Sib-pair Command: mztwin


ClassAnalysis and data manipulation command
Namemztwin
Arguments [<monozygosity_indicator> |(<zygosity_score> >|>=|<|<=|==|^= <threshold>)] [clean|delete]

Using a binary or quantitative trait which indicates which sib pairs are monozygotic twin pairs, list markers at which the twins carry discordant genotypes. Gives proportion discordance for each marker. This is useful for estimating genotyping error rates. The clean option deletes genotypes for pairs where there is an inconsistency, and fills in missing genotypes where that for the cotwin is available. The delete option drops the member of the pair with the fewest nonmissing phenotypes, and averages (across the pair) quantitative phenotypes where both are observed.

Example:

....
>> set locus mzdz quantitative
>> set twin mzdz merlin
>> mztwin clean

Monozygotic twin pair error checking.


MZ sibships        Number   Pedigrees
------------------ ------   -----------
MZ singletons *        23    004401 004401 003255 003476 003476 011069 011069
MZ pairs              483    002422 001986 009229 003554 003733 003120 003457
MZ triplets **          3    368023 500021 24340

Pedigree    Person1        Person2     Con     Dis   %Dis
45240       4524001        4524002      59       2    3.3  rs22141 rs2124132
23452       2345201        2345202     174       1    0.6  rs534370
23532       2353201        2353202     148       3    2.0  rs2360589 rs37378
....


Locus       Dis  Pairs    Prop
---------  ----- -----  ------
rs346345       6   150  0.0400
rs23432        6   153  0.0392
rs22141        6   161  0.0373
....

Checked   356 twin pairs.
Skipped   148 ungenotyped (same-sex) pairs.


Pedigree      Twin1          Twin2       Locus       Geno1   Geno2
45240       4524001        4524002       rs22141      A/G     A/A
45240       4524001        4524002       rs2124132    A/G     A/A
....

Reconciled 21019 MZ twin pair genotypes.
Deleted      148 inconsistent MZ twin pair genotypes.



ClassAnalysis and data manipulation command
Namemztwin find
Arguments [<monozygosity_indicator> ]

Using the currently active markers, identify likely MZ twin pairs as pairs of relatives (in the same pedigree) sharing 99.5% or greater marker concordance. A value indicating membership of an MZ twin pair will be written to the currently active twin indicator trait (see set twin) or to the named variable. value of one will be written for members of an MZ twin pair.

Example:


> mzt find                                                                   

------------------------------------------------
Searching for likely MZ twin pairs or duplicates
------------------------------------------------
Maximum number of marker loci = 1948
Writing MZ twin indicator to "mzdz".

Pedigree       ID1          ID2          Concordance
Ped0002        1            2            1808/1808 (1.0000)
Ped0003        1            2            1808/1808 (1.0000)
Ped0009        1            2            1808/1808 (1.0000)
Ped0010        1            2            1808/1808 (1.0000)
...
Ped9999        1            2            1582/1584 (0.9987)

Total putative MZ pairs = 1554

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