Original data are available at http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/2007-08_rel22/phased/ . If you use haplotypes from a single population as reference, you can download files from the above HapMap official website and feed the files directly to MaCH. You will need to turn on --hapmapFormat option. For details, see HapMap format reference files. If you use the panels below (already in MaCH input format), you do NOT need to turn on --hapmapFormat option.

 Original
    CEU.r22.orig.tgz
    JPT+CHB.r22.orig.tgz
    YRI.r22.orig.tgz
    CEU.r22.orig.map.tgz
    JPT+CHB.r22.orig.map.tgz
    YRI.r22.orig.map.tgz
  

 Consensus
    CEU.r22.tgz
    CHB+JPT.r22.tgz
    YRI.r22.tgz

    CEU+YRI+JPT+CHB.r22.tgz
    CEU+YRI.r22.tgz
    CEU+CHB+JPT.r22.tgz

    r22.consensus.map.tgz
  

  First, un-tar the files using the following commands:
tar -zxvf CEU+YRI+JPT+CHB.r22.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 .