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Personal Genomics for Bioinformaticians

Module 1 - Introduction

Chapter 1: Introduction to the human genome
Chapter 2: Overview of technologies for genome analysis
Tutorial 1: file formats for describing genetic variation
- T1.2 VCF files
- T1.2 Plink files

Module 2 - Ancestry

Chapter 3: Introduction to population genetics
Chapter 4: Global ancestry
- 4.1 Global ancestry analysis with PCA
- 4.2 Global ancestry analysis with ADMIXTURE
Chapter 5: Relative finding
Tutorial 2: Working with 1000 Genomes data and plink
- T2.1 The 1000 Genomes Project dataset (and wrangling VCF files)
- T2.2 Some tips and examples for using plink

Module 3 - From genotypes to phenotypes

Chapter 7: GWAS for complex traits
Chapter 8: Heritability
- 8.1 Measuring heritability in related individuals
- 8.2 Measuring SNP-based heritability using LMMs
Chapter 9: Polygenic risk scores
- 9.1 Clumping + Threshold (C+T) method
- 9.2 Bayesian methods for polygenic risk scores

Appendix 1 - glossary and notation

Chapter A1.1: Unix cheat sheet

Repository
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Index

By Melissa Gymrek

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