FI-Federated-Analytics

A Snakemake workflow to perform genome-wide association studies. Based on the workflow at https://github.com/Ax-Sch/asso_smk_smpl/tree/main.

Repository structure

config

• config.yaml file to set workflow parameters

workflow

• Snakefile

• envs

  • environments for each rule

• scripts

  • R scripts

Input files

• VCF file: one file for each chromosome or one file for the whole genome chr{contig}.merged.annotated.vcf.gz
• Sample sheet: a tsv file containing sample ID, covariates and phenotypes. The sample ID column should be called "sample"
• Pedigree file: pop{popul}_pedigree.fam in PLINK .fam file format

Running the workflow

Update config file

• Directory for the input files
• Populations
• Sample sheet filename
• Phenotype and covariate columns in the sample sheet
• Number of PCs to use
• Contigs

Building the container

Run the command below and save the .sif file in a folder called image

singularity build gwas_workflow.sif gwas.def

Run the worfklow

Running the workflow requires Snakemake version 7

snakemake --jobs 10 --use-singularity