This folder contains setup instructions for key tools used in the PRS analysis pipeline.
- Fast and flexible tool for LD clumping and threshold-based PRS calculation
- Used for baseline PRS score generation
- Nextflow-based pipeline from the Polygenic Score Catalog
- Core to ancestry-adjusted normalization (see separate section)
- Notes: Requires conda or Docker environment. Outputs include raw and ancestry-adjusted scores.
- Beagle 5.5: Java-based imputation tool used on Lyday VCFs
- conform-gt: Harmonizes genotype formats to match reference panel
- bcftools: For subsetting and filtering variants
- PLINK 2.0: Conversion and QC
Each tool folder contains installation instructions, links to documentation, and sample commands used in this project.