Sensitive Copy Ratio Pipeline compatibility with tool "mergeLevels"

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Gannon Cottone

• May 06, 2020 15:34

Can you please provide
a) GATK version used
b) Exact GATK commands used
c) The entire error log if applicable.

Hello, my group and I are new to this field. I have been following tutorial(s) 11682 and 11683 for sensitive detection of copy ratio alterations and applying it to benign tissue. I found a tool called (mergeLevels) and am wondering if the output from the sensitive copy ratio pipeline would be compatible for this tool or if anyone has used it in the past? If not, would there be any reason that the output from the pipline could not be used?

I appreciate any insight into this if anyone has tried before!

 

Thank you

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  Bhanu Gandham

  • May 06, 2020 22:40

  Hi ,

  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.

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