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Revision as of 00:03, 30 January 2015
, 00:03, 30 January 2015→Chromosome X Imputation
= 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 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.
Male Samples (Non-PAR)
* '''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 PAR is located on <font face=Courier>'''chrX:1-2709520'''</font> and <font face=Courier>'''chrX:154584238-154913754'''</font> on build hg18 and <font face=Courier>'''chrX:60001-2699519'''</font> and <font face=Courier>'''chrX:154931044-155260560'''</font> on build hg19. The split can be done for VCF files as follows (for build hg19):
vcftools --gzvcf males.gwas.data.vcf.gz \
--from-bp 2699520 \
--to-bp 154931043 \
--recode \
--out males.non.PAR.gwas.data
vcftools --gzvcf males.gwas.data.vcf.gz \
--exclude-positions males.non.PAR.gwas.data.recode.vcf \
--recode \
--out males.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)
# 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
Female Samples (Non-PAR)
# Female Samples (Non-PAR)
../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf --haps targetStudyChrX.females.vcf --prefix testRun
# Male Samples (PAR)
../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf --haps targetStudyChrX.males.vcf --prefix testRun
#Female Samples (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
