Minimac3 Cookbook : Pre-Phasing - Revision history

Santy.8128: /* Introduction */

2015-01-30T06:20:01Z

Introduction

← Older revision		Revision as of 02:20, 30 January 2015
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	= Introduction =		= Introduction =

	Once a quality controlled dataset is available we need to pre-phase the data followed by imputation. Pre-Phasing can be done using either [http://www.sph.umich.edu/csg/abecasis/MaCH/ MaCH] or [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html SHAPEIT], the most commonly used tools. This wiki page gives detailed instruction on pre-phasing GWAS data of different samples sizes. This also applies for phasing of the non-Pseudo-Autosomal Region ~~of female Chromosome X~~ and the Pseudo-Autosomal Region ~~of chromosome X~~ (for both males and females).		Once a quality controlled dataset is available we need to pre-phase the data followed by imputation. Pre-Phasing can be done using either [http://www.sph.umich.edu/csg/abecasis/MaCH/ MaCH] or [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html SHAPEIT], the most commonly used tools. This wiki page gives detailed instruction on pre-phasing GWAS data of different samples sizes. This also applies for phasing of the non-Pseudo-Autosomal Region (only for females) and the Pseudo-Autosomal Region (for both males and females) of chromosome X .

	= Pre-phasing with MaCH =		= Pre-phasing with MaCH =

Santy.8128: /* Introduction */

2015-01-30T06:19:24Z

Introduction

← Older revision		Revision as of 02:19, 30 January 2015
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	= Introduction =		= Introduction =

	Once a quality controlled dataset is available we need to pre-phase the data followed by imputation. Pre-Phasing can be done using either [http://www.sph.umich.edu/csg/abecasis/MaCH/ MaCH] or [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html SHAPEIT], the most commonly used tools. This wiki page gives detailed instruction on pre-phasing GWAS data of different samples sizes. This also applies for phasing of non-Pseudo-Autosomal Region of female Chromosome X and Pseudo-Autosomal Region of chromosome X (for both males and females).		Once a quality controlled dataset is available we need to pre-phase the data followed by imputation. Pre-Phasing can be done using either [http://www.sph.umich.edu/csg/abecasis/MaCH/ MaCH] or [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html SHAPEIT], the most commonly used tools. This wiki page gives detailed instruction on pre-phasing GWAS data of different samples sizes. This also applies for phasing of the non-Pseudo-Autosomal Region of female Chromosome X and the Pseudo-Autosomal Region of chromosome X (for both males and females).

	= Pre-phasing with MaCH =		= Pre-phasing with MaCH =

Santy.8128: /* Introduction */

2015-01-30T06:18:58Z

Introduction

← Older revision		Revision as of 02:18, 30 January 2015
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	= Introduction =		= Introduction =

	Once a quality controlled dataset is available we need to pre-phase the data followed by imputation. Pre-Phasing can be done using either [http://www.sph.umich.edu/csg/abecasis/MaCH/ MaCH] or [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html SHAPEIT], the most commonly used tools. This wiki page gives detailed instruction on pre-phasing GWAS data of different samples sizes.		Once a quality controlled dataset is available we need to pre-phase the data followed by imputation. Pre-Phasing can be done using either [http://www.sph.umich.edu/csg/abecasis/MaCH/ MaCH] or [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html SHAPEIT], the most commonly used tools. This wiki page gives detailed instruction on pre-phasing GWAS data of different samples sizes. This also applies for phasing of non-Pseudo-Autosomal Region of female Chromosome X and Pseudo-Autosomal Region of chromosome X (for both males and females).

	= Pre-phasing with MaCH =		= Pre-phasing with MaCH =

Santy.8128: /* Contact */

2015-01-30T03:31:25Z

Contact

← Older revision		Revision as of 23:31, 29 January 2015
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	--exclude-snp gwas.alignments.strand.exclude \		--exclude-snp gwas.alignments.strand.exclude \
	-O Gwas.Chr20.Phased.Output		-O Gwas.Chr20.Phased.Output

			= 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 at 02:03, 30 January 2015

2015-01-30T02:03:39Z

← Older revision		Revision as of 22:03, 29 January 2015
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			= Introduction =

	Once a quality controlled dataset is available we need to pre-phase the data followed by imputation. Pre-Phasing can be done using either [http://www.sph.umich.edu/csg/abecasis/MaCH/ MaCH] or [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html SHAPEIT], the most commonly used tools. ~~See our~~ wiki page ~~on [[Minimac3 Cookbook : Pre-Phasing\| Pre-Phasing]] for further details~~ on pre-phasing on GWAS of different samples sizes.		Once a quality controlled dataset is available we need to pre-phase the data followed by imputation. Pre-Phasing can be done using either [http://www.sph.umich.edu/csg/abecasis/MaCH/ MaCH] or [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html SHAPEIT], the most commonly used tools. This wiki page gives detailed instruction on pre-phasing GWAS data of different samples sizes.

