How to add Triticum aestivum snpEff4.3 genome database or appropriate wheat genome database in Galaxy for VCF annotation?

[jennaj]

@Pranav_Menon

I tried downloading the SnpEff database directly from sourceforge and uploading it to Galaxy. However SnpEff eff says this file is unavailable (similar to the problem above). I think the issue has got to do with the metadata, but autodetect does not work.

Right, this particular data does not work “from the history” when loaded this way. You have to create or download the database using the other tools.

@Pranav_Menon

The reason I tried the above method is because when I use the SnpEff download tool or SnpEff build tool, all I get is a file with 2 lines. Not sure why this happens.

The output with just a few lines is an internal link to the SnpEff database created on the server. The SnpEff tool form should recognize and accept it as a database input.

@wm75 explains more about this is one of the prior posts in this topic (scroll up) and in a new duplicated Topic/post here SnpEff errors while trying to run the tool.