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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.
Phase without External Reference
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 .
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).
Split Your Data
You can split your data using splitPed.
Phase/Imputation with External Reference
Questions and Comments?
Email Yun Li.