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fixed Mutect2 bug that overfiltered by one variant #6101

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merged 2 commits into from
Aug 21, 2019
Merged

fixed Mutect2 bug that overfiltered by one variant #6101

merged 2 commits into from
Aug 21, 2019

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davidbenjamin
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@takutosato This fixes two sources of the bug:

  • Threshold was equal to the error probability of the worst unfiltered variant, but filtering was based on errorProbability > threshold - EPSILON, which ends up filtering this variant.
  • Threshold was adjusted and filtering parameters were changed on the last pass, which means that error probabilities could shift slightly relative to those used to set the threshold.

takutosato
takutosato approved these changes Aug 20, 2019
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...ain/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/FilterMutectCalls.java Outdated
@@ -104,7 +104,7 @@
private static final int NUMBER_OF_LEARNING_PASSES = 2;

@Override
protected int numberOfPasses() { return NUMBER_OF_LEARNING_PASSES + 1; }
protected int numberOfPasses() { return NUMBER_OF_LEARNING_PASSES + 2; } // {@coode NUMBER_OF_LEARNING_PASSES} passes for learning, one for the threshold, and one for calling
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coode -> code

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fixed

@davidbenjamin davidbenjamin merged commit 7b2853f into master Aug 21, 2019
@davidbenjamin davidbenjamin deleted the db_threshold branch August 21, 2019 02:50
@andrewrech andrewrech mentioned this pull request Aug 27, 2019
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@takutosato takutosato takutosato approved these changes

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@davidbenjamin @takutosato