PRSice PRS calculation warning Mismatched SNPs. Is it due to using multi-covariate for SNP effect size?

Question

[landscape95]

Hi everyone, I am doing the PRS with PRSice since I want to evaluate the model with each P_threshold which is one of the function of PRSice, all I done was calculate the SNP effect size by Plink2 with --linear with Covariates information file of Discovery Samples, I'll then get the association result which contains BETA column with respect to each covariate (each SNP will have BETA for each Covariate, let say there are 10 covariates then SNP1 will have 10 Beta values) . Eg.

SNP1 ADD 0.5
SNP1 COVAR1 0.5
SNP1 COVAR2 0.5
...
SNP1 COVAR10 0.5

After that I put this association result with the Target samples in PRSice, I wonder because of using 10 covariates that make the program warns:

Warning: Mismatched SNPs detected between base and 
         target!You should check the files are based on the same 
         genome build, or that can just be InDels

Is this considered a problem? Do you have any experience and suggestion? Your help is really appreciated!

Answer 1

[Sam]

The mismatched SNPs warning suggest there are soe SNPs between the base and target that has conflicted information (e.g. coordinate, chromosome ID and / or alleles that doesn't match even after considered flipping and complementary sequences)