Question: fcGENE conversion error: Plink dosage to bed/bim/fam
0
gravatar for aldoc
3.0 years ago by
aldoc10
aldoc10 wrote:

Hi,

There are some PLINK dosage files (format=1) that I need to convert to bed/bim/fam (using best guesses of genotypes). Namely, the .dose files I have are like:

SNP    A1    A2    F1 I1    F2 I2    ...
rsXXX    A    T    1.692    1.699    ...
...

If I understand well (http://www.bx.psu.edu/~giardine/tests/tmp/fcgene-1.0.7.pdf, p.10), I could re-format them by using:

./fcgene --dosage file.dose --fam file.fam --map file.map --oformat plink-bed

However, I get this error:

ERROR: First line of plink dosage format file "file.dose" should start with the word "SNP", the second column with the word "A1" and the third column with the word "A2".

I have tried changing tabs for single spaces in "file.dose", but still I get the same message. Do you know how to fix it?

Thanks in advance,

plink fcgene dosage • 1.8k views
ADD COMMENTlink modified 12 months ago by bg11160 • written 3.0 years ago by aldoc10

I have exactly the same problem. Any clues about the solution?

ADD REPLYlink written 2.7 years ago by ansyr0

Same problem, even with the example files provided in v1.0.6 EROOR: First line of plink dosage format file "work_examples/plink/plink_dosage.dose" should start with the word "SNP", the second column with the word "A1" and the thrid column with the word "A2"

ADD REPLYlink written 19 months ago by uitde0070
0
gravatar for Teresa
17 months ago by
Teresa10
United States
Teresa10 wrote:

I have the same problem. Have you solved it?

ADD COMMENTlink written 17 months ago by Teresa10
0
gravatar for Wietje
17 months ago by
Wietje200
Germany
Wietje200 wrote:

How did you compile your dosage file? Did you enter the data or the header manually? Could it be that you have "hidden" symbols or characters in there so that PLINK cannot read the first line correctly?

ADD COMMENTlink written 17 months ago by Wietje200
0
gravatar for bg1116
12 months ago by
bg11160
bg11160 wrote:

Has anyone figured out the answer to this problem? I am having the same issue.

Thanks

ADD COMMENTlink written 12 months ago by bg11160
1

Just use plink 2.0 —import-dosage + —make-bed.

ADD REPLYlink written 12 months ago by chrchang5235.4k
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