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?
Thanks!
Debora
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