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Protocols

TrioDeNovo specifications

Information


Unique identifier OMICS_16467
Name TrioDeNovo
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format VCF, PED
Output format VCF
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 0.04
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Bingshan Li

Publication for TrioDeNovo

TrioDeNovo citations

 (4)
library_books

Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands

2017
Nat Genet
PMCID: 5675000
PMID: 28991257
DOI: 10.1038/ng.3970

[…] were analyzed. Synonymous variants were also filtered using the same criteria and analyzed separately to determine whether there is an inflation of background rate.DNMs were called by Yale using the TrioDenovo program and by HMS as previously described, and filtered using the same criteria, which have been shown to yield a specificity of 96.3% as described previously. These hard filters include: […]

call_split

Leveraging blood serotonin as an endophenotype to identify de novo and rare variants involved in autism

2017
Mol Autism
PMCID: 5361831
PMID: 28344757
DOI: 10.1186/s13229-017-0130-3
call_split See protocol

[…] nine bioinformatics tools provided in ANNOVAR. Each variant was assigned a deleterious score (DScore) between 0 and 9, denoting the number of damaging predictions from among these algorithms. We used TrioDenovo to call DNVs on both autosomes and X chromosome and obtained reliable candidates for validation after filtering []. We focused on two types of functional variants: loss of function (LoF; sp […]

library_books

Digenic mutations of human OCRL paralogs in Dent’s disease type 2 associated with Chiari I malformation

2016
Hum Genome Var
PMCID: 5143364
PMID: 28018608
DOI: 10.1038/hgv.2016.42

[…] e a history of renal involvement, it was suspected that the disease may be caused by either de novo or homozygous mutations in the context of recessive inheritance. To identify de novo mutations, the TrioDeNovo program was used and high-stringency filters were applied as described in the Methods section. We identified two de novo mutations in this trio. The first is a tolerated missense mutation i […]

library_books

Two locus inheritance of non syndromic midline craniosynostosis via rare SMAD6 and common BMP2 alleles

2016
eLife
PMCID: 5045293
PMID: 27606499
DOI: 10.7554/eLife.20125.029

[…] cribed in Materials and methods; summary data are shown in . Variants were called using the GATK pipeline (see Materials and methods) and de novo mutations in parent-offspring trios were called using TrioDeNovo (). The impact of identified missense variants on protein function was inferred using MetaSVM (). All de novo calls were verified by in silico visualization of aligned reads (), and all cal […]

Citations

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TrioDeNovo funding source(s)
This work was partially supported by National Institutes of Health [grant 1R01HG006857] and [1R01HG007358].

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