Documentation for the 2018 Workshop on Computational Methods to Analyse Human Genetic Variation

This is the documentation for the 2018 Workshop delivered at the Next Generation Genomics 2018 Symposium Workshops in Helsinki by Stephan Schiffels

Contents:

• Notes on Infrastructure
  • How to Connect to Jupyter
  • Basic Usage
  • Notebooks
• Principal Components Analysis (PCA)
  • Genotype Data
  • How PCA works
  • Preparing the parameter file
  • Population lists vs. Projection
  • Running smartPCA
  • Plotting modern populations
  • Adding ancient individuals
• F Statistics
  • F3 Statistics
  • Admixture F3 Statistics
  • F4 Statistics
  • Outgroup F3 Statistics
  • Outgroup F3 Statistics Biplot
• MSMC
  • Prerequisites
  • Data
  • Generating consensus sequences for each sample
  • Combining samples
  • Running MSMC2 for estimating the effective population size
  • Estimating population separation history
  • Plotting in Python
• Solution Notebooks

Indices and tables

• Index
• Module Index
• Search Page