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Reference haplotypes generated by the 1000 Genomes project and formatted so that they are ready for analysis are available from the [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G-2010-06.html MaCH download page]. The most recent set of haplotypes were generated in June 2010 by combining genotype calls generated at the Broad, Sanger and the University of Michigan. In our hands, this June 2010 release is substantially better than previous 1000 Genome Project genotype call sets.
 
== Estimating Model Parameters ==
 
The first step for genotype imputation analyses using MaCH is to build a model that relates your dataset to a reference set of haplotypes. This model will include information on the length of haplotype stretches shared between your sample and the reference panel (in a ''.rec'' file) and information on the similarity of marker genotypes between your sample and the reference panel (in a ''.err'' file). The contents of the second file reflect the combined effects of genotyping error and differences in genotyping assays between the two samples.
 
In our view, MaCH's ability to estimate these parameters makes it especially robust to problems in genotyping, differences in genotyping assays and in the ability to adjust to varying degrees of similarity between the sample being imputed and a reference panel.
== Step 1: Phasing ==
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