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  • © 2018

Copy Number Variants

Methods and Protocols

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

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

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-x
  2. Statistical Detection of Genome Differences Based on CNV Segments

    • Yang Zhou, Derek M. Bickhart, George E. Liu
    Pages 49-59
  3. Using HaMMLET for Bayesian Segmentation of WGS Read-Depth Data

    • John Wiedenhoeft, Alexander Schliep
    Pages 83-93
  4. Split-Read Indel and Structural Variant Calling Using PINDEL

    • Kai Ye, Li Guo, Xiaofei Yang, Eric-Wubbo Lamijer, Keiran Raine, Zemin Ning
    Pages 95-105
  5. Detecting Small Inversions Using SRinversion

    • Ruoyan Chen, Yu Lung Lau, Wanling Yang
    Pages 107-114
  6. Detection of CNVs in NGS Data Using VS-CNV

    • Nathan Fortier, Gabe Rudy, Andreas Scherer
    Pages 115-127
  7. Structural Variant Breakpoint Detection with novoBreak

    • Zechen Chong, Ken Chen
    Pages 129-141
  8. Versatile Identification of Copy Number Variants with Canvas

    • Sergii Ivakhno, Eric Roller
    Pages 155-168
  9. Analysis of Population-Genetic Properties of Copy Number Variations

    • Lingyang Xu, Liu Yang, Derek M. Bickhart, JunYa Li, George E. Liu
    Pages 179-186
  10. Structural Variation Detection and Analysis Using Bionano Optical Mapping

    • Saki Chan, Ernest Lam, Michael Saghbini, Sven Bocklandt, Alex Hastie, Han Cao et al.
    Pages 193-203
  11. Correction to: Analysis of Population-Genetic Properties of Copy Number Variations

    • Lingyang Xu, Liu Yang, Derek M. Bickhart, JunYa Li, George E. Liu
    Pages E1-E1
  12. Back Matter

    Pages 205-206

About this book

This volume offers detailed step-by-step instructions to allow beginners and experts alike to run appropriate copy number variants (CNV) detection software on a dataset of choice and discern between false positive noise and true positive CNV signals. Chapters guide readers through single nucleotide polymorphism (SNP) chips, optical mapping assembly techniques, and current open-source programs specializing in CNV detection.  Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Copy Number Variants: Methods and Protocols aims to provide guidance to Bioinformaticians and Molecular Biologists who are interested in identifying copy number variants (CNV) with a wide variety of experimental media

Editors and Affiliations

  • Research Microbiologist/Bioinformatician, USDA ARS DFRC, Madison, USA

    Derek M. Bickhart

Bibliographic Information

  • Book Title: Copy Number Variants

  • Book Subtitle: Methods and Protocols

  • Editors: Derek M. Bickhart

  • Series Title: Methods in Molecular Biology

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

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2018

  • Hardcover ISBN: 978-1-4939-8665-1Published: 24 July 2018

  • Softcover ISBN: 978-1-4939-9359-8Published: 10 December 2019

  • eBook ISBN: 978-1-4939-8666-8Published: 23 July 2018

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 206

  • Number of Illustrations: 11 b/w illustrations, 25 illustrations in colour

  • Topics: Bioinformatics

Buy it now

Buying options

eBook USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access