University of Michigan Center for Statistical 


HapMap3 r2 Phased Data Download

Original data are available at These files are in different format than HapMapII and are not compatible with MaCH's --hapmapFormat option. We provide converted files below, which can be fed directly to MaCH. If you use the files below, you do NOT need to turn on --hapmapFormat option.

Download Data

    Single Population Reference
    CEU: hm3_r2_b36_fwd.CEU.tgz
    YRI: hm3_r2_b36_fwd.YRI.tgz
    TSI: hm3_r2_b36_fwd.TSI.tgz 
    MEX: hm3_r2_b36_fwd.MEX.tgz
    JPT+CHB: hm3_r2_b36_fwd.JPT+CHB.tgz
    Combined Reference
    CEU+YRI: hm3_r2_b36_fwd.CEU+YRI.tgz
    CEU+TSI: hm3_r2_b36_fwd.CEU+TSI.tgz
    Map Files (Shared across populations)
    DIY:Convert HapMap III phased data to MACH format

  First, un-tar the files using the following command:
tar -zxvf hm3_r2_b36_fwd.CEU+YRI.tgz

  The files can be directly fed to mach. We recommend a 2-step imputation procedure: pre-phasing using MaCH and imputation using minimac. For details, please go to minimac .

Do not turn on --compact if memory is not an issue.
Report to Yun Li if you encounter any problems.


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