I have a bioinformatics pipeline for variant calling that I want to validate using Galaxy. For this, I need to use GATK version 4.4.0.0. Can someone please let me know if this version is available in Galaxy?
Thank you.
Welcome, @Deepa !
For GATK, there is only one tool available at the public Galaxy servers. Search the tool panel with that as a keyword to find it.
You will want to use a custom reference genome that is properly formatted for both
- Galaxy → see here for how FAQ: How to use Custom Reference Genomes?
- and GATK → see the original tool documentation for this
Alternative variant analysis tools like Freebayes are available instead. To review tutorials that include this and any tool, scroll to the bottom of the tool form for links.
Or, you can navigate the Galaxy Training Network (GTN) directly. Start here and notice the different domains/categories and the Learning Pathways at the top. If you have trouble finding something, please let us know and we will try to help more. https://training.galaxyproject.org/
Hope this helps! 