NHGRI Analysis Visualization and Informatics Lab-space

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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.
GATK Best Practices for Somatic CNV Discovery

GATK Best Practices for Somatic CNV Discovery

This workspace contains an example of the somatic copy number variation workflow, representing the Variant Discovery portion of the Somatic CNV Discovery pipeline. Launch Workspace

Optimus Pipeline for Analysis of 3’ Single-Cell Transcriptomic Data

Optimus Pipeline for Analysis of 3’ Single-Cell Transcriptomic Data

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

inferCNV Tumor Single-Cell RNA-Seq Analysis Pipeline

inferCNV Tumor Single-Cell RNA-Seq Analysis Pipeline

The inferCNV workflow compares RNA from tumor samples with corresponding “normal” samples to identify evidence for copy number variations in tumors. Launch Workspace

GWAS Pipeline Using Hail

GWAS Pipeline Using Hail

This workspace serves as a basic tutorial for using Hail, a python-based package containing additional data types and methods for working with genomic data. Launch Workspace

GATK Best Practices for Germline SNPs & Indels

GATK Best Practices for Germline SNPs & Indels

This is a fully reproducible example of Processing For Variant Discovery, HaplotypeCallerGVCF, and Joint Discovery workflows based on GATK Best Practices. Launch Workspace

Additional Example Workspaces

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

Bringing Your Own DataRunning GATK on Terra
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