Hi there,

I want to do QC for my data according to the text below, but I am not sure about the amount of these criteria that I wrote are true or not, especially for hwe. Please guide me if have a mistake.

"Quality control of genomic data retained SNP with call rates>0.9, minor allele frequencies >0.01, and departures from Hardy-Weinberg equilibrium (difference between expected and observed frequency of heterozygous) <0.15. "

--maf 0.01 --geno 0.1 --mind 0.1 --hwe 0.15

Thanks