I keep running into the following error when trying to follow GATKs 'best practice workflow' for Somatic short variant discovery (SNVs + Indels):
Warning: CreateSomaticPanelOfNormals is a BETA tool and is not yet ready for use in production
I have tried both gatk-220.127.116.11 and gatk-18.104.22.168, I have supplied a .list for --vcfs, and tried supplying each file for --vcfs.
I have Normal, Tumor, Recurrence samples for each patient. If I cannot get CreateSomaticPanelOfNormals working, can I emit it downstream for Mutect2?