MuTect specifications

Information


Unique identifier OMICS_00087
Name MuTect
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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MuTect article

MuTect citations

 (8)
2018
PMCID: 5843664

[…] 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. […]

2018
PMCID: 5789978

[…] more than three samples were discarded to minimize systematic errors. associated tumor and germline exome sequencing data was utilized for the patient example and somatic variants were called using mutect2 with default settings., all variants were annotated using snpeff and validated using the integrative genomics viewer49,50. bam-readcount was used to count the number of a/c/g/t’s in plasma […]

2018
PMCID: 5839396

[…] 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 […]

2017
PMCID: 5669905

[…] burrows-wheeler alignment (bwa) tool to human genomic reference sequences (hg19, ncbi built 37) [47]. to identify single nucleotide polymorphisms (snps) and short insertions and deletions (indels), mutect2 with recommended parameters was performed [48]. all mutations were annotated by the annovar software using some resources (details in supplementary method) [49]. a subset of somatic mutations […]

2017
PMCID: 5500377

[…] erbb2, and genes encoding small gtpases, level 1 sequencing data in bam format were downloaded via the cancer genomics hub. data from 906 tumor-normal pairs were subjected to mutation calling with mutect. to detect fusion transcripts, level 1 prealigned rna-seq data in bam format were downloaded from the cancer genomics hub. to determine er and her2 statuses, clinical information […]

MuTect institution(s)
The Broad Institute of Harvard and MIT, Cambridge, MA, USA

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