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Joint estimation of contamination for ancient DNA and endogenous mitochondrial genome inference

Download this project as a tar.gz file


Sequencing of mitochondrial DNA from ancient samples is often used as a preliminary strategy to ensure recoverable endogenous DNA, that is DNA endogenous to sample of interest. Deamination of the molecules, a common form of damage to aDNA, can interfere with alignment and consensus calling against a reference sequence. For hominin samples, contamination from modern humans involved in the excavation and experimental process can further complicate consensus calling meaning quantification of this contamination is crucial in evaluating which ancient samples have the most potential for further downstream analyses.



schmutzi is an iterative method to estimate contamination for ancient hominin samples and call the endogenous mitochondrial consensus. More precisely, schmutzi is a set of programs aimed at ancient DNA data which use a Bayesian maximum a posteriori algorithm that can :

The model used has been extended to the nuclear genome and implemented into a software called DICE:

Download and installation

To download, either download the tar.gz file from the link on top of the page or, if you have git installed, download the latest version using:
git clone  --depth=1 --recursive
Installation instructions are provided in the file


Documentation and usage is found in the file

Test Data

There is test data provided as part of the package along with command line. See for the data used in the manuscript.


Please cite the following:

Renaud, Gabriel, Viviane Slon, Ana T. Duggan, and Janet Kelso. "Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA." Genome Biology 16, no. 1 (2015): 1-18.

Support or Contact

The README contains several common problems, please refer to them. The program was developed and is maintained by Gabriel Renaud (@grenaud) at the Max Planck Institute for Evolutionary Anthropology.