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Add GATK3 Variant Refinement

I note that the GATK 4 pipelines have a joint_discovery workflow, e.g. the gatk-workflows/gatk4-germline-snps-indels repo. However, this doesn't exist for the GATK 3 pipelines: gatk-workflows/gatk3-germline-snps-indels.

Might it be possible to add this, so we can run a true end-to-end Best Practice with GATK 3?

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