Hi all, I am working with genotyped data with immunochip v1 and v2.
I have several cohorts, each with one dataset for cases and one for controls. All of them have passed the quality controls (maf, mind, geno, hwe, missing test, deletion of non autosomal chromosomes and indels, as well as AT/GC type SNPs with frequencies close to 0.5). After merging the case and control datasets from each cohort independently, I make the PCAs and they appear to form a homogeneous cloud and the genomic inflation factor is around 0.95.
The problem I have is when I impute these data (using TOPMED imputation server and its multiethnic reference panel), because when I impute them, and do the logistic regression (after filtering again by maf and hwe) I get very inflated results and many false positives in all chromosomes.
What can this be due to? Thanks in advance!