reaganmogire/lft-gwas-afr

Template scripts for multi-cohort GWAS of liver enzyme traits in African populations # Multi-cohort GWAS of Liver Enzyme Traits (ALP, ALT, AST, GGT) This repository contains **minimal, cohort-agnostic template scripts** illustrating the main analytical steps used for genome-wide association and downstream statistical genetics analyses of circulating liver enzyme traits. The goal is to document **methods and execution patterns**; it is not a drop-in, end-to-end reproduction of any single cohort pipeline. The repository accompanies the manuscript: *Multi-cohort genome-wide association analyses reveal loci underlying circulating liver enzyme levels in African-ancestry populations.* No individual-level data or cohort-specific configuration files are included. --- ## Repository scope The repository documents the following analytical components: 1. Genome-wide association analyses (**SAIGE**) 2. Meta-analysis across cohorts (**METASOFT**, Han–Eskin random effects) 3. Conditional analyses (**GCTA–COJO**) 4. Statistical fine-mapping (**SuSiE RSS**) 5. Colocalisation with cis-eQTLs (**FastENLOC**, GTEx liver) 6. Secondary colocalisation using a signal-isolated liver eQTL resource (**COLOC / coloc.abf**) 7. Genetic correlation analyses (**LD score regression**) Each component is represented by a single template script and/or an example command. --- ## End-to-end analysis outline **Step 1 — Run within-cohort GWAS (SAIGE).** Fit a null model per phenotype and cohort, then run association testing per chromosome. **Step 2 — Harmonize cohort GWAS summary statistics.** Ensure consistent variant identifiers, alleles, effect direction, and column schema across cohorts. **Step 3 — Meta-analyze across cohorts (METASOFT).** Perform Han–Eskin meta-analysis per phenotype using harmonized cohort-level summary statistics. **Step 4 — Test independence of “novel” signals (GCTA–COJO).** Condition lead signals on previously reported variants within the locus using an ancestry-matched LD reference. **Step 5 — Fine-map selected loci (SuSiE RSS).** Construct locus- …