README.md

Training Material for

This repository contains material to help users migrate their genomic analysis workflows to the AnVIL cloud platform.

Tutorials

Analysis	Inputs	Outputs	Features
GWAS	Local .csv, Cloud .vcf	Top variants	Terra, Dockstore, Jupyter, RStudio
GATK	Local .fastq	.vcf	Terra, Dockstore
scRNA-seq

Technology Overview

• Terra
  • Running Workflows, Getting Data, Interactive Analysis w/ Jupyter Notebooks
  • Architecture and Design Overview
• Dockstore
  • Intro to Dockstore, Brief Developer Details
• Gen3
  • User Perspective, Technical Overview

Dockstore Workflows

• GENESIS GWAS
• GATK collection
• BWA align by TOPMed
• 10x Genomics scRNA-seq by Human Cell Atlas

AnVIL Workspaces

• ASHG 2019 GWAS Tutorial
• GWAS Tutorial in NHLBI's BioData Catalyst
• Bioconductor using Jupyter Notebooks
• COVID-19 scRNA-seq
• Human Cell Atlas Optimus Pipeline for 10x Genomics scRNA-seq

Workshop Guidance

• Terra in the classroom

References

• Getting Started on Terra
• Terra Documentation
• Genomics in the Cloud O'Connor and Van der Auwera 2020 O'Reilly