All currently wrapped versions of GATK tools are deprecated due to the outdated versions and/or licensing issues.
There are plans to wrap the latest release but that is still a work-in-progress. Use Freebayes/VCFtools instead. Workflow examples are in the Galaxy tutorials: https://galaxyproject.org/learn/
Thanks! Jen, Galaxy team
Freebayes/VCFtools I want to use the VCF files to identify SNPs in control and variant sample populations. What is the best tool for doing this - I can generate the SNPs using Freebayes but I have not found a workflow example for this next step and it is very frustrating!!
Thank you for your response Carol