rmogire/liver-enzyme-gwas
Domain:
healthcareRecord type:
software
Creator:
rmo
Host:
Template scripts for “Multi-cohort GWAS of liver-enzyme traits in African-ancestry populations.” Reproducible, well-commented SAIGE→METASOFT→SuSiE→FastENLOC→LDSC workflow; no datasets included.
# Liver-Enzyme GWAS (African-Ancestry) – Template Scripts
_Companion code for Mogire RM *et al.*_
This repository contains **fully documented templates** that reproduce
every analysis step we ran for the manuscript
**“Multi-cohort genome-wide association analyses reveal loci underlying circulating liver enzyme levels in African-ancestry populations.”**
> ⚠️ **No data are included.**
> Each script has placeholder paths (`path/to/...`).
> Replace those with your own file locations before running.
---
## Directory map
| Path | Purpose |
|--------------------------|-------------------------------------------|
| `scripts/` | Bash / Python / R templates for each step |
| `configs/` | Optional config files (e.g. FUMA) |
| `results/ logs/` | Created at run-time; ignored by Git |
---
## Template overview
| Stage | Script / file |
|------------------------------------|---------------|
| Single-cohort GWAS (SAIGE) | `scripts/template_run_gwas_saige.sh` |
| Meta-analysis (METASOFT) | `scripts/template_meta_analysis_metasoft.sh` |
| Fine-mapping (SuSiE + PLINK) | `scripts/template_finemap_susie.py` |
| eQTL colocalisation (FastENLOC) | `scripts/template_colocalization_fastenloc.sh` |
| SNP-heritability & rg (LDSC) | `scripts/template_ldsc_rg.sh` or `template_ldsc_workflow.sh` |
| Manhattan / QQ plots (R) | `scripts/template_plot_manhattan_qq.R` |
Each file starts with a **usage block** showing the exact command to run after you have edited the paths.
---
## Software / environment
A minimal conda specification is provided in `environment.yml` with:
* Python ≥ 3.10 (pandas, numpy, seaborn, matplotlib, gwaslab, rpy2)
* R ≥ 4.2 (susieR, data.table, qqman)
* SAIGE, METASOFT, PLINK 2, LDSC
* Java 8 (for METASOFT)
> **FastENLOC** must be compiled separately; see its GitHub page.
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