Next-generation genotype imputation service and methods.
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Cites background or methods or result from "Next-generation genotype imputation..."
...Imputation accuracy for a variant generally increases with increasing reference panel size, and variants must be present in the reference panel in order to be accurately imputed.(4,5) Consequently, whenever a significantly larger reference panel becomes available, it is advantageous to re-impute target samples with the larger panel for subsequent analysis....
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...Minimac does not require a genetic map because recombination parameters are estimated and stored when producing the m3vcf format input file for the reference data.(4,24) Beagle 4....
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...The techniques developed thus far have made it possible to provide imputation using reference panels with tens of thousands of individuals as a free web service.(4) However, the total computational cost of imputation is substantial and increasing....
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...Current imputation methods are able to make use of a rich palette of computational techniques, including the use of identity-by-descent,(6,14,15) haplotype clustering,(4,16) and linear interpolation(5) to reduce the model state space, the use of pre-phasing to reduce computational complexity,(14,17,18) and the use of specialized reference file formats to reduce file size and memory footprint.(4,5,19) The techniques developed thus far have made it possible to provide imputation using reference panels with tens of thousands of individuals as a free web service....
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...Accuracy All the genotype imputation methods that we evaluated are based on the Li and Stephens probabilistic model(20) and have essentially the same imputation accuracy (Figure 3), which is consistent with previous reports.(4,5) The apparent difference in accuracy between Beagle 4....
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