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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].
