This is the place to post any questions, problems or bug reports for the GATK development team to look at.
We try to respond within a reasonably short amount of time, but keep in mind that we are not support agents -- we are programmers and scientists, with code to write and data to analyze. In the same spirit, because our resources are limited and our time precious, we ask that you please consult all available sources of information in the GATK Guide and previous posts in this forum before posting your question here, and above all, refrain from posting problems that are clearly identified as USER ERRORS in the GATK's output. Thank you!
We also welcome discussions and responses from everyone in the user community. If you know something, say something!