Computational-Genome-Analysis

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Computational-Genome-Analysis

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Website for Computational Exome and Genome Analysis

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# Companion Website for Computational Exome and Genome Analysis

This is the website for [Computational Exome and Genome Analysis](https://www.crcpress.com/Computational-Exome-and-Genome-Analysis/Robinson-Piro-Jager/p/book/9781498775984) 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.

# Feedback
Please send questions, comments, and suggestions to the authors using the Issue tracker on this site. We will keep a list of [errata](ERRATA.md).

# Additional Material
* Introduction to SVD: https://github.com/TheJacksonLaboratory/Computational-Genome-Analysis/blob/master/SVD-Intro.pdf

# Scripts
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.

# Contents of the Book
* 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

Computational-Genome-Analysis

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