No, pixel shift images can be processed by dcrawps, a fork of David Coffin's dcraw software, and freely available, just search for dcrawps.
It is command line, and available as binary for Win (and OSX I think) and source code as well...easily built in Linux and OSX.
It will process the 4 raw images and allow output of a 16 bit tiff.
One of it's nice features is that it will tell you if it finds any artefacts resulting from movement and will make corrections.
Movement artefacts are found by comparing the two raws that were aligned on the green filter, a technique which I think Pentax adopted with the movement correct in the K-1.
Cheers,
Terry