LD reference panel and target genotype

[Qiaolan]

Hi Bjarni,

Thanks for your time.

I have some questions about the reference panel and target genotype.

1. The reference panel should follow --gf and the target genotype should follow --vgf. Is this correct?

2. In step 3, the polygenic risk score is calculated based on the target genotype, i.e, --vgf in step 1?

3. If I don't want to use LD reference panel. I can just put the target genotype in --gf?

Thanks!

Qiaolan

[bbitarello]

Hey there,
I think I can help.

"The reference panel should follow --gf and the target genotype should follow --vgf. Is this correct?""

Yes

"In step 3, the polygenic risk score is calculated based on the target genotype, i.e, --vgf in step 1?"

"If I don't want to use LD reference panel. I can just put the target genotype in --gf?"

My understanding is an LD reference is required. If you put the same datasets in --gf and --vgf it will use as LD reference the target dataset (which is not advisable because of overfitting). Using the same dataset for LD reference that was used in the GWAS is fine, though.

Best