How --genome calculates its results

[Rocio Mariana]

Hi,

I was wondering if someone could help me to learn how does plink calculate some values for the --genome IBD relations.

    FID1    IID1    FID2    IID2   RT     EZ      Z0         Z1        Z2    PI_HAT   PHE      DST      PPC     RATIO

    0001    0001   0002   0002  UN    NA  0.8157  0.0180  0.1663  0.1753    -1     0.867248  0.3245  1.9714

This is a header and one example of a result of --genome in a relatedness.genome file.

I notice that PI_HAT, that is the "Proportion IBD" is calculated as: P(IBD=2) + 0.5*P(IBD=1), then it would be 0.1663 + 0.5*0.0180 that results on 0.1753.

Since, Z0 P(IBD=0), Z1 P(IBD=1) and Z2 P(IBD=2), my question is, how this values are calculated, and what does IBD=0 means?

Thanks!

[Christopher Chang]

This is explained in detail in the original PLINK paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950838/ ); start reading from "We use a method-of-moments approach"...

[Baraka Mkumbe]

How can I identify identical twins in my samples? I have already checked for relatedness using --genome cmd in plink and obtained the z0, z1,z2 and pihat value

[Christopher Chang]

The currently-recommended method is to use plink 2.0's --make-king-table command, which uses a formula that is more reliable than --genome's at identifying close relations.  E.g.

plink2 \

  --bfile <your fileset prefix> \

  --make-king-table \

  --king-table-filter 0.354 \

  --out identical_twins

(See the third paragraph of the linked documentation for an explanation of the 0.354 cutoff.)

[Baraka Mkumbe]

Thanks Christopher

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