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

Malaspinas, A.S.; Tange, O.; Moreno-Mayar, J.V.; Rasmussen, M.; DeGiorgio, M.; Wang, Y.; Valdiosera, C.E.; Politis, G.; Willerslev, E.; Nielsen, R.

doi:10.1093/bioinformatics/btu410

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

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Serval ID

serval:BIB_699EFB431D16

Type

Article: article from journal or magazin.

Collection

Publications

Institution

Production externe

Title

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

Journal

Bioinformatics

Author(s)

Malaspinas A.S., Tange O., Moreno-Mayar J.V., Rasmussen M., DeGiorgio M., Wang Y., Valdiosera C.E., Politis G., Willerslev E., Nielsen R.

ISSN

1367-4811 (Electronic)

ISSN-L

1367-4803

Publication state

Published

Issued date

15/10/2014

Peer-reviewed

Oui

Volume

Number

Pages

2962-2964

Language

english

Notes

Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish

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.

Keywords

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

DOI

10.1093/bioinformatics/btu410

Pubmed

24974206

Web of science

000343083600017

Open Access

Yes

Create date

16/06/2019 15:10