Welcome to AnVIL
User-centered solution for genomic data access, analysis, and visualization. Based on familiar software platforms. Engineered for cloud infrastructure.

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.