Variant Calling : Methods and Protocols / edited by Charlotte Ng, Salvatore Piscuoglio.

Format:

Book

Contributor:

Ng, Charlotte, Editor.

Piscuoglio, Salvatore, Editor.

SpringerLink (Online service)

Series:

Springer Protocols (Springer-12345)

Methods in molecular biology 1940-6029 ; 2493

Methods in Molecular Biology, 1940-6029 ; 2493

Language:

English

Subjects (All):

Genetics.

Bioinformatics.

Local Subjects:

Genetics.

Bioinformatics.

Physical Description:

1 online resource (XI, 354 pages) : 57 illustrations, 44 illustrations in color.

Edition:

1st ed. 2022.

Contained In:

Springer Nature eBook

Place of Publication:

New York, NY : Springer US : Imprint: Humana, 2022.

System Details:

text file PDF

Summary:

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. .

Contents:

Data Processing and Germline Variant Calling with the Sentieon pipeline

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

Octopus: Genotyping and Haplotyping in Diverse Experimental Designs

Accurate Ensemble Prediction of Somatic Mutations with SMuRF2

Detecting Medium and Large Insertions and Deletions with Transindel

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

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

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

Structural Variant Detection from Long-Read Sequencing Data with cuteSV

Identifying Somatic Mitochondrial DNA Mutations

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

PipeIT: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data

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

UMI-Varcal: a low-frequency variant caller for UMI-tagged paired-end sequencing data

Alignment-free genotyping of known variations with MALVA

Kmer2SNP: Reference-free heterozygous SNP calling using k-mer frequency distributions

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

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

Variant Annotation and Functional Prediction: SnpEff

Annotating Cancer-Related Variants At Protein-Protein Interface with Structure-PPi

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

Other Format:

Printed edition:

ISBN:

978-1-0716-2293-3

9781071622933

Access Restriction:

Restricted for use by site license.