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AS_QD annotation missing for GATK 184.108.40.206
I am no longer getting the AS_QD annotation when I use newer versions of GATK, didn;t have the problem with 220.127.116.11. I tried to force with -A AS_QualByDepth
java -Xmx64G -jar gatk-package-18.104.22.168-local.jar CombineGVCFs -R ref.fa -G StandardAnnotation -G AS_StandardAnnotation -V [...] -O combined.vcf.gz -A AS_QualByDepth
java -Xmx64G -jar gatk-package-22.214.171.124-local.jar GenotypeGVCFs -R ref.fa -V combined.vcf.gz -O genotyped.vcf.gz -G StandardAnnotation -G AS_StandardAnnotation -A AS_QualByDepth
Does this maybe have something to do with recent changes 126.96.36.199 quality calcs?