GATK4.1.5 GenotypeGVCFs --annotation-group

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hana lango allen

• March 12, 2020 16:06

Looking at various forum posts it seems the question has been asked but not answered yet: which annotations are used for different annotation groups?

There is no detail in tech documentation, and invoking gatk-4.1.5.0/gatk GenotypeGVCFs --help only tells us:

--annotation-group, -G:String  One or more groups of annotations to apply to variant calls. This argument may be specified 0 or more times. Default value: null. Possible Values: {AlleleSpecificAnnotation, AS_StandardAnnotation, ReducibleAnnotation, StandardAnnotation, StandardHCAnnotation, StandardMutectAnnotation}

This is a rather nice feature which I can obviously run to find out but would be good to have the details listed in the documentation pages.

Thanks, Hana

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• 

  Bhanu Gandham

  • March 13, 2020 18:34

  HI hana lango allen

   

  Thank you for your input and we will look into updating our documentation.

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