How to perform quality control for sex when there are no variants after thresholding for MAF? I am trying with PLINK.
Would it be accurate to merge with 1000 genomes European allele frequencies and redo the thresholding for this part of QC, as I have heard that in small sample sizes allele frequencies can be biased.
Does that make my genetic data less reliable? I didn't have a lot of individuals removed due to heterozygosity, etc.