487
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchMinimac3 Cookbook : Chromosome X Imputation (view source)
Revision as of 13:19, 10 September 2015
, 13:19, 10 September 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. 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.
* '''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 \
--chr X \
--from-bp 2699520 \
--to-bp 154931043 \
--recode \
--out Non.PAR.gwas.data
vcftools --gzvcf gwas.data.vcf.gz \
--exclude-positions Non.PAR.gwas.data.recode.vcf \
--recode \
--out PAR.gwas.data
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''': After this step, please verify that the male samples have only one haplotype in <font face=Courier>Non.PAR.gwas.data.recode.vcf</font> and two haplotypes in <font face=Courier>PAR.gwas.data.recode.vcf</font>
* '''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 \
--out Male.Non.PAR.gwas.data ## or Female.Non.PAR.gwas.data \
* '''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 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:
# Phased All Samples (PAR)
../bin/Minimac3 --refHaps refPanelChrX.Auto.vcf \
--haps Phased.PAR.gwas.data.vcf \
--prefix testRun.All.PAR
# Phased Female Samples (Non-PAR)
../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf \
--haps Phased.Female.Non.PAR.gwas.data.vcf \
--prefix testRun.females.Non.PAR
# Haploid Male Samples (Non-PAR)
../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf \
--haps Male.Non.PAR.gwas.data.recode.vcf \
--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.
= Download =
= Download =
