1,555
edits
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The specific numbers are that:
The specific numbers are that:
For variants with MAF >1%, the average r<sup>2</sup> correlation between imputed and true genotypes will be 0.8879 (Affymetrix) and 0.8590 (Illumina).
* For variants with MAF >1%, the average r<sup>2</sup> correlation between imputed and true genotypes will be 0.8879 (Affymetrix) and 0.8590 (Illumina).
For variants with MAF >5%, the average r<sup>2</sup> correlation between imputed and true genotypes will be 0.9458 (Affymetrix) and 0.9256 (Illumina).
* For variants with MAF >5%, the average r<sup>2</sup> correlation between imputed and true genotypes will be 0.9458 (Affymetrix) and 0.9256 (Illumina).
The fraction of variants imputed with r<sup>2<sup> > 0.80 will be:
The fraction of variants imputed with r<sup>2</sup> > 0.80 will be:
For variants with MAF >1%, 82.1% (Affymetrix) and 76.5% (Illumina)
* For variants with MAF >1%, 82.1% (Affymetrix) and 76.5% (Illumina)
For variants with MAF >5%, 94.6% (Affymetrix) and 89.2% (Illumina)
* For variants with MAF >5%, 94.6% (Affymetrix) and 89.2% (Illumina)
The evaluation is based on imputation of ~600 UK samples that have been whole genome and whole exome sequenced (comparing imputed genotypes and the sequenced based calls) and using a panel of 2,500 sequenced individuals from the T2D-Go Project (Altshuler, Boehnke, McCarthy) as a reference.
The evaluation is based on imputation of ~600 UK samples that have been whole genome and whole exome sequenced (comparing imputed genotypes and the sequenced based calls) and using a panel of 2,500 sequenced individuals from the T2D-Go Project (Altshuler, Boehnke, McCarthy) as a reference.
