bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS).
Where this comes from
- Record sourced from PubMed, PMID 24974206.
- Also identified by DOI 10.1093/bioinformatics/btu410 and PMC identifier 4184259.
- Licence recorded as CC BY-NC.
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Abstract
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. 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). bammds-users@nongnu.org Supplementary data are available at Bioinformatics online.
Medical subject headings
- Genomics
- Phylogeography
- Software