Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

GATK-SV HPC VM hardware requirements


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    Gökalp Çelik

    Hi Georgia Hosking

    As you can see from the documentation at the github repository 

    gatk-sv pipeline has been tested only on GCP and is currently unsupported on any other ways of execution. It consists of multiple steps of data collection and filtering from individual samples therefore you might need to run each sample in parallel or separate depending on the resources you can get from the HPC. Each tool utilized by the workflow may need different levels of resources and may have different ways of parallelization so estimating what is ultimately necessary is not trivial. 

    Main suggestion is to have a Cromwell instance using HPC as a back-end to begin with. As you may begin to execute different steps and tools you may end up facing different errors and issues which may all be addressed separately and will most likely to be different from what the team is experiencing with the GCP. 

    Once you begin your journey we wish to listen your experiences and we hope that we may have suggestions for your problems in gatk-sv workflow. 


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