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.

Originalsprog	Engelsk
Tidsskrift	Bioinformatics
Vol/bind	30
Udgave nummer	20
Sider (fra-til)	2962-2964
Antal sider	3
ISSN	1367-4803
DOI	https://doi.org/10.1093/bioinformatics/btu410
Status	Udgivet - 15 okt. 2014

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10.1093/bioinformatics/btu410Licens: CC BY-NC

btu410Forlagets udgivne version, 168 KBLicens: CC BY-NC

Citationsformater

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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

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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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JO - Bioinformatics

JF - Bioinformatics

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ER -

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

Abstract

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