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Adding annotations to the format field
I am struggling with adding AlleleBalanceBySample and StrandBiasBySample to my joint VCF file. The data through joint VCF were generated with GATK 3.2-2, and I have tried using the VariantAnnotator as well as repeating the GenotypeGVCF step specifying the annotations. I have also tried using the GenotypeGVCFs tool from 3.3-0, but am trying to avoid running the HC again in the interest of time. For the strand bias by sample I can see why the VariantAnnotator approach would fail, as the information is not contained in the joint VCF file, but it is there in the GVCF. For the allele balance by sample it seems the info is already in the joint VCF, so either VariantAnnotation or rerunning GenotypeGVCFs seem like they should work.
I should add that when I do try to add these annotations using GenotypeGVCFs, they are noted in the header ##FORMAT section, but not in the actual F:O:R:M:A:T.
Any clues or hints (or admonitions!) much appreciated.