How to do a conditional analysis (using a tagging SNP) with dosage data in PLINK?

Question

[joseuribesalazar]

Hi all,

I performed an association analysis with dosage data (.gen and .fam files) with PLINK 1.9 using imputated data and got back the association p-value for each SNP. Now, I want to do another association test with the same data, but using the SNP with the strongest association signal as a covariate (a conditional test).

The problem is that when i try to use the --condition option, a message appears saying "--dosage doesn't allow the conditional option".

Has anybody had the same problem? Any possible solutions or help are extremely welcome, since I'm breaking my head over here.

Thank you!

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Type of data that I have:

SNP     Position     A1       A2    ProbA1A1_Subject1   ProbA1A2_Subject1   ProbA2A2_Subject1... for 5000 subjects

[Kevin Blighe]

The dosage part of PLINK is under development, as far as I'm aware: https://www.cog-genomics.org/plink/1.9/order#dosage

Note that you can do what you want in R. I have processed whole genome genotyping PLINK data in R.