HapMap3 r2 Phased Data Download
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.
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 .
Notes:
Do not turn on --compact if memory is not an issue.
Report to Yun Li if you encounter any problems.
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