CHROMIBD computes IBD probabilities between a “target chromosome” and a set of “parental chromosomes” (the method works best without “phantom parental chromosomes”). These chromosomes need to be phased and the program relies only on phased (non-missing) markers in target and parental chromosomes. The program works only with bi-allelic markers such as SNPs.
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T. Druet and F. Farnir (2011)
Modeling of identity-bydescent processes along a chromosome between haplotypes and their genotyped ancestors.
Genetics. 2011 June; 188(2): 409–419.