Nutanix now provide a hypervisor agnostic platform, which is great however if you do not clearly state which hypervisor you want it will come out of the factory with KVM installed, as I found out on my last project.
When I contacted Nutanix to ask what to do to change it to Hyper-V I was braced for, send it back or when have to send you an engineer however I was told that it was simple and I could do it myself.
So, all you have to do is go to the Nutanix portal, download the hypervisor image you want. Once you have the ISO, you need to configure the IPMI interface with an IP address so you can connect to the BMC controller (think iLO or iDRAC), mount the ISO and boot to the virtual CD. Once booted, the installer will ask you if you want to keep the existing settings (name, serial number, etc) say yes and leave it to do its thing, once it has rebooted you will have a Hyper-V 2012 R2 Server with the Controller VM installed and working.
You can now go on and configure your Nutanix cluster.
I will add some pictures to this soon.