Longitudinal GWAS Pipeline (longGWAS)

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. The longGWAS computational pipeline was developed using Nextflow for researchers to deploy and perform custom GWAS analyses with ease.

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

• Getting Started
  • Requirements
  • Basic Usage
• Nextflow Configuration
• Command line Parameters
  • --ancestry
  • --assembly
  • --chunk_flag
  • --chunk_size
  • --covarfile
  • --covariates
  • --dataset
  • --input_vcf
  • --kinship
  • --longitudinal_flag
  • --mh_plot
  • --minor_allele_freq
  • --minor_allele_ct
  • --model
  • --out
  • --phenofile
  • --pheno_name
  • --plink_chunk_size
  • --r2thres
  • --study_col
  • --time_col
• Input File Format
  • Input Genotype
  • Input Covariates
  • Input Phenotype / Outcomes
• Example usage
  • Cross-sectional analysis
  • Longitudinal analysis
  • Survival analysis