Holiday Notice:
The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
Can GATK mutect2 detect MNPs?

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