If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
AS_QD annotation missing for GATK 220.127.116.11
I am no longer getting the AS_QD annotation when I use newer versions of GATK, didn;t have the problem with 18.104.22.168. I tried to force with -A AS_QualByDepth
java -Xmx64G -jar gatk-package-22.214.171.124-local.jar CombineGVCFs -R ref.fa -G StandardAnnotation -G AS_StandardAnnotation -V [...] -O combined.vcf.gz -A AS_QualByDepth
java -Xmx64G -jar gatk-package-126.96.36.199-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 188.8.131.52 quality calcs?