Welcome to the GDC Documentation!

This project provides tools and pipelines for interacting with the Genomic Data Commons (GDC). It is designed to run efficiently on high-performance clusters like the UMN MSI Agate cluster.

Contents:

• Installation
  • Automatic Software Installation
  • Prerequisite Software
  • Software Loading Methods
  • Software Environment Summary
  • External Dependencies
  • Software Environment Files
  • Container Images
  • Troubleshooting
• Genomics
  • Standard Procedure
  • Technical Implementation
• Usage
  • Software Environment Setup
  • Workflow Overview
  • Configuration
  • Running the Pipeline
  • Advanced Options
  • Master SLURM Job
  • Custom SLURM Script
• Tutorial: Quality Control Pipeline in Practice
  • Prerequisites
  • Discussion Points: Multi-Ancestry and Admixed Study Designs
  • Next Steps
• Tutorial: Ancestry Classification in Practice
  • Prerequisites
  • Lab Exercise: Running Ancestry Classification
  • Interpreting Pipeline Outputs
  • Next Steps
• Tutorial: Assembling 1000 Genomes Reference Data
  • Prerequisites
  • Lab Exercise: Assembling 1kG Reference Panel
  • Understanding the Processing Steps
  • Pipeline Outputs
  • Discussion Points
  • Next Steps
• Tutorial: Heritability Estimation with Multi-Ancestry Simulation
  • Prerequisites
  • Lab Exercise: Multi-Ancestry Heritability Estimation
  • Interpreting Results
  • Simulation Parameters: What to Explore
  • Discussion Points
  • Next Steps

Getting Started

Recommended Learning Pathway:

1. Installation - Set up software environment

2. Usage - Learn how to run the pipeline

3. Tutorial: Assembling 1000 Genomes Reference Data - Download reference data

4. Tutorial: Quality Control Pipeline in Practice - Run quality control

5. Tutorial: Ancestry Classification in Practice - Classify ancestry

6. Tutorial: Heritability Estimation with Multi-Ancestry Simulation - Estimate heritability (optional)

Quick Setup (MSI/UMN HPC):

module use /path/to/GDCGenomicsQC/envs
module load gdcgenomicsqc
conda activate snakemake
cd GDCGenomicsQC
snakemake --version

See also: Usage for detailed instructions on running the pipeline with module load or local snakemake.

Indices and tables

• Index

• Module Index

• Search Page