Welcome to plco-analysis’s documentation!

Contents:

• Installation
  • Overview
  • Short Version (for experts)
  • Long Version (for interested parties)
    • Environment Management with conda
    • Getting a Copy of the Pipeline
    • Build conda Environments
    • Environment Usage
    • Updating Project Configuration
• Preprocessing
  • Overview
  • Relatedness
  • Ancestry Estimation
  • Genotype Cleaning by Ancestry
  • Imputed Data Reformatting
  • 1000 Genomes Reference Data
  • LD Score/BOLT Reference Files
• Primary Analysis
• Meta-Analysis
• Postprocessing
• Globus Distribution
• User Vignette
• Advanced Development Notes
  • Overview of Make
    • Rule Structures
    • Job Tracking/Logging
    • Integration with Clusters
    • Conda Environments
    • Thread Safety/Directory Locking
  • Result Directory and Filename Conventions
  • Adding Analysis Modules
    • Inputs
    • Outputs
  • Adding Other Pipelines
    • Extension to Other Languages

Indices and tables

• Index

• Module Index

• Search Page