fastNGSadmix: admixture proportions and principal component analysis of a single NGS sample
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fastNGSadmix : admixture proportions and principal component analysis of a single NGS sample. / Jørsboe, Emil; Hanghøj, Kristian Ebbesen; Albrechtsen, Anders.
In: Bioinformatics, Vol. 33, No. 19, 01.10.2017, p. 3148-3150.Research output: Contribution to journal › Journal article › Research › peer-review
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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
VL - 33
SP - 3148
EP - 3150
JO - Computer Applications in the Biosciences
JF - Computer Applications in the Biosciences
SN - 1471-2105
IS - 19
ER -
ID: 185476071