Tool: DICE: Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans
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gravatar for Gabriel R.
3.7 years ago by
Gabriel R.2.6k
Danmarks Tekniske Universitet
Gabriel R.2.6k wrote:

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/

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Gabriel R.2.6k
1

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.

ADD REPLYlink written 3.7 years ago by genomax75k

A tool announcement, sorry forgot the link to the paper and software. Adding it now, thanks!!

ADD REPLYlink written 3.7 years ago by Gabriel R.2.6k
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