University of Michigan Center for Statistical 


Chromsome X Phased Data Download

Original data are available at HapMap website Below are files converted to MaCH and minimac input format.

Download Data

    HapMap2 r21
    CEU    : hm2_r21.chrX.CEU.non-par.tgz
    CHB+JPT: hm2_r21.chrX.CHB+JPT.non-par.tgz 
Latest Release from 1000 Genomes Project (currently 20101123 as of June 20, 2011) chrX.tgz

  First, un-tar the files using the following command:
tar -zxvf hm2_r21.chrX.CEU.non-par.tgz
tar -zxvf hm2_r21.chrX.CHB+JPT.non-par.tgz

  The files can be directly fed to MaCH and minimac. We recommend a 2-step (MaCH+minimac) imputation procedure:
(step 1) phase your own data using MaCH (if no missing genotypes in males, only need to phase females); and
(step 2) impute using minimac.

     # step1
     mach1 -d sample.dat -p sample.ped --states 200 -r 20 --phase -o sample.phased > sample.phased.log
     # step2
      minimac --refHaps hm2_r21_chrX_CEU/hm2_r21.chrX.non-par.hap.gz --refSnps hm2_r21_chrX_CEU/hm2_r21.chrX.non-par.snps --haps sample.phased.gz --snps sample.snps --rounds 5 --states 200 --prefix sample.imputed > sample.imputed.log

Refer to wiki page for more details.
Report to Yun Li if you encounter any problems.


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