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=== Split Your Data ===
=== Split Your Data ===
You can split your data using [http://www.sph.umich.edu/csg/yli/splitPed/ 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 [http://genome.sph.umich.edu/wiki/Minimac#Imputation minimac wiki] for more details.
You can split your data using [http://csg.sph.umich.edu//yli/splitPed/ 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 [http://genome.sph.umich.edu/wiki/Minimac#Imputation minimac wiki] for more details.
== Phasing/Imputation with External Reference ==
== 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. <br>
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. <br>
You can split the reference data using [http://www.sph.umich.edu/csg/yli/splitRef/ splitRef].
You can split the reference data using [http://csg.sph.umich.edu//yli/splitRef/ splitRef].
== Post Phasing/Imputation Ligation ==
== Post Phasing/Imputation Ligation ==
You can use [http://www.sph.umich.edu/csg/yli/ligateHap.V004.tgz LigateHaplotypes ] to ligate the parts.
You can use [http://csg.sph.umich.edu//yli/ligateHap.V004.tgz LigateHaplotypes ] to ligate the parts.
== Questions and Comments? ==
== Questions and Comments? ==
Email [mailto:yunli@med.unc.edu Yun Li].
Email [mailto:yunli@med.unc.edu Yun Li].
