eQTL & veQTL Mapping Pipeline

Snakemake workflow for cis/trans eQTL and veQTL mapping in Drosophila melanogaster across two treatment groups (Control and High Sugar).
Last updated: 03/20/2026 — Huiting

---

Overview

run_pipeline_cluster.sh
├── Snakefile_setup          # Step 1: build conda environment
└── Snakefile                # Step 2: run full mapping pipeline
    ├── rules/genotype_processing_eqtl.smk
    ├── rules/genotype_processing_veqtl.smk
    ├── rules/phenotype_processing_GRAMMAR.smk
    ├── rules/eqtl_mapping.smk
    └── rules/veqtl_mapping.smk

---

Setup

1. Clone the repository

git clone <repo-url>
cd <repo-dir>

2. Configure input files

Edit config.yaml to point to your data files:

3. Run the pipeline

Dry run to preview jobs

snakemake --dry-run

Local run

# Step 1: set up conda environment
snakemake \
    --snakefile Snakefile_setup \
    --use-conda \
    --cores 1

# Step 2: run pipeline locally
snakemake \
    --use-conda \
    --cores {cores}

SGE cluster run

bash run_pipeline_cluster.sh

This will:

1. Create conda environment
2. Submit all pipeline jobs to the SGE cluster via qsub

---

Pipeline Steps

Step	Rule module	Description
1	genotype_processing_eqtl.smk	Filter and reformat VCF for eQTL mapping
2	genotype_processing_veqtl.smk	Filter and reformat VCF for veQTL mapping
3	phenotype_processing_GRAMMAR.smk	GRAMMAR correction of phenotypes
4	eqtl_mapping.smk	Cis and trans eQTL mapping (tensorQTL)
5	veqtl_mapping.smk	Cis and trans veQTL mapping in parallel batches (veqtl-mapper)

---

Key Parameters

Parameter	Value	Description
GROUP	["Ctrl", "HS"]	Treatment groups
GENE_COUNT	8763	Genes after removing bimodal genes
CIS_CHUNK_SIZE	127	Genes per cis-veQTL batch job
TRANS_CHUNK_SIZE	30	Genes per trans-veQTL batch job

---

---

File Reference

File	Purpose
Snakefile_setup	Conda environment setup and package install
Snakefile	Main pipeline entry point
config.yaml	All input/output paths
run_pipeline.sh	One-command launcher
rules/	Individual rule modules (.smk)
envs/	Individual envs modules (.yaml)

---