1. bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS).
- Author
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Malaspinas AS, Tange O, Moreno-Mayar JV, Rasmussen M, DeGiorgio M, Wang Y, Valdiosera CE, Politis G, Willerslev E, and Nielsen R
- Subjects
- Genetics, Population, Genome, Human genetics, Genotype, Humans, Genomics methods, Phylogeography methods, Software
- 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., (© The Author 2014. Published by Oxford University Press.)
- Published
- 2014
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