Variant Calling

Methods and Protocols

Charlotte Ng, Salvatore Piscuoglio (Herausgeber)

Buch | Softcover

354 Seiten

2022 | 1st ed. 2022
Springer-Verlag New York Inc.
978-1-0716-2295-7 (ISBN)

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lt;p>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.

lt;p>1. Data Processing and Germline Variant Calling with the Sentieon pipeline

Rafael Aldana and Donald Freed

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

Shuangxi Ji, Matthew D. Montierth, and Wenyi Wang

3. Octopus: Genotyping and Haplotyping in Diverse Experimental Designs

Daniel P Cooke

4. Accurate Ensemble Prediction of Somatic Mutations with SMuRF2

Weitai Huang, Ngak Leng Sim, and Anders J Skanderup

5. Detecting Medium and Large Insertions and Deletions with Transindel

Ting-You Wang and Rendong Yang

6, DECoN: A detection and visualisation tool for exonic copy number variants

Anna Fowler

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

Arshi Arora, Ronglai Shen, and Venkatraman E. Seshan

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

Lixing Yang

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

Tao Jiang, Shiqi Liu, Shuqi Cao, and Yadong Wang

10. Identifying Somatic Mitochondrial DNA Mutations

Jisong An, Kyoung Il Min,and Young Seok Ju

11. Identification, Quantification, and Testing of Alternative Splicing Events from RNA-Seq data using SplAdder

Philipp Markolin, Gunnar Rätsch, and Andre Kahles

12. PipeIT: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data

Andrea Garofoli, Désirée Schnidrig, and Charlotte K Y Ng

13. Variant calling from RNA-seq data using the GATK joint genotyping workflow

Jean-Simon Brouard and Nathalie Bissonnette

14. 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, Philippe Ruminy Hélène Dauchel, Pierre Vera, and Fabrice Jardin

15. Alignment-free genotyping of known variations with MALVA

Giulia Bernardini, Luca Denti, and Marco Previtali

16. Kmer2SNP: Reference-free heterozygous SNP calling using k-mer frequency distributions Yanbo Li, Hardip Patel, and Yu Lin

17. Somatic Single Nucleotide Variant Calling from Single Cell DNA sequencing data using SCAN-SNV

Sajedeh Bahonar and Hesam Montazeri

18. Copy Number Variation Detection by Single-Cell DNA sequencing with SCOPE

Rujin Wang and Yuchao Jiang

19. Variant Annotation and Functional Prediction: SnpEff

Pablo Cingolani

20. Annotating Cancer-Related Variants At Protein-Protein Interface with Structure-PPi Miguel Vazquez and Tirso Pons

21. Preanalytical Variables and Sample Quality Control For Clinical Variant Analysis

Ilaria Alborelli and Philip M. Jermann

Erscheinungsdatum	28.06.2023
Reihe/Serie	Methods in Molecular Biology
Zusatzinfo	44 Illustrations, color; 13 Illustrations, black and white; XI, 354 p. 57 illus., 44 illus. in color.
Verlagsort	New York, NY
Sprache	englisch
Maße	178 x 254 mm
Themenwelt	Mathematik / Informatik ► Informatik ► Theorie / Studium
	Informatik ► Weitere Themen ► Bioinformatik
	Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
Schlagworte	copy number variants • downstream analyses • HLA typing • Nextflow • RNA-Seq data
ISBN-10	1-0716-2295-1 / 1071622951
ISBN-13	978-1-0716-2295-7 / 9781071622957
Zustand	Neuware