Dear CGA
I have found MuTect very useful and now would like to calling somatic indels. I understand that the SomaticIndelDetector is now depreciated in favor of a tool from the Broad Cancer Group:
Is it currently available?

best and/or latest versions for somatic indel detection

I have a couple of related questions:

Is there an updated version available for external users? If not, what is the best or most recent version for somatic indel detection? Would it be the latest version of SomaticIndelDetector from GATK even though it is deprecated or rather the jar file provided on this CGA site which was used for your publication?



Currently we do not have an updated version of Indelocator for external users.

Gordon Saksena