Hey,

In your shell, to go from PLINK's ped to MACH's impute ped you need to remove the phenotype column:

gawk '{ $6 = ""; gsub(FS "+", FS) }1' data.ped > data2.ped

Then create the dat file from PLINK's map file

gawk '{print "M",$2}' data.map > data.dat

Hope that helps.

DAT file:

awk '{$1="M";print $1,$2}' file.map > file.dat

SNP file:

cut -f2 file.map > file.snp

MAP file:

cut -f 1,2,4 file.map > file.V2.map

PED file:

If you want to have your ped file in this format (FAM1001 ID1234 0 0 M A/A A/C C/C)

cut -d ' ' -f1-5,7- file.ped > temp

awk 'BEGIN { 

    ORS = " "

 } {

    print "\n"

    print $1,$2,$3,$4,$5;

    for(i=6; i?NF; i+=2)

    {

            print $i "/" $(i+1) 

    }

}' temp | cut -f2- -d ' ' | tail -n+2 > newfile.ped

EDIT

Sorry, there was an error.

Replace the ? by < in the for loop and this should work.