Changes

= Chromosome X Imputation =  

= 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. Following should be the steps involved in 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 [[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.

  vcftools --gzvcf gwas.data.vcf.gz \

  vcftools --gzvcf gwas.data.vcf.gz \

           --from-bp 2699520 \

           --from-bp 2699520 \

           --to-bp 154931043 \

           --to-bp 154931043 \

* '''Pre-phase PAR data and female non-PAR data:''' Out of the three available data, only the PAR data and female non-PAR data have two haplotypes and thus need to be phased, while the male non-PAR data has haploids and need not be phased. See our wiki page on [[Minimac3 Cookbook : Pre-Phasing| Pre-Phasing]] and [[Minimac3 Cookbook : Converting Files to VCF| Converting to VCF]] for further details on pre-phasing and converting files back to VCF format.

* '''Pre-phase PAR data and female non-PAR data:''' Out of the three available data, only the PAR data and female non-PAR data have two haplotypes and thus need to be phased, while the male non-PAR data has haploids and need not be phased. See our wiki page on [[Minimac3 Cookbook : Pre-Phasing| Pre-Phasing]] and [[Minimac3 Cookbook : Converting Files to VCF| Converting to VCF]] for further details on pre-phasing and converting files back to VCF format.

* '''Impute Data:''' The following example illustrates how to impute into the pahsed PAR data (both males and females together), phased female non-PAR data and haploid male non-PAR data as follows:

* '''Impute Data:''' The following example illustrates how to impute into the phased PAR data (both males and females together), phased female non-PAR data and haploid male non-PAR data (same as obtained after splitting the non-PAR by sex) as follows:

  # Male Samples (Non-PAR)

  # Phased All Samples (PAR)

   ../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf \

   ../bin/Minimac3 --refHaps refPanelChrX.Auto.vcf \

                   --haps Phased.Male.Non.PAR.gwas.data.vcf \

                   --haps Phased.PAR.gwas.data.vcf \

                   --prefix testRun.males.Non.PAR

                   --prefix testRun.All.PAR

   

   

  # Female Samples (Non-PAR)

  # Phased Female Samples (Non-PAR)

   ../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf \

   ../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf \

                   --haps Phased.Female.Non.PAR.gwas.data.vcf \

                   --haps Phased.Female.Non.PAR.gwas.data.vcf \

                   --prefix testRun.females.Non.PAR

                   --prefix testRun.females.Non.PAR

   

   

  # All Samples (PAR)

  # Haploid Male Samples (Non-PAR)

   ../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf \

   ../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf \

                   --haps PAR.gwas.data.recode.vcf \

                   --haps Male.Non.PAR.gwas.data.recode.vcf \

                   --prefix testRun.All.PAR

                   --prefix testRun.males.Non.PAR

* '''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.

* '''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.