Does Galaxy.org have a BQSR tool?

Question

[LeandroF.]

Hi all! I'm creating a variant calling workflow/tutorial for biology students with no background in informatics, using almost exclusively the Galaxy platform tools.

Now, I'm aware that I can easily teach them to run Rstudio, install GATK using the shell and run the commands. However I'm being asked to avoid anything related to CLI usage for fresh students, besides I'm not that proficient in that myself.

I could not find implemented tools for creating a sequence dictionary from the ref-genome, updating the known-sites.vcf and index according to the ref-genome Galaxy uses, and application of BQSR. Are there any tools that perform any of the above mentioned processes?

In another post in this platform 6 yrs ago I read that this step might even be neglictible, and depends on the variant calling tool (in the case of Galaxy is Lofreq).

Thanks for your time and your knowledge!

Answer 1

[GenoMax]

It may be best to ask on Galaxy help forum: https://help.galaxyproject.org/

Galaxy does have a tutorial workflow for calling variants: https://training.galaxyproject.org/training-material/topics/data-science/tutorials/bash-variant-calling/tutorial.html

[LeandroF.]

Thanks for the feedback! Actually I am quite familiar with this workflow and its basically CLI using the Rstudio interactive tool, which, as I stated above, been asked by my supervisor to avoid.. additionally this tutorial does not possess a BQSR step.

Unfortunately I'm still waiting for a reply to this same query in the Galaxy forum.

[GenoMax]

You are perhaps also aware of galaxy toolshed that have many tools available including GATK3 and 4. Those will cover your need for BQSR.

If you are looking to use public galaxy for whatever you are trying to do then it may not be an option but if you are willing to host your own galaxy then you can make use of tools in toolshade to build any workflow you like.

[LeandroF.]

Your help is greatly appreciated! I'm using th implemented in toolshed.