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Jump to navigationJump to searchMinimac3 Cookbook : Chromosome X Imputation (view source)
Revision as of 01:41, 30 January 2015
, 01:41, 30 January 2015→Chromosome X Imputation
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. This wiki page gives further details on imputing chromosome X.
* '''Convert files to VCF Format''' : Start by converting the unphased, quality controlled data set into VCF format. See our wiki page on .
* '''Split the data by Sex''' : Start by splitting the unphased, quality controlled data set by sex.
* '''Split the data by Sex''' : Start by splitting the unphased, quality controlled data set by sex.
