Missing lots of SNP while clumping

Question

[landscape95]

Hi everyone, has anyone experienced this issue, I have around a million SNPs to do the PRS but with PRSice, after clumping, I only have around 100k SNPs remain. I wonder what situation this could be, thanks. Your help is really appreciated!

Base file:
plink.stat
1133273 variant(s) observed in base file, with:
1133273 total variant(s) included from base file

Start performing clumping

257682 MB RAM detected; reserving 10 MB for clumping
Allocated 10 MB successfully


Number of variant(s) after clumping : 112953


Phenotype is a continuous phenotype
57767 sample(s) with valid phenotype

[Sam]

Did you use imputed data? Imputed SNPs tends to have high LD with eachother and as a result most of those SNPs will be removed after clumping.