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-126.96.36.199 and gatk-188.8.131.52, 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?