MaCH: machX - Revision history

Ppwhite at 16:02, 2 February 2017

2017-02-02T16:02:50Z

← Older revision		Revision as of 12:02, 2 February 2017
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	This page documents how to perform X chromosome (non-pseudo-autosomal part) imputation using MaCH [http://~~www~~.sph.umich.edu/csg/yli/mach] and minimac [http://genome.sph.umich.edu/wiki/Minimac].		This page documents how to perform X chromosome (non-pseudo-autosomal part) imputation using MaCH [http://csg.sph.umich.edu/csg/yli/mach] and minimac [http://genome.sph.umich.edu/wiki/Minimac].

	== Getting Started ==		== Getting Started ==

Ppwhite: /* Reference Haplotypes */

2017-02-02T15:28:54Z

Reference Haplotypes

← Older revision		Revision as of 11:28, 2 February 2017
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	=== Reference Haplotypes ===		=== Reference Haplotypes ===

	You can download the reference haplotypes from MaCH download page [http://~~www~~.sph.umich.edu/~~csg~~/yli/mach/download/chrX.html].		You can download the reference haplotypes from MaCH download page [http://csg.sph.umich.edu//yli/mach/download/chrX.html].

	== Two-Step Imputation ==		== Two-Step Imputation ==

Ppwhite: /* Your Own Data */

2017-02-02T15:28:36Z

Your Own Data

← Older revision		Revision as of 11:28, 2 February 2017
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	=== Your Own Data ===		=== Your Own Data ===

	To get started, you will need to store your data in [[Merlin]] format pedigree and data files, one per chromosome. For details of the Merlin file format, see the Merlin tutorial [http://~~www~~.sph.umich.edu/~~csg~~/abecasis/Merlin/tour/input_files.html]. <br>		To get started, you will need to store your data in [[Merlin]] format pedigree and data files, one per chromosome. For details of the Merlin file format, see the Merlin tutorial [http://csg.sph.umich.edu//abecasis/Merlin/tour/input_files.html]. <br>

	Within each file, markers should be stored by chromosome position. Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele). <br>		Within each file, markers should be stored by chromosome position. Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele). <br>

Cfuchsb at 22:28, 10 February 2011

2011-02-10T22:28:20Z

← Older revision		Revision as of 18:28, 10 February 2011
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	== FAQ ==		== FAQ ==
	=== Shall I phase/impute males and females together or separately? ===		=== Shall I phase/impute males and females together or separately? ===
	~~When there is missing genotypes among~~ males~~, phasing is needed for males as well. But phasing them~~ together with or separately from females doesn't seem to affect imputation quality.		Phasing males together with or separately from females doesn't seem to affect imputation quality.

	Imputing males together with or separately from females doesn't seem to affect imputation quality either.		Imputing males together with or separately from females doesn't seem to affect imputation quality either.

Ylwtx at 12:29, 29 November 2010

2010-11-29T12:29:56Z

← Older revision		Revision as of 08:29, 29 November 2010
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	== FAQ ==		== FAQ ==
			=== Shall I phase/impute males and females together or separately? ===
			When there is missing genotypes among males, phasing is needed for males as well. But phasing them together with or separately from females doesn't seem to affect imputation quality.

			Imputing males together with or separately from females doesn't seem to affect imputation quality either.

			== Questions and Comments? ==

			Email [mailto:yunli@med.unc.edu Yun Li].

