期刊
BIOINFORMATICS
卷 33, 期 19, 页码 3148-3150出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btx474
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资金
- Lundbeck foundation
- Danish National Research Foundation [DNRF94]
- Initiative d'Excellence Chaires d'attractivite, Universite de Toulouse (OURASI)
- Lundbeck Foundation [R215-2015-4174] Funding Source: researchfish
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. Availability and implementation: The admixture estimation method is implemented in C++ and the PCA method is implemented in R. The code is freely available at http://www.popgen.dk/software/index.php/FastNGSadmix
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