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Please note the final planned GREGoR website downtime in April:

  • Friday, April 19  at 5 pm PT to Monday April 22 at 8 am PT (63 hours)

During this time the GREGoR website will be down and users will be unable to log into the DCC's AnVIL management web app to link their AnVIL accounts. Please contact the DCC at gregorconsortium@uw.edu if you have questions or need help during the downtime.

AnVIL Resources

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Introduction

The GREGoR Consortium is using the NHGRI Analysis Visualization and Informatics Lab-space (AnVIL) for data sharing and collaborative analysis in the cloud. This page provides basic information on how GREGoR is using AnVIL, as well as links to AnVIL related resources for Consortium members.

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Getting Started

To begin working with the GREGoR Data, we recommend researchers 

  1. Set up an AnVIL account (which is the same as a Terra account)
  2. Link their AnVIL account to their eRA commons ID
  3. Obtain access to GREGoR Data
  4. Clone the release workspace to conduct analysis

     
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GREGoR Data on AnVIL

Within AnVIL, GREGoR Data is separated into workspaces by participant consent group. Once you have access to GREGoR Data, you can find workspaces associated with the GREGoR Consortium on AnVIL searching for "GREGoR" on AnVIL’s Workspaces page. The data in these workspaces is structured as tables that conform to the GREGoR Data Model. Conceptually, researchers can think of this structure as a relational database and interrogate the data using approaches such as joining and filtering statements across the tables. The tables include pointers to the molecular data files (such as .bams and .vcfs) that may be used as inputs for running bioinformatic workflows.

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Interactive Analysis

Researchers can write code for interactive data analysis on AnVIL using RStudio, Jupyter notebooks, or Galaxy. AnVIL also supports interactive analysis with the Integrative Genomics Viewer (IGV) and seqr. AnVIL analysis tutorials and resources include:

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Workflows on AnVIL

AnVIL supports bulk data processing and analysis tasks encoded in theWorkflow Description Language (WDL). AnVIL users can write their own workflows, can publish workflows for others to use, and can use workflows shared by others on Dockstore.  If you would like to add a workflow to the  GREGoR organization on Dockstore, please contact the DCC to be added to the organization.

Links to Resources:

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