Class | Analysis and data manipulation command |
Name | mztwin |
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.
Class | Analysis and data manipulation command |
Name | mztwin 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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