README.md

nf-qtl

Nextflow QTL mapping pipeline using tensorQTL

Overview

Requirements

Python:

• tensorQTL
• PyTorch

R:

• qvalue

Usage

module load jdk/1.8.0_92
module load nextflow/0.29.1

# use an up to date version of nextflow instead of our creaky old decrepit one
export NXF_VER=21.04.1

Pipeline overview

Step 1: Normalize count matrix

Step 2: Convert VCF to plink & generate population genetic structure covariates

Step 3: Chunk genome

Step 4: Run QTL analysis for each chunk

Step 5: Compute FDR for permutation pass

Step 6: Apply FDR to a variant-phenotye pairs