I am trying to use GATK through Galaxy and trying to call variants from my vcf file. "Select Variants from VCF files (Galaxy Version 0.0.3)".
What to write in "Using reference genome"?
I have another issue while using ANNOVAR for annotation.
What to write in "Annotation Regions" and "Annotation Databases"?
All of Galaxy's currently wrapped GATK tools are considered deprecated, are based on older GATK releases, and may fail for a variety of reasons. For now, skip using GATK in Galaxy, whether at a public server or your own local Galaxy with the tools loaded from the ToolShed.
Important: The data content (not just the database assignment) must actually be based on the hg19 genome/build/version, otherwise, the tool will end with an error due to a genome mismatch. In other words, avoid assigning that database in hopes that it will retrieve annotation for VCF content based on a different genome/build/version.