SPLINK (Sib Pair Linkage analysis) is a program for linkage analysis using affected sib pairs. It uses the method of maximum likelihood to estimate the probability that two affected sibs share 0, 1 or 2 autosomal marker haplotypes identically by descent (IBD). For marker haplotypes on the X-chromosome, IBD sharing of maternal haplotypes only is considered. Parental marker data need not be present (although, of course, they help) and neither IBD status or phase of marker haplotype need be known. When full parental data are not available, the uncertainty in assigning parental haplotypes may be reduced by including data on sibs who are either unaffected or of unknown affection status. When all available data still permit ambiguity for parental haplotypes, the population haplotype frequencies become relevant, and these are estimated internally, again using the method of maximum likelihood.
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Holmans, P. and Clayton, D. (1995).
Efficiency of typing unaffected relatives in an affected sib-pair linkage study with single locus and multiple tightly-linked markers.
Am J Hum Genet 57:1221-1232.