Galaxy is currently using vcfPytools for vcf support in a few tools as well as for viewing in Trackster. Unfortunately, vcfPytools does not support the latest version of vcf (4.1) and thus is causing issues when used with the output of many newer variant callers such as Freebayes.
I contacted the author of vcfPytools about this and he had this to say:
I have actually completely rewritten the tool in C++ (now imaginatively called vcfCTools!). This supports v4.1, but is not quite complete and requires some additional testing. This should not take too long (perhaps another week), but then I will make this new version available on github and you are more than welcome to use this. I can let you know when I push the code. The rewrite is designed with freeBayes in mind and is being tested with vcf outputs from its most recent version. If there are specific problems/concerns that you have, please let me know and I'll make sure that I address these.
Al
Is anyone working on modifying Galaxy to use the new vcfCTools? I would be willing to lend my support to such an effort. If not, is there at least support from the Galaxy team for doing this?