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AS_QD annotation missing for GATK 4.1.3.0

timhtimh brissy, AUMember

Hi.
I am no longer getting the AS_QD annotation when I use newer versions of GATK, didn;t have the problem with 4.0.8.1. I tried to force with -A AS_QualByDepth

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

Does this maybe have something to do with recent changes 4.0.10.1 quality calcs?
Tim

Issue · Github
by Tiffany_at_Broad

Issue Number
6157
State
open
Last Updated

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