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Issue with genetic QC sex check

Hi,

I am doing a sex check on genetic data for a cohort I am working on, consisting of about 830 people. Most people seem to have incorrect sex assignment (around 560 problems). I have used plink QC and there were no people that showed excessive heterozygosity rates but the sex check seems bizarre really. Any suggestions on what may be going wrong would be much appreciated enter image description here

plink
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written by kl • kl

After setting set-hh-missing, I have the following boxplot, where a F statistic of 0.91 corresponds to a female in my phenotypic dataset which doesn't seem quite right enter image description here

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written by kl • kl

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