	=== MaCH ===		= Pre-phasing with MaCH =

	'''MaCH''' is a Markov Chain based haplotyper. It can resolve long haplotypes in samples of unrelated individuals. The source code is available for download [http://www.sph.umich.edu/csg/abecasis/MaCH/download/ here]. Check out their [http://www.sph.umich.edu/csg/abecasis/MaCH/ home-page] for further details.		'''MaCH''' is a Markov Chain based haplotyper. It can resolve long haplotypes in samples of unrelated individuals. The source code is available for download [http://www.sph.umich.edu/csg/abecasis/MaCH/download/ here]. Check out their [http://www.sph.umich.edu/csg/abecasis/MaCH/ home-page] for further details.
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	--prefix Gwas.Chr20.Phased.Output		--prefix Gwas.Chr20.Phased.Output

	=== SHAPEIT===		= Pre-phasing with SHAPEIT =

	'''SHAPEIT''' is a fast and accurate method for estimation of haplotypes (phasing) from genotype or sequencing data. The source code is available for download [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download here]. Check out their [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html home-page] for further details. It can be used to phase a small number of samples (a reference panel required) as well as a large number of samples (NO reference panel required). The reference panels and genetic map files required by SHAPEIT are available for download [https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#reference here].		'''SHAPEIT''' is a fast and accurate method for estimation of haplotypes (phasing) from genotype or sequencing data. The source code is available for download [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download here]. Check out their [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html home-page] for further details. It can be used to phase a small number of samples (a reference panel required) as well as a large number of samples (NO reference panel required). The reference panels and genetic map files required by SHAPEIT are available for download [https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#reference here].
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	--exclude-snp gwas.alignments.strand.exclude \		--exclude-snp gwas.alignments.strand.exclude \
	-O Gwas.Chr20.Phased.Output		-O Gwas.Chr20.Phased.Output

			= Contact =

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

Santy.8128: Created page with " Once a quality controlled dataset is available we need to pre-phase the data followed by imputation. Pre-Phasing can be done using either [http://www.sph.umich.edu/csg/abecas..."

2015-01-30T01:50:45Z

Created page with " Once a quality controlled dataset is available we need to pre-phase the data followed by imputation. Pre-Phasing can be done using either [http://www.sph.umich.edu/csg/abecas..."

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Once a quality controlled dataset is available we need to pre-phase the data followed by imputation. Pre-Phasing can be done using either [http://www.sph.umich.edu/csg/abecasis/MaCH/ MaCH] or [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html SHAPEIT], the most commonly used tools. See our wiki page on [[Minimac3 Cookbook : Pre-Phasing| Pre-Phasing]] for further details on pre-phasing on GWAS of different samples sizes.

=== MaCH ===

'''MaCH''' is a Markov Chain based haplotyper. It can resolve long haplotypes in samples of unrelated individuals. The source code is available for download [http://www.sph.umich.edu/csg/abecasis/MaCH/download/ here]. Check out their [http://www.sph.umich.edu/csg/abecasis/MaCH/ home-page] for further details.

A typical command line to phase using MaCH looks like this (<code>Gwas.chr20.Unphased.dat</code> and <code>Gwas.chr20.Unphased.ped </code> is the quality controlled GWAS data set in [http://www.sph.umich.edu/csg/abecasis/Merlin/ Merlin] format)

mach1 -d Gwas.chr20.Unphased.dat \
-p Gwas.chr20.Unphased.ped \
--rounds 20 \
--states 200 \
--phase \
--interim 5 \
--sample 5 \
--prefix Gwas.Chr20.Phased.Output

=== SHAPEIT===

'''SHAPEIT''' is a fast and accurate method for estimation of haplotypes (phasing) from genotype or sequencing data. The source code is available for download [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download here]. Check out their [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html home-page] for further details. It can be used to phase a small number of samples (a reference panel required) as well as a large number of samples (NO reference panel required). The reference panels and genetic map files required by SHAPEIT are available for download [https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#reference here].

* The following example shows a typical SHAPEIT command line to phase a LARGE number (>200) of GWAS samples (<code>Gwas.chr20.Unphased.vcf</code> is the quality controlled GWAS data set in VCF format).

shapeit -V Gwas.chr20.Unphased.vcf \
-M genetic_map_chr20.txt \
-O Gwas.Chr20.Phased.Output

* The following example shows a typical SHAPEIT command line to phase a SMALL number (<200) of GWAS samples (<code>Gwas.chr20.Unphased.vcf</code> is the quality controlled GWAS data set in VCF format).

## The following step splits out variants mis-aligned between the reference and gwas panel
shapeit -check \
-V Gwas.chr20.Unphased.vcf\
-M genetic_map_chr20.txt \
--input-ref reference.haplotypes.gz reference.legend.gz reference.sample \
--output-log gwas.alignments

## The following step phases gwas panel using the reference panel while excluding the markers found in the step above.
shapeit -B gwas \
-V Gwas.chr20.Unphased.vcf \
--input-ref reference.haplotypes.gz reference.legend.gz reference.sample \
--exclude-snp gwas.alignments.strand.exclude \
-O Gwas.Chr20.Phased.Output