4.3 years ago by
You are executing the tool on the public Main Galaxy instance at http://usegalaxy.org? If so, then the input VCF must be based on the hg19 reference annotation database and labeled as such to access additional annotation. Indexed reference annotation options appear in the tool form's "Annotation" boxes, where one or more can be selected to be incorporated into the run.
To run this tool with other reference genomes, please use the version in the Tool Shed with a cloud or local Galaxy. Instructions to get started are here:
Other public instances may host this tool for certain genomes. These change frequently and a list of potential sites can be reviewed here:
Hopefully one of these options will work out for you, Jen, Galaxy team