Guides and Tutorials

Key guides and tutorials grouped by user persona are listed below. For a general onboarding and getting-started tour, see the Learn section. See Getting Help with AnVIL Tools and Components to obtain personalized help for each of AnVIL's components and tools.

General

Getting Started - An overview of AnVIL with a focus on onboarding and preparing new users to run genomic analyses in the cloud.

Investigators

• Setting Up Lab Accounts - Follow these instructions to get your accounts, set up billing, and set up your team members to do research with AnVIL.
• Creating Cloud Cost Budget Justifications - Templates for calculating a cloud cost budget and writing a budget justification for using AnVIL in your grant applications.

Data Analysts

• Getting Started with Gen3 - An overview of the Gen3 platform and how to use Gen3 to access AnVIL datasets, create cohorts, and export them to Terra workspaces.
• Getting Started with Bioconductor - Guides helping R / Bioconductor users start RStudio or Jupyter for interactive analysis, and workflows for large-scale data processing.
• Getting Started with Galaxy - A step-by-step tutorial demonstrating how to compute quality metrics of unaligned reads, align the reads to a reference genome using bowtie2, plot a coverage histogram, call variants using FreeBayes, and then summarize the variant calls using bcftools.

Data Submitters

Data Submission Guide - An overview of the process of submitting data to AnVIL and confirming eligibility for submission.