Table of Contents
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.
Back to topGetting Started
To begin working with the GREGoR Data, we recommend researchers
- Set up an AnVIL account (which is the same as a Terra account)
- Link their AnVIL account to their eRA commons ID
- Obtain access to GREGoR Data
- View the GREGoR Consortium's workspaces
- Clone the release workspace to conduct analysis
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.
Back to topInteractive 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:
- Terra tutorial on Jupyter notebooks
- Terra documentation on RStudio
- Using the R/Bioconductor “AnVIL” package
- How to view IGV tracks of BAM and VCF Files
- Using Seqr in AnVIL
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:
- WDL training course with videos
- More on WDL from Terra support
- GREGoR Consortium Workflows on Dockstore
- Find existing workflows in Dockstore or the Broad Methods Repository
- Tutorial on writing a simple workflow (slides| video)