HapMap r22 Download
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.
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 .
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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