The R package has an implementation of a generalized version of CDH test to detect compound heterozygosity (CH).
Zhong K, Karssen LC, Kayser M, Liu F "CollapsABEL: an R library for detecting compound heterozygote alleles in genome-wide association studies." BMC Bioinformatics 2016 https://doi.org/10.1186/s12859-016-1006-9
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