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14 bytes added
, 07:00, 5 August 2011
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| :::: '''<End of the corresponding haplotype file>''' | | :::: '''<End of the corresponding haplotype file>''' |
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− | === Imputation quality evaluation ===
| + | == Imputation quality evaluation == |
| Minimac hides each of the genotyped SNPs in turn and then calculates 3 statistics: | | Minimac hides each of the genotyped SNPs in turn and then calculates 3 statistics: |
| * looRSQ - this is the estimated rsq for that SNP (as if SNP weren't typed). | | * looRSQ - this is the estimated rsq for that SNP (as if SNP weren't typed). |
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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.). | + | Be aware that, unfortunately, 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 == |
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| 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)]. |