iVar variants - Enhancement request: Include optional GFF3 reference annotation

usegalaxy.org support
1

Hi,

I would like to add a .gff file to my ivar variant analysis. Can I do this in Galaxy? (I’ve been having trouble installing the command line version)

Thank you!

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2

Hi @schweie

The ivar tool suite is installed at all UseGalaxy.* servers.

Search the tool panel with the keyword “ivar” to find them. Usage help is on the tool forms.

You can also search the tool panel with keywords like “vcf” and “variant” to find tools to manipulate vcf datasets.

And tutorials are here: Galaxy Training!

Thanks!

3

Hi jenny, thanks very much for your reply! I have been using ivar variants using Galaxy , and it works very well for me. However, I would like to add a gff file, that would be an option on the command line tool, but I can’t figure out how to add it if I use galaxy.

Thank you

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4

Hi @schweie

Ok, thanks for explaining. The option to incorporate a GFF3 annotation dataset has not been added to the Galaxy wrapper for the tool (yet).

I created an issue ticket for the enhancement request that you can follow and/or comment on here: Enhancement request: iVAR variants · Issue #3873 · galaxyproject/tools-iuc · GitHub

5

oh, fantastic, thank you very much!

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