bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)

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Malaspinas, Anna-Sapfo
Tange, Ole
Moreno-Mayar, J. Víctor
Rasmussen, Morten
DeGiorgio, Michael
Wang, Yong
Valdiosera, Cristina
Politis, Gustavo
Willerslev, Eske
Nielsen, Rasmus
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2014
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Summary: We present bammds, a practical tool that allows visualization of samples sequenced by second-generation sequencing when compared with a reference panel of individuals (usually genotypes) using a multidimensional scaling algorithm. Our tool is aimed at determining the ancestry of unknown samples—typical of ancient DNA data—particularly when only low amounts of data are available for those samples. Availability and implementation: The software package is available under GNU General Public License v3 and is freely available together with test datasets https://savannah.nongnu.org/projects/bammds/ . It is using R ( http://www.r-project.org/ ), parallel ( http://www.gnu.org/software/parallel/ ), samtools ( https://github.com/samtools/samtools ). Contact: bammds-users@nongnu.org Supplementary information: Supplementary data are available at Bioinformatics online.

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Bioinformatics

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30

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20

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© The Author(s) 2014. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Population, Ecological and Evolutionary Genetics

Mathematical Sciences

Biological Sciences

Information and Computing Sciences

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