I am trying to find the concordance for a sample (SOLiD data for a whole genome) against its Array data generated from Illumina 2.5M. To do this, I am using plink, but when I used this command
plink --bfile file1 --bmerge file2.bed file2.bim file3.fam --merge-mode 7 --out myfile1vs2
Concordance rate is nan
Is my data wrong or my command ?