Using Example Workspaces

Browsing and cloning example workspaces is a great way to get started using AnVIL.

The AnVIL project's example workspaces demonstrate common genomic analysis pipelines deployed using data and tools available on AnVIL.

These analyses utilize unrestricted public data along with reproducible workflows, allowing researchers to clone and execute the workspaces as a learning exercise or for adapting to their own research.

Prerequisites

The example workspaces listed below may be viewed with only a Terra account. To use the workspace and run or modify its associated tutorial, you will need to:

1. Link your Terra account with a Google billing account.
2. Clone the example workspace into your billing account before running the workspace's analysis pipeline or interactive analysis.

Featured Example Workspaces

GATK - Best practices for somatic CNV discoveryA somatic copy number variation workflow, representing the Variant Discovery portion of the Somatic CNV Discovery pipeline.

GATK - Best Practices for Germline SNPs & IndelsA fully reproducible example of Processing For Variant Discovery, HaplotypeCallerGVCF, and Joint Discovery workflows.

Hail GWAS PIPELINEA basic tutorial for using Hail, a python-based package for working with genomic data.

inferCNV Tumor Single-Cell RNA-Seq Analysis PipelineCompare RNA from tumor samples with corresponding “normal” samples to identify evidence for copy number variations in tumors.

Optimus PipelineThe Optimus pipeline processes 3-prime single-cell transcriptome data from the 10X Genomics v2 (and v3) assay.

Additional Example Workspaces

Terra contains many additional example workspaces that are useful for getting started.