Hi Chris,
Thanks for the quick response on this. I have a quick related question:
I've been exporting genotype data using "plink2 --export tped 12 --output-missing-genotype 0" and running a mixed model with EMMAX, which (I believe) generates its own additive coding for the tped data where 2=homozygous ALT, 0=homozygous REF, and 1=heterozygote.
I'm now running GWAS analysis using other tools, and would like to export genotype data using the same additive coding (2=homozygous ALT, 0=homozygous REF, and 1=heterozygote). Is this possible with plink2?
When I run "plink2 --export A", I believe the resulting additive coding is of the reverse form: 0=homozygous ALT, 2=homozygous REF, and 1=heterozygote (which is the opposite of what I want).
The reason I ask is that I'm working with very large files (10s of millions of snps), and I'm hoping not to have to write an adhoc program to reverse the additive coding in order to generate something that is consistent with my previous output (generated with "plink2 --export tped 12 --output-missing-genotype 0" and EMMAX tped data encoding).
Thanks very much for your input,
Esther