Result of gatk126.96.36.199
Result of gatk188.8.131.52
And the bug may result in an error in the filter step.
@xiucz Could you run it with --tumor-segmentation segments.tsv in 4.0.11 and 4.0.12 and then post both segments.tsv here? They are very small files. This will just take a minute because you do not need to re-run GetPileupSummaries
Also, could you try running both with and without a matched normal?
Finally, it's possible that the old output was not good.