Atlas: analysis tools for low-depth and ancient samples
- Link, Vivian Department of Biology, University of Fribourg, Switzerland, - Swiss Institute of Bioinformatics, Fribourg, Switzerland,
- Kousathanas, Athanasios Department of Biology, University of Fribourg, Switzerland, - Swiss Institute of Bioinformatics, Fribourg, Switzerland,
- Veeramah, Krishna Department of Ecology and Evolution, Stony Brook University, USA and
- Sell, Christian Institute of Anthropology, Johannes Gutenberg-University, Mainz, Germany.
- Scheu, Amelie Institute of Anthropology, Johannes Gutenberg-University, Mainz, Germany.
- Wegmann, Daniel Department of Biology, University of Fribourg, Switzerland, - Swiss Institute of Bioinformatics, Fribourg, Switzerland,
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24.03.2017
Published in:
- bioRxiv. - 2017, p. 105346
English
Summary: Post-mortem damage (PMD) obstructs the proper analysis of ancient DNA samples and can currently only be addressed by removing or down-weighting potentially damaged data. Here we present ATLAS, a suite of methods to accurately genotype and estimate genetic diversity from ancient samples, while accounting for PMD. It works directly from raw BAM files and enables the building of complete and customized pipelines for the analysis of ancient and other low-depth samples in a very user-friendly way. Based on 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.
- Faculty
- Faculté des sciences et de médecine
- Department
- Département de Biologie
- Language
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- English
- Classification
- Biological sciences
- License
- License undefined
- Identifiers
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- RERO DOC 288548
- DOI 10.1101/105346
- Persistent URL
- https://folia.unifr.ch/unifr/documents/305390
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