Hello,

I had .CEL files and than I converted those to plink format and did QC steps following https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6001694/ Then imputed those SNPs on Michigan imputation server and than I did QC steps on those file like this:

plink --vcf  chr1.dose.vcf.gz --biallelic-only --make-bed --double-id --out s1
plink --bfile s1 --bmerge s1 --merge-mode 6
plink --bfile s1 --exclude plink.missnp --make-bed --out s2
plink --bfile s2 --list-duplicate-vars
plink --bfile s2 --exclude plink.dupvar --make-bed --out s3
plink --bfile s3 --qual-scores chr1.info 7 1 1 --qual-threshold 0.5 --make-bed --out s4
plink --bfile s4 --maf 0.01 --hwe 0.000001 --snps-only --make-bed --out s5
plink --bfile s5  --geno 0.02 --mind 0.02 --make-bed --out FINAL_DATA_QC1

Is there is anything you would change in these parameters or do you have any GWAS QC workflow available which would be more relevant?

Thanks!