Original data are available at http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/2006-07_phaseII/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 combined panels below, you do NOT need to turn on --hapmapFormat option.

    CEU+YRI+JPT+CHB
    hm_phasing.r21.CEU+YRI+JPT+CHB.hap.tgz
    hm_phasing.r21.CEU+YRI+JPT+CHB.snps.tgz
  

    CEU+YRI
    hm_phasing.r21.CEU+YRI.hap.tgz
    hm_phasing.r21.CEU+YRI.snps.tgz
  

    CEU+CHB+JPT
    hm_phasing.r21.CEU+CHB+JPT.hap.tgz
    hm_phasing.r21.CEU+CHB+JPT.snps.tgz
  

    CEU: for those who prefer using MACH format reference files
    hm2.r21.CEU.tgz
    hm2.r21.CEU.map.tgz
  

  First, un-tar the files using the following commands:
tar -zxvf hm_phasing.r21.CEU+YRI+JPT+CHB.hap.tgz
tar -zxvf hm_phasing.r21.CEU+YRI+JPT+CHB.snps.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 .