schmutzi

Motivation.

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.

News

June 18, 2018

A new script has been added: bam2makeSchmutziHaplogrep2.pl. This script uses a new version of the command-line haplogrep to go directly from fasta to hsd which contains the haplogroups+confidence

March 23, 2018

bam2prof can now produce substitution rates on the PHRED scale.

Aug 21, 2017 Release v1.5.4

A wrapper script (bam2makeSchmutzi.pl) was updated to generate Makefiles to automate the processing of a large number of aligned bam files. Please note that the BAM files must have been aligned to the mitochondrial genome alone (excluding the nuclear genome).

About.

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 :

contDeam: estimate contamination based on deamination patterns alone (both nuclear and mitochondrial)
endoCaller: call a mitochondrial consensus for the endogenous genome accounting for both contamination and deamination.
mtCont: estimate mitochondrial contamination using the endogenous calls. By scanning a database of modern human putative contamination sources it can identify the most likely contaminant among the database records. An exhaustive non-redundant database of human MTs is provided with the package.

The model used has been extended to the nuclear genome and implemented into a software called DICE: http://grenaud.github.io/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 https://github.com/grenaud/schmutzi.git

Installation instructions are provided in the README.md file

Documentation

Documentation and usage is found in the README.md file

Test Data

There is test data provided as part of the package along with command line. See https://bioinf.eva.mpg.de/schmutzi/ for the data used in the manuscript.

Citing

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.