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Is there any example of a queue script calling variants with the HaplotypeCaller?
Yes @ericminikel, that script can be adapted -to run HaplotypeCaller instead of UnifiedGenotyper. You may need to add some arguments to the argument collection, but it should be fairly straightforward.
Geraldine Van der Auwera, PhD
Not at this time, but it will take you only minimal changes to adapt the existing scripts to use the HC instead of the UG.
Is ExampleUnifiedGenotyper.scala the existing script you're referring to?