Optional blacklist VCF to for labeling artifacts in Permutect weak-labeling mode #9136
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LeeTL1220
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Apr 3, 2025
src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/PermutectDatasetEngine.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/PermutectDatasetEngine.java
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LeeTL1220
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Apr 4, 2025
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@LeeTL1220 Small change for Permutect data here, usually irrelevant. In most use cases, it will be possible to train with a GIAB truth VCF to label data. When there is not, this PR allows users to optionally specify a PoN as a hint that unlabeled data are probably actually artifacts.
This should not in any way be interpreted as Permutect using a PoN for variant calling. It has zero effect on our DREAM and Linseq evaluations, which use an NA12878 sample for training.