Identifying important variants for ischaemic heart disease using genome-wide and phenome-wide association studies
This folder contains collection of scripts and Jupyter notebooks to perform genome-wide association studies (GWAS) analysis of Ischemic heart disease, aggregating significant variants using linkage disequilibrium (LD) clumping and subsequent phenome-wide association study (PheWAS).
| Order | Name | Description |
|---|---|---|
| 1 | gwas-phenotype-samples-qc.ipynb | Performs sample QC on cases and controls cohorts and select only those samples, for which imputed data are available. |
| 2 | liftover_plinks_bed.wdl | Lifts array data to the newer version of the reference genome - GRCh38 and merges files per chromosome as one file. |
| 3 | run_array_qc.sh | Performs QC on lifted array PLINK files. |
| 4 | bgen_qc.wdl | Performs QC on imputed data BGEN files and merges results for individual chromosomes into one file. |
| 5 | run_ld_clumping.ipynb | Performs LD clumping on significant GWAS variants. |
| 6 | get-phewas-data.ipynb | Create phenotype data in long format suitable for the PheWAS R package. Extract Genotype data for each variant selected by LD clumping. |
| 7 | run-phewas.ipynb | Run PheWAS analysis using PheWAS R package |