fcGENE conversion error: Plink dosage to bed/bim/fam
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5.5 years ago
aldoc ▴ 10

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?

plink fcGENE dosage • 3.2k views
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I have exactly the same problem. Any clues about the solution?

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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"

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3.9 years ago
Teresa ▴ 20

I have the same problem. Have you solved it?

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3.9 years ago
Wietje ▴ 220

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?

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3.6 years ago
bg1116 • 0

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

Thanks

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