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Can GATK mutect2 detect MNPs?
ugabronco
Member
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?
Thanks
Answers
@ugabronco
Hi,
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.
-Sheila