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EnsembleCNV
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EnsembleCNV

EnsembleCNV is a tool to detect and genotype copy number variation (CNV). It uses single nucleotide polymorphism (SNP) data. The algorithm eliminates batch effects on raw data, assembles CNV calls into regions by a heuristic algorithm, re-computes genotypes for each copy number variable region using an adjusted local likelihood model, computes refined CNV boundaries, and CNV genotypes with a confidence score.



EnsembleCNV

EnsembleCNV is a tool to detect and genotype copy number variation (CNV). It uses single nucleotide polymorphism (SNP) data. The algorithm eliminates batch effects on raw data, assembles CNV calls into regions by a heuristic algorithm, re-computes genotypes for each copy number variable region using an adjusted local likelihood model, computes refined CNV boundaries, and CNV genotypes with a confidence score.

Topic

Genetics

Details

  • Operation: Variation detection
  • Software interface: command-line user interface
  • Language: R;Perl
  • Operating system: Linux
  • License: Not stated
    • Cost: Free
  • Version name: -
  • Credit: National Institutes of Health [1R41DA042464-01, 1U01HD079068, 1R01ES029212-01, R01HL125863]; National Natural Science Foundation of China [91643201, 21876134]; Ministry of Science and Technology of China [2016YFC0206507]; Transatlantic Networks of Excellence Award from Foundation Leducq [12CVD02]. The FA study is supported in part by the Bunning Family Food Allergy Project/Food Allergy Initiative, Sacks Family Foundation Fund, Food Allergy Research and Education (FARE) and the National Institute of Allergy and Infectious Diseases [U01AI090727, R56AI080627 and R21AI088609, PI, Xiaobin Wang]. Funding for open access charge: Icahn School of Medicine at Mount Sinai Internal Research Fund.
  • Contact: ke.hao _at_ mssm.edu
  • Collection: -

Publications

Zhang Z, Cheng H, Hong X, Di Narzo AF, Franzen O, Peng S, Ruusalepp A, Kovacic JC, Bjorkegren JLM, Wang X, Hao K "EnsembleCNV: an ensemble machine learning algorithm to identify and genotype copy number variation using SNP array data." Nucleic Acids Res. 2019 Apr 23;47(7):e39. https://doi.org/10.1093/nar/gkz068
PMID: 30722045
PMCID: PMC6468244


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