Understanding the .diff file of plink1.9

[Wenbin Mei]

Hi!

I have a very basic question on comparing overlapping samples and variants between two filesets. I ran:

plink --bfile file1 \
       --bmerge file2 \
       --merge-mode 6 \
       --out strand_check

Here are the first few lines of strand_check.diff

                SNP                  FID           IID      NEW      OLD
        1:888659:T:C            fid1        iid1      T/T      0/0
        1:888659:T:C            fid1         iid2      T/T      0/0
        1:888659:T:C            fid1         iid3      T/T      0/0
        1:888659:T:C            fid1         iid4      T/T      0/0
        1:888659:T:C            fid1         iid5      T/T      0/0 

It appears that the genotypes are concordant but the coding is different: file1 is number-coded while file2 is letter-coded. Do you know what could have caused this? Aren't all the genotypes in .bed binary (so number-coded)? Is there any way to convert the genotypes to number-coded (0/0, 0/1, 1/1, ./.)?

Thanks a lot!