Variant Calling

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.

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

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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.