Question: error in merging data by two versions of plink
gravatar for fatima
3.5 years ago by
fatima10 wrote:

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.

bmerge plink • 1.5k views
ADD COMMENTlink written 3.5 years ago by fatima10

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

ADD REPLYlink written 3.5 years ago by fatima10

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?

ADD REPLYlink written 3.4 years ago by tz.rzezniczak0

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

ADD REPLYlink written 3.3 years ago by fatima10
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