How to perform quality control for sex when there are no variants after thresholding for MAF
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.
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The simple answer is you can't. Also, is there a reason why your title and your post body have the same content? Use a concise title and elaborate more in the body. You don't even mention what tools and which versions of them you're using.
I am trying with PLINK --check sex. Would an option be to merge my data with 1000 genomes European allele frequencies and redo the thresholding for this part of QC (hopefully I end up with more variants), 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.