Yes, this is a possible result. Please see this post for how to interpret vcf output from the GATK pipeline: https://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it
That said, all GATK tools currently wrapped for Galaxy have been deprecated. Problems can come up (functional and technical) and the tools should be avoided.
Please see the GTN Variant Analysis tutorials for help with using alternative tools/methods:
There was an earlier project to upgrade the GATK tool suite, but it looks like it has been delayed now (see GATK update to 3.4 · Issue #194 · galaxyproject/tools-iuc · GitHub & GATK update to 3.4 · Issue #194 · galaxyproject/tools-iuc · GitHub). I asked the IUC about future plans/status at their Gitter chat – please watch for their reply here and/or free to join in: https://gitter.im/galaxy-iuc/iuc?at=5c7d5c6153efa91203b107ca