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bioRxiv · 10.1101/039347

Efficient analysis of large datasets and sex bias with ADMIXTURE

Suyash S. Shringarpure·Carlos D. Bustamante·Kenneth L. Lange·David H. Alexander
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Abstract

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.\n\nResults: 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 5x 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.\n\nConclusions: These modifications make ADMIXTURE more efficient and versatile, allowing users to extract more information from large genomic datasets.

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Suyash S. Shringarpure, Carlos D. Bustamante, Kenneth L. Lange, David H. Alexander. 2016-02-10. Efficient analysis of large datasets and sex bias with ADMIXTURE. https://doi.org/10.1101/039347

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