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, 22:08, 29 January 2015
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| + | = Introduction = |
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− | Chromosome X has a pseudo-autosomal region (PAR) which can be imputed for males and females together. Imputing the PAR on chromosome X is same as usual imputation, since both males and females are diploids at these sites. However, the non pseudo-autosomal region needs to be imputed for males and females separately, as males are haploids while females are diploids. Of course, the PAR and non-PAR regions need to be imputed separately. See our wiki page on [[Minimac3 Cookbook : Chromosome X Imputation |Chromosome X Imputation]] for details on imputing chromosome X. | + | Chromosome X has a pseudo-autosomal region (PAR) which can be imputed for males and females together. Imputing the PAR on chromosome X is same as usual imputation, since both males and females are diploids at these sites. However, the non pseudo-autosomal region needs to be imputed for males and females separately, as males are haploids while females are diploids. Of course, the PAR and non-PAR regions need to be imputed separately. This wiki page gives further details on imputing chromosome X. |
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| The following example illustrates imputation on the non-PAR of chromosome X for males and females separately (files available in <code>Minimac3/test/</code> directory) | | The following example illustrates imputation on the non-PAR of chromosome X for males and females separately (files available in <code>Minimac3/test/</code> directory) |