I can't seem to run the IndelRealigner on reads that contain colons, ":" in the reference scaffold names. The RealignerTargetCreator step works correctly and generates the interval table, but the second, IndelRealigner, step fails. When I look at the generated interval table, I see the interval delimiter is a colon, which I imagine is the problem.
Unfortunately, I have a set of human references that have a colon in every scaffold name, so changing this would be a massive undertaking.
I believe this problem could be solved if you searched for the colon delimiter from the end of the interval string instead of from the beginning, so I'm hoping this a real simple fix.