Sib-pair Command: test duplicate


ClassAnalysis and data manipulation command
Nametest duplicate
Arguments [ids [merge]] [<indicator>].

Test if genetically identical individuals are present in the dataset. Write an indicator value for each individual tested to a phenotypic variable if specified. If the ids modifier is specified, then testing is limited to persons with the same individual ID in different pedigrees. If found, and the merge modifier has been specified, then Sib-pair will reciprocally fill in missing data in one record using data from the other record. A duplication indicator can be written to a phenotype variable if this is specified.

The total number of discordances per locus is written to the locstat variable, accessible using the summary and drop commands. This is to allow diagnosis of marker quality.

Example:

>> set loc m1 mar
>> set loc m2 mar
>> set loc m3 mar
>> set loc m4 mar
>> set loc m5 mar
>> set loc m6 mar
>> set loc m7 mar
>> set loc m8 mar
>> set loc m9 mar
>> set loc m10 mar
>> set loc m11 mar
>> set loc m12 mar
>> read pedigree inline
1 1 x x m 1/1 1/2 1/2 2/2 1/2 1/1 1/2 2/2 2/2 2/2 1/2 1/1
1 2 x x m 1/1 1/2 1/2 2/2 1/2 1/1 1/2 2/2 2/2 2/2 1/2 2/2
;;;;
>> run
>> set twin err 0.15 10

Monozygotic twin or duplicate mistyping rate = .1500    
Minimum number of markers to be used         = 10

>> test dup

Twin indicator variable is not currently defined.


------------------------------------------------
Searching for likely MZ twin pairs or duplicates
------------------------------------------------
Maximum number of marker loci = 12
Number of individuals tested  = 2
Number of individuals skipped = 0 (<10 markers)
Threshold for nonidentity     = 10 markers (0.833)

Ped1           ID1         Ped2           ID2          Concordance
1              1           1              2            11/12 (0.9167)

Total putative duplicates     = 1

>> sum

Test: "Number of discordances".

Total number of tests = 12

Locus              Chr Position   Statistic
------------------ --- ---------- -----------
m12                          (27)    1.000     
m4                           (19)    0.000     
m3                           (18)    0.000     
m2                           (17)    0.000     
m1                           (16)    0.000     

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