Joint estimation of demography and contamination for nuclear ancient DNA

Project maintained by Fernando Racimo and Gabriel Renaud

About.

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. For estimating present-day human contamination for mitochondrial data, please see schmutzi here: http://grenaud.github.io/schmutzi/.

How does it work?.

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:

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.

How do I download and install dice ?

We recommend to git clone the repository: 
git clone  --depth=1 --recursive https://github.com/grenaud/dice.git
The installation instructions are found in the README. Details about running the software are also found in the README. To build the software, please have installed the following:
For C++: