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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