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Minimac: 1000 Genomes Imputation Cookbook

14 bytes added, 11:19, 26 July 2013
Quality Control
With older genotyping platforms, low frequency SNPs are also often excluded because they are hard to genotype accurately. With more modern genotyping arrays, the accuracy of genotype calls for low frequency SNPs is less of a concern.
Two good ways to verify that you have used appropriate quality control steps are to generate a Q-Q plot for your dataset and to calculate a genomic control parameter. If these verifications are not satisfactory, it may be useful to investigate before proceeding to imputation.
=== Reference Haplotypes ===

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