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Efficient analysis of large datasets and sex bias with ADMIXTURE
BACKGROUND: A number of large genomic datasets are being generated for studies of human ancestry and diseases. The ADMIXTURE program is commonly used to infer individual ancestry from genomic data. RESULTS: We describe two improvements to the ADMIXTURE software. The first enables ADMIXTURE to infer...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877806/ https://www.ncbi.nlm.nih.gov/pubmed/27216439 http://dx.doi.org/10.1186/s12859-016-1082-x |
Sumario: | BACKGROUND: A number of large genomic datasets are being generated for studies of human ancestry and diseases. The ADMIXTURE program is commonly used to infer individual ancestry from genomic data. RESULTS: We describe two improvements to the ADMIXTURE software. The first enables ADMIXTURE to infer ancestry for a new set of individuals using cluster allele frequencies from a reference set of individuals. Using data from the 1000 Genomes Project, we show that this allows ADMIXTURE to infer ancestry for 10,920 individuals in a few hours (a 5 × speedup). This mode also allows ADMIXTURE to correctly estimate individual ancestry and allele frequencies from a set of related individuals. The second modification allows ADMIXTURE to correctly handle X-chromosome (and other haploid) data from both males and females. We demonstrate increased power to detect sex-biased admixture in African-American individuals from the 1000 Genomes project using this extension. CONCLUSIONS: These modifications make ADMIXTURE more efficient and versatile, allowing users to extract more information from large genomic datasets. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-1082-x) contains supplementary material, which is available to authorized users. |
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