General

Use snakefile as main pipeline and defines paths for files and directives

Conda environment

Run pipeline in Conda specified env

1. Install the conda environment found under envs/rbio.yaml (conda has to be installed on the system):

conda env create -f envs/rbio.yaml

2. Activate env after installation

conda activate rbio

3. Start R terminal
4. Install 1) devtools + MatrixEQTL and 2) annotation template

# matrixEQTL
install.packages("devtools")
devtools::install_github("andreyshabalin/MatrixEQTL")
# annotation package
BiocManager::install("IlluminaHumanMethylationEPICanno.ilm10b2.hg19")

Configuration

You may change the thresholds and cut-offs at configs/workflow.json

• maf : the minor allele frequency threshold

Converting impute2 genotypes to dosages.

• post_maf : the minor allele frequency threshold to be applied after matrixEQTL has been run.

Useful to define different summaries.

• cisDist : the maximal distance between SNP-CpGs pairs until which it counts as a 'cis-pairs'.

Cis-pairs will be reported in a separate file.

• pvThresholdCis : The P value threshold to be applied for cis-meQTLs.

Only associations with P value < pvThresholdCis will be reported

• pvThresholdTrans : The p-value threshold to be applied for trans-meQTLs.

Only associations with P value < pvThresholdTrans will be reported

• significant_pv_cutoff : For final results files.

P value significant threshold e.g.: 1e-14

Execution

Execute snakemake in the project directory to run the full pipeline
Manually call the all_dosage_to_matrixEQTL and the all_methylation_to_matrixEQTL rules

Run snakemake with parallel task processing

./scripts/run_pipeline.sh <num-parallel-tasks>

Configure the script above to your VM capacity with: [scripts/run_pipeline.sh](scripts/run_pipeline.sh)

Covariates

meth ~ geno + sex + age + bmi + wbc + PCs1..20 + houseman estimates (except gran) + plate + batch