Difference between revisions of "MaCH: machX"
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=== Phase Your Own Data === | === Phase Your Own Data === | ||
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| + | 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. | ||
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| + | mach1 -d sample.dat -p sample.ped --states 200 -r 20 --phase -o sample.phased > sample.phased.log | ||
=== Impute === | === Impute === | ||
== FAQ == | == FAQ == | ||
Revision as of 09:47, 26 November 2010
This page documents how to perform X chromosome (non-pseudo-autosomal part) imputation using MaCH [1] and minimac [2].
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 [3].
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).
Note that for males hemizygotes are coded as homozygotes.
Reference Haplotypes
You can download the reference haplotypes from MaCH download page [4].
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
