Minimac3 Cookbook : Chromosome X Imputation - Revision history

Santy.8128: /* Chromosome X Imputation */

2015-09-10T17:19:49Z

Chromosome X Imputation

← Older revision		Revision as of 13:19, 10 September 2015
Line 14:		Line 14:

	vcftools --gzvcf gwas.data.vcf.gz \		vcftools --gzvcf gwas.data.vcf.gz \
			--chr X \
	--from-bp 2699520 \		--from-bp 2699520 \
	--to-bp 154931043 \		--to-bp 154931043 \

Santy.8128: /* Chromosome X Imputation */

2015-01-30T06:02:06Z

Chromosome X Imputation

← Older revision		Revision as of 02:02, 30 January 2015
Line 35:		Line 35:
	* '''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.

Santy.8128: /* Chromosome X Imputation */

2015-01-30T05:57:38Z

Chromosome X Imputation

← Older revision		Revision as of 01:57, 30 January 2015
Line 7:		Line 7:
	= 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.

Santy.8128: /* Chromosome X Imputation */

2015-01-30T05:56:54Z

Chromosome X Imputation

← Older revision		Revision as of 01:56, 30 January 2015
Line 10:		Line 10:


	* '''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.

	* '''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 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

	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 \
			--recode \
			--out PAR.gwas.data

			'''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 \		--recode \
	--out ~~males~~.PAR.gwas.data		--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 ~~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

	# 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

	# ~~Male Samples (PAR)~~		# All Samples (PAR)
	~~../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf \~~
	~~--haps targetStudyChrX.males.vcf \~~
	~~--prefix testRun.males.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.

Santy.8128: /* Chromosome X Imputation */

2015-01-30T05:41:06Z

Chromosome X Imputation

← Older revision		Revision as of 01:41, 30 January 2015
Line 9:		Line 9:
	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. This wiki page gives further details on 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 .

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

Santy.8128: /* Chromosome X Imputation */

2015-01-30T04:07:01Z

Chromosome X Imputation

← Older revision		Revision as of 00:07, 30 January 2015
Line 47:		Line 47:
	--prefix testRun.females.PAR		--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.

	= Download =		= Download =

Santy.8128: /* Chromosome X Imputation */

2015-01-30T04:06:50Z

Chromosome X Imputation

← Older revision		Revision as of 00:06, 30 January 2015
Line 47:		Line 47:
	--prefix testRun.females.PAR		--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.

	= Download =		= Download =

Santy.8128: /* Chromosome X Imputation */

2015-01-30T04:06:19Z

Chromosome X Imputation

← Older revision		Revision as of 00:06, 30 January 2015
Line 27:		Line 27:
	* '''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

	# 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

	# 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 \
			--haps targetStudyChrX.males.vcf \
	#Female Samples (PAR)		--prefix testRun.males.PAR
	../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf --haps targetStudyChrX.females.vcf --prefix testRun
			# 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.

Santy.8128: /* Chromosome X Imputation */

2015-01-30T04:03:48Z

Chromosome X Imputation

@@ Line 7: / Line 7: @@
 = 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.
    ../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf --haps targetStudyChrX.males.vcf --prefix testRun
+ &nbsp;
-Female Samples (Non-PAR)
+# Female Samples (Non-PAR)
    ../bin/Minimac3 --refHaps refPanelChrX.Non.Auto.vcf --haps targetStudyChrX.females.vcf --prefix testRun

Santy.8128: /* Introduction */

2015-01-30T03:33:40Z

Introduction

← Older revision		Revision as of 23:33, 29 January 2015
Line 3:		Line 3:
	[http://genome.sph.umich.edu/wiki/Minimac3 '''Minimac3 '''] is a lower memory and more computationally efficient implementation of [http://genome.sph.umich.edu/wiki/Minimac2 minimac2]. It is an algorithm for genotypic imputation that works on phased genotypes and is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.		[http://genome.sph.umich.edu/wiki/Minimac3 '''Minimac3 '''] is a lower memory and more computationally efficient implementation of [http://genome.sph.umich.edu/wiki/Minimac2 minimac2]. It is an algorithm for genotypic imputation that works on phased genotypes and is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.

	This wiki page is designed to give users a '''detailed step-by-step description on ~~running typical GWAS imputation experiments~~'''.		This wiki page is designed to give users a '''detailed step-by-step description on imputing chromosome X'''.

	= Chromosome X Imputation =		= Chromosome X Imputation =