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,