Original data are available at http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/2009-02_phaseIII/HapMap3_r2/. 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.

    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)
    hm3_r2_b36_fwd.map.tgz
  

    DIY:Convert HapMap III phased data to MACH format
    hm32mach.tgz
  

  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 .