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'''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.
= 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.
==== 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>--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>
