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
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.
Does the
PHE
field depend on the specified affected status forIID1
andIID2
? In the pairwise code (AA
,AU
,UU
), doesA
stand for Affected andU
for unaffected?What I do not understand are the
DST
,PPC
andRATIO
fields, as well as theIBS0
,IBS1
,IBS2
,HOMHOM
andHETHET
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
What have you searched so far, dear Ram?
It's been 10 months, so the context has changed a LOT :-)
I think I managed some sort of solution, but cannot recall what it was.
Upvote for effort...