GCHap
This program finds maximum likelihood estimates of haplotype frequencies from a sample of genotyped individuals.
Usage: java GCHap input.par input.ped
where
- input.par is a LINKAGE parameter file
- input.ped is a LINKAGE pedigree file. Only the genotype data from this file are used, the individuals are assumed to be unrelated.
The program uses the gene counting method, or EM algorithm, to iterate between reconstructing the haplotypes and estimating haplotype frequencies.
The results are written to the standard output file. There is a line for each haplotype with a positive frequency MLE, the frequency is given first in the line followed by the alleles of the haplotype. These are followed by two lines for each individual giving the reconstructed haplotypes, one haplotype on each line.
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