebrafish (danrer7) or human (hg19) reference genomes using bwa [33]. mutation calling. mutation-calling was done using mutect [34]. manual curation. the mutation lists generated by mutect were curated via manual inspection of the alignment files at each location using the integrative genomics viewer (igv) [66]. […]

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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