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bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)
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.orgSupplementary information
Supplementary data are available at Bioinformatics online.Many UC-authored scholarly publications are freely available on this site because of the UC's open access policies. Let us know how this access is important for you.