Minimac3 Cookbook : Converting Files to VCF - Revision history

Santy.8128: /* Convert MaCH Files */

2015-01-31T03:32:17Z

Convert MaCH Files

← Older revision		Revision as of 23:32, 30 January 2015
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	= Convert '''MaCH''' Files =		= Convert '''MaCH''' Files =

	Use Mach2VCF (~~coming soon~~) as follows:		Use Mach2VCF (available [ftp://share.sph.umich.edu/minimac3/Mach2VCF.v1.Source.Binary.tar.gz here]) as follows:

	mach2VCF --haps Gwas.Chr20.Phased.Output.hap \		mach2VCF --haps Gwas.Chr20.Phased.Output.hap \

Santy.8128: /* Introduction */

2015-01-30T05:58:31Z

Introduction

← Older revision		Revision as of 01:58, 30 January 2015
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	= Introduction =		= Introduction =

	~~After the pre~~-~~phasing has been done, we can begin to run~~ the ~~imputation. But before that, we need to convert our phased GWAS panel files (obtained above) to VCF format (since Minimac3 can only use VCF format files). If pre-phased GWAS data is~~ available ~~in VCF format, users can skip this step. Otherwise, the following steps show how~~ to convert other format files to VCF format.		This wiki-page explains the main tools available to convert other format files to VCF format.

	= Convert '''PLINK''' Files =		= Convert '''PLINK''' Files =

Santy.8128: /* Contact */

2015-01-30T03:31:09Z

Contact

← Older revision		Revision as of 23:31, 29 January 2015
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	--input-haps Gwas.Chr20.Phased.Output \		--input-haps Gwas.Chr20.Phased.Output \
	--output-vcf Gwas.Chr20.Phased.Output.VCF.format.vcf		--output-vcf Gwas.Chr20.Phased.Output.VCF.format.vcf

			= Useful Wiki Pages =

			There are a few pages in this Wiki that may be useful to for '''Minimac3''' users. Here are links to a few:

			* [[Minimac3\| Minimac3 Overview Page]]

			* [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''')

			* [[Minimac3 Cookbook : Pre-Phasing \| Pre-Phasing ]]

			* [[Minimac3 Cookbook : Converting Files to VCF\| Converting Files to VCF]]

	= Contact =		= Contact =

	In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das].		In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das].

Santy.8128: /* Convert SHAPEIT Files */

2015-01-30T02:07:33Z

Convert SHAPEIT Files

← Older revision		Revision as of 22:07, 29 January 2015
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	--input-haps Gwas.Chr20.Phased.Output \		--input-haps Gwas.Chr20.Phased.Output \
	--output-vcf Gwas.Chr20.Phased.Output.VCF.format.vcf		--output-vcf Gwas.Chr20.Phased.Output.VCF.format.vcf


	= Contact =		= Contact =

	In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das].		In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das].

Santy.8128: /* Convert MaCH Files */

2015-01-30T02:07:29Z

Convert MaCH Files

← Older revision		Revision as of 22:07, 29 January 2015
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	--snps Gwas.Chr20.Phased.Output.snps \		--snps Gwas.Chr20.Phased.Output.snps \
	--prefix Gwas.Chr20.Phased.Output.VCF.format		--prefix Gwas.Chr20.Phased.Output.VCF.format


	= Convert '''SHAPEIT''' Files =		= Convert '''SHAPEIT''' Files =

Santy.8128: /* Convert PLINK Files */

2015-01-30T02:07:22Z

Convert PLINK Files

← Older revision		Revision as of 22:07, 29 January 2015
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	--recode vcf \		--recode vcf \
	--out Gwas.Chr20.Phased.Output.VCF.format		--out Gwas.Chr20.Phased.Output.VCF.format


	= Convert '''MaCH''' Files =		= Convert '''MaCH''' Files =

Santy.8128 at 02:07, 30 January 2015

2015-01-30T02:07:13Z

← Older revision		Revision as of 22:07, 29 January 2015
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			= Introduction =

	~~Consequently~~, we ~~would have~~ the following steps.		After the pre-phasing has been done, we can begin to run the imputation. But before that, we need to convert our phased GWAS panel files (obtained above) to VCF format (since Minimac3 can only use VCF format files). If pre-phased GWAS data is available in VCF format, users can skip this step. Otherwise, the following steps show how to convert other format files to VCF format.

	===Convert ~~GWAS Panel~~ Files ~~into VCF ==~~=		= Convert '''PLINK''' Files =

	~~If pre-phased GWAS data is available in VCF format, users can skip this step. Otherwise, the following steps show how to convert other format files to VCF format.~~		Use PLINK2 (available [https://www.cog-genomics.org/plink2 here]) as follows:

	* '''PLINK:''' Use PLINK2 (available [https://www.cog-genomics.org/plink2 here]) as follows:

	plink --bfile Gwas.Chr20.Phased.Output \		plink --bfile Gwas.Chr20.Phased.Output \
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	--out Gwas.Chr20.Phased.Output.VCF.format		--out Gwas.Chr20.Phased.Output.VCF.format

	* '''MaCH:''' Use Mach2VCF (coming soon) as follows:
			= Convert '''MaCH''' Files =

			Use Mach2VCF (coming soon) as follows:

	mach2VCF --haps Gwas.Chr20.Phased.Output.hap \		mach2VCF --haps Gwas.Chr20.Phased.Output.hap \
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	--prefix Gwas.Chr20.Phased.Output.VCF.format		--prefix Gwas.Chr20.Phased.Output.VCF.format

