Convert .gen file with only alternate allele dosage to plink files?

Question

[clyumath]

I have a .gen file with only alternate allele dosage (0~2) for each SNP, like a simple following (3 SNPs and 5 samples):

1       1:11008:C:G     11008   C       G       1.022   0.193   0.192   0.281   0.003
1       1:11012:C:G     11012   C       G       1.022   0.193   0.192   0.281   0.003
1       1:13110:G:A     13110   G       A       0.135   0.193   0.019   0.002   0.002

Is there a software that can convert this kind of gen file to plink files (bed/fam/bim)?

I understand, for a standard .gen file with SNPs of three probabilities (like CC,CG,GG) can be done by plink --gen --sample, but the gen file I have is only with alternate allele dosage (0~2) for each SNP. Any suggestion?

Thank you very much in advance!

Answer 1

[zx8754]

Read about plink --import-dosage flag:

• https://www.cog-genomics.org/plink/2.0/input#import_dosage

[clyumath]

Thanks, --import-dosage works well.