Is Gatk'S Somatic Indel Detector In A Galaxy Tool Somewhere?

Question

[corn8bit]

I'm working with some cancer data and want to run SomaticIndelDetector on it. It seems like all the GATK tools are wrapped so I thought I'd ask here before making my own to see if I'm missing something that google missed.

Or is this tool obsolete/replaced?

Answer 1

[Raony Guimarães]

Yes, this tool is officially deprecated ! :)

http://gatkforums.broadinstitute.org/discussion/2411/somaticindeldetector-is-deprecated

They are now recommending you to use Mutec

[User 59]

Not for indel calling they aren't - read your own link. "SomaticIndelDetector has been transferred to a different project and is now distributed directly by the Borad cancer group. If you are interested in using it, you should contact them directly to ask how you may obtain their software. Also, please note that MuTect (the tool I recommended in my previous post) is only meant for SNPs, not indels"