error in merging data by two versions of plink

Question

[fatima]

Dear all,

I tried to merge two binary file(my data set and the reference panel 1000G), but I get just fam file and log file :

Options in effect: --bfile mydata --bmerge ref.bim ref.bed ref.fam --make-bed --out mergefiles

Reading map (extended format) from [ mydata.bim ]

17838 markers to be included from [ mydata.bim ]

Reading pedigree information from [ mydata.fam ]

713 individuals read from [ mydata.fam ]

713 individuals with nonmissing phenotypes

Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)

Missing phenotype value is also -9

338 cases, 375 controls and 0 missing

226 males, 487 females, and 0 of unspecified sex

Reading genotype bitfile from [ CD_GermanyKielchr2_mod.bed ]

Detected that binary PED file is v1.00 SNP-major mode

Using merge mode 1 : consensus call (default)

**Could you tell me what is the problem?In addition when I try to run it by plink v1.9 I get this error:

Line 1 of ref.bed has fewer tokens than expected.

Thank you.

[fatima]

I found the problem. The order in bed, bim and fam file is important.

[tz.rzezniczak]

I seem to be having the same problem trying to use --filter in PLINK.
Can you specify what you mean by the order is important?

[fatima]

It means you should use bed file at first and bim and fam respectively (exactly in the same order is written in plink instructure).