An experimental extension to the discrete Laplace method for Y-STR haplotype frequency estimation

Frequency estimation for Y-STR haplotypes is a challenging problem because limited data are available and complex dependencies exist within the data. As a result, various statistical methods have been proposed for frequency estimation. The discrete Laplace method has been recommended in some contexts by the DNA commission of the ISFG. This method is limited to haplotypes with single integer repeat alleles only at all loci. We propose a generalisation of the method that handles duplicated loci such as DYS385 and less common alleles that are not integer repeats. The extension is implemented in an experimental R package called disclapmix2.