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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

 (16)
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Activating de novo mutations in NFE2L2 encoding NRF2 cause a multisystem disorder

2017
Nat Commun
PMCID: 5635015
PMID: 29018201
DOI: 10.1038/s41467-017-00932-7
call_split See protocol

[…] 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. Bas […]

library_books

Differences between germline and somatic mutation rates in humans and mice

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

[…] 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 was […]

library_books

Analysis of exome data for 4293 trios suggests GPI anchor biogenesis defects are a rare cause of developmental disorders

2017
Eur J Hum Genet
PMCID: 5477361
PMID: 28327575
DOI: 10.1038/ejhg.2017.32

[…] netic information available included full v4.1 VCFs, annotation for variants that have already been reported back to clinicians via DECIPHER and a list of Sanger validated de novo mutations called by DeNovoGear. Selected BAM files were downloaded from the European Genome-Phenome Archive (EGA; www.ebi.ac.uk/ega/datasets/EGAD00001001114). Other information included clinical details, which included a […]

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PUF60 variants cause a syndrome of ID, short stature, microcephaly, coloboma, craniofacial, cardiac, renal and spinal features

2017
Eur J Hum Genet
PMCID: 5392357
PMID: 28327570
DOI: 10.1038/ejhg.2017.27
call_split See protocol

[…] udy. High-resolution analysis for copy number abnormalities using array-based comparative genomic hybridization was also performed. Putative de novo variants were identified from exome data using the DeNovoGear software and then validated by targeted Sanger sequencing. For patients 7–12, alternative but similar trio exome sequence approaches were used, for example, for patient 10 a proband-based e […]

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Clinical and molecular consequences of disease associated de novo mutations in SATB2

2017
Genet Med
PMCID: 5548934
PMID: 28151491
DOI: 10.1038/gim.2016.211
call_split See protocol

[…] ir parents was extracted from blood or saliva and subjected to target capture using Agilent SureSelect 55MB Exome Plus and sequenced on Illumina HiSeq. De novo sequence variants were identified using DeNovoGear (https://github.com/denovogear) and the effect of each genomic variant was predicted with the Ensembl Variant Effect Predictor (grch37.ensembl.org/Homo_sapiens/Tools/VEP). For individual KA […]

library_books

Insulin resistance uncoupled from dyslipidemia due to C terminal PIK3R1 mutations

2016
JCI Insight
PMCID: 5070960
PMID: 27766312
DOI: 10.1172/jci.insight.88766

[…] 001001257, EGAN00001001835, and EGAN00001001824).Exome data for P1 and her parents were merged, and variants with a high posterior probability of being de novo (cutoff value 0.8) were extracted using DeNovoGear v0.5 (https://sourceforge.net/projects/denovogear/) (). Potential compound heterozygous mutations were also extracted. Variant annotation has previously been described in detail (). Potenti […]

Citations

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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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