Mutascope statistics

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Mutascope specifications

Information


Unique identifier OMICS_02074
Name Mutascope
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.0.2
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Olivier Harismendy <>

Publication for Mutascope

Mutascope in pipelines

 (2)
2015
PMCID: 4346117
PMID: 25881093
DOI: 10.1186/s12885-015-1077-4

[…] (celemics, seoul, korea). subsequently, each product was indexed, mixed, and deeply sequenced on hiseq2500. raw data was deindexed and mapped to the reference human genome (hg19) using novoalign. mutascope was used to call somatic mutations, and compared to the whole exome sequencing data []. only the loci with at least 500 reads of both normal and tumor tissue and >5% allelic fraction […]

2015
PMCID: 4422481
PMID: 25889843
DOI: 10.1186/s12967-015-0485-1

[…] them using illumina miseq sequencer for 2x150 bp reads. the sequencing reads were then aligned and mutation called using the illumina basespace cloud with truseq dna amplicon application or using mutascope locally []. to increase the detection sensitivity the reads spanning the expected 42 nt deletion in aa2476t tumor were aligned independently using blat []. to analyze the large deletion […]


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Mutascope in publications

 (3)
PMCID: 5585396
PMID: 28874753
DOI: 10.1038/s41467-017-00100-x

[…] and the following run set up: read 1: 301 cycles; read 2: 8 cycles; read 3: 8 cycles; read 4: 301 cycles., fastq files were retrieved from illumina basespace (https://basespace.illumina.com/). mutascope was used to process reads and to prepare them for variant calling because it is a high-sensitivity software suite designed to analyze data derived from high-throughput sequencing of pcr […]

PMCID: 4346117
PMID: 25881093
DOI: 10.1186/s12885-015-1077-4

[…] (celemics, seoul, korea). subsequently, each product was indexed, mixed, and deeply sequenced on hiseq2500. raw data was deindexed and mapped to the reference human genome (hg19) using novoalign. mutascope was used to call somatic mutations, and compared to the whole exome sequencing data []. only the loci with at least 500 reads of both normal and tumor tissue and >5% allelic fraction […]

PMCID: 4220156
PMID: 25312340
DOI: 10.1038/cr.2014.131

[…] at genome scale. existing algorithms for identifying psnms from whole-genome or targeted resequencing data require a matched control sample, such as jointsnvmix, varscan 2, strelka, ebcall, mutect, mutascope, and lofreq. as a result, fundamental patterns of the psnms in whole genomes of clinically unremarkable individuals remain largely unknown, such as the prevalence, allele fractions, […]


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Mutascope institution(s)
Bioinformatics Graduate Program, University of California San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA; Rady Children’s Hospital, University of California San Diego, La Jolla, CA, USA; Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA, USA; Department of Medicine, University of California San Diego, La Jolla, CA, USA; Clinical and Translational Research Institute, University of California San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
Mutascope funding source(s)
Supported by National Cancer Institute (1R21CA155615-01A1 and 1R21CA152613-01); NCATS (UL1RR031980); a pilot award from the NIH Center of Excellence Grant to the San Diego Center for Systems Biology (P50GM085764).

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