TrioCaller statistics

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TrioCaller specifications

Information


Unique identifier OMICS_07458
Name TrioCaller
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format VCF
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Requirements
BWA, samtools
Maintained Yes

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Maintainer


  • person_outline Wei Chen <>

Publication for TrioCaller

TrioCaller in publications

 (3)
PMCID: 4627508
PMID: 26366554
DOI: 10.1038/ng.3368

[…] finally, using the list of likely high-quality sites, genotypes were estimated using the haplotype-aware calling algorithms implemented in beagle, to generate initial haplotype estimates, and triocaller, to refine this initial haplotype set. the entire computational process required approximately 20 years of computing time (6 cpu years for quality control and alignment, and 14 cpu years […]

PMCID: 4494155
PMID: 26092298
DOI: 10.1186/s12915-015-0152-2

[…] to refine these genotype calls using pedigree-aware methods such as polymutt []. we therefore broke the pedigree into units (trios and parent-offspring duos) that could be analyzed with the programs triocaller [] and beagle 4.0 []. we broke full sibships into distinct trios by replicating parental information. similarly, for male monkeys who have had offspring with multiple different female […]

PMCID: 3605488
PMID: 23494190
DOI: 10.1007/s10142-013-0319-2

[…] to genome coverage, genotype calling and statistical power of the output data for gwas was discussed by abecasis from the computation point-of-view through the use of the abcd (kang et al. ) and triocaller (chen et al. ) software., the plenary lectures by eric perakslis and michael eisen debated different aspects of freedom to access information for scientific research. in the food and drug […]


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TrioCaller institution(s)
Division of Pediatric Pulmonary Medicine, Allergy and Immunology, Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Biostatistics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA; The Center for Human Genetics Research, Department of Molecular Physiology & Biophysics, and Neurology, Vanderbilt University Medical Center, Nashville, TN, USA; Istituto di Ricerca Genetica e Biomedica, Centro Nazionale di Ricerca (CNR), Monserrato, Cagliari, Italy; Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA; Dipartimento di Scienze Biomediche, Università di Sassari, Sardinia, Italy; Department of Genetics, Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
TrioCaller funding source(s)
Supported by the research grants HG007022, HG005581, and HG006292 from National Institutes of Health and startup funds from the Department of Pediatrics, University of Pittsburgh School of Medicine.

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