Some of the annotations I use in VQSR do not always vary significantly and hence I get the following error:
```A USER ERROR has occurred: Positive training model failed to converge. One or more annotations (usually MQ) may have insufficient variance. Please consider lowering the maximum number of Gaussians allowed for use in the model (via --max-gaussians 4, for example).```
I have found that removing the annotation (trail and error) tends to give better results than dropping the gaussians, probably because the one annotation happens to not show meaningful variation.
To prevent GATK from crashing on me every time I would like to automate this process rather than trail and error. In order to do so I need to identify and exclude the annotation that insufficiently varies (differs from one data set to the next), what does GATK consider insufficient variance and how is it calculated?
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