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LASER is a C++ software that can estimate individual ancestry directly from genome-wide shortgun sequencing reads without calling genotypes. The method relies on the availability of a set of reference individuals whose genome-wide SNP genotypes and ancestral information are known. We first construct a reference coordinate system by applying principal components analysis (PCA) to the genotype data of the reference individuals. Then, for each sequence sample, uses the genome-wide sequencing reads to place the sample into the reference PCA space. With an appropriate reference panel, the estimated coordinates of the sequence samples identify their ancestral background and can be directly used to correct for population structure in association studies or to ensure adequate matching of cases and controls.  

LASER is a C++ software that can estimate individual ancestry directly from genome-wide shortgun sequencing reads without calling genotypes. The method relies on the availability of a set of reference individuals whose genome-wide SNP genotypes and ancestral information are known. We first construct a reference coordinate system by applying principal components analysis (PCA) to the genotype data of the reference individuals. Then, for each sequence sample, uses the genome-wide sequencing reads to place the sample into the reference PCA space. With an appropriate reference panel, the estimated coordinates of the sequence samples identify their ancestral background and can be directly used to correct for population structure in association studies or to ensure adequate matching of cases and controls.  

= Workflow  =

= Workflow  =