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Minimac: 1000 Genomes Imputation Cookbook (view source)

Revision as of 22:53, 10 February 2011

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These statistics can be found in the *.info file
 
These statistics can be found in the *.info file
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Be aware that imputation quality statistics are not directly comparable between different imputation programs (MaCH/minimac vs. Impute vs. Beagle etc.).
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== Quality Filtering ==
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For 1000 Genome SNPs, we currently recommend that any markers with estimated r<sup>2</sup> of <0.5 should be treated with caution. This is a bit more conservative than the threshold of 0.3 we recommend for HapMap; but 1000 Genome SNP genotypes are also of lower quality. Be aware that imputation quality statistics are not directly comparable between different imputation programs (MaCH/minimac vs. Impute vs. Beagle etc.).
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== Questions and Comments ==
 
== Questions and Comments ==
    
Please contact [mailto:goncalo@umich.edu Goncalo Abecasis] or [mailto:cfuchsb@umich.edu Christian Fuchsberger (minimac)] or [mailto:yunli@med.unc.edu Yun Li (MaCH)].
 
Please contact [mailto:goncalo@umich.edu Goncalo Abecasis] or [mailto:cfuchsb@umich.edu Christian Fuchsberger (minimac)] or [mailto:yunli@med.unc.edu Yun Li (MaCH)].
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