I want to check the strand bias in the vcf file.
So I check default annotation (group).
> Mutect2 : Default annotation group = [StandardMutectAnnotation]
> HaplotypeCaller : Default annotation group = [StandardAnnotation, StandardHCAnnotation]
I think FOXOG(F1R2, F2R1) is the one to measure strand bias among Mutect2's default annotation variant calling.
also, I think SOR is the one to measure strand bias among HaplotypeCaller's default annotation variant calling, and I checked that SOR is printed on application StandardAnnotation group.
I have 2 questions ;
Q1 : Why does Mutect2 to StandardAnnotation group not apply by default, and therefore not print SOR?
Q2 : Because SOR is not printed by default, I thought I should see FOXOG to check the strand bias of the variant called with Mutect2. Does FOXOG represent strand bias better than SOR when calling with Mutect2? If yes, why?
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