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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

Calling somatic CNVs

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    Genevieve Brandt (she/her)

    Hi Yasin Uzun, the documentation for that workflow is still being developed. We do have two somatic CNV workflows available in Dockstore in the featured GATK Best Practices Workflows. The CNV Somatic Pair Workflow and CNV Somatic Panel Workflow. These are written in the Workflow Description Language which can be read to see all the steps. You can also run them as-is or with a few tweaks by downloading those WDLs and running them on your own machine. They have documentation about how to run them on the Dockstore site. 

    One other note - for the easiest usage, you can run all these workflows on our application Terra, which is a cloud platform and has excellent service to help you get set up and running. 

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    Yasin Uzun

    Thank you very much for the response. But I am confused a bit. Unfortunately, our servers don't support running Docker. Does that mean I can't use WDLs? Are the WDLs only for running in Docker? Or can they be run in Linux/Unix system shell with gatk binaries, without Docker?

    Is there any example commands or tutorials about how to compute CNVs in Linux/Unix system shells directly with gatk, without Docker or Terra?

    Thanks.

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    Beri

    Hi Yasin Uzun,

    You can follow along with the GATK CNV tutorials here.

    The workflow is written to mainly work using dockers, though if you are not able to use docker on your system you can edit the wdl to remove the runtime block for each task which is where the use of dockers are specified. Then edit the command block of the task to point to a local binary of the tool being executed. 

    Example:

    From

    task GeneralTask {
        input {
          File standardized_copy_ratios
        }
        command <<<
            gatk SomeGATKTool \
                --input ~{standardized_copy_ratios} 
        >>>
        runtime {
            docker: "~{gatk_docker}"
            memory: "400 MB"
            disks: "200 HDD"
            cpu: 1
            preemptible: 5
        }
        output {
            File output_file = "~{output_dir_}.denoised.png"
        }
    }

    to

    task GeneralTask {
        input {
          File standardized_copy_ratios
        }
        command <<<
            <local path to tool>/gatk SomeGATKTool \
                --input ~{standardized_copy_ratios} 
          >>>
        output {
            File output_file = "~{output_dir_}.denoised.png"
        }
    }
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    Emiliano Dalla

    Hi Genevieve Brandt, the OP said he has an unmatched tumor sample, could you confirm if it is still possible to perform somatic CNVs calling?

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    Genevieve Brandt (she/her)

    Hi Emiliano Dalla,

    The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

    Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

    We cannot guarantee a reply, however, we ask other community members to help out if you know the answer. Yasin Uzun, do you have any insights to this question?

    For context, check out our support policy.

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    Pamela Bretscher

    Hi Emiliano Dalla,

    Yes, you can still perform somatic CNV calling with an unmatched tumor sample, it will just be less accurate at distinguishing somatic and germline variants. Here is our Mutect2 FAQ which mentions tumor-only vs. tumor-normal mode and the updated workflow for somatic CNV calling.

    Kind regards,

    Pamela

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