Ylwtx: /* Impute */

2010-11-26T13:49:15Z

Impute

← Older revision		Revision as of 09:49, 26 November 2010
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	=== Impute ===		=== Impute ===

			Imputation will then be performed on the phased haplotypes using minimac [http://genome.sph.umich.edu/wiki/Minimac].

			minimac --refHaps ref.hap.gz --refSnps ref.snps --haps sample.phased.gz --snps sample.snps --rounds 5 --states 200 --prefix sample.imputed > sample.imputed.log

	== FAQ ==		== FAQ ==

Ylwtx: /* Phase Your Own Data */

2010-11-26T13:47:40Z

Phase Your Own Data

← Older revision		Revision as of 09:47, 26 November 2010
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	=== Phase Your Own Data ===		=== Phase Your Own Data ===

			If there is no missing genotypes in males, you will only need to phase the females. Make sure that alleles are all stored in forward strand before phasing.

			mach1 -d sample.dat -p sample.ped --states 200 -r 20 --phase -o sample.phased > sample.phased.log

	=== Impute ===		=== Impute ===

	== FAQ ==		== FAQ ==

Ylwtx: /* Reference Haplotypes */

2010-11-26T13:44:28Z

Reference Haplotypes

← Older revision		Revision as of 09:44, 26 November 2010
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	=== Reference Haplotypes ===		=== Reference Haplotypes ===

	You can download the ~~following~~ reference haplotypes from MaCH download page [http://www.sph.umich.edu/csg/yli/mach/download/chrX.html].		You can download the reference haplotypes from MaCH download page [http://www.sph.umich.edu/csg/yli/mach/download/chrX.html].

	== Two-Step Imputation ==		== Two-Step Imputation ==

Ylwtx at 13:44, 26 November 2010

2010-11-26T13:44:05Z

← Older revision		Revision as of 09:44, 26 November 2010
Line 5:		Line 5:
	=== Your Own Data ===		=== Your Own Data ===

	To get started, you will need to store your data in [[Merlin]] format pedigree and data files, one per chromosome. For details of the Merlin file format, see the Merlin tutorial [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html].		To get started, you will need to store your data in [[Merlin]] format pedigree and data files, one per chromosome. For details of the Merlin file format, see the Merlin tutorial [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html]. <br>

	Within each file, markers should be stored by chromosome position. Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele).		Within each file, markers should be stored by chromosome position. Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele). <br>

	Note that for males hemizygotes are coded as homozygotes.		Note that for males hemizygotes are coded as homozygotes. <br>

	=== Reference Haplotypes ===		=== Reference Haplotypes ===

Ylwtx at 13:43, 26 November 2010

2010-11-26T13:43:37Z

← Older revision		Revision as of 09:43, 26 November 2010
Line 1:		Line 1:
	This page documents how to perform X chromosome (non-pseudo-autosomal part) imputation using MaCH [http://www.sph.umich.edu/csg/yli/mach] and minimac [http://genome.sph.umich.edu/wiki/Minimac].		This page documents how to perform X chromosome (non-pseudo-autosomal part) imputation using MaCH [http://www.sph.umich.edu/csg/yli/mach] and minimac [http://genome.sph.umich.edu/wiki/Minimac].

	== Getting Started ==		== Getting Started ==

	=== Your Own Data ===		=== Your Own Data ===
	To get started, you will need to store your data in [[Merlin]] format pedigree and data files, one per chromosome. For details of the Merlin file format, see the Merlin tutorial [http:/www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html].
			To get started, you will need to store your data in [[Merlin]] format pedigree and data files, one per chromosome. For details of the Merlin file format, see the Merlin tutorial [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html].

	Within each file, markers should be stored by chromosome position. Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele).		Within each file, markers should be stored by chromosome position. Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele).
Line 10:		Line 11:
	Note that for males hemizygotes are coded as homozygotes.		Note that for males hemizygotes are coded as homozygotes.

	=== Reference Haplotypes ===		=== Reference Haplotypes ===
	You can download the following reference haplotypes from MaCH download page [http://www.sph.umich.edu/csg/yli/mach/download/chrX.html].
			You can download the following reference haplotypes from MaCH download page [http://www.sph.umich.edu/csg/yli/mach/download/chrX.html].

	== Two-Step Imputation ==		== Two-Step Imputation ==

	=== Phase Your Own Data ===		=== Phase Your Own Data ===

	=== Impute ===		=== Impute ===

	== FAQ ==		== FAQ ==