About "Third-Party Tools"

Geraldine_VdAuwera

Other teams have developed their own tools to work on top of the GATK framework. This section lists several of these software packages as well as links to documentation and contact information for their respective authors.

Please keep in mind that since this is not our software, we make no guarantees as to their use and cannot provide any support.

vyellapa

Most of the papers from Broad mention a tool called Indelocator for Indel detection in Cancer Genomes. Would it be possible to know the syntax to run it?

Thank you, Teja

Geraldine_VdAuwera

Hi Teja,

I'm not familiar with that tool, is it possible you're you asking about the SomaticIndelDetector? I think think that might be the same thing that has been renamed. If so, this tool used to be part of GATK, but we have transferred it to a different team's codebase -- still here at the Broad, but in the Cancer group. I'm not sure whether or how they're making that tool available to the community. I have passed the question along to the appropriate person and will let you know when I get an answer. In the meantime, you may find it interesting to look at their website, which includes a list of tools for cancer genome analysis: http://www.broadinstitute.org/cancer/cga/