In GATK 3.8, we used readbackedphasing to merge SNPs into a MNP, but I did not see this tool listed for 4.0
Does mutect2 do this now?
There is no tool in GATK4 to merge MNPs. You will need to look outside of GATK or use version 3.8. Note, there are plans to make a tool that does this, but it has not been implemented yet.