Great project, I started building something similar when Claude pointed me to your version. I've played around with the consumer chip to vcf translation and imputation a bit, and created a small PR fixing some issues https://github.com/dawndrain/genetic_prediction/pull/2
One of the bigger issues I've had is the Michigan server dropping all homozygous SNPs before imputation, I'm trying to understand it better and come up with a sample padding workaround so everything is kept and used. https://github.com/dawndrain/genetic_prediction/issues/5
Great project, I started building something similar when Claude pointed me to your version. I've played around with the consumer chip to vcf translation and imputation a bit, and created a small PR fixing some issues
https://github.com/dawndrain/genetic_prediction/pull/2
One of the bigger issues I've had is the Michigan server dropping all homozygous SNPs before imputation, I'm trying to understand it better and come up with a sample padding workaround so everything is kept and used.
https://github.com/dawndrain/genetic_prediction/issues/5
I'll look at the sco... (read more)