Changes

'''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.

= 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/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 ==

=== 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  ====

   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

|-  

|-  

| <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>  

| 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>--rs </code>  

| <code>--rs </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].

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 ===

= 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 [[minimac2]], please cite:

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

 

 

 

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.