How to perform quality control for sex when there are no variants after thresholding for MAF
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12 weeks ago
kl ▴ 10

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.

sex-check • 295 views
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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.

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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.

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