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

Authors :: Malaspinas AS
Tange O
Moreno-Mayar JV
Rasmussen M
DeGiorgio M
Wang Y
Valdiosera CE
Politis G
Willerslev E
Nielsen R
Source :: Bioinformatics (Oxford, England) [Bioinformatics] 2014 Oct 15; Vol. 30 (20), pp. 2962-4. Date of Electronic Publication: 2014 Jun 28.
Publication Year :: 2014
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.<br />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).<br />Contact: bammds-users@nongnu.org<br />Supplementary Information: Supplementary data are available at Bioinformatics online.<br /> (© The Author 2014. Published by Oxford University Press.)

Subjects :: Genetics, Population
Genome, Human genetics
Genotype
Humans
Genomics methods
Phylogeography methods
Software

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