GATK4 baserecalibrator

Hi, I am using GATK4 mutect2 for variant calling. I need baserecalibrator for the preprocessing process, but I can’t find it in Galaxy tools and Tool Shed.
Can you tell me how to use baserecalibrator or a tool that can replace it?

Variant Calling
Base (Quality Score) Recalibration


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Hi @bcg,
currently BaseRecalibrator is not available in the public Galaxy servers. I recommend you use Freebayes for performing the variant calling.


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Thanks for your reply,

Do you know why?
I wonder why it is because it was provided in the previous version.

Hi @bcg, here you can find some info about it: issue GATK.

Thank you! :grinning: