Dosage flip with --chr-id

[Federico Billeci]

HI! I am computing a PRS with PRsice2, my target data is ukbb imputed data and as base data I am using a summary statistic on type 2 diabetes. I saw in previous conversations that it is not necessary to flip manually the non matching alleles between base and target, since PRsice should do this automatically. I guess this works usually since the match between base and target is based on the RS-id. In my case, since my target data uses as identifier chromosome:position_ref-allele_minor-allele (where minor is referred to the UKBB), I put the --chr-id option in PRsice, so that I can use the same identifier as my target data. I guess that in this case I have to do the base-target matching by hand, is this correct? In particular, since I don't want to modify my target data, I am modifying the base data, such that the effect allele is always the minor allele, so everytime there is a mismatch, I flip them and multiply by -1  the beta. Is this correct?

Thank you very much and best, 

Federico