mamanambiya/exome_aibst_b38

Nextflow pipeline for whole-exome analysis of 12 African populations (PGx, population structure, HDV) — underlying the manuscript # African Exome Analysis Workflow A comprehensive Nextflow DSL2 pipeline for analysing whole-exome sequencing data from African populations, with a focus on pharmacogenomic (PGx) variants, population structure, and highly differentiated variants (HDV). This repository contains the analysis pipeline and scripts underlying the manuscript *"Pharmacogenomic diversity across 12 African populations"* (Mbiyavanga et al.). Whole-exome sequencing data are deposited in the European Genome-phenome Archive (EGA) under accession **EGAS00001008456** (controlled access). ## Overview The workflow processes joint-called VCFs through quality control, annotation, population-level analysis, and reporting: - Variant annotation (SnpEff, dbSNP, ClinVar, COSMIC, CADD, AlphaMissense, dbNSFP) - Population allele frequencies - Pharmacogenomic (PGx) star-allele and phenotype calling (PyPGx) - HLA typing (OptiType / arcasHLA) - Highly differentiated variants (HDV) between populations - F_ST analysis for population differentiation (Weir & Cockerham) - Principal Component Analysis (PCA, EIGENSOFT smartpca) - ADMIXTURE ancestry estimation - Novel-variant discovery (absent from dbSNP, gnomAD, AGVP) ## Quick Start ### Prerequisites - Nextflow (≥ 22.10) - Singularity (or Docker) - A SLURM HPC cluster (optional) — or a single machine with enough RAM, using Nextflow's built-in local executor (no cluster required) ### Run The manuscript results use the DeepVariant WES +2 kb-padded GRCh38 track, configured by layering the base config with the DeepVariant overlay. On a **SLURM cluster** (`slurm` profile submits each process as a job): ```bash nextflow run main.nf \ -profile singularity,slurm \ -c ILIFU/exome_analysis_nextflow.config \ -c ILIFU/dv_wes_padded_2kb.config ``` On a **single machine**, drop the `slurm` profile — Nextflow then runs every process locally: ```bash nextflow run main.nf \ -profile singularity \ -c ILIFU/exome_analysis_nextflow.config \ -c ILIFU/dv_wes_padded_2kb.con …