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'''You may want to learn about new and improved [[Minimac4]].'''
'''minimac''' is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation. 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.
'''minimac''' is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation. 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.
* [[Minimac Command Reference]] - Summary of minimac options
* [[Minimac Command Reference]] - Summary of minimac options
* [[Minimac Diagnostics]] - Summary of diagnostics for imputation performance generated by minimac
* [[Minimac Diagnostics]] - Summary of diagnostics for imputation performance generated by minimac
*[https://imputationserver.sph.umich.edu Imputation server] - We are running imputation (and pre-phasing) for you!
= Download =
= Download =
A binary Linux (64 bit) version of minimac is available [http://www.sph.umich.edu/csg/cfuchsb/minimac-beta-2012.7.17.tgz from here] and source code [http://www.sph.umich.edu/csg/cfuchsb/minimac.src.tgz from here]
A binary Linux (64 bit) version of minimac is available [http://csg.sph.umich.edu/cfuchsb/minimac-beta-2013.7.17.tgz from here] and source code [http://csg.sph.umich.edu/cfuchsb/minimac.src.tgz from here]
The current version of minimac should be stamped 2012.7.17 - if your version shows a different version number or date stamp when it runs, it is not current.
The current version of minimac should be stamped 2013.7.17 - if your version shows a different version number or date stamp when it runs, it is not current.
If you use this beta 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 beta 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.
== Change log ==
== Change log ==
2013.7.17
- minor bug fixes
- minor bug fixes
-- all variants in the reference VCF will be imputed (SNPs, InDels, SVs)
-- all variants (SNPs, InDels, SVs) in the reference VCF will be imputed - independent from the FILTER column setting
- improved performance (Thanks to David Hinds - see also [[minimac2]] for the full set of performance improvements)
2012.11.16
2012.11.16
=== 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).
|-
|-
|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>
==== using a VCF reference panel ====
==== using a VCF reference panel ====
minimac --vcfReference --refHaps ref.vcf.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200 --prefix results
minimac --vcfReference --refHaps ref.vcf.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200 --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; otherwise, please set the --rs flag
==== using a MaCH reference panel ====
==== using a MaCH reference panel ====
minimac --refHaps ref.hap.gz --refSnps ref.snps.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200 --prefix results
minimac --refHaps ref.hap.gz --refSnps ref.snps.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200 --prefix results
A detailed description of all minimac options is available [[Minimac Command Reference|elsewhere]]. Here is a brief description of the above parameters:
A detailed description of all minimac options is available [[Minimac Command Reference|elsewhere]]. Here is a brief description of the above parameters:
|-
|-
| <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>
=== 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]. As of this writing, the most recent set of haplotypes are based on genotype calls were generated in May 2011 and are an interim analysis of Project's Phase I data.
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]. As of this writing, the most recent set of haplotypes are based on genotype calls were generated in May 2011 and are an interim analysis of Project's Phase I data.
=== Imputation quality evaluation ===
=== Imputation quality evaluation ===
=== Additional Sources of Information ===
=== Additional Sources of Information ===
If the combination of MaCH and Minimac still runs too slowly for you, and you have access to a multi-processor compute cluster, you can look at [[ChunkChromosome]] page to learn how to conveniently split each chromosome into multiple segments that can be analyzed in parallel.
If the combination of MaCH and Minimac still runs too slowly for you, and you have access to a multi-processor compute cluster, you can look at [[ChunkChromosome]] page to learn how to conveniently split each chromosome into multiple segments that can be analyzed in parallel. For information on how to put the resulting chunks back together, see [[Ligate Minimac|this page]].
If you are especially interested in 1000 Genomes Imputation, then you should look at the [[Minimac: 1000 Genomes Imputation Cookbook]].
If you are especially interested in 1000 Genomes Imputation, then you should look at the [[Minimac: 1000 Genomes Imputation Cookbook]].
= 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 =
If you use minimac, please cite:
If you use [[minimac]] or [[minimac2]] please cite:
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.
