Featured Workspaces

The AnVIL project's featured 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.

The featured workspaces are hosted from within an AnVIL branded Terra instance.

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.

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.

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.

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.

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.

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