Covert Plink (Ped,Map) To Mach Format

Question

[Cirrus]

Dear All,

do anyone knows a tool or R function that converts plink files into mach format?

Thanks a lot

Answer 1

[Adrian Cortes]

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.

Answer 2

[Maxime Lamontagne]

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.

[somethingwithdata]

I used your code and it worked fine till i tried to get the ped: the erroroutput was this:

"awk: line 3: syntax error at or near print"

any suggestions what might be the problem?

my ped-file contains about 300000 SNPs and 2800 Samples

[Maxime Lamontagne]

Sorry, there was an error.

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

[JazminSP]

Thanks! Your solution functions perfectly! I already had my .ped and .dat files but MACH didn't recognise it correctly and it would say the markers were not bi-allelic.

Mil gracias!!!