Genomics in the Cloud: Using Docker, GATK, and WDL in Terra

Book Description

Data in the genomics field is booming. In just a few years, organizations such as the National Institutes of (NIH) will host 50+ petabytes—or over 50 million gigabytes—of genomic data, and they’re turning to cloud infrastructure to make that data available to the research community. How do you adapt tools and protocols to and analyze that volume of data in the cloud?

With this practical book, researchers will learn how to work with genomics using open source tools including the Genome Analysis Toolkit (GATK), Docker, WDL, and Terra. Geraldine Van der Auwera, longtime custodian of the GATK user community, and Brian O’Connor of the UC Santa Cruz Genomics Institute, guide you through the process. You’ll learn by working with real data and genomics from the field.

This book covers:

  • Essential genomics and computing background
  • Basic operations
  • Getting started with GATK, plus three major GATK Best Practices pipelines
  • Automating analysis with scripted workflows using WDL and Cromwell
  • Scaling up workflow execution in the cloud, including parallelization and cost optimization
  • Interactive analysis in the cloud using Jupyter notebooks
  • Secure collaboration and computational reproducibility using Terra

Book Details