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SISG Module 17: Computational Pipeline for WGS Data

July 29-31, 2020

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Who are we?

Ken�Rice

Stephanie�Gogarten

Tim�Thornton

Instructors

Affiliations: Biostatistics Dept., Univ. of Washington and Trans-Omics in Precision Medicine (TOPMed) Data Coordinating Center

Amarise Little

Anna Mikhaylova

Matt Conomos

Teaching Assistants

Andréa Horimoto

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What are we going to learn?

  • What sequencing data looks like and how to work with it
    • Caveat: variant calls, in one specific format
  • What are the steps involved in running a large-scale genome-wide association test (GWAS) with WGS data?
  • How do you handle related samples?
  • How do you effectively analyze rare variants?
  • How can you take advantage of computational platforms to make all this easier?

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Two websites

Official SISG page: (requires login)

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Github:�(what we’ll actually use!)

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Pre-assessment reminder

On the official site:

https://uwsurvey.qualtrics.com/jfe/form/SV_eht27L5t1EyxwYl��Thanks for doing this!

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What is the class format?

Sessions have:

  • Recorded lecture(s) - watch via Zoom in real time, or download/stream yourself
  • Exercises, in breakout sessions - for asking questions, working together, and learning from each other!
  • Short wrap-up discussion: instructors answer further questions, also address what was challenging in the exercises

Please use our Slack channel to ask questions! (We will also look for Zoom chat messages.) We’ve never done this class online either - expect awkwardness!

Course website: https://uw-gac.github.io/SISG_2020/

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Recordings

  • Only viewable by module participants
  • Breakout rooms not recorded
  • Video is recorded for active speaker only; please disable your camera if you want to be sure your face does not appear
  • We will post Zoom sessions recordings when they become available. But Zoom’s processing steps can take a few hours: thanks for your patience.

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How do I do the exercises?

  • Log into https://platform.sb.biodatacatalyst.nhlbi.nih.gov
  • Under “Public Projects”, select “GENESIS Tutorial -> Copy Project”
  • Select “SISG20 workshop” as the billing group
  • Click “Interactive Analysis” (top right)
  • Select “Data Cruncher”
  • Select “GENESIS tutorial”
  • Click “Start”
    • Wait a few minutes for your instance to start up
  • Click “Open in editor”

Watch the video to see all of this in action!