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Protocols

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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Documentation


Maintainer


  • person_outline Olivier Harismendy

Publication for Mutascope

Mutascope citations

 (4)
library_books

Analysis of amplicon based NGS data from neurological disease gene panels: a new method for allele drop out management

2016
BMC Bioinformatics
PMCID: 5123238
PMID: 28185542
DOI: 10.1186/s12859-016-1189-0

[…] ative allele or an artifact []. Advances in the bioinformatics field led to the creation and the development of algorithms to manage such artifacts during the analysis (e.g.: AmpliVar [], TSSV [] and Mutascope []). AmpliVar is based on the reduction of the number of input reads to be aligned to a reference genome by grouping for primer sequence in a key-value structure, where each group is analyze […]

call_split

BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma

2015
J Transl Med
PMCID: 4422481
PMID: 25889843
DOI: 10.1186/s12967-015-0485-1
call_split See protocol

[…] ced 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 in s […]

library_books

Tumor evolution and intratumor heterogeneity of an epithelial ovarian cancer investigated using next generation sequencing

2015
BMC Cancer
PMCID: 4346117
PMID: 25881093
DOI: 10.1186/s12885-015-1077-4

[…] ple (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 were us […]

library_books

Postzygotic single nucleotide mosaicisms in whole genome sequences of clinically unremarkable individuals

2014
Cell Res
PMCID: 4220156
PMID: 25312340
DOI: 10.1038/cr.2014.131

[…] s 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, mutation […]

Citations

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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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