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by Brian D. O'Connor, Geraldine A. Van der Auwera
Genomics in the Cloud
1. First steps on the Cloud
Setting up your Google Cloud account and first Project
Create a Project
Check your billing account and activate free credits
Running basic commands in Google Cloud Shell
Log into the Cloud Shell VM
Use gsutil to access and manage files
Pull a Docker image and spin up the container
Mounting a volume to access the filesystem from within the container
Setting up your own custom VM
Create and configure your VM instance
Set up the GATK container image
Configure the Integrated Genome Viewer to read data from GCS buckets
Wrap up and next steps
2. First steps with GATK
Getting started with GATK
Operating requirements
Command-line syntax
Multithreading with Spark
Running GATK in practice
Generate an output BAM to troubleshoot a surprising call
Understanding variant context annotations
Plotting variant context annotation data
Applying hard filters to germline SNPs and indels
Best Practices workflows covered in the book
Other supported use cases
Wrap up and next steps
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Genomics in the Cloud
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