ShivamSharma13/kidney-phenotype-gwas

Scripts and workflows for GWAS, ancestry-specific GWAS, and PRS analysis performed in our work: African ancestry-enriched variants in the GATM gene are associated with elevated serum creatinine levels ## This repository has scripts used for analyses in the following publication: African ancestry-enriched variants in the GATM gene are associated with elevated serum creatinine levels on _MedRxiv (2025)._ ## Overview of scripts and results ### **Step 1:** Phenotype QC and modeling + _01_PhenotypeQC.r_ - QC of serum creatinine and stage setup for GWAS. + _02_PhenotypeModeling.r_ - Simple statistical modeling of serum creatinine and covariates. ### **Step 2:** Standard and ancestry-specific GWAS using SAIGE + _03_GWASWorkflow.Saige.wdl_ - WDL workflow (ideal for cromwell) for GWAS using SAIGE. + _04_AnalyzeGWASResults.r_ - Analyzing and visualizing (manhattan plots) GWAS results. + _05_PerformAdmixtureMapping.r_ - Admixture mapping using bioconductor packages. + _06_AnalyzeTractorGWAS.r_ - Ancestry-specific GWAS using tractor. ### **Step 3:** Clumping and fine mapping + _08_LD&FineMapping.r_ - LD clumping and variant fine-mapping using Susie. ### **Step 4:** Polygenic scores estimation and modeling + _07_ClumpingAndPRS.ipynb_ - Stepwise PRS estimation and modeling. + _10_AnnotateVariants.wdl_ - Variant effect annotation using SnpEff.