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ATLAS: Analysis Tools for Low-depth and Ancient Samples

Vivian Link, Athanasios Kousathanas, Krishna Veeramah, Christian Sell, Amelie Scheu, View ORCID ProfileDaniel Wegmann
doi: https://doi.org/10.1101/105346
Vivian Link
1Department of Biology, University of Fribourg, Fribourg, 1700, Switzerland,
2Swiss Institute of Bioinformatics, Fribourg, 1700, Switzerland,
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Athanasios Kousathanas
1Department of Biology, University of Fribourg, Fribourg, 1700, Switzerland,
2Swiss Institute of Bioinformatics, Fribourg, 1700, Switzerland,
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Krishna Veeramah
3Department of Ecology and Evolution, Stony Brook University, 11794, Stony Brook, USA
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Christian Sell
4Institute of Anthropology, Johannes Gutenberg-University, Mainz, 55128, Germany.
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Amelie Scheu
4Institute of Anthropology, Johannes Gutenberg-University, Mainz, 55128, Germany.
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Daniel Wegmann
1Department of Biology, University of Fribourg, Fribourg, 1700, Switzerland,
2Swiss Institute of Bioinformatics, Fribourg, 1700, Switzerland,
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  • ORCID record for Daniel Wegmann
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Abstract

Summary Post-mortem damage (PMD) obstructs the proper analysis of ancient DNA samples. Currently, PMD can only be addressed by adjusting sequencing quality scores or by removing potentially damaged data. Here we present ATLAS, a suite of methods to analyze ancient samples that properly account for PMD. It works directly from raw BAM files and contains all necessary methods to infer patterns of PMD, recalibrate base quality scores and accurately genotype ancient DNA, along with many other useful tools. ATLAS enables the building of complete and customized pipelines for the analysis of ancient and low-depth samples in a very user-friendly way. Using simulations we show that, in the presence of PMD, a dedicated pipeline of ATLAS calls genotypes more accurately than the state of the art pipeline of GATK combined with mapDamage 2.0.

Availability ATLAS is an open-source C++ program freely available at https://bitbucket.org/phaentu/atlas.

Contact Daniel.Wegmann{at}unifr.ch

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted February 02, 2017.
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ATLAS: Analysis Tools for Low-depth and Ancient Samples
Vivian Link, Athanasios Kousathanas, Krishna Veeramah, Christian Sell, Amelie Scheu, Daniel Wegmann
bioRxiv 105346; doi: https://doi.org/10.1101/105346
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ATLAS: Analysis Tools for Low-depth and Ancient Samples
Vivian Link, Athanasios Kousathanas, Krishna Veeramah, Christian Sell, Amelie Scheu, Daniel Wegmann
bioRxiv 105346; doi: https://doi.org/10.1101/105346

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