Changes

* '''Convert files to VCF Format''' : Start by converting the unphased, quality controlled data set into VCF format. See our wiki page on .

* '''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.

* '''Split the data by Sex''' : Start by splitting the unphased, quality controlled data set by sex.

* '''Split the data into PAR and non-PAR:''' Separate the pseudo-autosomal part and non-pseudo-autosomal part into separate files. The non-PAR is located on <font face=Courier>'''chrX:2699520-154931043'''</font> on build hg19. The split can be done for VCF files as follows.

  vcftools --gzvcf gwas.data.vcf.gz \

 

  vcftools --gzvcf males.gwas.data.vcf.gz \

           --from-bp 2699520 \

           --from-bp 2699520 \

           --to-bp 154931043 \

           --to-bp 154931043 \

           --recode \

           --recode \

           --out males.non.PAR.gwas.data

           --out Non.PAR.gwas.data

  &nbsp;

  &nbsp;

  vcftools --gzvcf males.gwas.data.vcf.gz \

  vcftools --gzvcf gwas.data.vcf.gz \

           --exclude-positions males.non.PAR.gwas.data.recode.vcf \

           --exclude-positions Non.PAR.gwas.data.recode.vcf \

 

 

* '''Split the non-PAR data by Sex:''' Separate the non-PAR data by sex, which can also be done by vcftools as follows. Note that the <font face=Courier>PAR.gwas.data.recode.vcf</font> need NOT be separated since both males and females are diploids there.

 

vcftools --vcf Non.PAR.gwas.data.recode.vcf \

          --keep male.sample.list        ## or female.sample.list \

           --recode \

           --recode \

           --out males.PAR.gwas.data

           --out Male.Non.PAR.gwas.data   ## or Female.Non.PAR.gwas.data \

 

* '''Impute Sex and PAR/non-PAR separately:''' The following example illustrates how to do that (files available in <code>Minimac3/test/</code> directory)

* '''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:

  # Male Samples (Non-PAR)

  # Male Samples (Non-PAR)

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

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

                   --haps targetStudyChrX.males.vcf \

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

                   --prefix testRun.males.Non.PAR

                   --prefix testRun.males.Non.PAR

  &nbsp;

  &nbsp;

  # Female Samples (Non-PAR)

  # Female Samples (Non-PAR)

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

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

                   --haps targetStudyChrX.females.vcf \

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

                   --prefix testRun.females.Non.PAR

                   --prefix testRun.females.Non.PAR

  &nbsp;

  &nbsp;

  # Male Samples (PAR)

  # All Samples (PAR)

# Female Samples (PAR)

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

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

                   --haps targetStudyChrX.females.vcf \

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

                   --prefix testRun.females.PAR

                   --prefix testRun.All.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.