AnVIL Demos: Polygenic Risk Score (PRS) Analysis in AnVIL on June 17, 2026

AnVIL Demos
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Topic: Polygenic Risk Score (PRS) Analysis in AnVIL

June 17, 2026 at 10:00 AM ET on Zoom

10:00 AM - 10:30 AM ET – Demo on AnVIL

This Demo, run by Matt Lebo and Shruti Parpattedar, will feature a brief presentation for attendees to gain an understanding of polygenic scores and then a demonstration of how to use AnVIL-provided workflows to run PRS analyses in AnVIL using the WDL framework.

10:30 AM - 11:00 AM ET – Q&A

We’ll open up the floor to questions about the demo presented, and will have AnVIL and Terra support on call to answer any questions about AnVIL you might have!

:pencil: Sign up: Register for AnVIL Demos

What are AnVIL Demos?

AnVIL Demos are a monthly, virtual meeting where we highlight what you can do on the NHGRI Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org/), a cloud-based computing platform for genomic data science! AnVIL Demos will start out with a 30-minute demonstration on the platform followed by open time for Q&A and user support.

The demos will highlight a range of topics, from a capability of the platform to a scientific analysis powered by AnVIL. If you’re interested in showcasing how you use AnVIL at a future AnVIL Demos session, reach out to Natalie Kucher (nkucher3 / at / jhu.edu). After the demo, we’ll open up the floor to answer questions about the demo and to answer any general questions you might have about AnVIL.

:play_or_pause_button: Watch past AnVIL Demos recordings from our YouTube playlist!

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Upcoming Events

Sign up to hear about future AnVIL Demos and announcements at http://bit.ly/anvil-mailing-list and learn about upcoming events at https://anvilproject.org/events!

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Q: Is there a common step where users encounter errors?

A: Most common is input prep, because users will put in data that come from many sources. Usually the errors from mistakes in this step are well described in the error messages.

Q: What is the cost to run the demo workflow on AnVIL? I saw you had $0.18 somewhere. Is that a reflection of the cost? For the real runs, where can we expect the cost to vary?

A: That’s where you’ll see the cost - it did that $0.18 to prepare the input. It may take a bit to populate the final cost, and at the end it’ll show you the cost of the analysis on AnVIL, and the Google Cloud console will show as well.

The model prep took $0.01 and the scoring took $0.06.

The input step will take the most cost because it takes the most cost for cleanup.

You can run as single samples or as a batch. We’ve run it at least 6,000 samples at a time (within our biobank data), largest batch was 20,000 samples. It’s not prohibitive at all. Maybe even the larger batches are under $100.

A lot of the tasks call the cache, which is a major cost savings since it uses some cached data.

Q: When you copy the workflow, you copy the steps. Then you have to copy the data files into the bucket. Is there anything else?

A: I would recommend copying the data that are in the workspace to your workspace files. You can use the sample data to test things.

This workspace will show you exactly how to run things and show you what you have compared to the sample.

Q: Is this workflow being used in practice to evaluate folks risks?

A: It’s run on the biobanks for their scores, but it is also a fully validated pipeline used in clinical practice.

Q: Are there any cases when you wouldn’t recommend running the ancestry adjustment?

A: For cases where you wouldn’t want to bucket an individual - for a single genetic ancestry and for folks who are admixed genetic ancestry you likely wouldn’t need to do it. The adjustment helps to get each of the individual samples.