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…

Yes, it worked really well by checking that option. I tried the current version (5.2) of SnpEff eff and it worked just fine! Thank you so much! [image]

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 t…

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…

Thank you so much. Is there a way to use SnpEff4.3 in public Galaxy? Are they compatible?

Hi @xuanz01 Does this help? [image] FreeBayes variant calling and Snpeff variant annotation The earlier version works fine. If you rerun your original jobs, but switch to using 4.3+T.galaxy5 FAQ: Changing the tool version

Thank you for the reply. I’ve tried both SnpEff4.3+T.galaxy1 and SnpEff4.3+T.galaxy2 (there is not 4.3+T.galaxy5) (see image 1). However, after running MiModD report variants, the columns for affected genes and transcripts are blank (see image 2). Image 1: [image] Image 2: [image]

You still need to follow my earlier advice: SnpEff eff (version 5.2) - #3 by wm75

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SnpEff eff (version 5.2)

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jennaj January 23, 2026, 11:54pm 5

Hi @xuanz01

Does this help?