DICE is a program to infer nuclear contamination from present-day humans in ancient DNA datasets using a Bayesian Markov Chain Monte-Carlo (MCMC). It also co-infers the demography and determines the most likely contamination source.
DICE works by computing the likelihood of finding a certain derived allele as contaminant by using the derived allele frequency in a potentially contaminating population. It is also possible that this derived allele is found endogenously in the sample. Given drift parameters, we compute the probability of observing the 3 following genotypes:
(ancestral , ancestral)
(derived , ancestral)
(derived , derived)
given the derived allele frequency in an anchor population. Since both the contamination rate and the demographic parameters depend on each other, we jointly infer them.
Read our paper here: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005972
See the webpage here: http://grenaud.github.io/dice/
Is this supposed to be an announcement for DICE or a question about DICE? I don't see any links for the program, if former.
A tool announcement, sorry forgot the link to the paper and software. Adding it now, thanks!!