Minimac2 - Revision history

Santy.8128 at 16:53, 9 March 2018

2018-03-09T16:53:29Z

← Older revision		Revision as of 12:53, 9 March 2018
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	'''New Version [[~~Minimac3~~]] available ! Please Check out !!!'''		'''New Version [[Minimac4]] available ! Please Check out !!!'''

	'''minimac2''' is an improved version of [[Minimac]]. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, "mini", refers to the modest amount of computational resources it requires. The second, "mac", is short hand for [[MaCH]], our widely used algorithm for genotype imputation.		'''minimac2''' is an improved version of [[Minimac]]. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, "mini", refers to the modest amount of computational resources it requires. The second, "mac", is short hand for [[MaCH]], our widely used algorithm for genotype imputation.

Goncalo: /* Download */

2015-04-23T21:59:10Z

Download

← Older revision		Revision as of 17:59, 23 April 2015
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	= Download =		= Download =
	A binary Linux (64 bit) version of minimac2 is available [http://csg.sph.umich.edu/cfuchsb/minimac2.2014.9.15.tgz from here] and source code [http://csg.sph.umich.edu~~/cfuchsb/~~/cfuchsb/minimac2.2014.9.15.src.tgz from here]. For compiling the source code, you need a recent [https://gcc.gnu.org gcc] (>=4.8), [http://www.openblas.net OpenBlas ], and [https://gcc.gnu.org/fortran/ GFortran].		A binary Linux (64 bit) version of minimac2 is available [http://csg.sph.umich.edu/cfuchsb/minimac2.2014.9.15.tgz from here] and source code [http://csg.sph.umich.edu/cfuchsb/minimac2.2014.9.15.src.tgz from here]. For compiling the source code, you need a recent [https://gcc.gnu.org gcc] (>=4.8), [http://www.openblas.net OpenBlas ], and [https://gcc.gnu.org/fortran/ GFortran].

	The current version of minimac2 should be stamped 2014.9.15 - if your version shows a different version number or date stamp when it runs, it is not current.		The current version of minimac2 should be stamped 2014.9.15 - if your version shows a different version number or date stamp when it runs, it is not current.

Santy.8128 at 05:03, 31 January 2015

2015-01-31T05:03:28Z

← Older revision		Revision as of 01:03, 31 January 2015
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			'''New Version [[Minimac3]] available ! Please Check out !!!'''

	'''minimac2''' is an improved version of [[Minimac]]. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, "mini", refers to the modest amount of computational resources it requires. The second, "mac", is short hand for [[MaCH]], our widely used algorithm for genotype imputation.		'''minimac2''' is an improved version of [[Minimac]]. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, "mini", refers to the modest amount of computational resources it requires. The second, "mac", is short hand for [[MaCH]], our widely used algorithm for genotype imputation.

Cfuchsb: /* using a VCF reference panel */

2015-01-28T10:24:44Z

using a VCF reference panel

← Older revision		Revision as of 06:24, 28 January 2015
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	==== using a VCF reference panel ====		==== using a VCF reference panel ====
	minimac2 --vcfReference --refHaps ref.vcf.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200 --prefix results		minimac2 --vcfReference --refHaps ref.vcf.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200
			--vcfchr 20 --prefix results

	'''Note''': GWAS SNPs (file --snps target.snps.gz) are by default expected to be in the chr:pos format e.g. 1:1000 and on build37/hg19		'''Note''': GWAS SNPs (file --snps target.snps.gz) are by default expected to be in the chr:pos format e.g. 1:1000 and on build37/hg19
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	\| <code>--vcfReference </code>		\| <code>--vcfReference </code>
	\| This option specifies that the provided --refHaps file is provided in VCF format , no --refSNPs file needed.		\| This option specifies that the provided --refHaps file is provided in VCF format , no --refSNPs file needed.
			\|-
			\| <code>--vcfchr </code>
			\| Chromosome for which we will carry out imputation.
	\|-		\|-
	\| <code>--rs </code>		\| <code>--rs </code>

