Bacillus subtilis QTL Mapping

This repository provides an example analysis pipeline for association mapping of spore germination–related traits in Bacillus subtilis. The workflow includes:

• Phenotype quality control (MAD-based outlier removal)
• Mixed-model variance component and heritability estimation
• BLUP estimation (random effects)
• QTL mapping using GAPIT MLM
• Variant map visualization from VCF data

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🚀 Quick start

Set up the environment

# Create environment
conda env create -f envs/environment.yml

# Activate (conda or micromamba)
conda activate bsubtilis-qtl-r44
# OR
micromamba activate bsubtilis-qtl-r44

Run the full pipeline

Run the following commands from the repository root directory (Bsubtilis_qtl_mapping):

Rscript 1_remove_outliers.R \
  --input phenotypes_raw.tsv \
  --output phenotypes_outlier_removed.tsv \
  --mad_cutoff 6

Rscript 2_heritability_estimation.R \
  phenotypes_outlier_removed.tsv \
  heritability

Rscript 3_random_effect_model.R \
  --input phenotypes_outlier_removed.tsv \
  --outprefix blups \
  --traits spore_area,optical_density

Rscript 4_gwas_gapit.R \
  --pheno pheno_data_qtl_mapping.txt \
  --geno genotype_data_qtl_mapping_hmp.txt \
  --outdir gapit_results

Rscript 5_plot_variant_map.R \
  --vcf genomic_data_variant_map_10k_snps_200_strains.vcf \
  --out variant_map.png

📁 Input files

All required input files are included in this repository and can be used to run the pipeline directly.

• phenotypes_raw.tsv
  Raw phenotype data

• phenotypes_outlier_removed.tsv
  Cleaned phenotype data after outlier removal

• pheno_data_qtl_mapping.txt
  GAPIT-ready phenotype file (Taxa, Trait format)

• genotype_data_qtl_mapping_hmp.txt
  HapMap genotype file used for GWAS

• genomic_data_variant_map_10k_snps_200_strains.vcf
  VCF file used for variant visualization