The figures in this paper use pretty deceptive scales. To be clear, DeepVariant is 0.5% better than a tool built in ~2010 (GATK), on DeepVariant's best test.
GATK is still the standard, not because better variant callers don't exist, but because it's more important that everyone uses the same tool for comparisons between studies.
GATK is still the standard, not because better variant callers don't exist, but because it's more important that everyone uses the same tool for comparisons between studies.