XWAS Manual V3.0

• Background
• Downloading and Extracting XWAS
• Genotype Calling
  • Prerequisites and Set Up
  • Usage
    • Parameter File
    • Individuals File
  • Comparing Genotype Calls
  • Visualization
• Quality-Control
  • Usage
    • Parameter File
  • General Quality Control
  • X-Specific Quality Control
• Imputation
  • Data Preparation
  • Usage
    • Parameter File
    • Reference Files Preparation
  • Post Imputation Quality Control
• Variant Association Testing
  • General Flags
  • Allele Frequency
  • Sex-Stratified Association Test
  • Sex Difference in Effect Size
  • Meta Analysis
  • Variance Heterogeneity Test
  • Clayton's Test
  • Epistasis Test
  • PLINK Functions
  • Examples
• Gene-Based Association Testing
  • Automated Gene-Based Association Testing
    • Parameter File
    • Gene File
  • Gene-Based Association Testing
    • Parameter File
    • Association Results File
• Gene-Based Gene-Gene Interaction Testing
  • Usage
    • Parameter File
• Visualization
  • QQ Plots
  • Manhattan Plots
• Troubleshooting
• References