Journal article

+ 1 other files

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,
Show more…
    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
  • English
Classification
Biological sciences
License
License undefined
Identifiers
Persistent URL
https://folia.unifr.ch/unifr/documents/305390
Other files

Statistics

Document views: 106 File downloads:
  • weg_aat.pdf: 172
  • weg_aat_sm.pdf: 54