I am using the examples provided by the MiModD tutorial called Mapping-by-sequencing: identification of a phenotype-causing mutation in a nematode genome. Using the updated version of snpeff (version 5.2) followed by MiModD Report Variants doesn’t generate an output file as showed in the tutorial (e.g., the columns for affected genes and transcripts are blank and no information about the effects of the mutations). Any ideas on how to improve that? Thanks!
Hi @xuanz01
Hopefully we can help! It looks like the annotated wasn’t getting attatched in the output report correctly. This means it likely wasn’t considered correctly in the statistics.
Please try using the SnpEff4.3 versions of these tools instead.
This will allow you to perform this step in the tutorial you reference. Hands-on: Mapping and molecular identification of phenotype-causing mutations / Mapping and molecular identification of phenotype-causing mutations / Variant Analysis
The SnpEff5.N versions have some issues with how the database keys and minor tool revisions are managed in the downloaded precomputed indexes. This can lead to small issues with the downloaded indexes. This happens when the tool are used in Galaxy but also anywhere else. There was an update last summer but I haven’t personally seen it fully work correctly yet. The ticket with more details is here.
However, any version will work fine if you are creating your own index. If interested, please see. → Downloading SnpEff database into history: Create database instead!
I’m wasn’t sure if you were running through the tutorial with the tutorial data? Exact species? If yes, then using the other version should be be enough.
If you are working with something different, that advice might be enough. Or there could be some other conflict in the reference data – we can maybe help more here with that but would need to see the example since the file details are the important parts. How to share. → How to get faster help with your question
Let’s start there! Hope this helps but please let us know if it actually does or if we can help more. 
Hi @xuanz01,
I never tested the combination of MiModD with Snpeff 5, but there’s a good chance it will work if you select the Annotation Option: `Use 'EFF' field compatible with older versions (instead of 'ANN')`
This option is crucial because MiModD looks for and parses only EFF field information and will simply ignore the ANN field as you found.
Thank you so much. Is there a way to use SnpEff4.3 in public Galaxy? Are they compatible?