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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
Hi,
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?
Paul
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Answers
I can provide example BAM files that I think demonstrates the bug if that helps.
Hi Paul,
The devs have completely rewritten MuTect based on the HaplotypeCaller internals, and are in the final phases of validation before the new version is released, so we cannot commit any effort to fixing bugs in the old version which will soon be deprecated. Sorry for the inconvenience.