Variant Calling

Chapter 1 Data Processing and Germline Variant Calling with the Sentieon Pipeline

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

Chapter 3 Octopus: Genotyping and Haplotyping in Diverse Experimental Designs

Chapter 4 Accurate Ensemble Prediction of Somatic Mutations with SMuRF2.

Chapter 5 Detecting Medium and Large Insertions and Deletions with transIndel

Chapter 6 DECoN: A Detection and Visualization Tool for Exonic Copy Number Variants

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

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

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

Chapter 11 Identification, Quantification, and Testing of Alternative Splicing Events from RNA-Seq Data Using SplAdder

Chapter 12 PipeIT2: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data

Chapter 13 Variant Calling from RNA-seq Data Using the GATK Joint Genotyping Workflow

Chapter 14 UMI-Varcal: A Low-Frequency Variant Caller for UMI-Tagged Paired-End Sequencing Data

Chapter 15 Alignment-Free Genotyping of Known Variations with MALVA

Chapter 16 Kmer2SNP: Reference-Free Heterozygous SNP Calling Using k-mer Frequency Distributions

Chapter 17 Somatic Single-Nucleotide Variant Calling from Single-Cell DNA Sequencing Data Using SCAN-SNV.

Chapter 18 Copy Number Variation Detection by Single-Cell DNA Sequencing with SCOPE

Chapter 19 Variant Annotation and Functional Prediction: SnpEff

Chapter 20 Annotating Cancer-Related Variants at Protein–Protein Interface with Structure-PPi

Chapter 21 Preanalytical Variables and Sample Quality Control for Clinical Variant Analysis