From what I could find, Galaxy currently provides Varscan and UnifiedGenotyper for variant calling. It appears that there are other tools available and some seem to outperform Varscan and UnifiedGenotyper. For example, GATK's Haplotypecaller is recommended over UnifiedGenotyper, although it does seem to take more computer power to run. Other tools such as Platypus, SGA, DISCOVAR, Scalpel also have good online reputation, although I do not know how extensive these tools have been tested. Platypus does have one publication out and it seems to be a fast and lightweight tool. Is there a plan to provide them (?not sure if this is the correct verb) on Galaxy main server?
Freebayes and Naive Variant Caller are on the public Main Galaxy instance at http://usegalaxy.org. Going forward we cannot comment yet about additional tools, although I can let you know that the core tool set to be supported on the Main server is under review at this time.
Some of the variant analysis tools under review can be found on the public Test Galaxy instance at https://test.galaxyproject.org.
The Tool Shed is a good resource, as mentioned before (for use in a local or cloud Galaxy). As can be other public Galaxy instances hosted by other groups. Choices for how/where to use Galaxy, with links to resources/how to set up (when needed), can be found in our wiki here:
In addition, most any 3rd party tool can be wrapped and used within Galaxy (in a loca/cloud), if you have resource to do that.
Hopefully this helps some more, Jen, Galaxy team