Contents

• Introduction
  • COSGAP: COntainerized Statistical Genetics Analysis Pipelines
    • Documentation
    • Project status
    • Information
    • Cite
    • Installation
    • Legacy
    • Source files
    • Documentation build instructions
• Getting started
  • hello.sif container
    • Description
    • Getting Started
    • Helpful links to Singularity documentation
    • Installing Docker and Apptainer on your local machine
    • Mapping your data to containers
    • Running as SLURM job
    • TSD-specific instructions
    • Software
      • References
• Installation and set up
  • Conda environment (optional)
  • Clone the repository
  • Update the Singularity Image Files (containers)
  • Pulling and using Docker image
  • Systems without internet access
• Install (old)
• Containers
  • gwas.sif container
    • Description
    • Software
  • python3.sif container
    • Description
    • Software
  • r.sif container
    • Description
    • Invoking Rstudio-server
    • Software
      • Genetic analysis software
      • R packages
  • ldsc.sif container
  • HDL.sif container
  • MAGMA.sif container
  • MiXeR.sif container
  • MTAG.sif container
  • References
• Specifications
  • Genotype data spec
    • Change log
  • Phenotypes and covariates spec
    • Change log
  • Summary statistics spec
    • Comparison of columns names
    • Change log
• Reference
  • openSNP example data
  • Summary statistics
• Scripts
  • GWAS
  • LDpred2
    • Prerequisites
      • Note on help functions
      • Note on filtering of genotype data
      • Note on missing genotypes
      • Note on genomic builds
      • Optional: Estimating linkage disequilibrium (LD)
    • Running LDpred2 analysis
      • Effective sample-size
      • Summary statistics
      • Synthetic example (chr21 and chr22)
      • Optional: Append score to existing file
      • Height example
    • Output
    • Slurm job
      • Redirect temporary file output
• Usecases
• API reference
  • gwas.py
    • ActionAppendDeprecated
    • ActionStoreDeprecated
    • LoadFromFile
    • Logger
      • Logger.error()
      • Logger.log()
    • NumpyEncoder
      • NumpyEncoder.default()
    • sec_to_str()
• Contributing
  • Bug reports and feature requests
    • Did you find a bug?
    • Do you have a suggestion for an enhancement or new feature?
  • Making a pull request
  • Information for developers
    • Sphinx
    • Folder structure
    • Note about NREC machine
    • Testing container builds
    • Git clone ignoring LFS
• Changelog
  • [Unreleased]
    • Added
    • Updated
    • Fixed
    • Removed
    • Misc
  • 1.15.0 - 2026-02-23
    • Added
  • 1.14.0 - 2025-12-05
    • Updated
    • Fixed
  • 1.13.1 - 2025-11-27
  • 1.13.0 - 2025-11-27
    • Added
    • Updated
  • [1.12.0] - 2025-11-26
    • Fixed
    • Removed
  • [1.11.0] - 2025-09-17
    • Added
  • [1.10.0] - 2025-08-27
    • Updated
    • Removed
  • [1.9.1] - 2025-03-27
    • Added
    • Updated
  • [1.9.0] - 2025-02-20
    • Added
    • Updated
    • Fixed
    • Removed
  • [1.8.1] - 2024-03-05
    • Fixed
  • [1.8.0] - 2024-02-22
    • Added
  • [1.7.2] - 2024-02-14
    • Updated
    • Added
  • [1.7.1] - 2024-02-06
    • Fixed
  • [1.7.0] - 2024-02-02
    • Added
    • Updated
    • Fixed
  • [1.6.0] - 2023-12-12
    • Added
    • Updated
  • [1.5.1] - 2023-10-20
    • Fixed
  • [1.5.0] - 2023-10-17
    • Added
    • Updated
    • Removed
  • [1.4.0] - 2023-10-17
    • Added
    • Fixed
    • Updated
    • Removed
  • [1.3.9] - 2023-10-17
    • Added
  • [1.3.8] - 2023-10-17
    • Fixed
  • [1.3.7] - 2023-10-17
    • Added
  • [1.3.7] - 2023-10-12
  • [1.3.6] - 2023-08-17
    • Fixed
  • [1.3.5] - 2023-08-17
    • Updated
  • [1.3.4] - 2023-06-22
    • Updated
    • Fixed
  • [1.3.3] - 2023-06-14
    • Updated
  • [1.3.2] - 2023-06-12
    • Fixed
  • [1.3.1] - 2023-06-07
    • Added
    • Fixed
  • [1.3.0] - 2023-05-19
    • Added
    • Fixed
  • [1.2] - 2023-05-11
    • Added
    • Updated
    • Fixed
    • Removed
    • Misc
    • Misc
  • [1.1] - 2022-12-01
    • Added
    • Updated
    • Fixed
    • Removed
  • [1.0.0] - 2020-10-20
    • Added
• Internal usage
  • Docker
    • Software versions
    • Feedback
    • Building notes
      • Offline builds
    • Note about NREC machine (old)
    • Testing container builds
    • Git clone ignoring LFS