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AS_QD annotation missing for GATK

timhtimh brissy, AUMember

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

java -Xmx64G -jar gatk-package- CombineGVCFs -R ref.fa -G StandardAnnotation -G AS_StandardAnnotation -V [...] -O combined.vcf.gz -A AS_QualByDepth

java -Xmx64G -jar gatk-package- 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 quality calcs?

Issue · Github
by Tiffany_at_Broad

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