WDL Tutorials
Step-by-step tutorials for writing pipelines in WDL.
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(howto) Install software for WDL workshops
For our hands-on workshops, you will need to download the following programs: womtool The womtool toolkit is a utility package that provides accessory functionality for writing and running WDL scripts, including syntax validation and input templa...
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[1] (howto) Write your first WDL script running GATK HaplotypeCaller
Requirements This tutorial assumes that you have a (very) basic understanding of GATK tools and have read the Getting Started guide. You should also have installed the necessary tools. Lastly, you will need to download the zip bundle containing th...
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[2] (howto) Write a simple multi-step workflow
Requirements This walkthrough assumes a (very) basic understanding of GATK’s tools and that you have read the Getting Started guide. You should have installed the necessary tools, and gone through the previous tutorial, as we will be starting off ...
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[3] (howto) Run a sample variant discovery mini-pipeline
Requirements This walkthrough assumes a (very) basic understanding of GATK’s tools and that you have read the Getting Started guide. You should have installed the necessary tools, and gone through the previous tutorial, as we will be starting off ...
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[4] (howto) Use scatter-gather to joint call genotypes
Requirements This tutorial assumes that you have a (very) basic understanding of GATK tools and have read the Getting Started guide. You should also have installed the necessary tools and gone through the previous tutorial, as we will build off co...
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