AS_QD annotation missing for GATK 4.1.3.0

[tmm211]

A user reported that they are no longer getting the AS_QD annotation when using GATK 4.1.3.0.
Laura said this was a regression.

This is what the user ran:
java -Xmx64G -jar gatk-package-4.1.3.0-local.jar CombineGVCFs -R ref.fa -G StandardAnnotation -G AS_StandardAnnotation -V [...] -O combined.vcf.gz -A AS_QualByDepth

java -Xmx64G -jar gatk-package-4.1.3.0-local.jar GenotypeGVCFs -R ref.fa -V combined.vcf.gz -O genotyped.vcf.gz -G StandardAnnotation -G AS_StandardAnnotation -A AS_QualByDepth

This Issue was generated from your [forums]
[forums]: https://gatkforums.broadinstitute.org/gatk/discussion/24427/as-qd-annotation-missing-for-gatk-4-1-3-0/p1