Somatic copy number variants (CNVs) and Panel of Normals creation
Hello Terra help,
I am new to Terra and currently trying to understand the workspace for Somatic copy number variants (CNVs).
And I am interested to know if I only have one sample to analyze i,e 1 pair of normal & tumor exome data, can I still use to create panel of Normals or run the somatic CNV workflow to derive CNVs from exome data Please let me know.
Thanks for writing in. Your question may actually be better suited for the expert community on the GATK forum and there may be a post that already answers your question: https://gatk.broadinstitute.org/hc/en-us/community/topics.
As Terra Support, I can only make a recommendation based on the documentation in the Somatic-CNVs-GATK4 workspace. I believe you should be able to run the cnv_somatic_pair_workflow since the inputs required are a pair of tumor and normal BAM files, which you have.
Thank you for your reply Samantha. I will search and post at GATK community forum as without this answer I am not sure if I can use Terra or not.
Currently, I don't have any Azure billing account set but before I do that, is it possible from Terra support to show me with a webex or zoom how to run this "Somatic copy number variants (CNVs)" best practices with Azure. Please let me know.
At this time, the workflows in the Somatic-CNVs-GATK4 workspace are only available to run on Terra on GCP, not Azure. Fortunately, we have plenty of resources, including support articles and video tutorials, to help you get started on Terra and run the workflow.
Please see our Getting Started section for more information.
Thanks for your reply Samantha. The institution where I work doesn't have GCP set up yet,only azure is available. Is it possible to work with non-gmail with Terra and sep up billing.
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