Missing lots of SNP while clumping
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
• 2,162 views
•
link
written
by
landscape95
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Can't figure out plink --sample-diff
written by curious
-
Number of SNPs included in the PRS calculation (PRSice)
written by hello_genome •
-
PRSice clumping was not processed for almost 9 hours with a stopped progress rate of 3.33%
written by runye •
-
Many SNPs getting excluded during PRSice 2 analysis
written by m.shoaib •
-
Duplicate ID error with update-name flag
written by geno89 •
-
Preparing Target Data
written by Jenish •
-
PRSice PRS calculation warning Mismatched SNPs. Is it due to using multi-covariate for SNP effect s…
written by landscape95
-
Plink2 error: Skipping --glm regression on phenotype 'PHENO1' since variance inflation factor for c…
written by landscape95
-
Parallel in PLINK for linear association for SNP effects
written by landscape95
-
PLINK Error: No valid entries in --score file.
written by Cindy •
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.