WDL Tutorials
Step-by-step tutorials for writing pipelines in WDL.
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(howto) Install software for WDL workshops
This documentation is in the process of being updated. In the meantime, you may find that some GATK commands are out of date, or that the WDL information is incomplete. If you encounter any issues you can't solve, please let us know. For our hand...
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[1] (howto) Write your first WDL script running GATK HaplotypeCaller
This documentation is in the process of being updated. In the meantime, you may find that some GATK commands are out of date, or that the WDL information is incomplete. If you encounter any issues you can't solve, please let us know. Requirements...
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[2] (howto) Write a simple multi-step workflow
This documentation is in the process of being updated. In the meantime, you may find that some GATK commands are out of date, or that the WDL information is incomplete. If you encounter any issues you can't solve, please let us know. Requirements...
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[3] (howto) Run a sample variant discovery mini-pipeline
This documentation is in the process of being updated. In the meantime, you may find that some GATK commands are out of date, or that the WDL information is incomplete. If you encounter any issues you can't solve, please let us know. Requirements...
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[4] (howto) Use scatter-gather to joint call genotypes
This documentation is in the process of being updated. In the meantime, you may find that some GATK commands are out of date, or that the WDL information is incomplete. If you encounter any issues you can't solve, please let us know. Requirements...
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