I recently used "ANNOVAR Annotate VCF with functional information using ANNOVAR (Galaxy Version 0.2)" on usegalaxy.org using the following settings:
For gene annotations, I entered: refGene, gencodev19 For annotation regions, I entered: GenomicsSuperDups, phastConsElements46way For annotation databases, I entered: 1000g2012_apr_all, avsift, snp137nonflagged, esp6500si_all, snp137, cosmic67 For output data type, I selected tabular.
These settings successfully produced an annotated VCF file. However, when I transferred this tool to our local server running Galaxy, it no longer works, saying that there are "no options available" for these databases, and it doesn't allow me to type them in. I am still able to run the tool 'successfully' (i.e. producing a green entry on the history), but all that is returned is an empty VCF file with no annotations. Why is this happening? I looked into ways to download those databases onto our server, but was unable to figure out how to do that, nor do I know if that is even the right approach to solving this problem. Any advice is appreciated.