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m2 gatk4 oncotated maf output includes rejected mutations #4421

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sooheelee opened this issue Feb 16, 2018 · 1 comment

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commented Feb 16, 2018

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]
[forums]: https://gatkforums.broadinstitute.org/gatk/discussion/11440/m2-gatk4-oncotated-maf-output-includes-rejected-mutations/p1

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commented Feb 16, 2018

Lee has answered as had I.

@sooheelee sooheelee closed this Feb 16, 2018

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