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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 Merlin tutorial [http://wwwcsg.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html]. <br>
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). <br>
=== Reference Haplotypes ===
You can download the reference haplotypes from MaCH download page [http://wwwcsg.sph.umich.edu/csg/yli/mach/download/chrX.html].
== Two-Step Imputation ==
== FAQ ==
=== Shall I phase/impute males and females together or separately? ===
When there is missing genotypes among Phasing males, phasing is needed for males as well. But phasing them 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.
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