Chromsome X Phased Data Download
Original data are available at HapMap website
http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/2006-07_phaseII/phased/. Below are files converted to MaCH and minimac input format.
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
Notes:
Refer to wiki page for more details.
Report to Yun Li if you encounter any problems.
|