fastNGSadmix: admixture proportions and principal component analysis of a single NGS sample

TY - JOUR

T1 - fastNGSadmix

T2 - admixture proportions and principal component analysis of a single NGS sample

AU - Jørsboe, Emil

AU - Hanghøj, Kristian Ebbesen

AU - Albrechtsen, Anders

PY - 2017/10/1

Y1 - 2017/10/1

N2 - Motivation Estimation of admixture proportions and principal component analysis (PCA) are fundamental tools in populations genetics. However, applying these methods to low- or mid-depth sequencing data without taking genotype uncertainty into account can introduce biases. Results Here we present fastNGSadmix, a tool to fast and reliably estimate admixture proportions and perform PCA from next generation sequencing data of a single individual. The analyses are based on genotype likelihoods of the input sample and a set of predefined reference populations. The method has high accuracy, even at low sequencing depth and corrects for the biases introduced by small reference populations.

AB - Motivation Estimation of admixture proportions and principal component analysis (PCA) are fundamental tools in populations genetics. However, applying these methods to low- or mid-depth sequencing data without taking genotype uncertainty into account can introduce biases. Results Here we present fastNGSadmix, a tool to fast and reliably estimate admixture proportions and perform PCA from next generation sequencing data of a single individual. The analyses are based on genotype likelihoods of the input sample and a set of predefined reference populations. The method has high accuracy, even at low sequencing depth and corrects for the biases introduced by small reference populations.

UR - http://www.scopus.com/inward/record.url?scp=85030685978&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btx474

DO - 10.1093/bioinformatics/btx474

M3 - Journal article

C2 - 28957500

AN - SCOPUS:85030685978

SN - 1367-4803

VL - 33

SP - 3148

EP - 3150

JO - Bioinformatics

JF - Bioinformatics

IS - 19

ER -