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. If you follow our recommendation of using MaCH+minimac for imputation, you only need to use splitPed in the MaCH step (to phase your study sample), which does not involve external reference. In the minimac step, imputation finishes within a day for several thousand individuals even for the largest chromosome as a whole: A good rule of thumb is that minimac should take about 1 hour to impute 1,000,000 markers in 1,000 individuals using a reference panel with 100 haplotypes, see minimac wiki for more details.
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.