Running PGS on MIS

Setup

Several imputation servers are available, each hosting different reference panels. In this tutorial, we will use the main instance of the Michigan Imputation Server. Before starting, make sure you complete the following prerequisites:

  1. Create an account.
  2. Download the required array data for PGS calculation.

Prepare Your Data

The dataset used in this tutorial has already been prepared for the Michigan Imputation Server. For your own data, please follow our Data Preparation Guide.

In general, the following requirements must be met:

  • Create a separate .vcf.gz file for each chromosome.
  • Ensure that variants are sorted by genomic position.
  • Use either GRCh37 or GRCh38 coordinates.

Login

After a successful login, you can start a new job using the Run tab or check previously submitted jobs under the Jobs tab.

Polygenic Score Calculation

The Michigan Imputation Server offers several applications, including Genotype Imputation, HLA Imputation, and Polygenic Score Calculation. In this tutorial, we focus on Polygenic Score Calculation.

Note

Please note that this app does not return imputed datasets to users.

Start Calculation

After selecting the app, fill in the following fields and click Start Calculation:

  • Name: Any name of your choice
  • Reference Panel: HapMap 2
  • Input Files: gwas.array.hapmap.chr20.vcf.gz
  • Scores: Tutorial (Simulated Scores)
  • Ancestry Estimation: Worldwide

Job Queue

Once submitted, your job will go through Input Validation, Quality Control (QC), Phasing/Imputation, and Polygenic Risk Calculation. Jobs are queued, and you will receive a notification when your PGS calculation is complete.

Input Validation and QC

The screenshots below illustrate statistics from input validation and quality control:


Running Jobs

The job is now queued and typically runs for around 30 minutes, depending on queue availability.

Download Results

Once your job is complete, you will receive a notification. You can then download your results in one of the following ways:

  1. Click on one of the files to download the file directly.
  2. Or use the wget command in your terminal.

Next Steps

The available scores file (scores.txt) can be used to run the PGS analysis as described here.