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

Bioinformatics. 2014 Oct 15;30(20):2962-4. doi: 10.1093/bioinformatics/btu410. Epub 2014 Jun 28.

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: [email protected]

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genetics, Population
  • Genome, Human / genetics
  • Genomics / methods*
  • Genotype
  • Humans
  • Phylogeography / methods*
  • Software*