Sib-pair Command: haplotypes


ClassAnalysis and data manipulation command
Namehaplotypes
Arguments <marker1> <marker2> <newmarker> [<threshold>]
mitochondrial|yhaplotype <marker1>...<markerN> <newmarker>

This infers phased genotypes when the two markers are in complete (or near-complete) LD. The threshold sets the maximum number of the rare haplotype that is acceptable when LD is not complete.

If mit or yha have been specified, the marker data must be haploid, and there is no limit to the number of markers that can be combined into a haplotype.

Example:

>> set loc h22 mar
>> hap snp17652 snp18342 h22

Haplotype  Code   Count
--------- -----  ------
   A A      11        8
   A G      12       16
   G A      21       28
   G G      22        0

Created phased genotypes for    41 individuals.

>> hap mit rs2001030 rs3928306 mithap                                         


Mit-Markers: rs2001030-rs3928306
Writing haplotypes to locus "mithap".

 Hap  Count (Founder Prop)   Haplotype
 ----- --------------------  -----------------------
    1        309 (.7537)     G-G
    2         74 (.1949)     G-A
    3         22 (.0515)     A-G
 ----- --------------------  -----------------------

 Number of observed haplotypes =        405
 Number of founder haplotypes  =        272 (out of possible 328)


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