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.
Phasing without External Reference
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.
Phasing/Imputation with External Reference
When you phase/impute with external reference panel, you will only need to break the reference files into parts containing subsets of markers because SNPs in your own data (pedigree files) but not in reference files will be automatically ignored by MaCH and minimac.
You can split the reference data using splitRef.
Post Phasing/Imputation Ligation
You can use LigateHaplotypes to ligate the parts.
Questions and Comments?
Email Yun Li.