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MaCH: machX

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This page documents how to perform X chromosome (non-pseudo-autosomal part) imputation using MaCH [http://wwwcsg.sph.umich.edu/csg/yli/mach] and minimac [http://genome.sph.umich.edu/wiki/Minimac].
== Getting Started ==
=== Your Own 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].
Within each fileTo get started, you will need to store your data in [[Merlin]] format pedigree and data files, markers should be stored by one per chromosome position. Alleles should be stored in For details of the forward strand and can be encoded as 'A'Merlin file format, 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele)see the Merlin tutorial [http://csg.sph.umich.edu//abecasis/Merlin/tour/input_files.html]. <br>
Note that 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 males hemizygotes are coded as homozygoteseach allele). <br>
=== Reference Haplotypes ===You can download the following reference haplotypes from MaCH download page [http://www.sph.umich.edu/csg/yli/mach/download/chrX.html]Note that for males hemizygotes are coded as homozygotes.<br>
== Two-Step Imputation = Reference Haplotypes ===
=== Phase Your Own Data ===You can download the reference haplotypes from MaCH download page [http://csg.sph.umich.edu//yli/mach/download/chrX.html].
== Two-Step Imputation == === Phase Your Own Data === If there is no missing genotypes in males, you will only need to phase the females. Make sure that alleles are all stored in forward strand before phasing.   mach1 -d sample.dat -p sample.ped --states 200 -r 20 --phase -o sample.phased > sample.phased.log === Impute === Imputation will then be performed on the phased haplotypes using minimac [http://genome.sph.umich.edu/wiki/Minimac].  minimac --refHaps ref.hap.gz --refSnps ref.snps --haps sample.phased.gz --snps sample.snps --rounds 5 --states 200 --prefix sample.imputed > sample.imputed.log
== FAQ ==
=== Shall I phase/impute males and females together or separately? ===
Phasing males together with or separately from females doesn't seem to affect imputation quality.
 
Imputing males together with or separately from females doesn't seem to affect imputation quality either.
 
== Questions and Comments? ==
 
Email [mailto:yunli@med.unc.edu Yun Li].
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