TrioCaller statistics

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Citations per year

Number of citations per year for the bioinformatics software tool TrioCaller
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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 citations

 (4)
library_books

Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers

2015
Nat Genet
PMCID: 4627508
PMID: 26366554
DOI: 10.1038/ng.3368

[…] sition. 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 fo […]

library_books

Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits

2015
BMC Biol
PMCID: 4494155
PMID: 26092298
DOI: 10.1186/s12915-015-0152-2

[…] oving data from samples suspected of contamination or mislabeling, and updating the pedigree based on newly identified parent-offspring relationships, we repeated the genotype call refining (Beagle + TrioCaller) step, described in Stage 2. We then applied the following filters to generate our final mapping sets: 1) removed SNPs with >=5 Mendel errors between parents and offspring; 2) removed SNPs […]

library_books

Genomic and Phenotypic Characterization of a Wild Medaka Population: Towards the Establishment of an Isogenic Population Genetic Resource in Fish

2014
PMCID: 3962483
PMID: 24408034
DOI: 10.1534/g3.113.008722

[…] LD (r2) was computed from the TrioCaller SNPs from the 16 wild Southern trio founders as well as in 16 parents from human trios sequenced and annotated by Complete Genomics (). Computations were performed using VCFtools () with th […]

library_books

Advances in biotechnology and informatics to link variation in the genome to phenotypes in plants and animals

2013
PMCID: 3605488
PMID: 23494190
DOI: 10.1007/s10142-013-0319-2

[…] pect 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 Adm […]


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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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