5 months ago by
United States
Hello,
The tool was just updated and the tutorials do not reflect what changed yet (but will soon).
Right now, there are no native indexes on the server linked in. Use the "Genome Source >> Download on Demand" option. Available datasets can be reviewed at the help link (https://sourceforge.net/projects/snpeff/files/databases/v4_3/). The database names are in the archive names.
For example, if your input VFC is based on hg19 and has that database assigned, enter hg19 into the box for Snpff Genome Version Name.
I confirmed this by reviewing data at the help link and searching by database name.
Example: the hg19 archive is named like:
snpEff_v4_3_hg19.zip
This can get a bit tricky but most can be worked out (for later, if/when doing your own analysis). For example, this one would be for galGal4 (VCF database assignment in Galaxy) and with Galgal4.75 entered into Snpff Genome Version Name:
snpEff_v4_3_Galgal4.75.zip
Whether or not there is an extra annotation that corresponds to "Non-coding and regulatory annotation" isn't a known before the tool is executed with this method, so it cannot be used as a filter. No filtering is used in the tutorial anyway (prior defaults used instead). This is likely temporary and will be resolved soon so that a built-in index can be used (especially those used in tutorials).
Once built-in indexes are available, clicking on the "Non-coding and regulatory annotation" box will list options to select/de-select (or something similar). The tutorial will update to reflect the proper usage/form pictures.
Thanks! Jen, Galaxy team
