The AnnotatePairOrientation tool and non-Mutect2 VCF input - only "0,0:0,0" values in the output


I would like to annotate VCF files (not generated by Mutect2) with F1R2/F2R1 read support counts. I was happy to find out that a dedicated tool is now provided for this very purpose (AnnotatePairOrientation), but even though I have tried the tool in multiple versions of GATK 4 (ranging from to and never received an error, I am still left out without useful output: for all the annotated variants, the reported F1R2:F2R1values are "0,0:0,0". I do not expect the input BAM and VCF files to be at fault, because Mutect2 running on the same inputs (with the option "--genotyping-mode" set to "GENOTYPE_GIVEN_ALLELES") reports non-zero F1R2/F2R1 counts. The tool's documentation page doesn't seem to list any specific requirements regarding the input VCF files (anything that could, let's say, cause the tool to output default zero values due to some information missing from the INFO or FORMAT fields).
Is any good soul out there able to confirm that the tool either a) works as intended on their data, or b) only outputs zeroes for them as well?

With many thanks and best regards,


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