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Published on: December 7, 2021
bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)
Anna-Sapfo Malaspinas1, Ole Tange1, José Víctor Moreno-Mayar1
1Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina.
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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