GWAS Pipeline for Longitudinal Analysis using Nextflow + Docker

Documentation for the longitudinal GWAS pipeline project. This project aims to provide a reproducible and scalable solution to perform genome wide association studies (GWAS) on longitudinal outcomes. We have put together a Nextflow workflow and accompanying Docker image for researchers to deploy and use to analyze whole genome sequencing data.

Visit the Getting Started page below or from the sidebar to see instructions for installation and basic usage.

• Getting Started
  • Installation
  • Basic Usage
• Nextflow Container
• Nextflow Configuration
• Commandline Parameters
  • --ancestry
  • --assembly
  • --covarfile
  • --covariates
  • --dataset
  • --input_vcf
  • --kinship
  • --longitudinal_flag
  • --model
  • --out
  • --phenofile
  • --pheno_name
  • --r2thres
• Input File Format
  • Input Genotype
  • Input Covariates
  • Input Phenotype / Outcomes
• Software
• Examples