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

Anna Sapfo Malaspinas, Ole Tange, José Víctor Moreno-Mayar, Morten Rasmussen, Michael DeGiorgio, Yong Wang, Cristina E. Valdiosera, Gustavo Politis, Eske Willerslev, Rasmus Nielsen

Research output: Contribution to journalArticle

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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.

Original languageEnglish (US)
Pages (from-to)2962-2964
Number of pages3
JournalBioinformatics (Oxford, England)
Volume30
Issue number20
DOIs
StatePublished - Oct 15 2014

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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    Malaspinas, A. S., Tange, O., Moreno-Mayar, J. V., Rasmussen, M., DeGiorgio, M., Wang, Y., Valdiosera, C. E., Politis, G., Willerslev, E., & Nielsen, R. (2014). bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS). Bioinformatics (Oxford, England), 30(20), 2962-2964. https://doi.org/10.1093/bioinformatics/btu410