Cfuchsb at 07:36, 28 January 2015

2015-01-28T07:36:22Z

← Older revision		Revision as of 03:36, 28 January 2015
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	= Download =		= Download =
	A binary Linux (64 bit) version of minimac2 is available [http://~~www~~.sph.umich.edu~~/csg~~/cfuchsb/minimac2.2014.9.15.tgz from here] and source code [http://~~www~~.sph.umich.edu/~~csg~~/cfuchsb/minimac2.2014.9.15.src.tgz from here]. For compiling the source code, you need a recent [https://gcc.gnu.org gcc] (>=4.8), [http://www.openblas.net OpenBlas ], and [https://gcc.gnu.org/fortran/ GFortran].		A binary Linux (64 bit) version of minimac2 is available [http://csg.sph.umich.edu/cfuchsb/minimac2.2014.9.15.tgz from here] and source code [http://csg.sph.umich.edu/cfuchsb//cfuchsb/minimac2.2014.9.15.src.tgz from here]. For compiling the source code, you need a recent [https://gcc.gnu.org gcc] (>=4.8), [http://www.openblas.net OpenBlas ], and [https://gcc.gnu.org/fortran/ GFortran].

	The current version of minimac2 should be stamped 2014.9.15 - if your version shows a different version number or date stamp when it runs, it is not current.		The current version of minimac2 should be stamped 2014.9.15 - if your version shows a different version number or date stamp when it runs, it is not current.

	If you use this version, please be sure to stop by the [http://~~www~~.sph.umich.edu~~/csg~~/abecasis/MaCH/download/ MaCH download page] and fill out the registration form, so that we can let you know when an official release is available and keep you updated with respect to any bug fixes.		If you use this version, please be sure to stop by the [http://csg.sph.umich.edu/abecasis/MaCH/download/ MaCH download page] and fill out the registration form, so that we can let you know when an official release is available and keep you updated with respect to any bug fixes.

	== Multiprocessor Version ==		== Multiprocessor Version ==
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	=== Preparing Your Data ===		=== Preparing Your 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 [http://~~www~~.sph.umich.edu~~/csg~~/abecasis/Merlin/tour/input_files.html Merlin Tutorial].		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 [http://csg.sph.umich.edu/abecasis/Merlin/tour/input_files.html Merlin Tutorial].

	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).
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	\|-		\|-
	\|style=white-space:nowrap\|<code>-d sample.dat</code>		\|style=white-space:nowrap\|<code>-d sample.dat</code>
	\| Data file in [http://~~www~~.sph.umich.edu~~/csg~~/abecasis/Merlin/tour/input_files.html Merlin format]. Markers should be listed according to their order along the chromosome.		\| Data file in [http://csg.sph.umich.edu/abecasis/Merlin/tour/input_files.html Merlin format]. Markers should be listed according to their order along the chromosome.
	\|-		\|-
	\| <code>-p sample.ped</code>		\| <code>-p sample.ped</code>
	\| Pedigree file in [http://~~www~~.sph.umich.edu~~/csg~~/abecasis/Merlin/tour/input_files.html Merlin format]. Alleles should be labeled on the forward strand.		\| Pedigree file in [http://csg.sph.umich.edu/abecasis/Merlin/tour/input_files.html Merlin format]. Alleles should be labeled on the forward strand.
	\|-		\|-
	\| <code>--states 200</code>		\| <code>--states 200</code>
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	\|-		\|-
	\| <code>--refHaps ref.hap.gz </code>		\| <code>--refHaps ref.hap.gz </code>
	\| Reference haplotypes (e.g. from [http://~~www~~.sph.umich.edu~~/csg~~/abecasis/MACH/download/ MaCH download page])		\| Reference haplotypes (e.g. from [http://csg.sph.umich.edu/abecasis/MACH/download/ MaCH download page])
	\|-		\|-
	\| <code>--vcfReference </code>		\| <code>--vcfReference </code>
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	=== Reference Haplotypes ===		=== Reference Haplotypes ===

	Reference haplotypes generated by the 1000 Genomes project and formatted so that they are ready for analysis are available from the [http://~~www~~.sph.umich.edu~~/csg~~/abecasis/MACH/download/ MaCH download page].		Reference haplotypes generated by the 1000 Genomes project and formatted so that they are ready for analysis are available from the [http://csg.sph.umich.edu/abecasis/MACH/download/ MaCH download page].

