Computational Genomic Signatures PDF Download

Cover -- Half Title -- Series Editor -- Published Titles -- Title -- Copyright -- Dedication -- Contents -- Who is this book for? -- Preface -- Contributors -- Part I Introduction -- Chapter 1 Introduction: Whole Exome and Genome Sequencing -- Chapter 2 NGS Technology -- Chapter 3 Illumina Technology -- Chapter 4 Data -- Part II Raw Data Processing -- Chapter 5 FASTQ Format -- Chapter 6 Raw Data: Quality Control -- Chapter 7 Trimming -- Part III Alignment -- Chapter 8 Alignment: Mapping Reads to the Reference Genome -- Chapter 9 SAM/BAM Format -- Chapter 10 Postprocessing the Alignment -- Chapter 11 Alignment Data: Quality Control -- Part IV Variant Calling -- Chapter 12 Variant Calling and Quality- Based Filtering -- Chapter 13 Variant Call Format (VCF) -- Chapter 14 Jannovar -- Chapter 15 Variant Annotation -- Chapter 16 Variant Calling: Quality Control -- Chapter 17 Integrative Genomics Viewer (IGV): Visualizing Alignments and Variants -- Chapter 18 De Novo Variants -- Chapter 19 Structural Variation -- Part V Variant Filtering -- Chapter 20 Pedigree and Linkage Analysis -- Chapter 21 Intersection Analysis and Rare Variant Association Studies -- Chapter 22 Variant Frequency Analysis -- Chapter 23 Variant Pathogenicity Prediction -- Part VI Prioritization -- Chapter 24 Variant Prioritization -- Chapter 25 Prioritization by Random Walk Analysis -- Chapter 26 Phenotype Analysis -- Chapter 27 Exomiser and Genomiser -- Chapter 28 Medical Interpretation -- Part VII Cancer -- Chapter 29 A (Very) Short Introduction to Cancer -- Chapter 30 Somatic Variants in Cancer -- Chapter 31 Tumor Evolution and Sample Purity -- Chapter 32 Driver Mutations and Mutational Signatures -- Appendix A Hints and Answers -- References -- Index