Summary: determine likely haplotype for individuals Argument: < 'on' or 'off' > Default: displays the current setting
When the 'haplotype' option is turned on, the 'scan' command will report the most likely inferences made regarding the haplotypes of the individuals in each pedigree. The haplotypes for founders will be displayed on the screen and the haplotypes for all individuals analyzed will be stored in a file called haplo.dump. In addition, if the 'postscript output' option is 'on', the entire pedigree (with haplotypes and recombinations indicated) will be drawn in a postscript file suitable for printing and displaying.
The haplotypes displayed represent the maximum-likelihood set of inheritance vectors that explain the data. After all markers have been scanned in a pedigree the most likely path through all of the markers is recreated - thus yielding the most likely pattern of inheritance at each marker and likely positions of recombinants. Among nearby markers that show no recombination, these haplotypes are usually unambiguous, but in cases where recombinants are present (especially in small sibships of 2 or 3 individuals), the haplotypes may be imperfect and simply represent the most likely choice out of several valid choices. For example, the most likely position of recombinants is shown in the PostScript output but other placements may be possible but simply less likely due to considerations of map interval size and allele frequency at certain markers.
Haplotypes can be invaluable tools both analytically (in searching for shared genomic regions of distantly related affected individuals and indicating linkage disequilibrium between markers) and practically (in searching for errors in genotyping which usually manifest themselves as excessive obligate recombination in an individual or pedigree). In cases where two original parents are both untyped for all loci, haplotypes will be displayed for them as usual but it must be noted that the assignments could be reversed (i.e., the two haplotypes assigned to the original father could actually belong to the original mother and vice-versa).
N.B. - at this time the drawing code is not yet complete and while nearly complete, certain pedigree structures (such as those containing marriage loops, inbreeding loops, or individuals with many spouses) may not always be drawn properly. Refer to the results in the haplo.dump file if it appears the pedigree has not been drawn properly.
'Haplotype' is ON when GENEHUNTER is started.