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

Anna Sapfo Malaspinas; Ole Tange; José Victor Moreno Mayar; Morten Rasmussen; Michael DiGiorgio; Yong Wang; Cristina E. Valdiosera Morales; Gustavo Politis; Eske Willerslev; Rasmus Nielsen

doi:10.1093/bioinformatics/btu410

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

Anna Sapfo Malaspinas, Ole Tange, José Victor Moreno Mayar, Morten Rasmussen, Michael DiGiorgio, Yong Wang, Cristina E. Valdiosera Morales, Gustavo Politis, Eske Willerslev, Rasmus Nielsen

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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: [email protected]

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original language	English
Journal	Bioinformatics
Volume	30
Issue number	20
Pages (from-to)	2962-2964
Number of pages	3
ISSN	1367-4803
DOIs	https://doi.org/10.1093/bioinformatics/btu410
Publication status	Published - 15 Oct 2014

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Cite this

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title = "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: [email protected] INFORMATION: Supplementary data are available at Bioinformatics online.",

author = "Malaspinas, {Anna Sapfo} and Ole Tange and {Moreno Mayar}, {Jos{\'e} Victor} and Morten Rasmussen and Michael DiGiorgio and Yong Wang and {Valdiosera Morales}, {Cristina E.} and Gustavo Politis and Eske Willerslev and Rasmus Nielsen",

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doi = "10.1093/bioinformatics/btu410",

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T2 - a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)

AU - Malaspinas, Anna Sapfo

AU - Tange, Ole

AU - Moreno Mayar, José Victor

AU - Rasmussen, Morten

AU - DiGiorgio, Michael

AU - Wang, Yong

AU - Valdiosera Morales, Cristina E.

AU - Politis, Gustavo

AU - Willerslev, Eske

AU - Nielsen, Rasmus

PY - 2014/10/15

Y1 - 2014/10/15

N2 - 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: [email protected] INFORMATION: Supplementary data are available at Bioinformatics online.

AB - 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: [email protected] INFORMATION: Supplementary data are available at Bioinformatics online.

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DO - 10.1093/bioinformatics/btu410

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SN - 1367-4803

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EP - 2964

JO - Bioinformatics

JF - Bioinformatics

IS - 20

ER -

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

Abstract

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