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This is the MaCH Divide and Conquer page, documenting how to break the genome into smaller pieces before imputation/phasing and how to ligate after imputation/phasing.
This is the MaCH Divide and Conquer page, documenting how to break the genome into smaller pieces before imputation/phasing and how to ligate after imputation/phasing.
== Phase without External Reference ==
=== 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 Merlin tutorial [http://www.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>
== Phase/Imputation with External Reference ==
== Questions and Comments? ==
Email [mailto:yunli@med.unc.edu Yun Li].
