d) Where do I find the strand artifact score calculated by mutect2? I see how it is calculated in section II.D of the mutect2 white paper, but I'm wondering if it is possible to have the score emitted in the VCF? In my VCF header I see "STRANDQ: Phred-scaled quality of strand bias artifact" which sounds like the score strand artifact score described in the white paper, but none of the records in my VCF have "STRANDQ" in the INFO field. I am seeing this behavior in with both GATK 4.1.8 and 4.2.0. I tried running mutect2 with "--enable-all-annotations true" and now I see other INFO fields related to strand bias populated, including "FS: Phred-scaled p-value using Fisher's exact test to detect strand bias" and "SOR: Symmetric Odds Ratio of 2x2 contingency table to detect strand bias". However, from the white paper I believe that STRANDQ (not FS or SOR) is used for adding the "strand_bias" filter - is that correct? On a broader note it would be really helpful if the white paper more directly described how the calculations correspond to the INFO/FORMAT fields in the mutect2 VCFs (see this post for a more detailed request along these lines).
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