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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].

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.

== Phasing/Imputation with External Reference ==

== Phasing/Imputation with External Reference ==