--output-missing-genotype not working on binary PLINK files

[Vince Forgetta]

Hi,

I am trying the following on binary PLINK files that have 'N' as missing genotype:

plink --bfile infile --missing-genotype N --output-missing-genotype 0 --out outfile --make-bed

My goal is to convert missing genotype code from 'N' to 0.

However, the resulting outfile.bim retains 'N' as the missing genotype. It works if I create ped/map files first:

plink --bfile infile --missing-genotype N --output-missing-genotype 0 --out outfile recode

plink --file outfile --make-bed --out outbin

Is this behaviour expected?

Thanks,

Vince

[Christopher Chang]

Hmm, this behavior is technically expected -- PLINK 1.07 does the same thing -- but I agree that it's messed up, and I seriously hope that nobody depends on it.  I will post a patch tonight.

[Vince Forgetta]

Thanks. I can test if you need.

[Christopher Chang]

Sure, let me know if you have any problems with the Aug 4 builds.