Our team has been using the Exome Germline Single Sample WARP (https://app.terra.bio/#workspaces/warp-pipelines/Exome-Analysis-Pipeline/workflows/warp-pipelines/1-ExomeGermlineSingleSample) on Terra.
We noticed that the reduced GQ resolution due to the new 4 GQ band schema-based GVCF reblocking step severely impacts downstream de novo calling.
I was wondering if there is any specific approach that you would suggest to reverse the reblocking step and get the default HaplotypeCaller GVCF. We just kept the standard workflow outputs. Ideally, I would like to avoid rerunning all samples across the entire workflow and try to get the desired GVCFs directly on Terra starting from either the reblocked GVCFs or CRAMs stored in the analysis workspace.
Thank you in advance for your help.
Same post on General Discussion GATK forum: https://gatk.broadinstitute.org/hc/en-us/community/posts/17193888661275-Best-strategy-to-reverse-the-GVCF-reblocking-step-on-Terra