This is the website for Computational Exome and Genome Analysis by Peter Robinson, Rosario Piro, and Marten Jäger. Readers will find scripts, programs, files, and other supporting material for the book. The book aims to provide a practical introduction to all of the major areas in the field, in order to help readers to develop a comprehensive understanding of the technologies, the medical use cases, and the entire computational analysis pipeline.

Please send questions, comments, and suggestions to the authors using the Issue tracker on this site. We will keep a list of errata.

• Introduction to SVD: https://github.com/TheJacksonLaboratory/Computational-Genome-Analysis/blob/master/SVD-Intro.pdf

This repository contains scripts and other resources intended for the exercises in the book.

• Chapter 19: conifer.dat: see the data subdirectory.
• Chapter 20: pedigree files: fam1.ped, fam2.ped, fam3.ped and sample-GRC38.vcf: see the pedigree subdirectory.
• Chapter 32: files for running DrGAP: NA12878_annotated.vcf.gz, NA12878_filtered.vcf, hg38_refGene.exp: see the drgap subdirectory.
• convertGenomeAccessions.pl: a script to convert VCF coordinates, an annoying but inevitable task for genome bioinformatics: see the convertVCF subdirectory.

• Part I: Introduction
  • Chapter 1: Introduction
  • Chapter 2: NGS Technology
  • Chapter 3: Illumina Technology
  • Chapter 4: Data
• Part II: Raw Data Processing
  • Chapter 5: FASTQ
  • Chapter 6: Q/C: Raw Data
  • Chapter 7: Q/C: Trimming
• Part III Alignment
  • Chapter 8: Alignment
  • Chapter 9: SAM/BAM
  • Chapter 10: Postprocessing the Alignment
  • Chapter 11: Alignment Data: Quality Control
• Part IV: Variant Calling
  • Chapter 12: Variant Calling & Quality-Based Filtering
  • Chapter 13: VCF
  • Chapter 14: Jannovar
  • Chapter 15: Variant Annotation
  • Chapter 16: Variant Calling QC
  • Chapter 17: Integrative Genomics Viewer
  • Chapter 18: De Novo Variants
  • Chapter 19: Structural Variation
• Part V: Variant Filtering
  • Chapter 20: Pedigree Analysis
  • Chapter 21: Intersection and RVAS Analysis
  • Chapter 22: Variant Frequency
  • Chapter 23: Variant Pathogenicity
• Part VI Prioritization
  • Chapter 24: Prioritization
  • Chapter 25: Random Walk
  • Chapter 26: Phenotype Analysis
  • Chapter 27: Exomiser
  • Chapter 28: Medical Interpretation
• Part VII Cancer
  • Chapter 29: A (Very) Short Introduction to Cancer
  • Chapter 30: Somatic Variants
  • Chapter 31: Tumor Evolution and Sample Purity
  • Chapter 32: Driver Mutations and Mutational Signatures
• Appendix A: Hints and Answers