Changes

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

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

# Male Samples (Non-PAR)

# Male Samples (Non-PAR)

   ../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf --haps targetStudyChrX.males.vcf --prefix testRun

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

                  --haps targetStudyChrX.males.vcf \

                  --prefix testRun.males.Non.PAR

  &nbsp;

  &nbsp;

# Female Samples (Non-PAR)

# Female Samples (Non-PAR)

   ../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf --haps targetStudyChrX.females.vcf --prefix testRun

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

                  --haps targetStudyChrX.females.vcf \

                  --prefix testRun.females.Non.PAR

  &nbsp;

  &nbsp;

# Male Samples (PAR)

# Male Samples (PAR)

   ../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf --haps targetStudyChrX.males.vcf --prefix testRun

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

&nbsp;

                  --haps targetStudyChrX.males.vcf \

#Female Samples (PAR)

                  --prefix testRun.males.PAR

   ../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf --haps targetStudyChrX.females.vcf --prefix testRun

&nbsp;

# Female Samples (PAR)

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

                  --haps targetStudyChrX.females.vcf \

                  --prefix testRun.females.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.