Galaxy GATK tool


I am having exome seq data and wants to do somatic calling through GATK in galaxy. For variant callers, I found only one caller-unified genotyper. Is GATK Mutect2 is also available in galaxy?



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Welcome @pkb

GATK tools at Galaxy Main are considered deprecated. These are based on GATK 1.4

GATK tools at Galaxy EU include both the GATK 1.4 and 2 version. The 1.4 version should be avoided, the 2 versions you can try – but it won’t include this tool.

For installing GATK into your own Galaxy, the ToolShed can be searched with the keyword “gatk” to bring up all wrappers. The most currently updated is GATK2 here: (same set of tools as at Galaxy EU).

There are plans to update GATK but I don’t know the status. I asked for a status at the IUC Gitter chat room here:

Please feel free to join the chat there or they may reply back here.