The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
Bug reporting for MuTect
I believe there is a bug in MuTect's indel proximity filter. Specifically, in the way that it detects indels.
This was tested on precompiled 1.1.4 and 1.1.5. I have not tested the latest source code, but it looks like it's still there.
What's the procedure for reporting bugs?