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

  • Author(s): Malaspinas, Anna-Sapfo
  • Tange, Ole
  • Moreno-Mayar, José
  • Rasmussen, Morten
  • DeGiorgio, Michael
  • Wang, Yong
  • Valdiosera, Cristina
  • Politis, Gustavo
  • Willerslev, Eske
  • Nielsen, Rasmus
  • et al.
Abstract

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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