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DeNovoGear specifications

Information


Unique identifier OMICS_00083
Name DeNovoGear
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.1.1
Stability Stable
Maintained Yes

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Publication for DeNovoGear

DeNovoGear citations

 (17)
library_books

De novo mutations implicate novel genes in systemic lupus erythematosus

2017
PMCID: 5886157
PMID: 29177435
DOI: 10.1093/hmg/ddx407

[…] approval for the research was granted by the nres committee london (12/lo/1273 and 06/mre02/9)., three bioinformatics tools with conservative parameters were used for dnm screening: bcftools (), denovogear () and denovocheck (). a detailed description of the methods applied can be found in si methods. briefly, 454 variants were identified with bcftools and denovogear and eight additional […]

library_books

Direct estimation of de novo mutation rates in a chimpanzee parent offspring trio by ultra deep whole genome sequencing

2017
PMCID: 5666008
PMID: 29093469
DOI: 10.1038/s41598-017-13919-7

[…] duplication regions in chimpanzees. , *fp: false positive, #known segmental duplication regions in chimpanzees., for the estimation of fn calls in our analysis, we used a likelihood-based program, denovogear, on the same data set for the comparison. denovogear is a program designed to detect de novo mutations using ngs data as we have done in this study. when the posterior probability […]

library_books

Activating de novo mutations in NFE2L2 encoding NRF2 cause a multisystem disorder

2017
PMCID: 5635015
PMID: 29018201
DOI: 10.1038/s41467-017-00932-7

[…] exome aggregation consortium (http://exac.broadinstitute.org/)) variants, predicted to modify a protein sequence or to impair splicing, implicated by reduced maximum entropy scores (maxentscan). the denovogear software was used to identify de novo mutations. false positive and irrelevant variants were further reduced by taking advantage of the varbank inhousedb containing 511 epilepsy exomes. […]

library_books

A recurrent de novo mutation in ACTG1 causes isolated ocular coloboma

2017
PMCID: 5518294
PMID: 28493397
DOI: 10.1002/humu.23246

[…] with isolated oc and both unaffected parents. in three of these trios, there was a wider family history of eye malformation that would be compatible with nonpenetrance in the intervening parent. denovogear analysis (ramu et al., ), together with a maximum minor allele frequency in exac of <10−4, was used to identify candidate de novo mutations (dnm) among all technically robust variant […]

library_books

Differences between germline and somatic mutation rates in humans and mice

2017
PMCID: 5436103
PMID: 28485371
DOI: 10.1038/ncomms15183

[…] removed using samtools. the mapped reads were indel-realigned and base pair score quality recalibrated using gatk., de novo germline snvs from family trios were called using varscan2 (ref. ) and denovogear and unifiedgenotyper, using the default parameters and a minimum of × 20 coverage. candidates were further filtered out if reported previously in dbsnp or if any variant-supporting read […]

library_books

Disseminated Mycobacterium malmoense and Salmonella Infections Associated with a Novel Variant in NFKBIA

2017
PMCID: 5489571
PMID: 28417298
DOI: 10.1007/s10875-017-0390-x

[…] prepared for each sample and aligned to the reference genome (grch37) using bwa v0.6.2. genotype likelihoods were computed using samtools (0.1.19) and de novo mutations in the patient called with denovogear (0.5.4). variant consequences, determined using ensembl vep (75), were used to identify deleterious mutations. a de novo heterozygous c.94a>g missense mutation, not reported in the exac […]


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DeNovoGear institution(s)
Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA; Genome Mutation and Genetic Disease Group, Wellcome Trust Sanger Institute, Cambridge, UK; School of Life Sciences, Arizona State University, Tempe, AZ, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA

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