Genomics in the Cloud: Using Docker, GATK, and WDL in TerraData in the genomics field is booming. In just a few years, organizations such as the National Institutes of Health (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 analysis tools and protocols to access and analyze that volume of data in the cloud? With this practical book, researchers will learn how to work with genomics algorithms 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 algorithms from the field. This book covers:
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Contents
Chapter 1 Introduction | 1 |
A Primer for Newcomers to the Field | 13 |
Chapter 3 Computing Technology Basics for Life Scientists | 53 |
Chapter 4 First Steps in the Cloud | 79 |
Chapter 5 First Steps with GATK | 115 |
Chapter 6 GATK Best Practices for Germline Short Variant Discovery | 147 |
Chapter 7 GATK Best Practices for Somatic Variant Discovery | 183 |
Chapter 8 Automating Analysis Execution with Workflows | 209 |
Chapter 10 Running Single Workflows at Scale with Pipelines API | 269 |
Chapter 11 Running Many Workflows Conveniently in Terra | 295 |
Chapter 12 Interactive Analysis in Jupyter Notebook | 331 |
Chapter 13 Assembling Your Own Workspace in Terra | 373 |
Chapter 14 Making a Fully Reproducible Paper | 413 |
Glossary | 441 |
445 | |
About the Authors | 468 |
Chapter 9 Deciphering Real Genomics Workflows | 245 |
Other editions - View all
Genomics Analysis with Spark, Docker and Clouds Brian D. O'Connor,Geraldine van der Auwera No preview available - 2020 |