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A linkage-disequilibrium framework to genotype inference in parents-offspring trios. TrioCaller will facilitate genotype calling and haplotype inference for many ongoing sequencing projects.

Software type:
Command line interface
Restrictions to use:
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Computer skills:
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  • Wei Chen <weichen.mich at gmail.com>


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, Pennsylvania 15224, USA; Department of Biostatistics, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania 15224, USA; The Center for Human Genetics Research, Department of Molecular Physiology & Biophysics, and Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA; Istituto di Ricerca Genetica e Biomedica, Centro Nazionale di Ricerca (CNR), Monserrato, Cagliari 09042, Italy; Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48105, USA; Dipartimento di Scienze Biomediche, UniversitĂ  di Sassari, Sardinia 07100, Italy; Department of Genetics, Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA

  • (Chen et al., 2013) Genotype calling and haplotyping in parent-offspring trios. Genome research.
    PMID: 23064751
  • (Mainzer et al., 2015) Isaac, the Illumina variant calling workflow. bioRxiv.
    DOI: 10.1101/031021
  • (Liu et al., 2013) Variant callers for next-generation sequencing data: a comparison study. PloS one.
    PMID: 24086590
  • (Nielsen et al., 2011) Genotype and SNP calling from next-generation sequencing data. Nature reviews Genetics.
    PMID: 21587300
  • (Altmann et al., 2012) A beginners guide to SNP calling from high-throughput DNA-sequencing data. Human genetics.
    PMID: 22886560
  • (Pabinger et al., 2013) A survey of tools for variant analysis of next-generation genome sequencing data. Briefings in bioinformatics.
    PMID: 23341494
  • (Yi et al., 2014) Performance comparison of SNP detection tools with illumina exome sequencing data-an assessment using both family pedigree information and sample-matched SNP array data. Nucleic acids research.
    PMID: 24831545
  • (Pirooznia et al., 2014) Validation and assessment of variant calling pipelines for next-generation sequencing. Human genomics.
    PMID: 25078893

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