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Revision as of 22:00, 29 January 2015
, 22:00, 29 January 2015Created page with " 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..."
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.
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)
Male Samples (Non-PAR)
../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf --haps targetStudyChrX.males.vcf --prefix testRun
Female Samples (Non-PAR)
../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf --haps targetStudyChrX.females.vcf --prefix testRun
NOTE: For imputing non-PAR of chromosome X, user must analyze male and female samples separately, otherwise program would crash. User should also ensure that the reference panel consists of only PAR or non-PAR region of chromosome X, otherwise program would crash.
