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Estimated per allele error rate is 0.0293
Estimated per allele error rate is 0.0293
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].
'''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.
== How do I get reference files for an region of interest? ==
== How do I get reference files for an region of interest? ==
Note that you do not need to extract regional pedigree files for your own samples because SNPs in pedigree but not in reference will be automatically discarded. <br> 1. For HapMapII format, download haplotypes from http://www.sph.umich.edu/csg/ylwtx/HapMapForMach.tgz <br> 2. For MACH format, you can do the following:
Note that you do not need to extract regional pedigree files for your own samples because SNPs in pedigree but not in reference will be automatically discarded. <br> 1. For HapMapII format, download haplotypes from http://csg.sph.umich.edu//ylwtx/HapMapForMach.tgz <br> 2. For MACH format, you can do the following:
*First, find the first and last SNP in the region you are interested in. Say "rsFIRST" and "rsLAST", defined according to position.
*First, find the first and last SNP in the region you are interested in. Say "rsFIRST" and "rsLAST", defined according to position.
== 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>
== More questions? ==
== More questions? ==
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].
