Introduction

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.

Publications

  1. bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS).
    Cite this
    Malaspinas AS, Tange O, Moreno-Mayar JV, Rasmussen M, DeGiorgio M, Wang Y, Valdiosera CE, Politis G, Willerslev E, Nielsen R, 2014-10-01 - Bioinformatics (Oxford, England)

Credits

  1. Anna-Sapfo Malaspinas
    Developer

    Centre for GeoGenetics, Natural History Museum of Denmark, Argentina

  2. Ole Tange
    Developer

    Centre for GeoGenetics, Natural History Museum of Denmark, Argentina

  3. José Víctor Moreno-Mayar
    Developer

    Centre for GeoGenetics, Natural History Museum of Denmark, Argentina

  4. Morten Rasmussen
    Developer

    Centre for GeoGenetics, Natural History Museum of Denmark, Argentina

  5. Michael DeGiorgio
    Developer

    Centre for GeoGenetics, Natural History Museum of Denmark, Argentina

  6. Yong Wang
    Developer

    Centre for GeoGenetics, Natural History Museum of Denmark, Argentina

  7. Cristina E Valdiosera
    Developer

    Centre for GeoGenetics, Natural History Museum of Denmark, Argentina

  8. Gustavo Politis
    Developer

    Centre for GeoGenetics, Natural History Museum of Denmark, Argentina

  9. Eske Willerslev
    Developer

    Centre for GeoGenetics, Natural History Museum of Denmark, Argentina

  10. Rasmus Nielsen
    Investigator

    Centre for GeoGenetics, Natural History Museum of Denmark, Argentina

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Summary
AccessionBT006891
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionArgentina
Submitted ByRasmus Nielsen