How to get the avaliable snp list with corrected beta used in LDpred2-auto module

[koujiaodahan]

There is a summary statistic from the EAS population(No validation data, No bim, No genotype data), so how can I get the final snplist with corrected beta in the best prs module?
Because No Genotype. so I plan to use LDpred2-auto based on some other public LD data such as 1000genome EAS.
The snplist includes all the matched snps , corrected beta is that beta_auto ? "beta_auto <- rowMeans(sapply(multi_auto[keep], function(auto) auto$beta_est))"

By the way, there are two parts in the guidance (LDpred2-auto: automatic model vs Inference with LDpred2-auto) about LDpred2-auto, just the used parameter is different? which is better reference for my situation?

[privefl]

• If you have access to UKBB, you can adapt https://github.com/privefl/paper-misspec/blob/main/code/prepare-corr-UKBB-EAS.R to derive some LD ref.

• beta_auto are the final PGS effect sizes from LDpred2-auto

• If you are interested in prediction only, you can use the first one; use the second one if you are also interested in inferring parameters (it is also fine for prediction)

[privefl]

Any update on this?