I am following the command of the link of MACH
# To estimate model parameters ...
prompt> mach1 -d sample.dat -p sample.ped -s hapmap.snps -h hapmap.haplos --greedy --rounds 10 --prefix round1
# To fill in missing genotypes ...
prompt> mach1 -d sample.dat -p sample.ped -s hapmap.snps -h hapmap.haplos --greedy --errormap round1.erate --cross round1.rec --mle --mldetails
I have data in PLINK format and done QC of SNP data using PLINK and generate .dat file and .ped file in Merlin format using GenABEL package. Also may be the .snps file contains only snps name and is like .txt file.
How can I get the .haplos file or the information of that file.
Finally how I get the genotype data with filling the missing data and how I convert it to PLINK format.
Could you please help me to provide any detail protocol for imputation of missing genotye.
http://csg.sph.umich.edu//abecasis/MACH/tour/imputation.html