Hi,
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?
Thanks
PK
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Welcome @pkb
GATK tools at Galaxy Main https://usegalaxy.org are considered deprecated. These are based on GATK 1.4
GATK tools at Galaxy EU https://usegalaxy.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 https://usegalaxy.org/toolshed can be searched with the keyword “gatk” to bring up all wrappers. The most currently updated is GATK2 here: https://toolshed.g2.bx.psu.edu/view/lz_hust/gatktools/01ff8dd37d4d (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: https://gitter.im/galaxy-iuc/iuc?at=5d97734d3220922ffb2a87a9
Please feel free to join the chat there or they may reply back here.
Thanks!