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all mutations in tumor filtered out as 'artifact_in_normal'


I am trying to run mutect2-gatk4 (Snapshot 13) with the parameters set as in the featured "help-gatk/Somatic-SNVs-Indels-GATK4" firecloud-workspace (including "run_orientation_bias_filter" set as "False") on a previously published WGS cohort of tumor/normal pairs (Bender, Sebastian, et al. Nature medicine (2016)). To create the PON, I used the "mutect2_pon" method from the same workspace.

In the resulting vcf files all mutations found are filtered out as 'artifact_in_normal'. I also tried to run the same method in tumor-only mode on the normals and tumors separately (with a PON created from WGS normals of a different cohort) and I do get a number of different mutations between the tumor and it's paired normal. Do you know what's going on? Is this a format issue, another filter I should deactivate or something else I'm missing?



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