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TrioDeNovo specifications


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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  • person_outline Bingshan Li <>

Publication for TrioDeNovo

TrioDeNovo in publications

PMCID: 5675000
PMID: 28991257
DOI: 10.1038/ng.3970

[…] 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: […]

PMCID: 5361831
PMID: 28344757
DOI: 10.1186/s13229-017-0130-3

[…] 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; […]

PMCID: 5143364
PMID: 28018608
DOI: 10.1038/hgv.2016.42

[…] variant server and exac (v3)., the relationship between the proband and parents was estimated using the pairwise identify-by-descent calculation in plink., de novo variants were called using the triodenovo program. triodenovo calculates the posterior likelihood of a mutation being a bona fide de novo event and assigned a data quality (dq) score to each variant call. de novo candidates […]

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

[…] 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 (), […]

PMCID: 4389250
PMID: 25809527
DOI: 10.1038/ncomms7684

[…] no additional candidates were added to the validation data set from this analysis., de novo mutations were called on the variants supplied by bcftools using denovogear version 0.5 (ref. ) and triodenovo ( using standard settings. denovogear called 3,303, 3,284, 4,245, 3,500, 3,593 and 3,480 snvs and small indel candidates in the autosomes […]

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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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