	* '''SHAPEIT:''' Use SHAPEIT (available [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download here]) as follows:
			= Convert '''SHAPEIT''' Files =

			Use SHAPEIT (available [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download here]) as follows:

	shapeit -convert \		shapeit -convert \
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	--output-vcf Gwas.Chr20.Phased.Output.VCF.format.vcf		--output-vcf Gwas.Chr20.Phased.Output.VCF.format.vcf

	~~=== Download Reference Panel ===~~

	Commonly used reference panels are 1000 Genomes Phase 3 (2,535 samples), 1000 Genomes Phase 1 (1,094 samples), HapMap2 (269 samples), Haplotype Reference Consortium (32,914 samples) etc. Users are advised to use either 1000 Genomes Phase 3 (available for download in [[#Reference Panels for Download \|Reference Panels ]]) or the Haplotype Reference Consortium (which due to data privacy issues cannot be shared publicly but can be used for imputation remotely on a server through a [http://imputationserver.sph.umich.edu/ imputation server] setup at University of Michigan). Reference panels for different versions of 1000 Genomes, in both VCF and <code>M3VCF</code> format, are available for download in [[#Reference Panels for Download \|Reference Panels]].

	~~=== Impute Samples ===~~

	The final step for imputation involves running '''Minimac3''' to perform the imputation analysis. Now that we have the pre-phased GWAS panel (in VCF format) and the appropriate reference panel (in VCF or <code>M3VCF</code> format), we can run Minimac3 as follows. In the following examples, the first one uses a VCF file for reference (that can be obtained as explained above) and the second example uses a <code>M3VCF</code> file (that might have been downloaded from the links [[#Reference Panels for Download\|below]] or created on a previous run of Minimac3).

	~~../bin/Minimac3 --refHaps ReferencePanel.Chr20.1000Genomes.vcf \~~		= Contact =
	~~--haps Gwas.Chr20.Phased.Output.VCF.format.vcf \~~
	~~--prefix Gwas.Chr20.Imputed.Output~~

	..~~/bin/Minimac3 --refHaps ReferencePanel.Chr20.1000Genomes.m3vcf \~~		In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das].
	~~--haps Gwas.Chr20.Phased.Output.VCF.format.vcf \~~
	~~--prefix Gwas.Chr20.Imputed.Output~~

Santy.8128: Created page with " Consequently, we would have the following steps. ===Convert GWAS Panel Files into VCF === If pre-phased GWAS data is available in VCF format, users can skip this step. Othe..."

2015-01-30T01:54:36Z

Created page with " Consequently, we would have the following steps. ===Convert GWAS Panel Files into VCF === If pre-phased GWAS data is available in VCF format, users can skip this step. Othe..."

New page

Consequently, we would have the following steps.

===Convert GWAS Panel Files into VCF ===

If pre-phased GWAS data is available in VCF format, users can skip this step. Otherwise, the following steps show how to convert other format files to VCF format.

* '''PLINK:''' Use PLINK2 (available [https://www.cog-genomics.org/plink2 here]) as follows:

plink --bfile Gwas.Chr20.Phased.Output \
--recode vcf \
--out Gwas.Chr20.Phased.Output.VCF.format

* '''MaCH:''' Use Mach2VCF (coming soon) as follows:

mach2VCF --haps Gwas.Chr20.Phased.Output.hap \
--snps Gwas.Chr20.Phased.Output.snps \
--prefix Gwas.Chr20.Phased.Output.VCF.format

* '''SHAPEIT:''' Use SHAPEIT (available [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download here]) as follows:

shapeit -convert \
--input-haps Gwas.Chr20.Phased.Output \
--output-vcf Gwas.Chr20.Phased.Output.VCF.format.vcf

=== Download Reference Panel ===

Commonly used reference panels are 1000 Genomes Phase 3 (2,535 samples), 1000 Genomes Phase 1 (1,094 samples), HapMap2 (269 samples), Haplotype Reference Consortium (32,914 samples) etc. Users are advised to use either 1000 Genomes Phase 3 (available for download in [[#Reference Panels for Download |Reference Panels ]]) or the Haplotype Reference Consortium (which due to data privacy issues cannot be shared publicly but can be used for imputation remotely on a server through a [http://imputationserver.sph.umich.edu/ imputation server] setup at University of Michigan). Reference panels for different versions of 1000 Genomes, in both VCF and <code>M3VCF</code> format, are available for download in [[#Reference Panels for Download |Reference Panels]].

=== Impute Samples ===

The final step for imputation involves running '''Minimac3''' to perform the imputation analysis. Now that we have the pre-phased GWAS panel (in VCF format) and the appropriate reference panel (in VCF or <code>M3VCF</code> format), we can run Minimac3 as follows. In the following examples, the first one uses a VCF file for reference (that can be obtained as explained above) and the second example uses a <code>M3VCF</code> file (that might have been downloaded from the links [[#Reference Panels for Download|below]] or created on a previous run of Minimac3).

../bin/Minimac3 --refHaps ReferencePanel.Chr20.1000Genomes.vcf \
--haps Gwas.Chr20.Phased.Output.VCF.format.vcf \
--prefix Gwas.Chr20.Imputed.Output

../bin/Minimac3 --refHaps ReferencePanel.Chr20.1000Genomes.m3vcf \
--haps Gwas.Chr20.Phased.Output.VCF.format.vcf \
--prefix Gwas.Chr20.Imputed.Output