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

被引：39

作者：

Malaspinas, Anna-Sapfo ^{[1
]}

Tange, Ole ^{[1
]}

Moreno-Mayar, Jose Victor ^{[1
]}

Rasmussen, Morten ^{[1
,2
]}

DeGiorgio, Michael ^{[3
]}

Wang, Yong ^{[4
,5
,6
]}

Valdiosera, Cristina E. ^{[1
,7
]}

Politis, Gustavo ^{[8
,9
]}

Willerslev, Eske ^{[1
]}

Nielsen, Rasmus ^{[1
,4
,5
]}

机构：

[1] Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, DK-1350 Copenhagen K, Denmark

[2] Stanford Univ, Sch Med, Dept Genet, Stanford, CA 94305 USA

[3] Penn State Univ, Dept Biol, University Pk, PA 16802 USA

[4] Univ Calif Berkeley, Ctr Theoret Evolutionary Genom, Dept Integrat Biol, Berkeley, CA 94720 USA

[5] Univ Calif Berkeley, Ctr Theoret Evolutionary Genom, Dept Stat, Berkeley, CA 94720 USA

[6] Ancestry Com DNA LLC, San Francisco, CA 94107 USA

[7] La Trobe Univ, Fac Humanities & Social Sci, Dept Archaeol Environm & Community Planning, Melbourne, Vic 3086, Australia

[8] Univ Ctr Prov Buenos Aires, INCUAPA CONICET, RA-7600 Olavarria, Argentina

[9] Fac Ciencias Nat & Museo, RA-1900 La Plata, Argentina

来源：

BIOINFORMATICS | 2014年 / 30卷 / 20期

基金：

新加坡国家研究基金会;

关键词：

SEQUENCE; NEANDERTHAL; PATTERNS;

D O I：

10.1093/bioinformatics/btu410

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A 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.

引用

页码：2962 / 2964

页数：3

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