GATK4 Best Practices -- SetNmMdAndUqTags

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Alijah O'Connor

• April 28, 2020 23:37

In some places, I'm seeing that running SetNmMdAndUqTags before BQSR is not part of the GATK best practices, but in other places (including the GATK GitHub page) this tool is included.  I'm just curious what the current official opinion for using this tool is? 

I've not been using this tool in my Somatic Variant Calling workflow and I haven't noticed any problems arising from its exclusion.  On that note, are there any consequences for not using this tool if I'm not getting runtime errors?

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  Bhanu Gandham

  • April 29, 2020 16:42

  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.

  For context, check out our support policy.

   

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