Welcome to the Genome Analysis Workshop

Attention

Please note that the content of this Workshop is quite outdated. Please check My Homepage <https://www.stephanschiffels.de/resources> for newer material.

This is the central documentation / handout for a workshop held May 9 - May 11 2016 by Dr. Stephan Schiffels, Alexander Peltzer and Stephen Clayton at the Max-Planck-Institute for the Science of Human History, Jena/Germany.

Contents:

• Introduction
  • Basic software
  • The command line environment
• Schmutzi Workshop
  • Detection of contamination on mitochondrial data
  • Sample preparation
  • Damage based contDeam
  • Mitochondrial based schmutzi
  • Output interpretation
  • Consensus Calling for Downstream analysis
• Sex Determination and X chromosome contamination estimate
  • Sex determination
  • Nuclear contamination estimates in Males
• Genotype Calling from Bam Files
  • Genotyping the test samples
  • Merging the test genotypes with the Human Origins data set
• Principal Component Analysis
  • Running SmartPCA
  • Plotting the results
• Outgroup F3 Statistics
  • Analysing groups of samples (populations)
  • Analysing individual samples
  • Plotting
• ADMIXTURE analysis
  • Converting to Plink format
  • Running ADMIXTURE
  • Plotting in R

Indices and tables

• Index

• Module Index

• Search Page