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, 11:22, 2 February 2017
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| Estimated per allele error rate is 0.0293 | | Estimated per allele error rate is 0.0293 |
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− | A better approach is to mask a small proportion of SNPs (vs. genotypes in the above simple approach). One can generate a mask.dat from the original .dat file by simply changing the flag of a subset of markers from M to S2 without duplicating the .ped file. Post-imputation, one can use [http://genome.sph.umich.edu/wiki/CalcMatch CalcMatch ]and [http://www.sph.umich.edu/csg/ylwtx/doseR2.tgz doseR2.pl ]to estimate genotypic/allelic error rate and correlation respectively. Both programs can be downloaded from [http://www.sph.umich.edu/csg/ylwtx/software.html http://www.sph.umich.edu/csg/ylwtx/software.html]. | + | A better approach is to mask a small proportion of SNPs (vs. genotypes in the above simple approach). One can generate a mask.dat from the original .dat file by simply changing the flag of a subset of markers from M to S2 without duplicating the .ped file. Post-imputation, one can use [http://genome.sph.umich.edu/wiki/CalcMatch CalcMatch ]and [http://csg.sph.umich.edu//ylwtx/doseR2.tgz doseR2.pl ]to estimate genotypic/allelic error rate and correlation respectively. Both programs can be downloaded from [http://csg.sph.umich.edu//ylwtx/software.html http://csg.sph.umich.edu//ylwtx/software.html]. |
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| '''Warning''': Imputation involving masked datasets should be performed separately for imputation quality estimation. For production, one should use all available information. | | '''Warning''': Imputation involving masked datasets should be performed separately for imputation quality estimation. For production, one should use all available information. |
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| == Install MaCH == | | == Install MaCH == |
− | We have source codes available through the MaCH download page: http://www.sph.umich.edu/csg/yli/mach/download/ <br> | + | We have source codes available through the MaCH download page: http://csg.sph.umich.edu//yli/mach/download/ <br> |
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| == More questions? == | | == More questions? == |
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| Email [mailto:yunli@med.unc.edu Yun Li] or [mailto:goncalo@umich.edu Goncalo Abecasis]. | | Email [mailto:yunli@med.unc.edu Yun Li] or [mailto:goncalo@umich.edu Goncalo Abecasis]. |