Hello,

I am looking to understand the PLINK .genome file, and I would appreciate any help you could give me with a few questions I have.

The plink --genome operation results in a .genome output file whose headers are outlines here: http://zzz.bwh.harvard.edu/plink/ibdibs.shtml

1. I can understand the Z0, Z1 and Z2 fields as percent-unrelated, percent-half-identical and percent-full-identical. PI_HAT is derived, so I understand how it's calculated, but I'd love some insight on the significance of the number and why it is calculated the way it is.

2. Does the PHE field depend on the specified affected status for IID1 and IID2? In the pairwise code (AA, AU, UU), does A stand for Affected and U for unaffected?

3. What I do not understand are the DST, PPC and RATIO fields, as well as the IBS0, IBS1, IBS2, HOMHOM and HETHET fields in the extended output. If someone could point to me material on this "PPC test", as well as what the "non missing loci" mean in the IBS fields, I can better understand this file.

Thank you!

--
Ram