I've been looking at the release notes for GATK 3.7. I would like to know if turning on the -newQual setting for HaplotypeCaller would be considered Best Practice for WGS and WES pipelines.
No, it's not yet used in our production pipeline because we are still waiting on some final evaluations, but it will be the default in GATK4. So expect to see an announcement to that effect later this quarter.
Thank you for your help.