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m2 gatk4 oncotated maf output includes rejected mutations #4421
Lee, just letting you know I've tagged you in a forum question.
The oncotated maf output includes many rejected mutations (using the configuration from the public spaces). This is bad practice. The unfiltered VCF (or preferably a tsv) should have these sites but we should not be annotating them or putting them in final outputs.
This Issue was generated from your [forums]