Computational Exome and Genome Analysis

Description

Exome and genome sequencing are revolutionizing medical research and diagnostics, but the computational analysis of the data has become an extremely heterogeneous and often challenging area of bioinformatics. Computational Exome and Genome Analysis provides a practical introduction to all of the major areas in the field, enabling readers to develop a comprehensive understanding of the sequencing process and the entire computational analysis pipeline. Content: Introduction. Whole Exome and Genome Sequencing. NGS Technology. Illumina Technology. Obtaining WES/WGS Data for this book. Raw Data Processing. FASTQ Format. Raw Data: Quality Control. Trimming. Alignment. Alignment: Mapping reads to the reference genome. SAM/BAM Format. Postprocessing the Alignment. Alignment Data: Quality control. Variant Calling. Variant Calling & Quality-based Filtering. Variant Call Format. Jannovar. Variant Annotation. Variant Calling: Quality Control. Integrative Genomics Viewer (IGV): Visualizing Alignments and Variants. De novo variants. Structural variation. Variant Filtering. Pedigree and Linkage Analysis. Intersection Analysis and Rare Variant Association Studies. Variant Frequency Analysis. Variant Pathogenicity Prediction. Prioritization. Variant Prioritization. Prioritization by Random Walk Analysis. Phenotype Analysis. Exomiser and Geniomiser. Medical Interpretation. Cancer. A (Very) Short Introduction to Cancer. Somantic variants in cancer. Tumor Evolution and Sample Purity. Driver Mutations and mutational signatures.