GATK Haplotype Caller Project

This tutorial demonstrates how to run the GATK Haplotype Caller pipeline using GenomeAnalysisTK-3.2-2 from the Broad Institute. These pipelines currently support GATK version 3.2-2 (md5 3163cbeef8fd50d8cb85096758b801a3) (keep content hash 2e98fdc8e90f4c48a0714b711767c9ce+76). You must obtain your own GATK jar file in order to run this pipeline. You can obtain this software by going to the Broad Institute’s GATK licensing site. Further instructions on how to upload your file can be found on the Arvados documentation page or the tutorial below. If you run into any problems, please contact

This tutorial introduces the following Arvados features:

How to run GATK3 using Arvados
How to access your pipeline results.
How to browse and select your input data for GATK3 and submit re-run the pipeline.
Start at the Curoverse website and click Log In at the top. We currently support all Google / Google Apps accounts for authentication. By simply choosing a Google-based account, your account will be automatically created and redirect to the Arvados Workbench.
In the Active pipelines panel, click on the Run a pipeline… button. Doing so opens a dialog box titled Choose a pipeline to run.
Select Demo GATK3 Haplotype Caller Pipeline and click the Next: choose inputs button. Doing so loads a new page to supply the inputs for the pipeline.
The default inputs from the GATK3 source code repository are already pre-loaded. Click on the Run button. The page updates to show you that the pipeline has been submitted to run on the Arvados cluster.
After the pipeline starts running, you can track its progress by watching log messages from jobs. This page refreshes automatically. You will see a complete label under the job the column when the pipeline completes successfully. The current run time of the job in CPU and clock hours is also displayed. You can view individual job details by clicking on the job name.
Once the job is finished, the output can be viewed to the right of the run time.
Click on the download button to the right of the file to download your results, or the magnifying glass to quickly view your results.