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Revision as of 18:08, 10 February 2011
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== Estimating Model Parameters ==
=== 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.
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.
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.
=== Selecting a Subset of Samples ===
==== Selecting a Subset of Samples ====
Using all availalble samples to estimate model parameters can be quite time consuming and is typically not necessary. Instead, we recommend that you select a set of 200 samples to use in this step of analysis. If you are not worried about batch effects, you could just take the first 200 samples in your pedigree file, for example:
Using all availalble samples to estimate model parameters can be quite time consuming and is typically not necessary. Instead, we recommend that you select a set of 200 samples to use in this step of analysis. If you are not worried about batch effects, you could just take the first 200 samples in your pedigree file, for example:
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== Imputation ==
=== Imputation ===
Once model parameters have been estimated, you are ready to impute. This step should be comparatively fast, at least on a per individual basis.
Once model parameters have been estimated, you are ready to impute. This step should be comparatively fast, at least on a per individual basis.
