Apt-format-result provides .map file (for exporting plink format) with all null values except affymetrix id column

Question

[tvibhaps]

Hi, I am trying to get plink format of gt call file (call code file) using apt-format-result and i am getting the map file as below (sample)

Chromosome    Marker ID      Genetic distance  Physical position
0             AX-86908953    0.000             0
0             AX-86930057    0.000             0

ped file looks as below (few portion of top lines)-

Sample                                  Filename  Genotypes
Sample1_259972_F24.CEL_call_code        A A       A A        T T
Sample2_02109_259972_H24.CEL_call_code  A A       A A        T T

MyCall code input file looks as below (few portion of top lines)-

probeset_id     sample1_00419_259972_F24.CEL_call_code
AX-86908953     BB      BB      BB      BB      AB
AX-86930057     BB      BB      BB      BB      BB

I can suspect only at input call code format in this situation i guess.

I am following the the apt-format-result link http://media.affymetrix.com/support/developer/powertools/changelog/apt-format-result.html.

Can we get call code format using apt-format-result as per the link says?iI do not see the input files used for exporting call-code-format.

1. What should be the format of call code file to get plink output using apt-format-result?
2. What should be input files to export call code format suing apt-format-result?

Any help is appreciated. Thank you.