gemma-nf

A pipeline for multi-trait genome-wide association studies (GWAS) using GEMMA.

The pipeline performs the following analysis steps:

• Split genotype file
• Preprocess genotype and phenotype data
• Compute kinship
• Test for association between phenotypes and genetic variants
• Collect summary statistics

The pipeline uses Nextflow as the execution backend. Please check Nextflow documentation for more information.

Requirements

• Unix-like operating system (Linux, MacOS, etc.)
• Java 8 or later
• Docker (v1.10.0 or later) or Singularity (v2.5.0 or later)

Quickstart (~2 min)

1. Install Nextflow:

   curl -fsSL get.nextflow.io | bash
   

2. Make a test run:

   nextflow run dgarrimar/gemma-nf -with-docker
   

Notes: move the nextflow executable to a directory in your $PATH. Set -with-singularity to use Singularity instead of Docker.

(*) Alternatively you can clone this repository:

git clone https://github.com/dgarrimar/gemma-nf
cd gemma-nf
nextflow run gemma.nf -with-docker

Important: Since release 22.12.0-edge, DSL1 is not further supported in Nextflow. Until gemma-nf is migrated to DSL2, the pipeline should be run using an older Nextflow release. This can be done using NXF_VER before Nextflow commands, e.g. NXF_VER=22.04.0 nextflow run dgarrimar/gemma-nf -with-docker.

Pipeline usage

Launching the pipeline with the --help parameter shows the help message:

nextflow run gemma.nf --help

N E X T F L O W  ~  version 22.04.0
Launching `gemma.nf` [modest_ritchie] DSL1 - revision: a8f7d96105

G E M M A - N F
============================================================================================
Performs multi-trait GWAS using GEMMA (https://github.com/genetics-statistics/GEMMA)

Usage:
    nextflow run gemma.nf [options]

Parameters:
 --geno GENOTYPES            genotype data in VCF format, indexed
 --pheno PHENOTYPES          (covariate-adjusted) phenotype data
 --maf MAF                   MAF filter (default: 0.01
 --l VARIANTS/CHUNK          number of variants tested per chunk (default: 500)
 --t THREADS                 number of threads (deafault: 1)
 --dir DIRECTORY             output directory (default: result)
 --out OUTPUT                output file prefix (default: gemma.tsv)