December 14, 2011

Segmented HAPlotype Estimation and Imputation Tool (Delaneau et al. 2011)

The ShapeIT website seems to be very well-designed and informative.

Nature Methods (2011) doi:10.1038/nmeth.1785

A linear complexity phasing method for thousands of genomes

Olivier Delaneau et al.

Human-disease etiology can be better understood with phase information about diploid sequences. We present a method for estimating haplotypes, using genotype data from unrelated samples or small nuclear families, that leads to improved accuracy and speed compared to several widely used methods. The method, segmented haplotype estimation and imputation tool (SHAPEIT), scales linearly with the number of haplotypes used in each iteration and can be run efficiently on whole chromosomes.


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