	=== Imputation quality evaluation ===		=== Imputation quality evaluation ===
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	= Post-imputation Association Analysis =		= Post-imputation Association Analysis =
	== Quantitative Traits ==		== Quantitative Traits ==
	Please use [http://~~www~~.sph.umich.edu~~/csg~~/yli/mach/download/mach2qtl.source.V108.tgz mach2qtl].		Please use [http://csg.sph.umich.edu/yli/mach/download/mach2qtl.source.V108.tgz mach2qtl].

	== Binary Traits ==		== Binary Traits ==
	Please use [http://~~www~~.sph.umich.edu~~/csg~~/yli/mach/download/mach2dat.source.1.0.18.tgz mach2dat]. Versions 1.0.18 and above accommodate to minimac output.		Please use [http://csg.sph.umich.edu/yli/mach/download/mach2dat.source.1.0.18.tgz mach2dat]. Versions 1.0.18 and above accommodate to minimac output.

	= Reference =		= Reference =

Cfuchsb: /* Reference */

2014-10-23T10:12:46Z

Reference

← Older revision		Revision as of 06:12, 23 October 2014
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	If you use [[minimac]] or [[minimac2]] please cite:		If you use [[minimac]] or [[minimac2]] please cite:

	Fuchsberger C, Abecasis GR, Hinds DA. minimac2: faster genotype imputation. Bioinformatics 2014 ~~(accepted)~~		Fuchsberger C, Abecasis GR, Hinds DA. minimac2: faster genotype imputation. Bioinformatics 2014 [http://bioinformatics.oxfordjournals.org/content/early/2014/10/22/bioinformatics.btu704.short]

	Howie B, Fuchsberger C, Stephens M, Marchini J, and Abecasis GR.		Howie B, Fuchsberger C, Stephens M, Marchini J, and Abecasis GR.

Cfuchsb: /* Reference */

2014-10-22T15:55:44Z

Reference

← Older revision		Revision as of 11:55, 22 October 2014
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	= Reference =		= Reference =

	If you use [[minimac2]], please cite:		If you use [[minimac]] or [[minimac2]] please cite:

	Fuchsberger C, Abecasis GR, Hinds DA. minimac2: faster genotype imputation. Bioinformatics 2014 (accepted)		Fuchsberger C, Abecasis GR, Hinds DA. minimac2: faster genotype imputation. Bioinformatics 2014 (accepted)


	~~If you use [[minimac]] please cite:~~


	Howie B, Fuchsberger C, Stephens M, Marchini J, and Abecasis GR.		Howie B, Fuchsberger C, Stephens M, Marchini J, and Abecasis GR.

Cfuchsb: /* Reference */

2014-10-21T00:17:59Z

Reference

← Older revision		Revision as of 20:17, 20 October 2014
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	= Reference =		= Reference =

	If you use ~~[[minimac]] or~~ [[minimac2]], please cite:		If you use [[minimac2]], please cite:

			Fuchsberger C, Abecasis GR, Hinds DA. minimac2: faster genotype imputation. Bioinformatics 2014 (accepted)

	~~Fuchsberger C, Abecasis GR, Hinds DA. minimac2~~: ~~faster genotype imputation. Bioinformatics 2014 (accepted)~~
			If you use [[minimac]] please cite:

Cfuchsb: /* Reference */

2014-10-21T00:17:18Z

Reference

← Older revision		Revision as of 20:17, 20 October 2014
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	Fuchsberger C, Abecasis GR, Hinds DA. minimac2: faster genotype imputation Bioinformatics 2014 (accepted)		Fuchsberger C, Abecasis GR, Hinds DA. minimac2: faster genotype imputation. Bioinformatics 2014 (accepted)

Cfuchsb: /* Reference */

2014-10-21T00:16:55Z

Reference

← Older revision		Revision as of 20:16, 20 October 2014
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	If you use [[minimac]] or [[minimac2]], please cite:		If you use [[minimac]] or [[minimac2]], please cite:


			Fuchsberger C, Abecasis GR, Hinds DA. minimac2: faster genotype imputation Bioinformatics 2014 (accepted)


	Howie B, Fuchsberger C, Stephens M, Marchini J, and Abecasis GR.		Howie B, Fuchsberger C, Stephens M, Marchini J, and Abecasis GR.