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

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.

authors

  • Malaspinas, A-S
  • Tange, O
  • Moreno-Mayar, JV
  • Rasmussen, M
  • DeGiorgio, M
  • Wang, Y
  • Valdiosera, CE
  • Politis, G
  • Willerslev, E
  • Nielsen, R

publication date

  • 2014