Microbiome GWAS data preparation starting from a phyloseq object. Careful about the setup files, those need to be tweaked Here is a quick tutorial on how to run it with Nextflow Regenie and some utility functions provided by Michele Filosi:

1. Create the working directory and cd there (i.e. "/scratch/work/mbGWAS")

mkdir /scratch/work/mbGWAS
cd /scratch/work/mbGWAS

2. clone Michele Filosi's repository

git clone https://gitlab.gm.eurac.edu/mfilosi/regenie_pipeline

3. Launch the phyloseq preparation file. This is rather case-specific, so make sure you modify it accordingly:

   • covariates to include
   • their transformation
   • other stuff...

Rscript 00_data_generation_script_CHRISMB.R
	-b "/scratch/work/mbGWAS"
	-i "path/to/phyloseq.Rds"
	-l "Genus"
	-g "TOPMed"
	-t "IRN"
	-d 10
	-p 0.2

4. Check sanity of phenotype, covariates and configuration files in the working directory

5. Now you are ready to go:

sbatch regenie_pipeline/bin/run_pipeline.sh