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Copy Number Variants pp 1–28Cite as

Identification of Copy Number Variants from SNP Arrays Using PennCNV

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1833))

Abstract

High-resolution single-nucleotide polymorphism (SNP) genotyping arrays offer a sensitive and affordable method for genome-wide detection of copy number variants (CNVs). PennCNV is a hidden Markov model (HMM)-based CNV caller for SNP arrays, first released 10 years ago. A typical CNV calling procedure using PennCNV includes preparation of input files, CNV calling, filtering CNV calls, CNV annotation, and CNV visualization. Here we describe several protocols for CNV calling using PennCNV, together with descriptions on several recent improvements to the software tool.

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Authors and Affiliations

  1. Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA

    Li Fang & Kai Wang

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  1. Li Fang
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  2. Kai Wang
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Editors and Affiliations

  1. Research Microbiologist/Bioinformatician, USDA ARS DFRC, Madison, WI, USA

    Derek M. Bickhart

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Fang, L., Wang, K. (2018). Identification of Copy Number Variants from SNP Arrays Using PennCNV. In: Bickhart, D. (eds) Copy Number Variants. Methods in Molecular Biology, vol 1833. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8666-8_1

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  • DOI: https://doi.org/10.1007/978-1-4939-8666-8_1

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8665-1

  • Online ISBN: 978-1-4939-8666-8

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