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/