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, 01:57, 30 January 2015
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| = Chromosome X Imputation = | | = Chromosome X Imputation = |
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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 (non-PAR) 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. | + | 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 (non-PAR) 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. Following should be the steps involved in imputing chromosome X. |
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| * '''Convert files to VCF Format:''' Start by converting the unphased, quality controlled data set into VCF format. See our wiki page on [[Minimac3 Cookbook : Converting Files to VCF| Converting to VCF]] for more details on how to convert. | | * '''Convert files to VCF Format:''' Start by converting the unphased, quality controlled data set into VCF format. See our wiki page on [[Minimac3 Cookbook : Converting Files to VCF| Converting to VCF]] for more details on how to convert. |