GWAS Pipeline in R

A pipeline for conducting genome-wide association studies (GWAS) using bash & R.

Table of Contents

• Introduction
• Parts
• Input Data Required

Introduction

Pipeline for performing genome-wide association studies (GWAS) using R. It supports data preprocessing, statistical analysis, and visualization of results.

Parts

• Subsetting and filtering imputed germline vcf
• SNP filtering based on Allele sequenced and frequency
• Merging with covariates datasets
• Elastic net feature selection & coxph
• Visualization of FDR-significant SNPs with kaplan-meier curve
• roc-test of FDR-significant SNPs
• Visualization of results with Manhattan and QQ plots
• Fine-mapping

InputDataRequired

• .vcf file containing population of interest
• .info file containing imputation information
• list of patients in 0_TCGA-.-._TCGA-.-. line-delimited format

Notes

Refer to the Rmd directory The order is the same for both Rmd and scripts