SAIGE-QTL Dynamic

SAIGE-QTL Dynamic is an advanced extension of SAIGE-QTL, which facilitates the analysis of heterogeneous genetic effects across different cell level and donor contexts directly from single-cell data efficiently, eliminating the need for pseudobulk aggregation.

Analysis Workflow

SAIGE-QTL Dynamic workflow overview showing the multi-step analysis pipeline

Docker Installation

Prerequisites

  • Docker installed on your system
  • Access to pull images from Docker Hub

Pull the SAIGE-QTL Docker Image

The pre-built Docker image can be pulled directly from Docker Hub:

docker pull yijia0802/saigeqtldynamic0.2.5.1:latest

SAIGE-QTL Dynamic consists of three steps. Step 1 fits the null model, Step 2 obtains variant-level summary statistics for each gene, and Step 3 uses the ACAT method to calculate gene-level p-values. I’ve attached example shell scripts for running all three steps. Steps 1 and 2 can be executed directly within the Docker container.

step1_fitNULLGLMM_qtl.R
step2_tests_qtl.R

Step 3 can be excuted outside of the container with the provided script.

Support

This work is in progress. For any questions, please contact Christiana Liu: liuyijia@broadinstitute.org.

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