Hallo Galaxy users,

I would like to annotate variants (in vcf file) found in my bacterial genomes and look which of them cause non-synonymous mutations. I have found two tools in the Main Galaxy that I can use for this purpose (snpEff and Annovar), but I have problems with them.

How can I change the input genome in snpEff? The only available choice in C. elegans. How can I choose my genome, already uploaded in my history?

Regarding Annovar, which file formats are required as Gene annotations/ Annotation Regions/ Annotation Databases? Reading the tool manual, it seems I can create my own txt/tabular files and use them for annotation, but the tool in Galaxy doesn't allow me to select any file, even if I have txt files in my history.

Any other suggested tool I can use?

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