Hi, guys! I am trying to detect mutations among RNAseq cancer and normal prostate samples in dogs. Fastq files passed quality filters after trimming process, and were mapped (STAR 2-passes) in galaxy. I am following the GATK best practices pipeline but I found that galaxy does not have any of the GATK tools (except GATK Mutec2) needed (splitNcigarReads, BaseRecalibration, IndelRealigner, etc). Can I keep up with this process using other available tools in galaxy? or is there any other pipeline that I can use which all its tools available in galaxy?
Hi, @alejandrogzi,
You might find that another instance of Galaxy has the tools you need. If not, you can request that tools be added. Check here for more info.
Hi, @jaredbernard,
Thanks for your response. I did look other instances for the tools needed, including the tool shed. I will try to open an issue to request the tools; however I am not too familiar with github yet but I will try to search for examples. Do you have any example or manual maybe?
If you go to the GitHub page, you can see examples under the Issues tab. If you click on New Issue, you can start one, and an administrator will assign it a label as a tool request.
Was the tool you needed in the Tool Shed already? If so, you could load it onto your own instance if you have one, or request that admin loads it onto the public instance.
Hope it works! 
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Hi @alejandrogzi,
GATK tools are considered deprecated due to reported malfunctioning: GitHub issue. I suggest you to use Freebayes as a replacement. You can find some information about it in the Galaxy Training tutorials.
Regards.