Adding 'dummy' parents using PLINK
The majority of programs that handle pedigree data require the each pedigree be graphically connected. For example, since Merlin requires that each pedigree be graphically connected, you cannot use Mega2 to convert to Merlin format unless you've adjusted your pedigree structures to be graphically connected. For example, if a pedigree file contains two siblings but it only contains their mother, then it is not clear from the pedigree file itself if the siblings are full siblings (sharing a common father) or half siblings (each with a different father). The missing father(s) would need to be inserted into the pedigree file before Mega2 could process the pedigree.
As the Mega2 documentation states:
Mega2 is designed so that it either needs both Father and Mother to be defined or for both to be undefined, you cannot have one defined and the other set to unknown. As the SimWalk2 documentation explains: “To reconstruct the relationships between individuals properly