This tool requires the variant annotation software SnpEff, which is not part of the MiModD package! It also needs the correct SnpEff genome database for your organism and reference sequence version installed with SnpEff.
What it does
This tool uses SnpEff to annotate the variants in the VCF input dataset with the effects that these variants have on known genomic features, i.e. on genes and transcripts.
To do its job, SnpEff requires a database of known genome annotations for your organism of interest. If you know the exact name of the genome database that you want to use, you can enter it directly. Otherwise, you should use the MiModD List Installed SnpEff Genomes tool first to generate a new dataset in your history that lists all SnpEff genome databases currently available to SnpEff on the system, then when you select this dataset as the List of available SnpEff Genomes above, you will be able to choose the SnpEff Genome from a dropdown list.
The tool will create a new dataset in VCF format with the annotations added to the corresponding variant records. Do not expect this format to be very readable, but use the MiModD Variant Reports tool to turn it into a human friendly form.
In addition, you can instruct the tool to produce an additional dataset with a summary of the variants and their effects in html format.
For additional help see these resources: