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Variant Calling

Methods and Protocols

  • Book
  • © 2022

Overview

Editors:
  1. Charlotte Ng

    1. Department of BioMedical Research, University of Bern, Bern, Switzerland

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    You can also search for this editor in PubMed   Google Scholar

  2. Salvatore Piscuoglio

    1. Department of Biomedicine, University of Basel, Basel, Switzerland

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    You can also search for this editor in PubMed   Google Scholar

  • 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 2493)

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Table of contents (21 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Data Processing and Germline Variant Calling with the Sentieon Pipeline

    • Rafael Aldana, Donald Freed
    Pages 1-19

  3. MuSE: A Novel Approach to Mutation Calling with Sample-Specific Error Modeling

    • Shuangxi Ji, Matthew D. Montierth, Wenyi Wang
    Pages 21-27

  4. Octopus: Genotyping and Haplotyping in Diverse Experimental Designs

    • Daniel P. Cooke
    Pages 29-51

  5. Accurate Ensemble Prediction of Somatic Mutations with SMuRF2

    • Weitai Huang, Ngak Leng Sim, Anders J. Skanderup
    Pages 53-66

  6. Detecting Medium and Large Insertions and Deletions with transIndel

    • Ting-You Wang, Rendong Yang
    Pages 67-75

  7. DECoN: A Detection and Visualization Tool for Exonic Copy Number Variants

    • Anna Fowler
    Pages 77-88

  8. FACETS: Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing

    • Arshi Arora, Ronglai Shen, Venkatraman E. Seshan
    Pages 89-105

  9. Meerkat: An Algorithm to Reliably Identify Structural Variations and Predict Their Forming Mechanisms

    • Lixing Yang
    Pages 107-135

  10. Structural Variant Detection from Long-Read Sequencing Data with cuteSV

    • Tao Jiang, Shiqi Liu, Shuqi Cao, Yadong Wang
    Pages 137-151

  11. Identifying Somatic Mitochondrial DNA Mutations

    • Jisong An, Kyoung Il Min, Young Seok Ju
    Pages 153-165

  12. Identification, Quantification, and Testing of Alternative Splicing Events from RNA-Seq Data Using SplAdder

    • Philipp Markolin, Gunnar Rätsch, André Kahles
    Pages 167-193

  13. PipeIT2: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data

    • Andrea Garofoli, Désirée Schnidrig, Charlotte K. Y. Ng
    Pages 195-204

  14. Variant Calling from RNA-seq Data Using the GATK Joint Genotyping Workflow

    • Jean-Simon Brouard, Nathalie Bissonnette
    Pages 205-233

  15. UMI-Varcal: A Low-Frequency Variant Caller for UMI-Tagged Paired-End Sequencing Data

    • Vincent Sater, Pierre-Julien Viailly, Thierry Lecroq, Élise Prieur-Gaston, Élodie Bohers, Mathieu Viennot et al.
    Pages 235-245

  16. Alignment-Free Genotyping of Known Variations with MALVA

    • Giulia Bernardini, Luca Denti, Marco Previtali
    Pages 247-256

  17. Kmer2SNP: Reference-Free Heterozygous SNP Calling Using k-mer Frequency Distributions

    • Yanbo Li, Hardip Patel, Yu Lin
    Pages 257-265

  18. Somatic Single-Nucleotide Variant Calling from Single-Cell DNA Sequencing Data Using SCAN-SNV

    • Sajedeh Bahonar, Hesam Montazeri
    Pages 267-277

  19. Copy Number Variation Detection by Single-Cell DNA Sequencing with SCOPE

    • Rujin Wang, Yuchao Jiang
    Pages 279-288

  20. Variant Annotation and Functional Prediction: SnpEff

    • Pablo Cingolani
    Pages 289-314
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Keywords

About this book

This volume provides practical guidance on a variety of techniques and steps to ensure successful variant calling. Chapters detail methods for variant calling from single-nucleotide variants to structural variants, variant calling in specialized data types such as RNA-seq and UMI-tagged sequencing, alignment-free genotyping and SNP calling, variant detection in single-cell DNA sequencing data, variant annotation, and preanalytical quality control to ensure successful variant calling. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists step-by-step protocol to execute the algorithms, describes the input and output data, and includes tips on troubleshooting and known pitfalls.

 

Authoritative and cutting-edge, Variant Calling: Methods and Protocols aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field.  

Editors and Affiliations

  • Department of BioMedical Research, University of Bern, Bern, Switzerland

    Charlotte Ng

  • Department of Biomedicine, University of Basel, Basel, Switzerland

    Salvatore Piscuoglio

Bibliographic Information

  • Book Title: Variant Calling

  • Book Subtitle: Methods and Protocols

  • Editors: Charlotte Ng, Salvatore Piscuoglio

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2293-3

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-2292-6Published: 26 June 2022

  • Softcover ISBN: 978-1-0716-2295-7Published: 26 June 2022

  • eBook ISBN: 978-1-0716-2293-3Published: 25 June 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 354

  • Number of Illustrations: 13 b/w illustrations, 44 illustrations in colour

  • Topics: Genetics and Genomics, Bioinformatics

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